How did you create the mask? It should be a surface overlay in fsaverage space, ie, you should be able to view it with
tksurfer fsaverage lh inflated -ov mask.mgz -fminmax .1 1 On 07/21/2016 01:51 PM, Mihaela Stefan wrote: > Hello freesurfers, > > I would like to use mri_glmfit with --mask but I get this error: > dimension mismatch 1 between y and mask. > I created a binary mask from 22 aparc labels (using mri_binarize) and > I would like to run a surface-based analysis only on those regions. > The command I use is: > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > lh.group.diff.mtx --surf fsaverage lh --mask lh22mask.mgz --glmdir > lh.group_diff_g2v0.glmdir > > The input file was generated with this command: > mris_preproc --fsgd g2v0.fsgd --cache-in thickness.fwhm15.fsaverage > --target fsaverage --hemi lh --out lh.g2v0.thickness.15.mgh > > From the error, it seems that I am not using the right input file. > What kind of input file should be used with a mask? > > I also thought to use --label but I am not sure how to combine my 22 > labels in one single label. mris_label2annot can combine them but the > output is an annotation file not a label. > > As a note, we will want to do FDR correction, not MC. > > Thanks! > Mihaela > > > _______________________________________________ > 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 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.
