External Email - Use Caution
Thank you so much for that! The README file instructs to download
make_average_subject and platform specific mri_aparc2aseg. However, the mac
version of mri_aparc2aseg is missing in the patch. Could it be possible to
download it from elsewhere?
- Nandita
On 12/5/19, 12:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Greve, Douglas N.,Ph.D." <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
dgr...@mgh.harvard.edu> wrote:
USE CAUTION: External Message.
See the REAME file here
https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_pub_dist_freesurfer_6.0.0-2Dpatch_&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=Bk3PG21nu20V-TX_S982zJE-KkrgCuPol41Dhbe_0mI&m=HRcVNlmwdK9YHH6teQ4oW9oc6SDFzz79TS63mOlbWIY&s=6p4504imNdnEktx-WXKqAlxMvMCQ1EYnJW_deB2CAWI&e=
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://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_SurfaceRegAndTemplates&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=Bk3PG21nu20V-TX_S982zJE-KkrgCuPol41Dhbe_0mI&m=HRcVNlmwdK9YHH6teQ4oW9oc6SDFzz79TS63mOlbWIY&s=LmIaVqBLyDekwkZsc46m3nOdn25B7E96m_UuRzDu3Ew&e=
>
> 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
>
>
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