sorry, it is not clear to me what is going wrong here. Did the mri_annotation2label command fail? or mris_anatomical_stats command?

On 11/17/19 9:55 PM, Samson Nivins wrote:

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Hi FreeSurfer Team,

I am interested in individual lobular volume and thickness. So I have extracted based on the Q and A I created few script to run and extract the data.

However, I got few questions regarding thickness and WM

For extracting lobular GM I used

mri_annotation2label --subject 1014  --hemi lh --lobesStrict lh.lobesStrict.annot

mri_annotation2label --subject 1014  --hemi lh --annotation lobesStrict --outdir '/home/samson/Volume/freesurfer/subjects/recon-all_working/lh'

for computing stats I used

mris_anatomical_stats -l '/home/samson/Volume/freesurfer/subjects/recon-all_working/lh/lh.occipital.label' -b 1014 lh

I am not sure, whether any command is there to export the data.

And, the average cortical thickness which we obtain in the terminal window during individual extraction, does it correspond to the lobular thickness or as whole

For example

I extracted stats for left frontal cortex:

I got the following details in Terminal window

Number of vertices, Total surface area, total gray matter, average cortical thickness ….

In this average cortical thickness – correspond to the ROI specifc are as a whole?

Thanks for you help.

Looking forward to hearing from you

Cheers

Best regards,

Sam

*Samson Nivins  |**PhD Student*

**

*A*The University of Auckland, Liggins Institute

Building 505, Level 2, 85 Park Road, Auckland

*Ph *+(64) 21 256 5964

*E*samson.nivins@gmail.com mailto:samson.nivins@gmail.com

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