External Email - Use Caution
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