Re: [Icatb-discuss] FIT: How does the tool accept correlation matrix?

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Hi Kai Wang,

It needs to be saved as a vector in a ascii file one per subject. Usually
lower triangular portion needs to be selected as the rest of the elements
are not of use. You can select behavioral as the modality type. If you can
wait until Friday this week I can add  FNC as a feature. I am assuming you
have multiple subjects in your analysis.

Thanks,
Sri

> ---------- Forwarded message ---------
> From: Kai Wang <Kai...@co...>
> Date: Sun, Nov 4, 2018, 11:20 PM
> Subject: Re: [Icatb-discuss] FIT: How does the tool accept correlation
> matrix?
> To: ica...@li... <
> ica...@li...>
>
>
> 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
> >
> > _______________________________________________
> > Icatb-discuss mailing list
> > Ica...@li...
> > https://lists.sourceforge.net/lists/listinfo/icatb-discuss
>
>
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