Hi Ajay
can you explain your entire processing stream, including the details of
the acquisition? What sequence/coil/scanner was used? You could fix your
problem by looking at the defects on the inflated.nofix, overlaying
lh.defect_labels on it to see where they are, then figuring out what caused
them in the volume. However, there is a bug in mris_fix_topology that only
comes up when it encounters a large enough defect (with nvertices>200,000).
The code tries to avoid running it's normal genetic algorithm as it would
take days (or weeks) to finish, since it scales with the square of the
number of vertices. I haven't figured out what is going wrong yet, but
hopefully will have a code fix soon.
cheers
Bruce
On Tue, 1
Dec 2015, Ajay Kurani wrote:
Hi Bruce, When looking at my top slices in brain ask I noticed that the
gray/white matter shows but the darker areas surrounding it are not present
(this usually goes to the edge of the brain). Could the large defects be a
result of having masked this out on the input file? I multiplied the
template with the GM/WM/CSF masks they provided to get the brain extracted
so I only see this missing in the very top few slices of the brain.
Thanks,
Ajay
On Tuesday, December 1, 2015, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Falk
I don't think you need to rerun the qsphere. I'm pretty sure
this is a bug in mris_fix_topology for giant defects, but
haven't finished tracking it down yet
cheers
Bruce
On Tue, 1 Dec 2015, Falk Lüsebrink wrote:
Hi Ajay,
you should
cp ?h.orig.nofix ?h.orig
cp ?h.inflated.nofix ?h.inflated
with ? being l or r depending your hemisphere.
After the fixing stage the
surfaces got damaged somehow, therefore you have to
recreate it them. I’m
not entirely sure about the qsphere. Probably you
have to run the -qsphere
stage again also.
Best,
Falk
Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com]
Gesendet: Montag, 30. November 2015 21:50
An: Falk Lüsebrink
Cc: Freesurfer support list; Bruce Fischl
Betreff: Re: [Freesurfer] Freesurfer 6.0 -
Autorecon2 failure
(mris_euler_number) using high res (0.5mm
isotropic) T1 image
Hi Falk,
I used the command and got the following error:
Command: ris_topo_fixer -mgz -warning -seed 1234
ICBM lh
mris_topo_fixer -mgz -warning -seed 1234 ICBM lh
INFO: assuming .mgz format
setting seed for random number genererator to 1234
reading
inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
lin_sym
_09b/ICBM/surf/lh.orig...
mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn
i_icbm152_nlin_sym
_09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215,
but face 46196 not in
vertex 24215 face list
mris_topo_fixer -mgz -warning -seed 1234 ICBM rh
INFO: assuming .mgz format
setting seed for random number genererator to 1234
reading
inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
lin_sym
_09b/ICBM/surf/rh.orig...
mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn
i_icbm152_nlin_sym
_09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903,
but face 35822 not in
vertex 18903 face list
Any suggestions would be appreciated.
Thanks,
Ajay
On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink
<falk.luesebr...@ovgu.de>
wrote:
Hi Ajay,
I ran into the same error processing hires data a
while ago using a nightly
build of centos 6 with the hires flag only. Disk
space or alike wasn't an
issue. I ran mris_topo_fixer instead of
mris_fix_topology to get working
surfaces.
Best,
Falk
-----Ursprüngliche Nachricht-----
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im
Auftrag von Bruce Fischl
Gesendet: Sonntag, 29. November 2015 22:48
An: Freesurfer support list
Betreff: Re: [Freesurfer] Freesurfer 6.0 -
Autorecon2 failure
(mris_euler_number) using high res (0.5mm
isotropic) T1 image
Hi Ajay
are you sure you didn't run out of disk space? That
error is a sanity check
on the surfaces that should never occur
cheers
Bruce
On Sun, 29 Nov 2015, Ajay
Kurani wrote:
> Hello Freesurfer experts,
> I am trying to run Freesurfer 6.0 beta
(downloaded 10/15/15
> version) with the -hires flag to process an MNI
template image which
> is 0.5mm isotropic. Stage 1 ran well and on
stage 2 there is an error
> during
> pocessing:
>
> Command run:
> recon-all -s ICBM -autorecon2 -openmp 8 -3T
-hires -expert expert.opts
>
> I supplied a skull stripped brain which was nu
corrected and so I used
> the T1.mgz and copied it to brainmask.mgz and
nu.mgz in autorecon1
> stage. I then ran autorecon2 and it was working
well until I was at
> the -fix stage and ran into the following error:
>
>
> Error:
> mris_euler_number ./surf/lh.orig
> mrisFindNeighbors: ./surf/lh.orig:
face[46196].v[0] = 24215, but face
> 46196 not in vertex 24215 face list
>
>
>
> I am not sure if this is due to the fact that we
have a very high
> resolution image (template) and if there are any
modifications needed
> aside from the hires flag. Are there any
suggestions you have?
>
> Thanks,
> Ajay
>
>
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