I think you SUBJECTS_DIR is set to the wrong place. What happens if you run
ls $SUBJECTS_DIR/s_001
Do you see your subject there?
On 9/8/2020 12:33 PM, Marina Fernández wrote:
External Email - Use Caution
Hi Doug,
I used the command that you sent me but I have the same error message
(ERROR: stating file /usr/local/freesurfer/...).
Do you know other options?
Thank you in advance.
Marina
-----------------------------------------------------
Douglas N. Greve
<https://www.mail-archive.com/[email protected]&q=from:%22Douglas+N.+Greve%22>
Tue, 08 Sep 2020 08:14:19 -0700
<https://www.mail-archive.com/[email protected]&q=date:20200908>
Try something like this
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.lobe.stats -b -a ../label/lh.lobe.annot fsm010 lh white
On 9/8/2020 7:58 AM, Marina Fernández wrote:
External Email - Use Caution
Dear experts,
I would like to get a .stats file this the volume and thickness of
lobe annotation, so I am following the steps indicated in this
link https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation.
Specifically, I used these commands:
mri_annotation2label --subject s_001 --hemi lh --lobesStrict lobe.annot
cd /usr/local/freesurfer/subjects/; mris_anatomical_stats -a
s_001/label/lh.lobe.annot -f s_001/stats/lh.lobe.stats -b s_001
lhThe output file that I get (lh.lobe.stats) seems normal and
contains the measurements that I need (volume and thickness). The
problem is that the terminal output contains this error message:
ERROR: stating file
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot
(below you can find the full terminal output)
What I have to do to obtain the lh.lobe.stats file (with the same
or similar stucture) without the error message?
Best regards,
Marina
% /TERMINAL OUTPUT / % /
subject = s_001
annotation = aparc
hemi = rh
surface = white
Reading surface
/usr/local/freesurfer/subjects/s_001/surf/rh.white
Loading annotations from
/usr/local/freesurfer/subjects/s_001/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Seg base 2000
MRISmergeAnnotations: parcCount=11, newparcname=frontal
mri_annotation2 supposed to be reproducible but seed not set
MRISmergeAnnotations: parcCount=9, newparcname=temporal
MRISmergeAnnotations: parcCount=5, newparcname=parietal
MRISmergeAnnotations: parcCount=4, newparcname=occipital
MRISmergeAnnotations: parcCount=4, newparcname=cingulate
computing statistics for each annotation in s_001/label/rh.lobe.annot.
reading volume /usr/local/freesurfer/subjects/s_001/mri/wm.mgz...
reading input surface
/usr/local/freesurfer/subjects/s_001/surf/rh.white...
Using TH3 vertex volume calc
Total face volume 176610
Total vertex volume 173305 (mask=0)
reading input pial surface
/usr/local/freesurfer/subjects/s_001/surf/rh.pial... reading input
white surface /usr/local/freesurfer/subjects/s_001/surf/rh.white...
reading colortable from annotation file...
colortable with 8 entries read (originally none)
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
ERROR: stating file
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot
atlas_icv (eTIV) = 1198953 mm^3 (det: 1.624839 )
37262 24668 63218 2.363 0.474 0.124 0.029 414 43.8 frontal
3602 2412 6370 2.374 0.615 0.137 0.027 54 3.8 cingulate
12917 8443 18251 2.024 0.428 0.134 0.030 171 15.6
occipital 19235 12890 36112 2.488 0.535 0.119 0.028
211 21.0 temporal 26568 17417 41499 2.204 0.466 0.119
0.024 287 25.6 parietal
2510 1617 4741 3.018 0.820 0.126 0.036 28 3.9 insula/
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