Hi
i run recon-all on 13 subjects (severe TBI) using the condor cluster
environment, 10 of them were stopped with, mostly ending with this error (found
in SUBJECTS_DIR/subj/scripts/recon-all.log) :
ncvarput: ncid 4: Input/output error
miicv_put: MINC package entry point
Dear Freesurfers,
Is there a way to export a large number of tkmedit images? I would like to
show other people how certain areas evolve as I change coordinates, and I
find myself capturing a lot of screenshots.
Thank you very much!
Sincerely,
Ye
___
Hi,
I just wanted to let you know that I solved the problem by creating a new
virtual machine on which I installed the newest version of Ubuntu (13.04),
FSL, and Freesurfer manually. I guess there could have been a solution with
the virtual machine running Xubuntu via the Freesurfer virtual disk
hi bruce and others:
i'm getting a recon failure on this particular brain: H0351.1009
the quality isn't great, but if you can take a quick look at the brain to
see if you can spot any particular issues, that would be great.
4 of the others finished recon and 3 are almost there.
cheers,
satra
hi doug,
bbregister was running into an error trying to do T2pial refinement
sequence of commands and output here:
https://gist.github.com/satra/5934639
and it looks like the absence of FSLDIR
i didn't have FSL installed on this machine - i thought that freesurfer had
it's own version of
Hi Sebastian
can you email us the first couple of lines of the control.dat file?
thanks
Bruce
On Fri, 5 Jul 2013, Sebastian Urchs wrote:
Hi,
I am trying to migrate to freeview from tkmedit and started comparing edits
in both programs. I found that when I set control points in tkmedit and
Hi Ye
you can use tcl to script it, or use freeview which I think can save
slice-flythroughs as a movie.
cheers
Bruce
On Fri, 5 Jul 2013, ye tian wrote:
Dear Freesurfers,
Is there a way to export a large number of tkmedit images? I would like to
show other people how certain areas evolve as
Hi Satra
what was the error? Pretty poor gray/white contrast in the data.
cheers
Bruce
On Fri, 5 Jul 2013, Satrajit Ghosh wrote:
hi bruce and others:
i'm getting a recon failure on this particular brain: H0351.1009
the quality isn't great, but if you can take a quick look at the brain to
Dear Doug,
Some time ago we e-mailed about the optimazation of the timing ou our
experimental design. Based on that conversation I have used the folling
command line:
--ntp 255 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1.0 --ev Gain2 4.0 8.0
--ev Gain4 4.0 8.0 --ev Gain6 4.0 8.0 --ev Gain8 4.0
hi bruce,
mri_watershed failed.
cheers,
satra
mri_watershed -T1 -brain_atlas
/nitrc/usr/local/freesurfer//average/RB_all_withskull_2008-03-26.gca
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume
Mode: Use the information of atlas
Hi,
I found that in some of my subjects there are - after manual correction -
focal regions with zero cortical thickness. On closer inspection, I can see
that the white matter and pial boundaries are touching in these regions -
hence probably the zero thickness.
My question is: should I manually
Hi Sebastien
check the aseg - it is probably regions that are not cortex (where the
surface passes adjacent to a noncortical structure like the callosum or the
basal ganglia
Bruce
On Fri, 5 Jul 2013,
Sebastian Urchs wrote:
Hi,
I found that in some of my subjects there are - after manual
I think the problem may be this:
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
you can also update bbregister with the version here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister
doug
On 07/05/2013 09:55 AM, Satrajit Ghosh wrote:
hi doug,
An Input/output error is a message from the operating system (not
related to FS). It usually means that the disk is corrupted.
doug
On 07/05/2013 06:47 AM, LAOUCHEDI MAKHLOUF wrote:
Hi
i run recon-all on 13 subjects (severe TBI) using the condor
cluster environment, 10 of them were
or maybe full?
On Fri, 5 Jul 2013, Douglas N Greve wrote:
An Input/output error is a message from the operating system (not
related to FS). It usually means that the disk is corrupted.
doug
On 07/05/2013 06:47 AM, LAOUCHEDI MAKHLOUF wrote:
Hi
i run recon-all on 13 subjects (severe
Hi,
I never got an answer to this problem, which affected numerous programs
including mris_resample, but I solved it with help from my local sysadmin.
I think the problem is that there is a versioning difference between Centos and
other Linux flavors (I use Linux Mint 14). But anyway, I:
1)
thanks doug, i'll try that version right now.
cheers,
satra
On Fri, Jul 5, 2013 at 11:37 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
I think the problem may be this:
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
you can also update bbregister with the version
hi doug,
same error with the updated one when i don't have FSL installed.
writing to
/data/subjects/H0351.2002/mri/transforms/tmp.bbregister.7856/template.nii...
fslregister --s H0351.2002 --mov
/data/subjects/H0351.2002/mri/transforms/tmp.bbregister.7856/template.nii
--re
g
Dear Freesurfer experts,
for one subject (out of over 80 already processed) I get i nthe last step
an error I am unable to locate. The output from the tracula -path command
says at the end: option 0 unknown.
There are no reported problems in -prep, and -bedp. The script uses default
values (I run
hey doug,
fslregister already uses flirt.fsl from freesurfer. you only need to
provide the schedule file and update the path. i just ran it copying the
schedule file over from fsl to a new location and setting the environment
variable FSLDIR, which i presume could be replaced with
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