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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
