Sounds like it. View the label on the volume while displaying the surfaces in the volume and see if they intersect
On 09/29/2016 01:12 PM, Crawford, Anna wrote: > 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. >>> >>> >>> >> =================================== >> >> >> 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. > > -- 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
