External Email - Use Caution Hello,
I am trying to make a study specific template based on the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates However, on running the first step: make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ... I get an error while running the recon-all is trying to run the aparc to aseg step: #@# AParc-to-ASeg aparc Thu Dec 5 11:29:33 EST 2019 /Users/nandita/FreeSurfer_recon/newtemplate \n mri_aparc2aseg --s newtemplate --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt \n relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /Users/nandita/FreeSurfer_recon subject newtemplate outvol /Users/nandita/FreeSurfer_recon/newtemplate/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /Users/nandita/FreeSurfer_recon/newtemplate/surf/lh.white Reading lh pial surface /Users/nandita/FreeSurfer_recon/newtemplate/surf/lh.pial Loading lh annotations from /Users/nandita/FreeSurfer_recon/newtemplate/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /Users/nandita/FreeSurfer_recon/newtemplate/label/tmpdir.annot2std.41916/seg.1.100110189.ctab) Reading rh white surface /Users/nandita/reeSurfer_recon/newtemplate/surf/rh.white Reading rh pial surface /Users/nandita/FreeSurfer_recon/newtemplate/surf/rh.pial Loading rh annotations from /Users/nandita/ADRC/FreeSurfer_recon/newtemplate/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /Users/nandita/FreeSurfer_recon/newtemplate/label/tmpdir.annot2std.47059/seg.1.100110189.ctab) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/nandita/FreeSurfer_recon/newtemplate/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /Users/nandita/FreeSurfer_recon/newtemplate/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter Segmentation fault Darwin Nanditas-MacBook-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Sun Jun 2 20:31:42 PDT 2019; root:xnu-4570.71.46~1/RELEASE_X86_64 x86_64 recon-all -s newtemplate exited with ERRORS at Thu Dec 5 11:29:52 EST 2019 On inspecting the mri folder, it seems the norm.mgz file has not been created at all. Looking at the flowchart of steps for the recon-all command, norm.mgz is supposed to be created in the CA Normalize step, which requires the talairach.lta in the newtemplate/mri/transforms folder, which seems to be missing as well. The only transform created in the transform folder is talairach.xfm. The talairach.lta is created in the EM GCA registration step. Do I re-run the EM GCA registration, CA normalize, and then contonue from aparc to aseg? I am not sure if since I am creating my own template, the EM GCA step requires any modifications? Any help will be appreciated. Thanks, Nandita
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