OK. Does that mean there is not a problem? I'm just not sure if you need
anything from us.
On 12/12/2019 7:37 PM, Joshi, Nandita wrote:
External Email - Use Caution
Hi Dr. Greve,
I apologize, maybe I should have been more specific. What I meant to say was,
for example, in the attached area and volume distribution graphs over regions,
we have most outliers in the superior frontal, and inferior parietal regions.
However, on examining these regions for the subjects that are outliers, in
comparison to the other subjects that are not, there doesn't seem to be an
increased inclusion of voxels in these regions which could possibly explain why
these might be outliers compared to the rest of the group.
- Nandita
On 12/12/19, 7:02 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Greve, Douglas
N.,Ph.D."<mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D.>
<freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
dgr...@mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofdgr...@mgh.harvard.edu>
wrote:
When you say that you looked at the labels/segmentations and that
nothing looked horribly wrong, would that mean that the labels are
accurate and that they are not really outliers?
On 12/5/19 7:26 PM, Joshi, Nandita wrote:
> External Email - Use Caution
>
> Hi Dr. Greve,
>
> Thanks so much for your response. The primary reason for my wanting to do
this is due to a large number of outliers in terms of area and volume. Our
subject population is cognitively impaired older adults > 60 yrs. The custom
surface based template might help in investigating the area outliers, but it
wouldn't help in investigating the volume outliers. Since the DK atlas is
constructed from a population 18-86 years including 10 people with Alzheimer's
Disease, I am not even sure if making a new volume atlas would help.
>
> Attached are graphs showing the distribution of the region wise area,
volume, and thickness of all subjects in lh (filled circles) and rh (open
circles). I looked into the aparc and aseg labels in specific regions for the
subjects that are outliers, but nothing seems to have gone horribly wrong in
terms of parcellation. Any pointers on how I can investigate and if a custom
volume template might help?
>
> Thanks,
> Nandita
>
>
>
> On 12/5/19, 1:36 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Greve, Douglas
N.,Ph.D."<mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D.>
<freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
dgr...@mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofdgr...@mgh.harvard.edu>
wrote:
>
> We currently do not have a mac build of mri_aparc2aseg, and we
recommend
> downloading the freesurfer dev release to resolve this issue.
>
>
>
> On 12/5/19 1:00 PM, Joshi, Nandita wrote:
> > 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."<mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D.>
<freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
dgr...@mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofdgr...@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
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > >
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> > >
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