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 <greve@nmr.mgh.harvard.edu>
An: Alexandru Hanganu <hanganu.alexandru@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.
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard..edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Von: Doug Greve <greve@nmr..mgh.harvard.edu>
An: Alexandru Hanganu <hanganu.alexandru@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.
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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