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/FreeSurferColorLUT) 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.hansen@regionh.dk / morten.sejer.hansen@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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