Thank you very much, Doug, it works indeed with your command! I am also curious about your advices to run the PCA on surface on resting state data (I know that mri_glmfit is not designed for that, but wonder there is a way to specify a contrast matrix and a design matrix such that the residuals are equal to the initial signal in order to run the PCA on my input resting state signal?).
Thank you very much, Florence 2017-10-04 9:41 GMT-04:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > what command are you using to view the data? It should be something like > > tksurferfv fsaverage lh inflated -ov v.mgh -fminmax .0001 .1 > > On 10/3/17 4:27 PM, Florence Campana wrote: > > > Dear freesurfers, > > I contact you since I ran a PCA with mri_glmfit. I do not manage to load > the output v.mgh as an overlay as suggested in the documentation, which > makes me wonder what is wrong. The output file or me loading it? > > For clarification, I ran the command: mri_glmfit --surf fsaverage lh --y > fmcpr.siemens.sm4.fsaverage.lh.nii.gz --pca --osgm --glmdir > /Users/Florence/Documents/test_glm_pca to run the PCA in surface. > > v.mgh is of size 1*163842(nb of vertices)*1*300 (number of components). > On the one hand, the output seems to make sense (its size, and the values > are centered around 0), on the other hand I do not understand why I do not > see anything when I load it as an overlay in tksurfer, despite modifying > the thresholds and color parameters etc. Or should I then save separately > each spatial component contained in v.mgh, and load each of them as one > overlay? > I would also like to specify that my input data > (fmcpr.siemens.sm4.fsaverage.lh.nii.gz) are of size 1*163842(nb of > vertices)*1*300 (time points). This is the data from a single subject for > now (before getting group data via mris_preproc) and I am not sure of > whether it has the proper format. Indeed, it is specified that —y is the “path > to input file with each frame being a separate input”. I do not understand > what it means: does frame refer to one time point, and should I then have > 300 input files (which seems a lot!)? > > Thank you very much, > > Florence > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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