i used dmax white. I now can see it on the inflated surface. Thank you for all your help in getting this working. Sorry, it took so long since I'm trying to figure all of this out still. The next step will be to take a volume that already has a selected region defined and projecting that region onto the inflated surface which I'm guessing will be somewhat similar to this.
Thanks again, Anna ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 1:14 PM To: Douglas N Greve Cc: freesurfer@nmr.mgh.harvard.edu; Crawford, Anna; Anna Crawford Subject: Re: [Freesurfer] Infalted/Label you can also look at the vertex index of the first entry in the label file and type that into the "cursor" field in freeview so it will go to that point. My guess is that it does intersect the surface, otherwise the label indices would have stayed -1 On Thu, 29 Sep 2016, Douglas N Greve wrote: > 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. 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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. 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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. 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