Dear all,
we observe some segmentation faults in the temporal lobe in single patients.
Gyri are within the brain mask but outside the pail boundaries. Editing brain
mask.mgz or wm.mgz does not resolves the problem.
Examples are attached.
How can we add missing brain? we are using free surfer v5
Are there any other groups of labels which are, by default, produced in
comparable less vs more restrictive ways?
Regards,
Don
>
>
> On 14-09-08 12:39 PM, Anastasia Yendiki wrote:
> > Hi David - On the difference between .thresh and "not .thresh" labels:
> > The BA labels come from averagi
Dear Bruce,
I've uploaded 2 subjects, both with the same problems, it'll be great
if you can take a look.
https://dl.dropboxusercontent.com/u/6070302/GUSTO_01_04002.tar.gz
https://dl.dropboxusercontent.com/u/6070302/GUSTO_01_04011.tar.gz
Yes, I've gone through the tutorials. I've added back wm
Hi Anastasia and FS-community
Thanks for your quick and helpful answer. I hope your server doesn’t treat me
like SPAM already. ;-)
Anyways I have some several other questions. Is there a way to run bedpostX for
different subjects in a row? Or do I have to run it for each subject
separately. I’
Hi Michele - The anatomical segmentation does look good, but from the
screenshot the DWI data seems to be noisy in the orbitofrontal area, which
may be affecting the uncinate. It's hard to tell just from one slice.
If you upload all the tracula output directories of this subject (dmri,
dmri.
uploaded (and activated).
Thanks!
On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Michele - The anatomical segmentation does look good, but from the
> screenshot the DWI data seems to be noisy in the orbitofrontal area, which
> may be affecting th
Thanks, Michele. Hard to tell what's causing this, perhaps a bit of
distortion orbitofrontally. You may be able to fix this type of thing by
reinitializing the tract reconstruction: Add "set reinit = 1" to your
configuration file, set the pathlist to include only the left and right
uncinate,
Hi Doug,
Running it as you suggested didn't work either. I tried it as follows:
1) /homes/8/hhe0/Documents/mri_glmfit-sim --glmdir --sim mc-z
1 1.3 mcz1_1.3 --sim-sign abs --cwpvalthresh .05
It says:
'nknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
Then I though
Not sure what is wrong. Is it executable? Were you able to save the file
from your email or did you cut and paste it into a file and save the file?
On 09/10/2014 04:03 PM, Eryilmaz, Huseyin Hamdi wrote:
> Hi Doug,
>
> Running it as you suggested didn't work either. I tried it as follows:
>
> 1)
Yes I could save the file from my email into '/homes/8/hhe0/Documents'. Under
'Permissions' tab of this file, 'Allow executing file as program' option is
checked.
I can try cd'ing into that folder then run the command as :
>> mri_glmfit-sim --glmdir --sim mc-z 1 1.3 mcz1_1.3
>> --sim
Hey everyone,
i have tried to run the mri_cvs_register command but it returned an error in the second step. It returned:
"VolumeMorph load - failed to open input stream"
I have entered: "mri_cvs_register --mov sub1 --template sub2"
What could i do to fix it?
Thanks for your help
Hi Ben,
What version of freesurfer are you using?
Lilla
On Wed, 10 Sep 2014, bigben2...@web.de wrote:
Hey everyone,
i have tried to run the mri_cvs_register command but it returned an error in
the second step. It returned:
"VolumeMorph load - failed to open input stream"
I have entere
Could you also send the log file along?
Thanks, Lilla
On Wed, 10 Sep 2014, bigben2...@web.de wrote:
> I'm using the version stable v5.3.0.
> Ben
>
>
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Hi,
I'm trying to compile Freesurfer current dev version from read only cvs
repo according to developers guide on my machine with Ubuntu 14.04, gcc
4.8.2, I proceed as follows in dev/ directory:
1- ./setup_configure: which finishes without error
2- ./configure with vxl and mni library dir
*News from the Human Connectome Project (HCP)*
*September 10, 2014*
*HCP Processing Pipelines Released *
The WU-Minn HCP Consortium is pleased to announce the open source release
of HCP data processing pipelines at
https://github.com/Washington-University/Pipelines. To download, click
*release
Thanks again, for the record, I'm using freesurfer version 5.3.0 on Centos
6.
On 9/09/2014 11:00 PM, <_andre...@sapo.pt> wrote:
> Hi Will,
>
> Just to clarify, what version of FS are you using? I think it might not be
> 5.0 and I don't know if everything aplies if we are using different
> version
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