That is a volume-based label. Try using the --paint option to mri_label2label to convert it to a surface-based label (assuming it is actually on the surface). Run mri_label2label with --help to get an example
On 09/29/2016 12:38 PM, Crawford, Anna wrote: > This is the output on label2label. The first colum of the created column is > -1. > > mri_label2label --srcsubject segfs --srclabel > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label > --trgsubject segfs --trglabel Testing1N.label --regmethod volume > > srclabel = > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label > srcsubject = segfs > trgsubject = segfs > trglabel = Testing1N.label > regmethod = volume > > usehash = 1 > Use ProjAbs = 0, 0 > Use ProjFrac = 0, 0 > DoPaint 0 > > SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ > FREESURFER_HOME /tools/freesurfer > Loading source label. > Found 216 points in source label. > Starting volumetric mapping 216 points > Src2TrgVolReg: ----------------- > 1.000 0.000 0.000 0.000; > 0.000 1.000 0.000 -0.000; > 0.000 -0.000 1.000 -0.000; > 0.000 0.000 0.000 1.000; > 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 > 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 > 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 > 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 > 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 > Writing label file Testing1N.label 216 > mri_label2label: Done > > Thanks, > Anna > ________________________________________ > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, September 29, 2016 12:29 PM > To: Crawford, Anna > Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve > Subject: RE: Infalted/Label > > I'll cc the list, which I should have done the first time. No, you > didn't do anything wrong. This is what mri_label2label should do - sample > these locations onto the surface you specify and fill in the vertex > indices. Check the output of label2label and see if it has values >= 0 > cheers > Bruce > > On Thu, 29 Sep 2016, Crawford, Anna wrote: > >> Hi, >> >> I just checked all the labels I created and they all have -1 in the first >> column (the file name ending in 'N' should be the one created from >> mri_label2label). So, I did something wrong when originally creating the >> label I assume. When I created it, under the ROI tab, I created a new one >> and then drew it in the viewer with a volume (I did both white matter and >> brain mask) also loaded. Was this wrong? >> >> Thank you, >> Anna >> ________________________________________ >> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >> Sent: Thursday, September 29, 2016 12:00 PM >> To: Crawford, Anna >> Cc: Anna Crawford; Douglas N. Greve >> Subject: RE: Infalted/Label >> >> Hi Anna >> >> the label you send me hasn't been sampled onto the surface, which is why >> it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You >> can tell this is the case as the first column has all -1. If it had been >> sampled onto the surface these values would be in [0, nvertices]. >> >> Does you newer one have non-zero values in this column? >> >> cheers >> Bruce >> >> On Thu, 29 Sep 2016, >> Crawford, Anna wrote: >> >>> It is in the left hemisphere. >>> ________________________________________ >>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >>> Sent: Thursday, September 29, 2016 10:38 AM >>> To: Anna Crawford >>> Cc: Crawford, Anna; Douglas N. Greve >>> Subject: Re: Infalted/Label >>> >>> are the labels lh or rh? >>> On Wed, 28 Sep 2016, Anna Crawford wrote: >>> >>>> Hopefully this works better for you. Thank you, >>>> >>>> Anna >>>> >>>> >>> >>> 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 . 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If >> you have received this communication in error, please contact the sender >> immediately and destroy the material in its entirety, whether electronic or >> hard copy. >> >> Thank you. >> >> >> > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News > & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of > our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by 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 the reader of this message is not the intended recipient or the > employee or agent responsible for delivering the message to the intended > recipient, you are hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If you have received > this communication in error, please contact the sender immediately and > destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > -- 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
