glad it worked out Bruce On Thu, 29 Sep 2016, Crawford, Anna wrote:
> 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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