Dear all,
I would like an accurate segmentation of the brain without skull in native
space. I am running a recon-all with Freesurfer 6 and Ubuntu 16.04. When it
finishes, I find mistakes and I erase some skull voxels from brainmask.mgz. I
run recon-all again and it finished without errors.
Wh
Dear FreeSurfer experts,
I am using mris_preproc command with following options:
mris_preproc --s s_001 --s s_002 --s s_003 --target my_subject_average
--hemi lh --meas my_input_surf.mgh --out /my_output_path/output_file
I observe mris_preproc uses mri_surf2surf. My question is related
Thanks you for your reply.
I have used surfreg script and now it runs correctly. However, my subject list
is very long, I have 100 subjects and running surfreg with all subject takes 13
hours (using all my cpus in a parallel way). Is there any option to reduce this
long time? Any cuda file?
T
Thanks you anyway, Douglas
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Dear Freesurfer experts,
I have a question related to make_average_subject command and Freesurfer
versions.
When I used to create my average subject with Freesurfer 5.3, I got
lh.cortex.label and rh.cortex.label files inside label folder with 149955
vertexs. Moreover, lh.Medial_Wall.label and
Hi,
We are not using the make_average_subject 6.0.0-patch. Do you think it would be
a possible solution? Where can I find that patch?
On the other hand, we've noticed that recon-all, which is a final
make_average_subject step, fails. I send you the recon-all.log. However, maybe
it is not rel
Hi,
I have installed the patch and it doesn't fix the label files problem. We have
tried make_average_subject with the other 56 subjects and Medial_wall.label
contains about 300 vertexs. It is very different from the other 60 subjects.
Nevertheless, we have also repeated the test with Freesurf
Hello,
I have upload the data. Recipient mail was ahoo...@mgh.harvard.edu. Please,
check you have received it.
Thanks very much,
M del Mar
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Hi,
Have you take a look at our data? Have you find any possible cause? We need to
continue with our analysis and it is now stopped.
Thanks you in advance,
M del Mar
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Hi Andrew,
Thanks very much! I have tried the new version of make_average_surface and it
works fine. I am very gratefull.
Best,
M del Mar
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Hi,
I am sorry for insisting, but I have found a new mistake in your new version of
make_average_surface.
rh.medial_wall.label contains 13733 vertex, it is a desired result. However,
rh.cortex.label contains all 163842 vertex, i.e, it covers medial wall area
too. That's why we still have the s
Hi Andrew,
My test in December with last version of make_average_surface worked correctly.
However, now I am trying to make another average subject and medial_wall.label
is not created. I am using the last patch as last time. It is unusual because
last time label folder was correctly created. I
Yes, it solves medial_wall label problem but not mri_aparc2aseg error.log. I
attached you in a previous message:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56610.html
Many thanks,
M del Mar
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