Hi Morten
the insula you should be able to get out of the cortical labels in the
various *.annot files. The substantia nigra we don't segment at the
moment, and I suspect it would be hard to do so from only a T1-weighted
scan.
cheers
Bruce
On Tue, 22 Mar 2016, Morten Sejer Hansen wrote:
Dear Experts,
I am interested in retrieving the volume of the insula and substantia nigra
from T1W
structural scans converted to nii.gz files. All scans have undergone the
recon-all
process without error.
I have seen volume estimations of Insula and substantia nigra performed in
several
studies, but I can’t seem to figure out how I retrieve these volumes.
I ran the command:
asegstats2table --subjects 1_T1W_recon-all 2_T1W_recon-all 3_T1W_recon-all
4_T1W_recon-all 5_T1W_recon-all --meas volume --tablefile Subcortical.txt
SUBJECTS_DIR : /Applications/freesurfer/subjects
Parsing the .stats files
Building the table..
Writing the table to Subcortical.txt
following this I get at fine output with several volume estimation of
subcortical
structures, but without the Insula (left and right), and without the substantia
nigra
(left and right).
I tried to run the same command on “Bert”, and ended up with the same result
(with
the insula and substania nigra still missing). I also tried to add the
--all-segs
But without any change in the output.
On the
FreeSurferColorLUT(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorL
UT) I can see that the structures I am interested in have the following
numbers: 19,
27, 55 and 59.
Could you provide me answers on how to extract the volumes of the insula and
substantia nigra?
Thanks a lot!
Kind regards
Morten Sejer Hansen
Morten Sejer Hansen
MD
Direct: + 45 26373611
Mail: morten.sejer.han...@regionh.dk / morten.sejer.han...@dadlnet.dk
Department of anaesthesiology 4231
Centre of head and orthopaedics
Copenhagen University Hospital, Rigshospitalet
Blegdamsvej 9
2100 Copenhagen
Tel: +45 35 45 35 45
Web: www.regionh.dk
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