It's surface-based analysis. On Fri, Jul 22, 2016 at 1:43 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:
> Are you doing volume or surface-based analysis? If volume, then you'll > need a volume mask and the --label is not appropriate. > > On 07/22/2016 01:36 PM, Mihaela Stefan wrote: > > I tried that, too and it seemed to work. I extracted the ROIs from > > ?h.aparc.annot and merged them into a single label with > > mri_mergelabels then I ran mri_glmfit. Now I am not sure I used the > > correct command to mask the search: > > > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > > group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir > > lh.group_diff_g2v0.glmdir > > > > So I used my own label instead of ?h.aparc.annot. Does the above > > command look right? > > > > Thanks again! > > Mihaela > > > > On Fri, Jul 22, 2016 at 12:34 PM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > What was your visualization command? You should probably run > > mri_vol2surf with --projfract 0.5 and --interp nearest to get a > > surface > > map. But it begs the question as to why you would do binarize the > > aparc+aseg to get surface ROIs (you should just use the > > ?h.aparc.annot). > > doug > > > > On 07/22/2016 10:38 AM, Mihaela Stefan wrote: > > > Hi Doug, > > > > > > I used this command: > > > mri_binarize --match 1035 1028 1003 1027 1031 1008 1002 1026 > > 1018 1020 > > > 1019 --i aparc+aseg.mgz --o lh22mask.mgz > > > > > > When I checked it first time, I opened it as a volume and it looked > > > okay to me. > > > Now I was able to view it in tksurfer but it looks weird. See > > attachment. > > > > > > > > > Alternatively, I was able to create a label with mri_mergelabels: > > > mri_mergelabels -i rh.insula.label -i rh.superiorfrontal.label -i > > > rh.caudalmiddlefrontal.label -i rh.rostralmiddlefrontal.label -i > > > rh.supramarginal.label -i rh.inferiorparietal.label -i > > > rh.caudalanteriorcingulate.label -i > > rh.rostralanteriorcingulate.label > > > -i rh.parsopercularis.label -i rh.parstriangularis.label -i > > > rh.parsorbitalis.label -o rh.22mask.label > > > > > > The mri_glmfit command seemed to have run successfully. However, > the > > > results from the ROI analysis are almost identical with the whole > > > brain analysis. I find that surprising. Does it make sense > > statistically? > > > > > > Here is the command I used for the whole brain analysis: > > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > > > group.diff.mtx --surf fsaverage lh --cortex --glmdir > > > lh.group_diff_g2v0WB.glmdir > > > > > > And the command with the label for the ROI analysis: > > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > > > group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir > > > lh.group_diff_g2v0.glmdir > > > > > > Thanks! > > > Mihaela > > > > > > > > > On Thu, Jul 21, 2016 at 5:55 PM, Douglas N Greve > > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > > > 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 > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >> > > > Phone Number: 617-724-2358 <tel:617-724-2358> > > <tel:617-724-2358 <tel:617-724-2358>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > > <tel:617-726-7422>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://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 > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto: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. > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://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 <mailto: > Freesurfer@nmr.mgh.harvard.edu> > > https://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 > > -- > 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 >
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