Activity for PsPM
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Dominik Bach posted a comment on discussion Help
Hi Mark. PsPM has moved to github: https://github.com/bachlab/PsPM Kindly post your follow-up questions there and please make sure you use the latest version of the software. Regarding your question, I was not sure what you wanted to infer: tonic arousal during the 1-minute VR experience (which would favour the SF-DCM module in PsPM), or event-related arousal? Dominik
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Mark Sloan posted a comment on discussion Help
Hello, I am brand new to PsPM and its SCR capabilities. I have been using Ledalab, but running into issues so exploring alternatives. I read the GLM vs Ledalab article, and the PsPM user manual, and I am trying to determine (A) whether GLM or DCM modelling is more appropriate for my data (almost 1,000 cases), and (B) if DCM is more accurate than Ledalab's CDA (CDA.SCR) analysis. My Data Setup: I have collected the skin conductance (MuS) responses of 975 virtual reality video experiences (13 one-minute...
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Yufei Wu posted a comment on discussion Help
Thanks Dominik! I fixed import problem and have posted another question on github discussion, could you please take a look? Thanks again for your help!
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This software has moved to https://github.com/bachlab/PsPM. Please make sure to use the latest version available there, and please post all remaining questions on https://github.com/bachlab/PsPM/discussions.
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Hi Dominik and all, I have a dataset with 40 participants and 54 trials for each participant, and I would like to model it as a time series data, my question is, what analysis is suitable in this case? Should I just model it as GLM with 54 conditions for each person or should I use DCM (which I didn’t find on the latest version)? Plus, the stimuli in the experiment is short visual stimuli. Thank you very much, Yufei
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And, I also have a question about the right text file to import: my first column is time stamp which can be excluded after I specify the sampling rate, my second column is the signal, and third column is the marker channel. However it reported error when I tried to import the file, could you specify where is the problem? Thanks again!
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="Generator" content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:DengXian; panose-1:2 1 6 0 3 1 1 1 1 1;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} @font-face {font-family:"\@DengXian"; panose-1:2 1 6 0 3 1 1 1 1 1;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal...
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Teddy posted a comment on discussion Help
Dear Maria, Thank you for the feedbacks. After checking the record of previous developments, I can see we designed the second level to give the warning, but the first level contrast did not give the warning. I have proposed an issue on GitHub and will add this warning for first level contrast in our PsPM develop version. We will let you know when the feature has been added so that you can use the beta version if you would like to. Hope it helps. Many thanks. Best wishes Teddy
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Maria Ploumitsakou posted a comment on discussion Help
Dear Teddy, Thank you very much for your prompt response. I managed to find out why this was happening so I will explain here in case it is useful for other users. My experiment included EDA and fMRI. I thus trimmed the EDA files based on the first non-dummy MRI trigger and the last MRI trigger because each of the experiment tasks was in a separate MRI run. However, trimming at the last trigger apparently did not leave enough time for the DCM to consider it as the window where it would look for the...
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Dear Maria, Thank you for explaining the issue with us. To allow us resolve this issue for you, could you please provide some information that can better demonstrate how the issue appears and are really helpful for us to investigate the issue, as below? Which version of PsPM did you use, e.g. 5.1 or 6.0? You can find this by typing “pspm” in the command line or find it at the bottom of the main GUI. How was the data processed, through the GUI or through the command line scripts? Can we have some...
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Dear professor Bach, I have trace fear conditioning data and I am using DCM as suggested in this case. After running the first level and contrasts, I went on with the second level. The output graph of reporting 2nd level was produced fine but only when looking at the 2nd level file did I realize that only a part of my subjects were included (less than half). However, I did not get any warning when running the 2nd Level to notify me about it. Trying to figure it out, I saw that the subjects excluded...
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PsPM has moved to GitHub; could you post your question there? https://github.com/bachlab/PsPM
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Grace Lei posted a comment on discussion Help
Hi there, I would like to ask about the eyetracker distance in the import batch for data type .asc. We are using Tower Mont. I wonder how shall I measure the eyetracker distance. Thank you very much!
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Hi Maria thanks for reaching out. Could you kindly share your full script, either on Github (https://github.com/bachlab/PsPM) or via email? This sourceforge page is not serviced regularly any longer. Best wishes Dominik
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Maria Ploumitsakou modified a comment on discussion Help
Hello, I am trying to make a script that will loop over participants and import and trim their data. I have made the correspondent batch and it works fine. However, when I try to run the script that loops over participants, I get the error: Unrecognized function or variable 'cfg_dep'. Error in import_trim_batch_job (line 32) matlabbatch{2}.pspm{1}.prep{1}.trim.datafile(1) = cfg_dep('Import: Output File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));...
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Hello, I am trying to make a script that will loop over participants and import and trim their data. I have made the correspondent batch and it works fine. However, when I try to run the script that loops over participants, I get the error: Unrecognized function or variable 'cfg_dep'. Error in import_trim_batch_job (line 32) matlabbatch{2}.pspm{1}.prep{1}.trim.datafile(1) = cfg_dep('Import: Output File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));...
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Ivan Rojkov posted a comment on discussion Help
Hi Jelka, Please excuse us for this late reply ! Since the end of last year we moved to GitHub (https://github.com/bachlab/PsPM), so if you could open a new Issue there it would be amazing ! About your issue: unfortunatelly it is very difficult to say you what is the error you are making without having the raw data :/ But as you described it, it seems that your error is in the import structure that you are using. To be entirely sure may I ask you while opening the new issue on GitHub to upload a...
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Jelka Stojanov posted a comment on discussion Help
Hello, I am new to PsPM and I am having trouble with importing .acq files. The data was originally in Acqknowledge 5, which I then exported as Acqknowledge 3 files. After many attempts and errors, I think the problem is in the way I am specifying channels - I initially used number 13 for SCR channel and 47 for marker channel (please see the screenshot attached), but these channels are not recognized and no pspm file is saved. After that, I used the numbers 3 (for SCR) and 10 (for markers) relying...
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PsPM released /Tutorial_dataset_DCM.zip
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Kasim Acar posted a comment on discussion Help
Hi everyone, made a similar post in GitHub about a week ago, hoping to get a response here. OS: macOS Catalina Matlab: R2019b PsPM: 4.2.1 When following the tutorials for both GLM and Non-Linear Model, I get errors: For GLM: 23-Dec-2019 19:48:58 - Running 'Import' Pulse data was converted to waveform with a sampling rate of 5000.00 Hz, to allow 10-fold oversampling. Warning: call of pspm_butter failed In pspm_prepdata (line 102) In pspm_pulse_convert (line 75) In pspm_get_spike (line 82) In pspm_import...
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Number of marker names and number of marker onsets mismatch
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pspm_get_events misses markers that correspond to the first sample row
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Fixed on github (see https://github.com/bachlab/PsPM/issues/15). I close the ticket.
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Dear Sasa, What you have to remember is that PsPM will always return you the pupil size in units of diameter. Here is how the import and conversion are done : At first, pspm_get_eyelink receives your data either in 'diameter' or 'area' (depending on how you have recorded them) but these data are still in 'au' and scalled. Then this function determines to which case your data belong ('diameter' or 'area') and transfers them to another function (lines 321, 328) called pspm_convert_au2unit with the...
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Sasa Redzepovic posted a comment on discussion Bug reports (Deprecated)
Hi Ivan, thank you for your reply. If I record all my data as area and use your scaling factor, then all the data is scaled the same way. But what if only some of the data is recorded as area and some is recorded as diameter? In this case the scaling is off. This is not a big issue if you standardize you data later on. But it does affect conversion to mm, which is needed for the new preprocessing toolbox. Doesn't it? All the best, Sasa
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Dear Sasa, Indeed the SR Research team is using a scaling factor between area and diameter of the pupil in order to have the right scaling during their conversion process. In PsPM on the other hand we scale that values in pspm_get_eyelink funtion, then when we use area2diameter we only worry about the standard conversion formula (A=pi*r^2). Regards, Ivan
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Hi Tobias, is there a particular reason for why you use a scaling factor of 2 and the SR Research Team 256? https://www.sr-support.com/forum/eyelink/data-viewer/53455-conversion-from-area-to-diameter All the best, Sasa
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Sure https://box.uke.de/f/8231317
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Eshref Yozdemir posted a comment on ticket #17
Dear Sasa, Thank you for letting us know about this issue. Could you please verify whether my understanding of the issue as explained below is correct? The current Eyelink import code loads markers incorrectly 1. when there are multiple markers with the same timestamp, and/or 2. when there is a marker whose timestamp value is either less than the smallest timestamp of a data sample or greater than the largest timestamp of a data sample. In case I understood it correctly, I agree with you that the...
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Please let me know if this is a valid work around or if I am seeing a bug where there is none. PSPM v4.2.0 import_eyelink.m line 259 % construct markers markers.markers = false(size(dataraw, 1), 1); markers.times = []; markers.names = {}; for idx = msg_indices msgline = messages{idx}; parts = split(msgline); time = str2num(parts{2}); markers.markers(bsearch(timecol, time)) = true; markers.times(end + 1, 1) = time; markers.names{end + 1, 1} = cell2mat(join(parts(3:end), ' ')); end My work around %...
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Number of marker names and number of marker onsets mismatch
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Anna posted a comment on discussion Help
Hi Dominik, thank you very much for that hint, that is really interesting! Indeed, also in our data, even though high-pass filtering improves the overall model fit and leads to smaller RSS across particpants, the effect size of a control contrast (here: CS+ vs. CS- during fear conditioning) is considerably (!) greater for a model with default settings for PSR GLM and no additional high-pass filter. I found it surprising first, but guess it reflects that improved model fit does not necessarily imply...
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Hi Anna it is not obvious that slow fluctuations of the pupil size would influence your GLM estimates at all. Korn & Bach 2016 and Korn et al. 2017 did not find that a high-pass filter improves the validity of the ensuing estimates. So you may also do without. (But perhaps there is a specific reason if filtering turns out to be better in your case.) Dominik
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Hi Ivan, my apologies, I somehow assumed that all filtering would be done during pre-processing of the pupil data, but it does make sense that this step is part of the GLM for PSR. I enabled the filter settings and it works flawlessly. Thanks for your help! Anna
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Dear Sara, I'm glad to hear that the solution worked for you. For your other questions, I have to apologize. In my answer for the previous topic, I've forgotten to specify that you have to apply a high-pass filter to your data otherwise the model would not fit correctly. Please excuse me for that omission. Here are the steps if you use PsPM Batch Editor: To apply a high-pass filter, in the module "GLM for SEBR", you have to select Filter Settings, enable it and then select High-Pass Filter, you choose...
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Dear Ivan, many thanks for your cotninuous support and for looking into this! Changing the accepted range of min and max values, as you suggested, addresses the issue. When proceeding with the analysis I noticed that the data fluctuates slowly over the course of the experiment which naturally heavily affects the response estimates of the GLM (see GLM for that subject attached). For this reason I'd like to high-pass filter the data. If I understand the pupil pre-processing correctly (but I might be...
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Dear Anna, Thank you very much for the details you have sent us and I am sorry for the delay I have taken to respond you. Here is my answer: I have achieved to reproduce entirely your error message except for the first line which is Warning: Escaped character '\M' is not valid. See 'doc sprintf' for supported special characters. Let us know if it persists after the following advice. Apparently you are using arbitrary units for diameters of the pupil and these arbitrary units do not correspond to...
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Hi Ivan, Thanks for the quick reply! Please find the entire error message below. Best, Anna Warning: Escaped character '\M' is not valid. See 'doc sprintf' for supported special characters. > In pspm_pupil_pp>preprocess (line 352) In pspm_pupil_pp (line 230) In pspm_cfg_run_pupil_preprocess (line 31) In cfg_run_cm (line 29) In cfg_util>local_runcj (line 1708) In cfg_util (line 968) In pspm_jobman (line 122) In PsPM_pupil_import_preprocess (line 29) Warning: Error using preprocess', 'PsPM_4.2.0\v4.2.0\pspm_pupil_pp.m',...
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Dear Anna, We managed to partially reproduce your error. Can you nevertheless send us more lines of your error message please ? It would help us to fully understand the problem and provide you a good support. Kind regards, Ivan. P.S: You can even copy/paste the whole error and use paragraph to highlight it.
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Hi, Thanks for the recent support on the SEBR analysis again! I now ran into problems trying to preprocess pupil data recorded with Eyelink. During interpolating/smoothing the data I receive the following Matlab error message: Warning: Escaped character '\M' is not valid. See 'doc sprintf' for supported special characters. In pspm_pupil_pp>preprocess (line 352) ... I hope you can replicate it with attached sample pupil data and script. Best regards, Anna
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Dear Ivan, thanks a lot for looking into this! As you suggested, down-sampling indeed solves the file size problem and, as hoped, the flexible latency models capture the inter-trial/inter-individual onset latency differences really well. Thanks again! Best, Anna
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Dear Anna, Thank you for relating this issue. What you are doing is correct - but the output files shouldn't get so big. We looked at it and the problem comes from your input data. Indeed, you input two arrays of size 1403368x1 without filtering it so during exetution PsPM will create five arrays of same size and three matrices of size 1403368x65. This is a huge file that MatLab tries to save. In theory it could do it but for that we have to modify our code. We will maybe implement that in a later...
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Thank you very much for providing this fantastic toolbox! We are interested in trial-by-trial responses in fear conditioning studies and are using PsPM already for skin conductance data. For our type of paradigm (CS duration: 6.5 sec, ITI: mean 16.5 sec, range: 15-18 sec, startle probe delivery 6000 ms after CS onset, US delivery 6450 ms after CS onset) a single-trial GLM seems to provide the most robust results for SCR. In order to make the analysis coherent across different measures we would like...
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Disable data filtering in pspm_display and pspm_ecg_editor
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Remove output channel length test from ecg2hb_amri test
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Change import_eyelink output structure
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Actually change blink_saccade_edge_discard_factor to 0
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Return NaN channel when there isn't enough hb to interpolate
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Return r-peak seconds (not logic vector) from ecg2hb_amri
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Latest version of release notes source code
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Add 4.2.0 user and dev manuals
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Release 4.2.0
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Update version numbers
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Add the author names in acknowledgements section
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Hi Marleen sorry for the late reply. Separating SCR in short succession and determining their amplitude is a great application of PsPM. However, what you need (as with any peak-scoring analysis) is a clear idea of when the SCR occur. Often this is precisely mandated by the experimental timing, but in your case, the pre-stimulus anticipation and the dynamic nature of the stimuli appear to preclude such deterministic approach, and DCM which allows to estimate the timing from the data, could be more...
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Change default eyelink edge discard factor to 0
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Bug in pspm_get_eyelink function expand_mask
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[r802] fixes this bug.
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Fix ticket #16 : iterate manually and fix index order
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Hi Ulrike, Thank you for your detailed bug report. You are definitely right in both of your observations. I will incorporate your suggested changes to PsPM in the next revision.
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Hi Ulrike, Thank you for your detailed bug report. You are definitely right in both of your observations. I will incorporate your suggested changes to PsPM in the next revision. Thank you.
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Ulrike Horn created ticket #16
Bug in pspm_get_eyelink function expand_mask
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Marleen Huebenr posted a comment on discussion Help
Hi Dominik, I am new to PSPM and modelling the EDA data, so I have a few fundamental questions regarding the analyses of my experiment. We are presenting videos of faces changing from neutral to a fearful or happy face. The videos are about 3 seconds long (changes detection occurs at about 1,5 sec after stimulus onset) followed by a ISI of 4 seconds before the next video is presented. First, I wanted to set up a GLM in response to the stimulus onset. Based off what I was observing at the single subject...
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Tatjana Schmidt posted a comment on discussion Help
Thank you so much for your answer, this clarified everything for me!
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Dominik Bach posted a comment on discussion Help
Hi Tanja SCR amplitude or magnitude measures from peak-scoring analysis are sometimes square-root or log-transformed to render their distribution more "normal", similar to a link function in a generalised linear model. However, I am not aware of any systematic investigation under which conditions this is meaningful or necessary - and the choice often seems to be based on tradition. This is why PsPM does not transform the estimates and leaves this to the user. In peak-scoring (and DCM), the distribution...
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Hi everyone, I am new to PsPM and I'm using it to analyse SCR with a DCM. With peak scoring, SCR is usually square root transformed. I was wondering if this is also done in PsPM by default? If yes, is this done before downsampling, filtering and normalizing, or after? Thank you in advance! Tanja
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Make correct_eyelink screen parameters conditionally optional
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Update manual with release notes and GLM/DCM notes
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Allow pupil_correct_eyelink to work with converted gaze data
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Update manual and batch with new DCM documentation
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Update pspm_dcm doc with new min ITI calculation
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Update manual with new fields and default options
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Update matlabbatch cfg scripts for new chan_action
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Use channel_action in all channel producing pspm functions
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Implement new formatting functions for PsPM infos.history
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Don't use last ITI during min_iti calculation in pspm_dcm
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Add new tests to pspm_test script and make sure they pass
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Implement resp_pp invalid arg test
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Fix pspm_extract_segments incorrect onset usage
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Implement set_blinks_saccades_to_nan test and fix bug
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Implement pspm_path tests and update dev guide test table
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Write extended release checklist in markdown
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Change correction default mode to manual in batch
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Update and improve documentations of batch,manual,code
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Add pupil preprocessing functions to PsPM pulldown menu
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Manual
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.m file help texts
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Implement LAST channel of a modality in pspm_glm
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Implement pupil loading precedence order in pspm_load_data
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Expand matlabbatch documentation of pupil functions
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Store extensive historical data upon channel preprocessing
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Too small ITI due to DCM session splitting
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Too small ITI due to DCM session splitting
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Too small ITI due to DCM session splitting
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Update manual with new comments and geometry page from Hayes & Petrov, 2015
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