Hi Morten
not yet. The STN is on our list of things to segment (as is the SN),
although both will likely require good T2* (or maybe T2) weighted images.
cheers
Bruce
On
Tue, 22 Mar 2016, Morten Sejer Hansen wrote:
Dear Bruce,
Thank you for your quick and precise answer.
One last question. Is it possible to segment the Nucl. Subthalamicus? It is a
subcortical anatomical structure, and is a part of the basal ganglia. It is not
included in the output following 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
Kind regards
Morten
-----Oprindelig meddelelse-----
Fra: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne af Bruce Fischl
Sendt: 22. marts 2016 14:02
Til: Freesurfer support list
Emne: Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are
not reported
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/FsTutoria
l/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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