I added the --paint option which seemed to run successfully. I loaded it as a label on the inflated surface and it did not crash, but I do not see it anywhere on the surface. Does this just mean that I didn't actually draw it on the surface? As in, everything was done correct, the location of the label isn't on the surface though.
Thank you! Anna ________________________________________ From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:45 PM To: Crawford, Anna; Bruce Fischl Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu Subject: Re: Infalted/Label 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 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. >> >> >> > =================================== > > > 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/ =================================== 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
