Can you run it with --debug as the first option and send the resulting terminal output?

On 11/9/2023 12:54 PM, Mirsol Choi wrote:

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Hello Freesurfers, 

I am trying to segment the hippocampus into its subfields and take the FA values from each subfield area. 

I am able to segment the hippocampus using the command 

(segmentHA_T1.sh) and I was also able to perform the dt-recon function on dwi data. 

I am trying to map the fa.nii file from dt-recon into the hippocampus subfield volume rh.hippoAmygLabels-T1.v22.HBT.mgz, however when I run the code that is provided by vol2subfield -help:

vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v21.HBT.mgz --outreg outreg.lta

or 

vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v21.HBT.mgz --o fa.rh.hbt.mgz

I am met with a message stating "set: Variable name must contain alphanumeric characters."

How can I fix this "variable name must contain alphanumeric characters" issue and run this command?

Thank you all for your time, help and expertise. 

M

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