External Email - Use Caution
Hi Douglas,
Thank you so much for your response. Attached is the message I receive when I input the --debug.
[image: Screenshot 2023-11-16 at 4.26.05 PM.png]
On Wed, Nov 15, 2023 at 7:50 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
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:
External Email - Use CautionHello 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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