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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
