mri_label2vol will transfer it into the volume, no need for surf2vol On 10/04/2016 03:54 PM, Joel Bruss wrote: > Doug (Bruce and Trisanna)- > > Thank you all for your help. I do, indeed, have a volume, then label, > and see now how to load and view this properly. I've gotten through the > "label2label" step and now have a label (from subA) in subB space. If > I now want to back-project this label to subB's input MRI volume, would > I run the following? > > (Assuming I invert the steps I did to get the original binary mask to > subA's surface, as a label) > > mri_label2vol --label $SUBJECTS_DIR/subA/tmpdir/rh.roi_to_subB.label \ > --subject subB \ > --temp brainmask.mgz \ > --regheader brainmask.mgz \ > --o $SUBJECTS_DIR/subA/tmpdir/roi_to_subB.mgz \ > --surf pial > > mri_surf2vol --surfval $SUBJECTS_DIR/subA/tmpdir/roi_to_subB.mgz \ > --volregidentity subB --template $SUBJECTS_DIR/subB/mri/orig.mgz --hemi rh \ > --o $SUBJECTS_DIR/subA/tmpdir/roi_to_subB_orig.mgz > > > "label2vol" works but I'm now stuck on the "surf2vol" command. I end up > with the following error: > > ERROR: dimension inconsistency in source data > Number of surface vertices = 128997 > Number of value vertices = 16777216 > > -Joel > > > > > > On 10/04/2016 02:45 PM, Douglas N Greve wrote: >> The rh.roiS.mgh file is a surface overlay (ie, one value per vertex), >> not a surface itself (which would have a list of vertices, the XYZ for >> each, and neighborhood relations). When you loaded rh.roiS.mgh as a >> surface overlay, did you change the threshold to be 0.5? The default is >> 2, and if your ROI is binary (0,1), then no voxels would ever appear >> above threshold >> >> >> On 10/03/2016 03:20 PM, Joel Bruss wrote: >>> Sorry, it sent before I finished. I'll try this again. >>> >>> On 09/30/2016 02:00 PM, Douglas N Greve wrote: >>>> 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. >>> Yes, this looks fine >>>> Then run mri_vol2surf so sample the binary ROI volume onto >>>> the surface. >>> This is what I ran: >>> >>> mri_vol2surf --src $SUBJECTS_DIR/subA/tmpdir/roi.mgz \ >>> --out $SUBJECTS_DIR/subA/tmpdir/rh.roiS.mgh \ >>> >>>> You can view the ROI on the surface by loading it as an >>>> overlay. >>> This is a volume or a surface now? Is it just a volume resampled to the >>> >>> surface space? I can't get it to load in freeview as a surface (it just >>> crashes), and it doesn't look like anything 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. >>> I next ran this: >>> mri_cor2label --id 1 --c $SUBJECTS_DIR \ >>> --i $SUBJECTS_DIR/subA/tmpdir/rh.roiS.mgh \ >>> --l $SUBJECTS_DIR/subA/tmpdir/rh.roi.label \ >>> --surf subA rh >>>> You can also view this label in the surface in freeview. >>> At this point, it just kept loading and loading and loading and I'd >>> finally have to kill the process. I never could visualize this output. >>>> Finally, >>>> run mri_label2label using the --regmethod surface >>> At this point, I must just be feeding bad data into good commands: >>> mri_label2vol --label $SUBJECTS_DIR/subA/tmpdir/rh.roi_to_subB.label \ >>> --subject subB \ >>> --temp brainmask.mgz \ >>> --regheader brainmask.mgz \ >>> --o $SUBJECTS_DIR/subA/tmpdir/roi_to_subB.mgz \ >>> --surf pial >>> >>> I don't know where things went wrong or how to view the output to diagnose. >>> >>> >>> >>> ________________________________ >>> 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. 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-- 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 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.
