Is it just those few vertices that are appear to be on the sphere? Can you send me the terminal output from the mri_label2label with the --close operation?
On 05/10/2017 12:16 PM, Hengda He wrote: > Hi Freesurfer Developers, > > I'm trying to map the vertices of caudal middle frontal in one subject > into the space of another subject by using mri_label2label. And I used > the method mentioned in this > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2015-November/042298.html > > We are using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I > noticed the mri_label2label in v5.1 has the bug of getting holes in > the mapped > labels(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42600.html). > > So I am using the > /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin from > freesurfer-x86_64-unknown-linux-gnu-dev5-20160513. > > For example, we have source Labels(aparc-lh-003_5thCol.label), which > are all in SurfaceRAS coordinates: > #!ascii label , from subject FreeSurfer vox2ras=TkReg > 8 > 104996 -35.679 16.281 25.156 1 > 104997 -36.480 16.439 25.362 2 > 104998 -37.443 16.702 25.369 3 > 105705 -41.554 16.840 28.930 4 > 105716 -40.445 17.153 28.046 5 > 105720 -39.570 17.200 26.959 6 > 131017 -29.315 12.915 45.422 7 > 131030 -31.304 12.514 46.455 8 > > By running this: > /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin > --srclabel aparc-lh-003_5thCol.label --srcsubject FreeSurfer > --trglabel aparc-lh-003_5thCol_Reg2MNI.label --trgsubject > FreeSurferMNI152 --regmethod surface --hemi lh > > We got mapped Labels(aparc-lh-003_5thCol_Reg2MNI.label), which are all > in SurfaceRAS coordinates: > 119096 -39.670 37.222 12.833 3.0000000000 > 117433 -44.642 35.253 14.575 4.0000000000 > 118250 -43.206 35.844 14.273 5.0000000000 > 119091 -42.114 36.692 14.044 6.0000000000 > 120517 -26.436 38.614 21.780 7.0000000000 > 121236 -25.959 39.757 24.739 8.0000000000 > 1321 -22.346 -82.436 -9.530 0.0000000000 > 121253 -26.213 39.504 23.711 8.0000000000 > > But the mapped labels I got from the mri_label2label in v5.1 and that > from using mri_label2label.bin in dev are quite similar to each other > when applying the method to around 3500 labels. > > So I am wondering if the bug of getting holes was fixed by providing > morphological operations in the updated mri_label2label like close > operation. If it is true, I am confused about the mapped labels from > mri_label2label with close operation. > > For example, with the same source labels above, I ran > > /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin > --srclabel aparc-lh-003_5thCol.label --srcsubject FreeSurfer > --trglabel aparc-lh-003_5thCol_Reg2MNI_close2.label --trgsubject > FreeSurferMNI152 --regmethod surface --hemi lh --close 2 > > And we got mapped Labels(aparc-lh-003_5thCol_Reg2MNI_close2.label): > 119096 -39.670 37.222 12.833 3.0000000000 > 117433 -44.642 35.253 14.575 4.0000000000 > 118250 -43.206 35.844 14.273 5.0000000000 > 119091 -42.114 36.692 14.044 6.0000000000 > 120517 -26.436 38.614 21.780 7.0000000000 > 121236 -25.959 39.757 24.739 8.0000000000 > 1321 -22.346 -82.436 -9.530 0.0000000000 > 121253 -26.213 39.504 23.711 8.0000000000 > 1045 -1.690 -91.572 -40.145 0.0000000000 > 118251 -18.413 75.394 63.061 0.0000000000 > 118258 -21.026 75.715 61.847 0.0000000000 > 119092 -19.797 75.786 62.165 0.0000000000 > > The problem is that four additional labels 1045, 118251, 118258 and > 119092 are not actually on the white matter surface but seem to be > right on a sphere(ex. label 1045, 1.690^2+91.572^2+40.145^2=100^2). > But I checked all other mapped labels like 119096, they are on the WM > surface in the SurfaceRAS coordinates. > > I am using CentOS release 6.9. > > Thanks! > > All the Best, > Hengda > > > _______________________________________________ > 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 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.
