Alex, The second one is for your label. The first one is for everything else outside the label.
Nick On Thu, 2009-01-22 at 18:04 +0000, Alexandru Hanganu wrote: > Hi Everyone, > > Could you please tell us why in the summary file (segstats-ROI5.txt) > there are two datas about thickness for the Mask that we applyed ? > > Index SegId NVoxels Volume_mm3 Mean StdDev Min > Max Range > 1 0 148111 148111.0 2.4249 0.9403 > -0.5673 5.00 5.5673 > 2 1 15731 15731.0 2.3929 0.7417 > 0.8352 4.45 3.6158 > > > Sincerely, > Alex. > > > > > ______________________________________________________________________ > Von: Doug Greve <gr...@nmr.mgh.harvard.edu> > An: Alexandru Hanganu <hanganu.alexan...@yahoo.de> > CC: FS Mailing List <Freesurfer@nmr.mgh.harvard.edu> > Gesendet: Montag, den 8. Dezember 2008, 19:41:52 Uhr > Betreff: Re: [Freesurfer] Statistic analysing for a mask > > what's your cmd? You need to make sure to add --in lh.thickness to get > thickness in the summary file > > Alexandru Hanganu wrote: > > Thank you Nick, and Doug for your answers. I used both "--reshape" > > flag and "--noreshape" flag and the results after "mri_segstats" > > were in both cases: > > > > . > > . > > . > > Voxel Volume is 1 mm^3 > > Generating list of segmentation ids > > Found 2 segmentations > > Computing statistics for each segmentation > > 0 0 134504 134504 > > 1 1 29338 29338 > > > > Reporting on 2 segmentations > > > > So I understand that these are the thickness data of the mask I > > used. Are these data in mm ? Because when using > > "mris_anatomical_stats" command line to see the thickness - the data > > is in mm, and is very different. > > > > Sincerely, > > Alex. > > > > > > > > ____________________________________________________________________ > > > > _______________________________________________ > > 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 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > ______________________________________________________________________ > Von: Doug Greve <gr...@nmr..mgh.harvard.edu> > An: Alexandru Hanganu <hanganu.alexan...@yahoo.de> > CC: FS Mailing List <Freesurfer@nmr.mgh.harvard.edu> > Gesendet: Montag, den 8. Dezember 2008, 18:51:32 Uhr > Betreff: Re: [Freesurfer] Statistic analysing for a mask > > Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd > lines. > > doug > > Alexandru Hanganu wrote: > > Dear Freesurfer users, > > > > We have an MNI mask and we want to apply this mask on a group of > > subjects for small volume correction. > > so we did the following steps: > > > > 1. cd $SUBJECTS_DIR/fsaverage/surf > > fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg > > TT_avg152T1_to_fsaverage.dat > > > > 2. cd $SUBJECTS_DIR/fsaverage/surf > > mri_vol2surf --mov /path/to/ROI5.nii --reg > > TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest > > --hemi lh --out lh.fsaverage.ROI5.mgh > > > > 3. cd $SUBJECTS_DIR/subjid/surf > > mri_surf2surf --s subjid --trgsubject fsaverage --hemi lh --sval > > lh.thickness --tval lh.thickness.fsaverage.mgh > > . > > . > > . > > Surf2Surf: Dividing by number of hits (163842) > > INFO: nSrcLost = 0 > > nTrg121 = 147410, nTrgMulti = 16432, MnTrgMultiHits = 2.25237 > > nSrc121 = 86069, nSrcLost = 0, nSrcMulti = 42416, MnSrcMultiHits > > = 2.31875 > > Saving target data > > > > > > > > 4. Next step was just for verifying, but we received an error (maybe > > it's not so important): > > cd $SUBJECTS_DIR/subjid/surf > > mri_segstats --seg > > $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh --in > > lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt > > > > Loading /usr/local/freesurfer/subjects/fsaverage/surf/lh.fsaverage.ROI5.mgh > > Loading lh.thickness.fsaverage.mgh > > ERROR: dimension mismatch between input volume and seg > > > > We want to determine the statistics only for this mask for the whole > > group of subjects (qdec, or mri_glmfit). > > If the mapping of our subjects thickness data was good, what should > > we do next in order to achieve our goal ? > > > > Thank you. > > > > Best regards, > > Dr. Alexandru Hanganu > > ___________________________________ > > Department of Neurology, > > Schleswig-Holstein University Hospital, Kiel Campus > > Arnold-Heller-Str. 3, building no. 41 > > D-24105 Kiel, Germany. > > > > > > ____________________________________________________________________ > > > > _______________________________________________ > > 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 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > _______________________________________________ > Freesurfer mailing list > 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
