Sorry, we don't have anything to do that.
On 10/04/2017 02:18 PM, Florence Campana wrote: > 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 > <mailto: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 list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
