Hello Freesurfers,

My name is Mirsol and I am currently trying to obtain FA values from particular hippocampus subfields by registering our fractional anisotropy map (FA.nii.gz) from dt_recon command and our hippocampus segmentations from the command segmentHA_T1.sh.

I have followed the protocol on the website "Segmentation of hippocampal subfields and nuclei of the amygdala" to perform the segmentation, and at the bottom of the website, it mentions:

"6. Multimodal integration

To extract values within the subfields from another modality (eg, DTI or fMRI), use vol2subfield. Run with --help for examples."

Upon using vol2subfield --help on UNIX (macOS), I was shown these scripts:

1. To get a registration between an input volume and a subfield volume

vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v22.HBT.mgz --outreg outreg.lta

2. To map the input volume into the subfield volume space

vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v22.HBT.mgz --o fa.rh.hbt.mgz

3. To compute segmentation statistics of the input volume

vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v22.HBT.mgz \

--o fa.rh.hbt.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol avgwfvol.mgz

I have tried all three codes presented here, but I am met with this message when I do.

"set: Variable name must contain alphanumeric characters."

I am quite unsure what to do from here and have not been able to troubleshoot this issue.

If someone out there could offer some advice or support, I will be forever grateful.

Thank you so much for your time,

Mirsol