See the REAME file here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
On 12/5/19 11:47 AM, Joshi, Nandita wrote: > > 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 Dec5 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 Jun2 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 Dec5 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
