Hi Doug,
my command line is
aparcstats2table --subjects subject1 subject2 subject3 --hemi rh --meas
thickness --tablefile aparc_stats.txt
I tried it on single subjects randomly chosen from the complete list and it
worksanyway it's still not working on the complete list while it works
fine
it seems that it is failing on a particular subjectwhen I exclude this
subject from the list then the command works and when I try to give the
command on that particular subject I get the error:
SUBJECTS_DIR : /usr/local/freesurfer/subjects
Parsing the .stats files
Traceback (most recent
Dear Doug,
thank you so much, the fix works great.
The problem now is that when I mris_convert the newly generated surface to .gii
the volume geometry is lost again and the offset reintroduced.
Is there a way to fix this? I have tried to give mri_surf2surf a register.dat
that would correct for
Dear freesurfer people,
Any idea whether I can apply transformation that was calculated by fsl
fnirt on the white/pial surfaces calculated using the freesurfer stream?
Thanks!
Shani
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Dear Anastasia and FreeSurfers,
I was preprocessing some data using tracula and found this error after
running trac-all -bedp -c dmrirc:
INFO: SUBJECTS_DIR is /data-02/joana/Last
INFO: Diffusion root is /data-02/joana/tracula/
Actual FREESURFER_HOME /usr/local/freesurfer-5.3
WARN: Running FSL's
Hi Pietro, that would not be the problem, at least not directly. The
problem is with the stats file itself. Compare the file to others to see
if it looks different. Is the disk full?
doug
On 9/2/13 4:38 AM, pietro de rossi wrote:
it seems that it is failing on a particular subjectwhen I
What if you specify the output of surf2surf to be a gii file?
On 9/2/13 6:47 AM, Franz Liem wrote:
Dear Doug,
thank you so much, the fix works great.
The problem now is that when I mris_convert the newly generated surface to
.gii the volume geometry is lost again and the offset
Hi Shani, I don't think you can apply a FNIRT transform to a surface.
doug
On 9/2/13 8:20 AM, Shani Ben Amitay wrote:
Dear freesurfer people,
Any idea whether I can apply transformation that was calculated by fsl
fnirt on the white/pial surfaces calculated using the freesurfer stream?
you might check on the FSL list. I think I've seen some traffic
indicating that there are some tools for doing this. I'l cc Saad as he
might know
cheers
Bruce
On Mon, 2 Sep 2013, Douglas Greve wrote:
Hi Shani, I don't think you can apply a FNIRT transform to a surface.
doug
On 9/2/13
Dear FreeSurfer experts,
how can I increase the font size on the tkmedit scale bar?
Cheers
Joerg
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The information in
A veritable game of telephone! Thanks Jesper. Matt?
On Mon, 2 Sep 2013, Jesper Andersson wrote:
Hi guys,
I didn't think we had any tools for doing that, and said so much on the FSL
mailbase. But apparently the WashU people has something that does just that
for you. I think the best person to
Hi Joerg
sorry, there doesn't seem to be any way to do this other than recompiling
the code. I could build you a version with a specific font if that would
help, assuming glut supports it
cheers
Bruce
On Mon, 2 Sep 2013, Jörg Pfannmöller wrote:
Dear FreeSurfer experts,
how can I increase
On 9/2/13 12:02 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote:
Hi Bruce,
Connectome Workbench commandline utilities can do this with FSL warp
fields:
wb_command -surface-apply-warpfield
One needs to use the inverse warp as the warpfield argument and the
forward warp as the -fnirt
Hi Doug,
this gives exactly the same surface as surf2surf followed by mris_convert (i.e.
with offset).
Thanks,
Franz
Am 02.09.2013 um 16:50 schrieb Douglas Greve:
What if you specify the output of surf2surf to be a gii file?
On 9/2/13 6:47 AM, Franz Liem wrote:
Dear Doug,
thank you
thanks Matt
Bruce
On Mon, 2 Sep 2013, Glasser, Matthew wrote:
Hi Bruce,
Connectome Workbench commandline utilities can do this with FSL warp
fields:
wb_command -surface-apply-warpfield
One needs to use the inverse warp as the warpfield argument and the
forward warp as the -fnirt
Hi Joana - What system are you running this on?
a.y
On Mon, 2 Sep 2013, Joana Braga Pereira wrote:
Dear Anastasia and FreeSurfers,
I was preprocessing some data using tracula and found this error after
running trac-all -bedp -c dmrirc:
INFO: SUBJECTS_DIR is /data-02/joana/Last
INFO:
This is an FSL problem. You can try the FSL list, and check out some links:
https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge
http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
This info is probably not stored in the gii header. I'll have to take a
look which could take a while. Depending on what you are doing, it might
not be important.
doug
On 9/2/13 2:58 PM, Franz Liem wrote:
Hi Doug,
this gives exactly the same surface as surf2surf followed by mris_convert
Thanks for the pointers, Chris. I'd call it an opportunity for FSL
customization rather than an FSL problem per se :o)
On Mon, 2 Sep 2013, Watson, Christopher wrote:
This is an FSL problem. You can try the FSL list, and check out some links:
https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge
Indeed. It's actually really easy to set up, too.
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Monday, September 02, 2013 3:46 PM
To: Watson, Christopher
Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer]
Hi All,
This may seem to be an easy question, I would just like to confirm...
I have two groups that underwent different types of training and were measured
at two time points (before and after training).
My understanding is that I should use the longitudinal scheme in freesurfer to
run
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