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Hi Doug,

That would do it. Thanks! However, I ran bbregister, got out the register.dat file, input that into the vol2subfield command and now it’s giving me an error stating: "dst or src volume is invalid. Inverse likely wrong…error: mir_concatenate_lta: unknown transform type for LTA1. My apologies if these are newbie mistakes, I’m still learning my way around Freesurfer.

Thanks!

Erin

On Jul 30, 2020, at 12:50 PM, Erin Moe <Erin.Moe@colorado.edu> wrote:

Hi Doug,

Thanks for the quick response. I've attached a text file of the terminal output after running vol2subfield with the --dubug option.

Thanks!

Erin

---

From: Erin Moe <Erin.Moe@colorado.edu>
Sent: Tuesday, July 28, 2020 11:26 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Thalamic nuclei in FSL

 

Hi Freesurfer experts,

I ran segmentThalamicNuclei on my dataset and would like to use the segmentations on BOLD data in FSL using Featquery. I tried running vol2subfield but got an error: “set: Variable name must contain alphanumeric characters. I’ve tried a mired of other things to get the thalamic nuclei output into the mean_func.nii.gz space but haven’t had much success. What would you recommend I try?

Terminal input for vol2subfield (note the dashes are double, my email client automatically changes them to single dashes):

vol2subfield —i mean_func.nii.gz —reg $subject —$subject/mri/ThalamicNuclei.v12.T1.mgz —BOLD_thalamus.mgz

Thanks!
Erin

<vol2subfield_debug.txt>

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