Hi Wei-Ta
if the remaining skull and dura don't affect the pial surface then it
doesn't matter. Run it all the way through recon-all and you'll probably
find it doesn't matter.
cheers
Bruce
On Fri, 19 Aug
2011, Wei-Ta Chen wrote:
Hi
I did autorecon1 on T1 structural brain images acqu
Hi
I did autorecon1 on T1 structural brain images acquired by
GE magnet. However, a small piece of skull with dura
still remained on brainmask.mgz (around the occiput), even after adjustment
of watershed threshold to 10. (Some brain would loss
when threshold was lowered to 7 or 5). I wondered if I
I'll try to write a tutorial this weekend
-- iOS 5
Em 18/08/2011, às 20:01, Nolan Nichols escreveu:
Hi Pedro,
I came across your post on the FreeSurfer mailing list and am trying to find
the AMI you created (
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018272.html).
I have
Thanks for the suggestion with upx, Nick. I gave it a try and decompressed
mri_info and mri_convert, but after decompressing neither worked and only
returned a message of 'error' as the stdout. I also tried a 32 bit install
on Ubuntu and an install on CentOS, and I am getting the same issue across
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: specify the size (mm) -
> useful for upsampling or downsampling
> filo@filo-Precision-M6500:~$ mri_convert --voxsize
> mr
A tiny typo in mri_convert:
filo@filo-Precision-M6500:~$ mri_convert | grep voxsize
-vs, --voxsize: specify the size (mm) -
useful for upsampling or downsampling
filo@filo-Precision-M6500:~$ mri_convert --voxsize
mri_convert --voxsize
mri_convert: unknown flag "--voxsize"
type mri_convert -
Dear Doug,
I will be very grateful if you can advise me with the following issue: if I
finished running the GLM what is the best way to further analyse my data in
order to see if there is any relation between age (at seizure onset) and
cortical thickness for my patients versus control group.
Dear Doug,
I just checked my results for the average thickness from each subject
generated in the csdbase.y.ocn.dat file in different clusters (e.g. I have 5
clusters for p<0.05). For cluster #1 - posteriorcingulate, the average
thickness for subject 1 is different from the average thic
Then I'm sorry, I don't know what could've gone wrong there. Perhaps try
asking on the FSL list?
On Thu, 18 Aug 2011, Moiyadi, Ammar wrote:
> I believe I'm running the latest version of fsl for Ubuntu, 4.1.4
>
> Ammar Moiyadi, BS
> Professional Research Assistant
> Department of Psychiatry
> Un
I believe I'm running the latest version of fsl for Ubuntu, 4.1.4
Ammar Moiyadi, BS
Professional Research Assistant
Department of Psychiatry
University of Colorado Anschutz Medical Campus
303-724-5490
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
S
No you don't. This is the reason I wrote mri_glmfit-sim -- so you don't
need to specify things that it can figure out automatically.
doug
Antonella Kis wrote:
> Hi Doug,
>
> When I run the:
>
> mri_glmfit-sim \
> --glmdir lh.age.glmdir \
> --cache 4 neg \
> --overwrite
>
> do I need to specify t
Hi Doug,
When I run the:
mri_glmfit-sim \
--glmdir lh.age.glmdir \
--cache 4 neg \
--overwrite
do I need to specify the --fwhm and/or to use the residual fwhm obtained from
the y.fsgd file? If not when I have to input this value during my GLM analysis?
Thank you.
Antonella
Was this by any chance an older version of bedpost that you ran? Older
versions didn't use to create mean_dsamples.nii.gz.
On Thu, 18 Aug 2011, Moiyadi, Ammar wrote:
> Hi Freesurfers - I am encountering an error in trac-all -paths where it
> cannot find the mean_dsamples.nii.gz file in my dmri
Hi Freesurfers - I am encountering an error in trac-all -paths where it cannot
find the mean_dsamples.nii.gz file in my dmri.bedpostX directory since it was
not created during the bedpost step. Because I ran the original bedpost (not
the Seychelles version) I was wondering if this output file w
Yes, I was able to run FSL commands, but normally I usually use the FSL GUI,
but now you're pointing this out, I try to run the commands that did not run
with tracula and shows me the same error about loading shared libraries.
How I can fix this?
Carolina
2011/8/18 Anastasia Yendiki
>
> Hm, it
Hm, it seems like all FSL commands give you a shared library error. Were
you able to run FSL commands properly before updating freesusrfer?
On Thu, 18 Aug 2011, Carolina Valencia wrote:
Hi,After update the FS version to 5.1, I follow the Tracula tutorial and run
the command
trac-all -prep -c
Hi,
After update the FS version to 5.1, I follow the Tracula tutorial and run
the command
trac-all -prep -c
$TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject
It starts to run but finish with errors:
writing to
/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tut
They are in the header now (see below for example). Those values in the
old file should not be used (which is why we removed them for later
versions).
doug
# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter
volume, 253760.315035, mm^3
# Measure rhCortex, rhCortexVol, Right h
Hi all,
In the aseg.stats and wmparc.stats output files in *version 4.2.0*, there
were four volumes named:
Left-Cerebral-White-Matter
Left-Cerebral-Cortex
Right-Cerebral-White-Matter
Right-Cerebral-Cortex
Does anyone happen to know what the corresponding volumes are in *version
5.1*? They don't a
On Wed, Aug 17, 2011 at 5:03 PM, Leo Souza wrote:
> Can you provide quick instructions on how to run those tests? I am new to
> FreeSurfer.
I'll have to defer to others on running those two programs - it's been
too long since I worked on Freesurfer. I believe the website has some
general informa
Dear Nick, dear all,
I am still having problem with loading the Project FIle.
When I save the Project File, one of the lines I get in the terminal window is:
cp: /Applications/freesurfer/subjects/qdec/*.levels: No such file or directory
I have several folders in /qdec, and a separate *.levels fi
Hi,
We (Aapo Nummenmaa and I) are developing cross-platform software that
would allow translating third-party coordinates back and forth with
Freesurfer segmentations.
Our example structural image is MEMPRAGE_4e_p2_1mm_iso (1 mm isotropic,
192 sagittal slices, T1 weighting).
Our third-party sys
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