[Freesurfer] read_surf surface

[Shizuka Hayashi]

External Email - Use Caution

Dear Freesurfer team,

I have a question about the inconsistency between the vertex read from 
read_surf and vertex shown in Freeview.
I have a volume from the hippocampal subfield pipeline and I converted it to 
surface mesh using
mri_tessellate mri/lh.hippoAmygLabels-T1.long.v21.mgz -an 
surf/lh.hippoAmygLabels-T1.long.v21.surf.

Then I smoothed the surface using mris_smooth 
surf/lh.hippoAmygLabels-T1.long.v21.surf 
surf/lh.hippoAmygLabels-T1.long.v21.surf

Now I want to get the corresponding voxel of lh.hippoAmygLabels-T1.long.v21.mgz 
with the vertex. In Freeview, for example, the vertex 0 is [5.17, -19.5, 4.83]. 
I know how to convert this vertex to the corresponding voxel.
However, when I read the surf/lh.hippoAmygLabels-T1.long.v21.surf from Matlab 
using read_surf, the first vertex ( vertex(1,:,:)) is equal to 
[165.4900,217.3600,-159.7300].

Are there any ways to solve the issue?

Thank you.

Regards,
Shizuka
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[Freesurfer] longitudinal hippocampal subfield

[Shizuka Hayashi]

External Email - Use Caution

Dear Freesurfer team,

I'm studying in longitudinal hippocampal changes. Currently I have output from 
recon-all with T1 and T2-FLAIR across each subject for each time point and 
output from the longitudinal pipeline for each subject.
Now, I want to run the longitudinal hippocampal subfield but the documentation 
states that it is for T1 scans only.
Can I run segmentHA_T1_long.sh with above output or do I need to rerun all 
above process with only T1 scans.

Thank you.

Best regards,
Shizuka
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