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My mistake, I think that fixed it.
Thank you!
Anna
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Monday, July 20, 2020 11:45 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] PetSurfer Crashing
Did you really mean to pass subject/mri/gtmseg.lta ? The registration is supposed to be the registration of the input (PET.template.nii.gz) to the anatomical. subject/mri/gtmseg.lta is the registration of gtmseg.mgz to the anatomical.
On 7/20/20 11:21 AM, Crawford, Anna wrote:
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Hello,
I am trying to run the PetSurfer process for the first time. I was able to run gtmseg and mri_coreg which seemed to go okay. When I tried running mri_gtmpvc, it is crashing, but I am not sure why. The command I am using and output are below. Do you have any guidance as to what is going wrong?
Thank you,
Anna
mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o subject/gtmpvc.output Loading input ../CTPET/PET.template.nii.gz done loading input 1 frames
$Id: mri_gtmpvc.c,v 1.69.2.1http://1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /mnt/netRAID18/7T/study709/S2sdt/ cd /mnt/autofs/netRAID18/7T/study709/S2sdt mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o subject/gtmpvc.output sysname Linux hostname fmri15 machine x86_64 user crawforda vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 20 avail.processors, using 1 Creating output directory subject/gtmpvc.output Loading seg for gtm subject/mri/gtmseg.mgz Loading seg ctab subject/mri/gtmseg.ctab Reading subject/mri/gtmseg.lta Replacing 18 Pruning ctab Checking tissue type done with seg vol maxFWHM = 2.95567 (voxels), PadThresh=0.0001, nPad=10 Computing auto mask Automask, reducing FOV region 256 256 109 reduced to 21 11 3 235 245 106 ERROR: LTAconcat(): LTAs 0 and 1 do not match LTA 0 ------------------- type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 10000.0000 1 4 4 9.999997615814209e-01 0.000000000000000e+00 -8.381903171539307e-09 -7.629394531250000e-06 7.450580596923828e-09 9.999998807907104e-01 0.000000000000000e+00 0.000000000000000e+00 -7.450580596923828e-09 7.450580596923828e-09 9.999998211860657e-01 -1.525878906250000e-05 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999999403953552e-01 src volume info valid = 1 # volume info valid filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = 4.125000000000000e+00 3.554792785644531e+01 -2.000000000000000e+01 dst volume info valid = 1 # volume info valid filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = 4.125000000000000e+00 3.554792785644531e+01 -2.000000000000000e+01 subject subject fscale 0.150000 LTA 1 ------------------- type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 10000.0000 1 4 4 9.999999403953552e-01 0.000000000000000e+00 0.000000000000000e+00 -2.099999237060547e+01 0.000000000000000e+00 9.999999403953552e-01 0.000000000000000e+00 -1.100000762939453e+01 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -3.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = ../CTPET/PET.template.nii.gz volume = 256 256 109 voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.029999971389771e+00 xras = -1.000000000000000e+00 -0.000000000000000e+00 0.000000000000000e+00 yras = -0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 zras = -0.000000000000000e+00 -0.000000000000000e+00 1.000000000000000e+00 cras = 3.660461425781250e+00 1.723927307128906e+02 1.247645019531250e+03 dst volume info valid = 1 # volume info valid filename = volume = 235 245 106 voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.029999971389771e+00 xras = -1.000000000000000e+00 -0.000000000000000e+00 0.000000000000000e+00 yras = -0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 zras = -0.000000000000000e+00 -0.000000000000000e+00 1.000000000000000e+00 cras = -1.861288452148438e+01 1.840597229003906e+02 1.250690063476562e+03 -------------------------- Data load time 10.9 sec nmask = 3714389, nsegs = 100, excluding segid=0 FWHM: 6 6 6 Std: 2.54797 2.54797 2.54797 nPad 10, PadThresh 0.0001 Checking Ref Ids Segmentations used for rescaling 174 Pons Computing Seg PVF Segmentation fault (core dumped)
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