Naomi Hannaway posted a comment on discussion Open Discussion

Dear GIFT experts, I have outputs from FSL dual regression, which I would like to use as inputs for dFNC within GIFT. I am trying to replicate the methods from a prior paper, which has structured their analysis this way. I am struggling with setting up the dFNC analysis, and have a couple of questions: I am usure what to use for the parameter file to set-up the analysis. Would it be reasonable to set-up but not run an ICA analysis within GIFT just to get this parameter file. Will it be possible to...

Jared posted a comment on discussion Help

Hi all, I am using GIFT for group-ICA for the first time and have a very basic questions. I have a dataset of task fMRI which were completed x2 for each subject. However, some participants did not complete all tasks and others only completed one run of the tasks. We are trying to run a group-level ICA across all of the different tasks and runs. It seems like I should/can only include participants in the group ICA if they have completed all task and all runs. Is that correct?

Muneeza Ayub posted a comment on discussion Open Discussion

Dear GIFT Development Team, I hope this message finds you well. I am beginner in brain imaging, and currently using the GIFT toolbox to perform constrained group ICA on resting-state fMRI data. While I have successfully run the constrained ICA, I am having difficulty extracting the average loading coefficient per component for each subject. I found the individual subject loading coefficients for each component at each TR (in the _ica_c.mat file), but it would be great to be able to extract the average...

Muneeza Ayub posted a comment on discussion Help

Dear GIFT Development Team, I hope this message finds you well. I am beginner in brain imaging, and currently using the GIFT toolbox to perform constrained group ICA on resting-state fMRI data. While I have successfully run the constrained ICA, I am having difficulty extracting the average loading coefficient per component for each subject. I found the individual subject loading coefficients for each component at each TR (in the _ica_c.mat file), but it would be great to be able to extract the average...

Mira Sinha posted a comment on discussion Open Discussion

Hi everyone, I’m working with a small sMRI dataset (14 individuals) and running a group-ICA SBM analysis in GIFT. When estimating the number of components, MDL only gives me one component, while Entropy Rate (Finite Memory Length) estimates 12 components. This seems unusual, as it only slightly reduces the dimensionality. I have a few questions: Is Entropy Rate (Finite) a reliable method for estimating components? I couldn’t find details in the manual on how it differs from MDL or whether it’s appropriate...

Erin Kim posted a comment on discussion Open Discussion

Dear GIFT experts! I have 2 groups (CON, PT) and each with 2 scanning sessions (rest1, rest2). I have fun group ICA with all subjects/sessions and got 20 meaningful components. Now I want to run temporal dynamic FNC (ICA) analysis but SEPARATELY for session 1 and session 2 to compare whether there is a group difference in rest1 and rest 2. When I click on the setup/run analysis, it asks for the icn_param.mat file and it automatically loads all subjects/session files this problem remains the same...

Wentao Zeng posted a comment on discussion Open Discussion

Hello, I want to lear the exact process of the entropy rate enhanced MDL to determine how many ICs I need. I read the original paper of Yi-Ou Li in 2007 but did not understand fully the formula then I found out in a paper of Xi-Nian Zuo in 2010 that GIFT toolbox includes this function but I don't know the name of it.

Eilish Fitzpatrick posted a comment on discussion Help

Hi all, A bit of background first. We have resting state fMRI data from patients and controls, scanned on 2 different sites with different scanning parameters. The aim of this study is to pool these datasets together, to determine within and between networks functional connectivity differences among these groups. Because the 2 datasets have different TRs and other parameters e.g. (one study used TR=1ms and MB=4; one study used TR=2s), we thought we would derive similar IC maps using spatially constrained...

Eilish Fitzpatrick posted a comment on discussion Open Discussion

Hi all, A bit of background first. We have resting state fMRI data from patients and controls, scanned on 2 different sites with different scanning parameters. The aim of this study is to pool these datasets together, to determine within and between networks functional connectivity differences among these groups. Because the 2 datasets have different TRs and other parameters e.g. (one study used TR=1ms and MB=4; one study used TR=2s), we thought we would derive similar IC maps using spatially constrained...

Anastasia Cherednichenko posted a comment on discussion Help

Hello, I pre-processed my data using intensity normalization followed by no scaling during ICA, and now have a question regarding the units of the output. I've read that the units from the back reconstruction are arbitrary, but I´ve also seen that this is unless prior normalization is performed. Therefore, my question is: are, in my case, the resulting values expressed in arbitrary units? if not, which is the scale of the back reconstruction values? I've already tried to find an answer, but I haven't...

armin posted a comment on discussion Help

Hi Rosella, Yes, you can run group ICA on mice data and use it as a template. Thanks, Armin On Wed, Apr 17, 2024 at 9:25 AM Rosella rosa1@users.sourceforge.net wrote: Good morning, I am a researcher at University of Genoa, Italy, in the field of neuroimaging. I am introducing to the rs-fMRI field applied to mice brain data. Specifically, I am going into details of the work Explainable fuzzy clustering framework reveals divergent default mode network connectivity dynamics in schizophrenia (https://pubmed.ncbi.nlm.nih.gov/36824777/)...

Rosella posted a comment on discussion Help

Good morning, I am a researcher at University of Genoa, Italy, in the field of neuroimaging. I am introducing to the rs-fMRI field applied to mice brain data. Specifically, I am going into details of the work Explainable fuzzy clustering framework reveals divergent default mode network connectivity dynamics in schizophrenia (https://pubmed.ncbi.nlm.nih.gov/36824777/) and trying to reproduce its step applied to mice brain. In this regard, I was wondering if the Neuromark pipeline of the Group ICA...

Rosella posted a comment on discussion Open Discussion

Good morning, I am a researcher at University of Genoa, Italy, in the field of neuroimaging. I am introducing to the rs-fMRI field applied to mice brain data. Specifically, I am going into details of the work Explainable fuzzy clustering framework reveals divergent default mode network connectivity dynamics in schizophrenia (https://pubmed.ncbi.nlm.nih.gov/36824777/) and trying to reproduce its step applied to mice brain. In this regard, I was wondering if the Neuromark pipeline of the Group ICA...

Carissa Weis posted a comment on discussion Open Discussion

Hello - I keep running into an error when generating a mask in the initial set up step. Does this pertain to an SPM error? It's possible my OS and software have updated since the last time I ran this but the batch script itself hasn't changed. I'm using GIFT v4.0.4.11, MATLAB 2022b, and spm12. Carissa

Carissa Weis posted a comment on discussion Help

Hello - I keep running into an error when generating a mask in the initial set up step. Does this pertain to an SPM error? It's possible my OS and software have updated since the last time I ran this but the batch script itself hasn't changed. I'm using GIFT v4.0.4.11, MATLAB 2022b, and spm12. Carissa

Stuart Washington posted a comment on discussion Help

I am running MATLAB 2023a. I might be running into a compatibility issue with MATLAB 2023. When I try to display my results from GIFT, I get the error below the asterisks: Opening display GUI. Please wait ... ...................................... Group ICA Error Information: Error using text Text cannot be a child of ColorBar. Error in ==> icatb_drawMComponents at 374 Error in ==> icatb_componentExplore at 191 Error in ==> displayButtonCallback at 1209 ...................................... Error...

Xiangyu Long posted a comment on discussion Open Discussion

Dear GIFT expert, Recently I found the article: "Joint connectivity matrix independent component analysis: Auto‐linking of structural and functional connectivities" published in Human Brain Mapping, and I'm very interested in this method to apply on my own data. However I didn't find the proposed method joint cmICA in the GIFT toolbox. I was wondering if this tool was available or not, thanks. Best, Xiangyu

Tanmayee Samantaray posted a comment on discussion Open Discussion

Hi Srinivas, Thanks for your kind reply. We did a 30 component SBM decomposition of Healthy controls (HC) and Parkinson's (PD) data. Almost all the maps had predominant positive regions. Next, we obtained the mean of the HC and PD loading coefficients for all 30 components. We observed 15 components showing PD > HC (meaning PD has more grey matter than HC), and the rest 15 components showing HC>PD (meaning HC has more grey matter than PD). This seems to imply half of the brain regions have higher...

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi Tanmayee, You need to take a look the spatial maps as well. Positive regions in spatial maps correspond to regions where patients > controls, negative regions healthy > patients in this example. Thanks, Srinivas From: discussion@icatb.p.re.sourceforge.net discussion@icatb.p.re.sourceforge.net on behalf of Tanmayee Samantaray tanmayeesam@users.sourceforge.net Sent: Friday, August 4, 2023 5:23 AM To: [icatb:discussion] 309910@discussion.icatb.p.re.sourceforge.net Subject: [icatb:discussion] sMRI...

Tanmayee Samantaray posted a comment on discussion Open Discussion

Hi!! I decomposed structural MRI of healthy controls and patient group using GIFT toolbox and obtained loading matrix and component matrix. The mean of the loading coefficients of healthy control is coming negative, while that of patients is coming positive. Does this mean that the tissue content of healthy is more than that of patients? If so, how is it even practically possible? Please explain on the directionality of the loading coefficients. Looking forward to this.

Tanmayee Samantaray posted a comment on discussion Help

Hi!! I decomposed structural MRI of healthy controls and patient group using GIFT toolbox and obtained loading matrix and component matrix. The mean of the loading coefficients of healthy control is coming negative, while that of patients is coming positive. Does this mean that the tissue content of healthy is more than that of patients? If so, how is it even practically possible? Please explain on the directionality of the loading coefficients. Looking forward to this.

Jooyeon Im posted a comment on discussion Open Discussion

Never mind! I found it. For those who runs into the same question as above, there is "Sort Components" option after clicking the Display GUI in the menu and selecting the ica_parameter_info.mat file.

Jooyeon Im posted a comment on discussion Open Discussion

Hello! I'm trying to perform spatial sorting but I could only find "Temporal Sorting" under Utilities. Does anyone know where I can find "Spatial Sorting" or just sorting option? Thank you.

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi Federica Colombo, Yes, there is option to do dimensionality estimation via GUI. There are two approaches like MDL and CCA based estimation. Permutation testing is not implemented for MCCAR. Will keep you posted on this. You can set the lambda value in ica_fuse_defaults.m. Please see MCCAR_LAMBDA Thanks, Srinivas From: discussion@icatb.p.re.sourceforge.net discussion@icatb.p.re.sourceforge.net on behalf of Federica Colombo fcolombo8@users.sourceforge.net Sent: Sunday, May 14, 2023 2:13 PM To: [icatb:discussion]...

BJ posted a comment on discussion Open Discussion

Also, when we run dFNC stats, is the order group1 - group2 (group 1 being the first group we enter during the setup for stats and group2 the second group)?

BJ modified a comment on discussion Open Discussion

Hi Srinivas, I have two groups and two sessions (baseline and follow-up). Within the dynamic FNC toolbox, there are three options for stats analysis: one-sample, two-sample, and paired t-test. I am interested in running a two-sample t-test between the groups, specifically focusing on session 2 (follow-up). However, I can only select subjects for each group, not the sessions themselves. It seems that the dFNC toolbox averages the sessions for the two-sample t-test, resulting in no significant FDR-corrected...

BJ posted a comment on discussion Open Discussion

Hi Srinivas, I have two groups and two sessions (baseline and follow-up) in the dynamic FNC toolbox. Within the toolbox, there are three options for stats analysis: one-sample, two-sample, and paired t-test. I am interested in running a two-sample t-test between the groups, specifically focusing on session 2 (follow-up). However, I can only select subjects for each group, not the sessions themselves. It seems that the dFNC toolbox averages the sessions for the two-sample t-test, resulting in no significant...

Federica Colombo posted a comment on discussion Open Discussion

Dear all, I'm interested in performing MCCAR+jICA using multimodal structural neuroimaging and depressive symptoms scores as reference. Currently, I'm running analysis using the batch script (input_data_fusion_1.m), but I have a few questions about its implementation: 1. Is there the possibility to estimate the number of components based on the minimum description length (MDL) criterion also in batch? 2. Is it possible to perform a permutation test within the FIT toolbox to assess the significance...

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi Doo, Could you upload the image on the dropbox or some other shared website? Thanks, Srinivas From: discussion@icatb.p.re.sourceforge.net discussion@icatb.p.re.sourceforge.net on behalf of Doo Blah dooblah@users.sourceforge.net Sent: Friday, March 31, 2023 2:24 AM To: [icatb:discussion] 309910@discussion.icatb.p.re.sourceforge.net Subject: [icatb:discussion] Bad image handle dimensions in GIFT When setting up the ICA, it all goes well for selecting the data, then it returns with the following...

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi Julia, You can set numOfPC1 to the number of components if you have one subject and numOfPC2 to the number of components if you have multiple components. To make things easier you can follow the icatb/icatb_batch_files/Input_spatial_ica.m settings for changing the parameters. Thanks, Srinivas

Doo Blah posted a comment on discussion Open Discussion

When setting up the ICA, it all goes well for selecting the data, then it returns with the following error. I've copy pasted the function of another version, even used the same variable V that worked on another computer, and it still gives me the same error. I recieve the following message: "Group ICA Error Information: Error using icatb_spm_slice_vol Bad image handle dimensions. Error in ==> icatb_spm_read_vols at 34 Error in ==> icatb_read_data at 194 Error in ==> icatb_loadData at 52 Error in...

Germana posted a comment on discussion Help

Hi, I'm trying to use GIG-ICA alghoritm on 5 different patiens. I have used the spatially sorting. I don't know if I did it right, but I don't understand exactly what is the output obtained. which is the GIG-ICA ouput? what is the mean result? sorry, I'm a bit confused. every help will be very usefull

Germana posted a comment on discussion Help

Hi. I'm new in this forum and I'm new using GIFT toolbox. I'm studying for my thesis and I need to use GIG-ICA alghoritm to study my resting states data. I can't find this alghoritm in GIFT toolbox and I don't know how to implement it. could someone please help me?

Julia May Brooks posted a comment on discussion Open Discussion

Hello, I am running group ICA on fMRI data using a batch script, and am hoping to choose the number of components that ICA produces so that we can compare results when 25, 50, 100, etc. components are ran for each dataset. How can I manually select the number of components for ICA to run in a batch script (In the input_data_subjects_2.m file)? Thank you!

Meng Yang posted a comment on discussion Open Discussion

This is the setup file Thank you for your help!

Marcello Giunta posted a comment on discussion Open Discussion

Dear GIFT and FIT experts, I have an issue with FIT toolbox. I have set an analysis with structural, FA and fMRI sequences, all loaded as nifti files with structural, DTI and fMRI labels, respectively. After completing the PGICA processing (without errors claimed) the GUI creates a result summary in which I can visualize only structural and fMRI components, while DTI components are cited just in the analysis (t-test) paragraph. Looking at output folders I can find DTI components, but in asc extension....

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi M.H., Could you send the fusion mat file which contains the settings in zip file? Thanks, Srinivas From: discussion@icatb.p.re.sourceforge.net discussion@icatb.p.re.sourceforge.net on behalf of Meng Yang reader2714@users.sourceforge.net Sent: Tuesday, October 11, 2022 9:14 AM To: [icatb:discussion] 309910@discussion.icatb.p.re.sourceforge.net Subject: [icatb:discussion] The error problem occurred when analyzing SNP and MRI data with FIT Hi every one, We tried to use FIT to analyze SNP data and...

Meng Yang posted a comment on discussion Open Discussion

Hi every one, We tried to use FIT to analyze SNP data and brain image, but the parallel ICA was interrupted by errors. First of all, the message "Out of memory." pops up in the MDL step. "Requested 6008.5GB array exceeds maximum array size preference." Then, if we continue the ICA analysis, we will get "Error using ica_fuse_calculate_parallelICA Too mamy output arguments." The above analysis was done with 3 modalities: VBM gray matter image, DTI RD image and SNP data. (SNP data have been coded with...

Carissa Weis posted a comment on discussion Open Discussion

Hello, following up on this question again. Are there any other suggestions for how to view the components without the resutls summary working?

Khalil Thompson posted a comment on discussion Open Discussion

This issue has been rectified but now I am running into another issue during the temporal sorting process. While beta weights are being computed, the process is halted midway through and I receive a message about "Unrecognized field name 'SPM'". Any ideas about whats going on here?

Khalil Thompson posted a comment on discussion Open Discussion

I am trying to temporally sort the components I have extracted from a task-based dataset. Every subject has a SPM design matrix produced during the initial first level modelling completed on the dataset. However, when I tried to apply these matrices to ICA for temporal sorting I receive this message that the Field "nscan" does not exist in the structure of the SPM.mat file. However, each SPM.mat does in fact have a nscan field or my earlier model specification efforts using traditional GLM modelling...

Carissa Weis posted a comment on discussion Open Discussion

Hello, I updated that default as suggested, but I still don't get any HTML output saved to my output directory. No browser is opened and I don't get any errors. Is this some issue with MATLAB connecting the browser on my computer? Carissa

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi Carissa, Try setting GICA_RESULTS_SUMMARY.display_option = 1 in icatb_defaults.m and see if you can see any error in the browser. Thanks, Srinivas From: discussion@icatb.p.re.sourceforge.net discussion@icatb.p.re.sourceforge.net on behalf of Carissa Weis cnweis@users.sourceforge.net Sent: Friday, July 22, 2022 9:17 AM To: [icatb:discussion] 309910@discussion.icatb.p.re.sourceforge.net Subject: [icatb:discussion] results summary not generated Hello, My group ICA has successfully completed and I...

Carissa Weis posted a comment on discussion Open Discussion

Hello, My group ICA has successfully completed and I wanted to generate the HTML results summary output to review components for additional analysis. After clicking the results summary button in the GUI window, the MATLAB terminal window says "Generating summary ... Done" but I don't see the HTML output anywhere. This file is created but nothing else: *tmp_results_struct.mat. Does this suggest there are no results? Carissa

katharina voigt posted a comment on discussion Open Discussion

Hi, I’m new to gift and I’m having issues with the temporal sorting of my ICA components. I have 240 scans, they are alternating for every 40 scans between rest and task block. So I have created a design matrix that looks like this below (shortened) and used the ascii_to_spm.mat file to create my spm.mat file needed for the temporal sorting. Rest Task Constant 1 0 1 1 0 1 1 0 1 ... 0 1 1 0 1 1 0 1 1 ... 1 0 1 1 0 1 1 0 1 … However, I’m getting the following error (see below) when I apply the temporal...

Jungwon Cha posted a comment on discussion Open Discussion

Hi Srinivas, I have another question about FDR correction. After validating components, I have decided to use 12 network, and I have performed MANCOVAN toolbox to find the difference between two groups using network. When I tried to display Mancovan results (univariate results) with FDR correction option, does this FDR correct over the number of components I am using (in my case, this is 12 networks)? If so, if I change the number of components for this MANCOVAN, the significant results with FDR...

Jungwon Cha posted a comment on discussion Open Discussion

Hi GIFT experts, I am using Component labeller to find higher correlated ICA components with RSN template network. Is there any defined threshold of correlation, for example, 0.15 or 0.3? Thanks, JC

Jungwon Cha posted a comment on discussion Open Discussion

Thank you!! JC

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi JUngwon, There is an option to select threshold criteria (fdr or none) in display mancova gui. It should be FDR corrected (p < 0.01) Yes, it is uncorrected p < 0.01 Thanks, Srinivas From: Jungwon Cha jungcha@users.sourceforge.net Sent: Friday, May 6, 2022 8:21 AM To: [icatb:discussion] 309910@discussion.icatb.p.re.sourceforge.net Subject: [icatb:discussion] FDR correction in MANCOVAN toolbox Hi GIFT expert! I have performed MANCOVAN toolbox to find the difference between two groups. When I tried...

Jungwon Cha posted a comment on discussion Open Discussion

Hi GIFT expert! I have performed MANCOVAN toolbox to find the difference between two groups. When I tried to display Mancovan results (univariate results), I got some points which I want to make clear. 1) As 'Threshold criteria (univariate results) : FDR' and ' P-threshold (univariate results): 0.01' , I got Figure 'Significant effects of GroupA - GroupB (p<0.01)' with the correlation diagram among components. Does it mean that these components are showing the group difference significantly at FDR...

katharina voigt posted a comment on discussion Help

Hi, I'm also after an answer please

katharina voigt posted a comment on discussion Help

Hi, I didn't preprocess data in SPM and also did not my first level analyses in SPM. So I don't have a SPM.mat file. How can I still do a temporal sorting of my ICA components if I have my onset times for events of my design matrix handy?

Jennie Chen posted a comment on discussion Open Discussion

Hi there, I'm interested in using joint ICA to look at ALFF, FA and gray matter volume in HIV vs. controls. From what I've gathered from the review papers on fusion techniques, I thought mCCA+jICA is a good option for me as I have 3 modalities. I have these images for 45 HIV and 16 control subjects, all in the same resolution/template space and smoothed by 10mm kernel. I was able to get 5 components out of my data but when I looked closely, it seems to be along the outlines of the masks I'm using...

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi Fazaneh, You can use select mask in setup-defaults menu and select the created mask from GIFT (mask.nii) or specify your mask. You can select constrained ica or moo-icar algorithms and select the agg​compnii files from previous analysis as template. Thanks, Srinivas From: Farzaneh Shayegh fshayegh@users.sourceforge.net Sent: Tuesday, March 29, 2022 10:57 PM To: [icatb:discussion] 309910@discussion.icatb.p.re.sourceforge.net Subject: [icatb:discussion] How to extract components of a new subject...

Farzaneh Shayegh posted a comment on discussion Open Discussion

Hi every one, I am running group ica on some subjects, and get the spatial maps, time course, etc.. Now I want to use these maps for a non-seen subject, without computing the maps once more. Do you have any suggestion. p.s. my main problem is to apply the used mask in the gift to my new subject. please guide me

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi Jordan, Could you send parameter file in zip format (icaparam*mat)? Also, screenshot of the components Thanks, Srinivas From: Jordan jordansbm@users.sourceforge.net Sent: Wednesday, March 9, 2022 8:03 AM To: [icatb:discussion] 309910@discussion.icatb.p.re.sourceforge.net Subject: [icatb:discussion] Mirrored spatial maps Dear experts, I have been using the source-based morphometry module for a while but I have run into a problem. I demeaned the images as a pre-processing step to start the analysis...

Jordan modified a comment on discussion Open Discussion

Jordan posted a comment on discussion Open Discussion

Dear experts, I have been using the source-based morphometry module for a while but I have run into a problem. I demeaned the images as a pre-processing step to start the analysis but now all the spatial maps are mirrored. Attached to the mail you can find an example of how it looked before the demeaning and after. Do you have an idea how to fix this? Best regards, Jordan

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi Jordan, Yes mean is removed from each image before doing data reduction. Thanks, Srinivas From: Jordan jordansbm@users.sourceforge.net Sent: Tuesday, February 22, 2022 9:34 AM To: [icatb:discussion] 309910@discussion.icatb.p.re.sourceforge.net Subject: [icatb:discussion] Demeaning before SBM Dear experts, I am working on a project where I am trying to identify components with the SBM module. I am using a self-made mask that eliminates signals from outside the brain. My question is: Is it necessary...

Jordan posted a comment on discussion Open Discussion

Dear experts, I am working on a project where I am trying to identify components with the SBM module. I am using a self-made mask that eliminates signals from outside the brain. My question is: Is it necessary to subtract the mean within this mask for each scan? Or is this done automatically by the PCA step? Best regards, Jordan

Andrew You posted a comment on discussion Help

Hello I ran group ICA and notice that it produces a mean, std, and tmap nii file for the components. I was wondering if I can produce a z map so I can produce a mask at a certain z threshold. I assume the mean.nii file is beta? In addition, does the remove components regress out the component from each individual file or simply remove the component from the results? Thank -Andrew

Teodora Stoica posted a comment on discussion Open Discussion

I am trying to estimate the number of components using MDL and I keep getting this error - any idea how to fix it? Any help would be appreciated! Opening GIFT ... Creating Mask Default mask includes voxels >= mean. Using first file of each subject to create default mask ... Done Creating Mask ...................................... Group ICA Error Information: Undefined function 'mat2file' for input arguments of type 'struct'. Error in ==> subfun at 164 Error in ==> subsasgn at 85 Error in ==> fun...

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi QingYuan, Its in MNI space. Please see more info @ https://academic.oup.com/cercor/article/22/1/158/366732 Thanks, Srinivas From: QingYuan alannormal@users.sourceforge.net Sent: Wednesday, November 3, 2021 1:34 AM To: [icatb:discussion] 309910@discussion.icatb.p.re.sourceforge.net Subject: [icatb:discussion] create new templates Dear experts: Hello, I have a question about the templates in icatb/icatb_templates/RSN.zip. I'd like to know the basics of the way to distinguish those networks(like...

QingYuan posted a comment on discussion Open Discussion

Dear experts: Hello, I have a question about the templates in icatb/icatb_templates/RSN.zip. I'd like to know the basics of the way to distinguish those networks(like a paper, maybe?), and which space is used? When I display it in an MNI space, I find there are some parts out of the brain. Is it defined in a Talairach space? Looking forward to your reply,thank you! Best regards

QingYuan posted a comment on discussion Help

Dear experts: Hello, I have a question about the templates in icatb/icatb_templates/RSN.zip. I'd like to know the basics of the way to distinguish those networks(like a paper, maybe?), and which space is used? When I display it in an MNI space, I find there are some parts out of the brain. Is it defined in a Talairach space? Looking forward to your reply,thank you! Best regards

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi Cici, May be the algorithm didn't do well estimating number of clusters. You can try using elbow/AIC/BIC criteria. Did you change the number of clusters and see if you get good results? Thanks, Srinivas From: Xi yang xiyang303@users.sourceforge.net Sent: Wednesday, October 27, 2021 1:29 PM To: [icatb:discussion] 309910@discussion.icatb.p.re.sourceforge.net Subject: [icatb:discussion] Temporal dFNC Dear expert of Gift I am use temporal dFNC method to analysis my data, in my results, according to...

Xi yang posted a comment on discussion Open Discussion

Dear expert of Gift I am use temporal dFNC method to analysis my data, in my results, according to the silhouette algorithm，the number of cluster was 2, But there are still some participants (in both group) occurrences for state 2 is 100%, I think it is a little strange ，I want to know is this reasonable? Looking forward to your professional reply , thank you very much for your help Best regards Cici

Alessio Pio Mimmo posted a comment on discussion Help

Dear all, I'm trying to run a Deep Fusion Analysis by using FIT_Manual (Jan 21, 2020, https://trendscenter.org/trends/software/fit/docs/v2.0e_fit.pdf), but unfortunatly the analysis has crashed, due to the following error: 'Could not find a version that satisfies the requirement mkl-service (from versions: ) No matching distribution found for mkl-service' Usually it appears when using python version 2.7. The same error occurs when trying install libpython and m2w64-toolchain. I have also tried to...

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi Nele, Group ICA requires voxel dimension to be the same across subjects. You can average the binary masks (with some threshold) and input them into GIFT. Thanks, Srinivas From: Nele De Bruyn neledebruyn@users.sourceforge.net Sent: Thursday, September 2, 2021 7:53 AM To: [icatb:discussion] 309910@discussion.icatb.p.re.sourceforge.net Subject: [icatb:discussion] Gift mask in stroke population dear GIFT users, I work with a stroke population, so every subject has a unique lesion location which I...

Nele De Bruyn posted a comment on discussion Open Discussion

dear GIFT users, I work with a stroke population, so every subject has a unique lesion location which I would like to mask out of the analysis. I do have subject-specific binary lesionmaps. So, is there a possibility to use these subject-specific lesions maps as subject-specific masks into the GIFT setup ICA step? thank you for your help, greetings, Nele

Ilka Böhm modified a comment on discussion Help

Hello, which specific despiking method is implemented in the dFNC toolbox in the section dFNC options --> pre-processing Thanks Ilka

Ilka Böhm posted a comment on discussion Help

sorry, I mean the processing post dFNC analysis

Ilka Böhm posted a comment on discussion Help

Hello, which specific despiking method is implemented in the dFNC toolbox in the section post-processing? Thanks Ilka

QingYuan posted a comment on discussion Open Discussion

Dear expert: Thanks for your reply! I will try it. Best regards! Get Outlook for Androidhttps://aka.ms/AAb9ysg From: Srinivas Rachakonda rnsk123@users.sourceforge.net Sent: Tuesday, August 17, 2021 12:28:05 PM To: [icatb:discussion] 309910@discussion.icatb.p.re.sourceforge.net Subject: [icatb:discussion] Re: SPM design matrix doesn't match with the data Hi, There is a default mask step in GIFT which removes voxels < mean value. If you want to specify a mask, you can use user specified mask. By the...

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi, There is a default mask step in GIFT which removes voxels < mean value. If you want to specify a mask, you can use user specified mask. By the way, I find a function in the Group ICA package, could I use this ? BTW. There is an option to use spatial temporal regression in GIFT which does the same thing. Thanks, Srinivas From: QingYuan alannormal@users.sourceforge.net Sent: Monday, August 16, 2021 6:17 AM To: [icatb:discussion] 309910@discussion.icatb.p.re.sourceforge.net Subject: [icatb:discussion]...

QingYuan posted a comment on discussion Open Discussion

Dear experts: Sorry, I still have some problems about the mask_ind. The mask of my preprocessed data is a .nii file, whose parameter is 617361, but the mask_ind that is generated by my data during ICA has 57549 voxels, which means there are 57549 values in each IC. Now I operate these IC(compSet.ic in ica_br.mat) to generate a new vector that has 57549 elements, and I want to create a .nii file based on it. How can I do this? I know this step needs the value of each voxel and a mask, but the mask...

Khalil Thompson posted a comment on discussion Help

Good morning everyone, I am thankful to have been connected to this email list through Jessica Turner! I have a question concerning a Task-Based ICA I am attempting to run on my fMRI dataset. In my experiment, participants played 3 games of the Prisoner's Dilemma task. Due to the flexibility of decision-making options from both the participant and the computer opponent algorithm in this game, no participant's data resembles the other in regards to stimulus presentation over the course of the task....

QingYuan posted a comment on discussion Help

Dear experts: The mask of my preprocessed data is a .nii file, whose paramter is 617361 .but the maskind that is generated by my data during ICA has 57549 voxels, which means there are 57549 values in each IC. Now I operate these IC(compSet.ic in ica_br.mat) to generate a new matix which has 57549 elements, and I want to create a .nii file based on it. How canI do this? I know this step need value of each voxel and a mask, but where can I find the mask? By the way, I find a function in the Group...

QingYuan posted a comment on discussion Open Discussion

Dear experts: Thank for your reply! I find that every network in the template should be separated in different 3D.nii file, and be named as 1,2,3... then putting them in one 4D nii file. Now the problem has been solved, thank you! Best regards! QingYuan

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi QingYuan, Template should be converted to a nifti file and labels (nifti file numbers) should be specified for each label. Example label file is located in icatb/icatb_templates/RSN.txt file. Thanks, Srinivas

QingYuan posted a comment on discussion Open Discussion

Dear experts: I want to use Yeo's Cortical Parcellation, and I download the templates from https://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011 , but I'm confused about how to change it to a format which can be used by 'component labeller'. Can you teach me how can I done this? I will be so grateful to receive your reply, thank you! Best regards! QingYuan

Susanna Gobbi posted a comment on discussion Open Discussion

Hi Srinivas, Thanks for your suggestion. Best, Susanna

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi Susanna, Yes FDR correction is applied on the univariate spatial maps. You can use mafdr (MATLAB function) on spatial maps as samples are greater than 500. Thanks, Srinivas

Susanna Gobbi posted a comment on discussion Open Discussion

Dear GIFT expert, I am using GIFT to analyze resting states in 2 groups (control/patients) each one with two sessions (before/after treatment) and I want to test the interaction effect of treatment and group. So, I am using the Univariate analysis (MANCOVA toolbox) with a GLM to correct for nuisance regressors as age, sex, and sites differences. I apologize if this is a naive question, but it is not clear to me if in the univariate analysis of the SMs there is by default a correction for multiple...

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi QingYuan, Number of rows in mask_ind is from default mask or custom mask specified. This value should be the same across components unless you are running group ica for each group separately. Thanks, Srinivas

QingYuan posted a comment on discussion Open Discussion

Dear expert: I'm confused that what determines the number of row of the mask_ind in 'ica_parameter_info.mat'? All IC have same number of mask_ind, but the number is different between conditions. I have two group of subjects, which recept different conditions. Both groups of subjects were treated with group ICA. Now I find that in these two groups, the number of columns of ic matrix in 'icac1-1.mat'is different. Is there any way to make them the same? Looking forward your reply, thank you! Best r...

QingYuan posted a comment on discussion Help

Dear expert: I'm confused that what determines the number of row of the mask_ind in 'ica_parameter_info.mat'? All IC have same number of mask_ind, but the number is different between conditions. I have two group of subjects, which recept different conditions. Both groups of subjects were treated with group ICA. Now I find that in these two group, the number of columns of ic matrix in 'icac1-1.mat'is different. Is there any way to make them the same? Looking forward your reply, thank you! Best re...

QingYuan posted a comment on discussion Open Discussion

Dear experts: That's useful, I've got what I want. Thanks! Best regards! QingYuan

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi QingYuan, Tried it on my end. Component labeler should work fine with RSN.zip file. 'File "\icatbtemplates\RSN.zip" path shows icatbtemplates instead of icatb_templates. Try fixing it if you are using command line. Thanks, Srinivas

QingYuan posted a comment on discussion Open Discussion

Dear experts: Thank you for your answer, my problem about timporal sorting has been solved perfectly! But there are another question: After finding the spacial components which correlate with design matrix, I need to label these component. Before I selected the RSN.zip in icatb_templates file as template, but now I can't use it, Matlab show that 'File "\icatbtemplates\RSN.zip" is not of a recognised type', how can I solve this? Looking forward to your reply, Thank you! Best regards! QingYuan

Haeme posted a comment on discussion Open Discussion

Hi Srinivas, thank you for your suggestion - that makes perfect sense!

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi QingYuan, Yes run or session means the same when selecting data. Estimation tool only gives an approximate number of components in the data. You can select slightly higher number for PC1 compared to PC2 like 40 for PC1 and 30 for PC2 assuming there are 40 timepoints or degrees of freedom in the data. Yes refFunNames is used when doing semi blind ica. For temporal sort, you can click on the display GUI and select yes for temporal sort when the analysis is finished. Yes refFiles is used for constrained...

QingYuan posted a comment on discussion Open Discussion

Dear experts: I'm so grateful to receive your prompt reply! I read the manual and change some parameters and directory path based on the Input_spatial_ica.m . I'd like to clarify something further: Is the word "session" in your letter means "run"? Every subject has 2 runs so each subject has 2 sessions? I am accustomed to choose "yes" for "Do you want to estimate the number of independent components?". If I write"doEstimation = 1",what about the "numOfPC1" and "numOfPC2"? Should I select Semi-blind...

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi Qingyuan, When you select the data, you can select "no" for Is your data stored in one group directory? and select number of subjects and sessions. This will let you select files for each subject and session. Optionally you can use batch template icatb/icatb_batch_files/Input_spatial_ica.m and run batch script or gica_cmd tool (Instructions in the manual) Thanks, Srinivas

QingYuan posted a comment on discussion Open Discussion

I think I haven't describe my question clearly, because there are 30 participants, and I make a group level ICA, so the diffTimePoints is a matrix：1x30 double, and each element here is 240. The nscan of the SPM.mat shows [120,120]. I'm looking forward to receive your reply! Best regards! Qingyuan

QingYuan posted a comment on discussion Open Discussion

Dear experts: Hello, I have a problem when I want to get Temporal Sorting Components. My data has two runs, and each run has 120 scans. The nscan of the SPM.mat shows [120,120]. But when I use these two runs to do ICA, the diffTimePoint shows 240, when I use one run, it shows 120. So I wonder how to match these two files? I will be sincerely grateful to receive your reply, thank you.

Srinivas Rachakonda posted a comment on discussion Open Discussion

Hi Haeme, Looks like session information is missing in design matrix (SPM.Sess field). When you create design in SPM, you need to select five sessions and for each session enter the onsets, duration etc. After that in GIFT, you can select different regressors for sessions in temporal sort. Thanks, Srinivas

Haeme posted a comment on discussion Open Discussion

And a SPM.mat attached!