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
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
________________________________
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.
________________________________
_______________________________________________
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
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
