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 Caution
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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