Those are giant defects. Check the inflated.nofix to see if the skull or
cerebellum is attached
On Aug 19, 2011, at 11:38 AM, Catherine Wan wrote:
> Dear List,
>
> I've been encountering a series of error messages when I did recon-all on a
> number of subjects, using Freesurfer v5.1
>
>
I am trying to use the output meshes from freesurfer (lh/rh.pial and
lh/rh.white converted to .stl) with the BET meshes from FSL. They seem to
be in different coordinate systems and have to be moved and scaled to match
correctly. Is there an easy transform that can do this. I have tried
several
Hi Knut - What are the permissions of this file? One thing you could try
is to run bedpostx on /media/Elements/freesurfer/dti/1/dtsave/1/dmri
directly from the command line instead of through trac-all and see if that
works (monitor is a script that bedpostx launches that prints to the
screen t
Dear List,
I've been encountering a series of error messages when I did recon-all on a
number of subjects, using Freesurfer v5.1
Below are the error messages for 3 different subjects (all with lesions). I
tried them using both dicom and nifti, and on various computers, but the
same messages appea
the default 'area' measure is for the white surface (while area.pial is
for the pial surface).
n.
On Fri, 2011-08-19 at 13:22 +0200, Tetiana Dadakova wrote:
> Dear list,
>
> In qdec in "Measure" option I can choose either area or area.pial.
> What is the difference between them?
>
> Thank you,
can you visually inspect the talairach xform in tkmedit and see if it
looks correct (or tkregister2)? What format were the images you gave to
recon-all? If analyze, make sure that the orientation is correct
cheers
Bruce
On Fri, 19 Aug 2011, Ahmed, F, Me
wrote:
Hello Freesurfers,
I got
Hi
I have started to run tracula on my own data. However when I run the
second stage I get this erros bedpostx_seychelles: line 260:
/media/Elements/freesurfer/dti/1/dtsave/1/dmri.bedpostX/monitor:
Permission denied. I have tried running is as root as well but it did
not help. Is there anythin
Hi Y'all, I recently found a bug in the way that FS converts
surface-based area (eg, lh.area) and volume (eg, lh.volume) into
standard space. I'm testing a fix now, but you should not use area or
volume measures until I've posted the fix and you re-run either
mris_preproc or qcache. The files
Hello Freesurfers,
I got this error on my processing and wondered what the problem may be:
Talairach Failure Detection Mon Aug 15 16:26:35 SAST 2011
/mnt/hgfs/VBM/freesurfer_EONCS/EONCS/NN117/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: tr
both :)
On Fri, 19 Aug 2011, Chris Filo Gorgolewski wrote:
> Did you go for backwards compatibility or between flags consistency?
>
> On 18 August 2011 20:17, Bruce Fischl wrote:
>> fixed, thanks
>> On Thu, 18 Aug 2011, Chris Filo Gorgolewski wrote:
>>
>>> A tiny typo in mri_convert:
>>>
>>> filo
Dear list,
In qdec in "Measure" option I can choose either area or area.pial.
What is the difference between them?
Thank you,
Tanja.
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Did you go for backwards compatibility or between flags consistency?
On 18 August 2011 20:17, Bruce Fischl wrote:
> fixed, thanks
> On Thu, 18 Aug 2011, Chris Filo Gorgolewski wrote:
>
>> A tiny typo in mri_convert:
>>
>> filo@filo-Precision-M6500:~$ mri_convert | grep voxsize
>> -vs, --voxsize
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