First, bring up the ROI on the volume along with the surface in the volume. You can do this with FreeView. Make sure that the ROI intersects the surface. Then run mri_vol2surf so sample the binary ROI volume onto the surface. You can view the ROI on the surface by loading it as an overlay. Then run mri_cor2label using the surface-sampled ROI as input and specifying --surf (see the --help) to make this a surface-based label. You can also view this label in the surface in freeview. Finally, run mri_label2label using the --regmethod surface
On 09/29/2016 01:58 PM, Joel Bruss wrote: > Ah, I see. The ROI will be subject-dependent (I want to do this for > multiple subjects) but the majority, if not all, should be cortical. > Any help you'd be willing to provide would be much appreciated. > > > On 09/29/2016 11:31 AM, Douglas N Greve wrote: >> The way you have it configured now, this is a volume-based ROI, so you >> need to use the volume-based reg method. This will map between the two >> subjects using the affine (12 dof) talairach registration which will not >> be as accurate as the surface-based registration. If this is a cortical >> ROI, I can show you how to redo this using a surface-based label. >> >> >> On 09/29/2016 11:37 AM, Joel Bruss wrote: >>> Another bump. >>> >>> On 09/21/2016 04:18 PM, Joel Bruss wrote: >>> >>>> 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. >>>> >>> ________________________________ >>> 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 >>> >>> > > > ________________________________ > 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
