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Re: [Icatb-discuss] FIT: How does the tool accept correlation matrix?
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From: Kai W. <Kai...@Co...> - 2018-11-05 06:18:06
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Thank you, Vince, for the advice.
However, I tried both ways and still didn't get the job through. Please see the error messages below for each type of trial:
a. resting-state correlation matrix saved as a vector in asc2 format and a modality of "eeg" was selected.
b. the matrix saved as a vector in asc2 format and a modality of "gene" was selected.
c. the matrix saved as a vector in asc2 format and a modality of "behavioral" was selected.
d. the matrix was transformed to nifty format (dimensions: 136 by 1 by 1) with fsl command "save_avw". A modality of "fmri" was selected.
e. the matrix was transformed to nifty format (dimensions: 136 by 136 by 136) where the vector was save in the first column and all other cells were set to zero. A modality of "fmri" was selected.
We wanted to deal with the resting state modality pretty much like the way you did it in the following paper.
Lerman-Sinkoff, D. B., Sui, J., Rachakonda, S., Kandala, S., Calhoun, V. D., & Barch, D. M. (2017). Multimodal neural correlates of cognitive control in the Human Connectome Project. NeuroImage, 163, 41-54.
Thank you very much,
Kai Wang
Postdoc at University of Colorado Boulder
## error log
a. eeg
...
Loading data for read & nback & area & thickness & lgi & rest ...
......................................
FIT Error Information:
Error using ica_fuse_applyMask (line 32)
Check the mask for eeg data
Error in ==> ica_fuse_applyMask at 32
Error in ==> ica_fuse_prepare_data at 73
Error in ==> ica_fuse_run_analysis at 225
Error in ==> run_analysis_Callback at 133
Error in ==> gui_mainfcn at 95
Error in ==> CCA_ICA_fusion at 42
Error in ==> @(hObject,eventdata)CCA_ICA_fusion('run_analysis_Callback',hObject,eventdata,guidata(hObject)) at 0
b. gene
...
Doing SVD on feature lgi
100% of (non-zero) eigenvalues retained in feature lgi
Doing SVD on feature rest
......................................
FIT Error Information:
Index exceeds matrix dimensions.
Error in ==> pcawhiten at 48
Error in ==> ica_fuse_mccaN at 24
Error in ==> ica_fuse_dataReduction at 157
Error in ==> ica_fuse_run_analysis at 265
Error in ==> run_analysis_Callback at 133
Error in ==> gui_mainfcn at 95
Error in ==> CCA_ICA_fusion at 42
Error in ==> @(hObject,eventdata)CCA_ICA_fusion('run_analysis_Callback',hObject,eventdata,guidata(hObject)) at 0
c. behavioral
...
Doing SVD on feature rest
......................................
FIT Error Information:
Index exceeds matrix dimensions.
Error in ==> pcawhiten at 48
Error in ==> ica_fuse_mccaN at 24
Error in ==> ica_fuse_dataReduction at 157
Error in ==> ica_fuse_run_analysis at 265
Error in ==> run_analysis_Callback at 133
Error in ==> gui_mainfcn at 95
Error in ==> CCA_ICA_fusion at 42
Error in ==> @(hObject,eventdata)CCA_ICA_fusion('run_analysis_Callback',hObject,eventdata,guidata(hObject)) at 0
d. nifti (136 by 1 by 1)
...
Creating mask from the data ...
......................................
FIT Error Information:
Error using ==
Matrix dimensions must agree.
Error in ==> ica_fuse_createMask at 87
Error in ==> ica_fuse_pre_stack_data at 12
Error in ==> applyCallback at 1107
e. nifti (135 by 136 by 136, zeros padded)
Doing SVD on feature rest
......................................
FIT Error Information:
Index exceeds matrix dimensions.
Error in ==> pcawhiten at 48
Error in ==> ica_fuse_mccaN at 24
Error in ==> ica_fuse_dataReduction at 157
Error in ==> ica_fuse_run_analysis at 265
Error in ==> run_analysis_Callback at 133
Error in ==> gui_mainfcn at 95
Error in ==> CCA_ICA_fusion at 42
Error in ==> @(hObject,eventdata)CCA_ICA_fusion('run_analysis_Callback',hObject,eventdata,guidata(hObject)) at 0
-----Original Message-----
From: Vince Calhoun <vca...@mr...>
Sent: 2018年10月21日 14:39
To: Kai Wang <Kai...@Co...>; ica...@li...
Subject: RE: [Icatb-discuss] FIT: How does the tool accept correlation matrix?
Hi Kai,
Yes, that should work fine. You could also add to a nifti image.
Best,
VDC
> -----Original Message-----
> From: Kai Wang <Kai...@Co...>
> Sent: Saturday, October 20, 2018 11:06 PM
> To: ica...@li...
> Subject: [Icatb-discuss] FIT: How does the tool accept correlation matrix?
>
> Dear experts,
>
> I'm using FIT to fuse data from several modalities. One modality of
interest is resting-state
> correlation matrix (between 17 networks; 17 by 17). I guess I can convert
the matrix to a
> vector, save it in a plain text format (e.g, csv) and feed it to FIT, just
like EEG or SNP data.
> But I'm not sure. Please advise.
> Thank you,
>
> Kai Wang
> Postdoc at University of Colorado Boulder
>
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> Icatb-discuss mailing list
> Ica...@li...
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