I have two subjects, subA and subB.  subA has a binary ROI mask, native
space, that I'd like to place in subB's native space. Both subjects have
been run through all stages of recon, edited, etc. Is there a better or
easier way to achieve this than what I've run?:

#Resample the native space binary ROI file into "brainmask" space
mri_convert -rl /subA/mri/brainmask.mgz -rt nearest --no_scale 1
ROI.nii.gz /subA/mri/ROI.mgz

#Convert ROI file into a label
mri_cor2label --id 1 --c /subA/mri --i ROI.mgz --l ROI.label

#Move label from subA to subB
mri_label2label --srcsubject subA --srclabel /subA/mri/ROI.label
--trgsubject subB --trglabel /subB/mri/ROI_to_subB.label --regmethod volume

#Convert warped ROI label to a volume
mri_label2vol --label /subB/mri/ROI_to_subB.label \
--subject subB \
--temp brainmask.mgz \
--regheader brainmask.mgz \
--o /subB/mri/ROI_to_subB.mgz

#Convert the volume back to native subB space
mri_convert -rl subB_native.nii.gz -rt nearest --no_scale 1
/subB/mri/ROI_to_subB.mgz ROI_to_subB_native.nii.gz

A few follow-up questions:

1) When running mri_label2label, is better to use surface or volume for
the "regmethod"?  Which method will give me a better fit for my output?
2) The output I'm getting looks striped (there are holes in the binary
mask) and doesn't quite fit the anatomy (the final file is shifted up
and away from where I would expect it to be although in the general
vicinity of what I would expect).  It's almost as if I've chosen a wrong
target or file along the way.  I don't expect the fit to be perfect, but
did I do something wrong?

Thanks in advance to any and all replies.

Notice: This UI Health Care e-mail (including attachments) is covered by the 
Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only 
for the use of the individual or entity to which it is addressed, and may 
contain information that is privileged, confidential, and exempt from 
disclosure under applicable law. If you are not the intended recipient, any 
dissemination, distribution or copying of this communication is strictly 
prohibited. If you have received this communication in error, please notify the 
sender immediately and delete or destroy all copies of the original message and 
attachments thereto. Email sent to or from UI Health Care may be retained as 
required by law or regulation. Thank you.

Freesurfer mailing list

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Reply via email to