Dear Doug,
thanks a lot for responding. Here my command lines and attached the image.
*So command line to perform the GLM analysis and get the sig.mgh file was:*
mri_glmfit --y
/data_august/Geo/freesurfer_OCD/freesurf_steps/2_mris_preproc/education_out/rh.all_gender_age.volume.10.mgh
\
--f
MRIwrite() writes out the image as a float, whereas FS insists that it
be UCHAR or INT. To get this, run
mri_convert aseg.mgz -odt int --no_scale 1 aseg.mgz
View aseg.mgz to make sure it looks right, then rerun recon-all
-autorecon2-cp -autorecon3
On 08/24/2016 05:51 PM, Silas wrote:
>
> Dear
THere is not an easy way to do this from the command line. You can do it
from matlab, something like
[Yvertices Ylabel Ycolortable] =
read_annotation('lh.Yeo2011_7Networks_N1000.annot')
[Cvertices Clabel Ccolortable] =
read_annotation('cache.th13.abs.sig.ocn.annot');
Then find the vertices in
Try using --o instead of --ocp
On 08/25/2016 05:50 AM, Oana Georgiana Rus wrote:
>
> Dear Doug,
>
> thanks a lot for responding. Here my command lines and attached the image.
>
> *So command line to perform the GLM analysis and get the sig.mgh file
> was:*
>
> mri_glmfit --y
> /data_august/Geo/
Does this file exist?
$FREESURFER_HOME/subjects/fsaverage/label/lh.BA1_exvivo.label
If not, what version of FS are you using?
On 08/24/2016 08:14 PM, Elpiniki Andrew wrote:
>
> Thankyou! It worked when I removed the trailing “ / “. However after
> it finished running, I received this error:
>
Dear all,
After running through recon-all ,I have obtained wmparc parcellation file
(see the attached figure ). I would like to obtain parcellation at specific
regions of interest for my study i.e Brain stem region and Thalamus
region, could you please let me know how i could perform parcellati
Hi Vasudev - These regions are part of the subcortical segmentation (aseg)
volume:
http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.ppt
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
a.y
On Thu, 25 Aug 2016, Dev vasu wrote:
Dear all,
After running through recon-al
Hi Freesurfer Experts,
I am trying to use freesurfer's mri_glmfit-sim tool to run permutation
testing on cortical thickness data (as recommended by Doug in my previous
post:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html )
Most of the tutorials I found were not relat
Can you tar up the glmdir and drop it to me at our filedrop (link
below)? Also,what version of FS are you using? Also, can you try running
it without backgrounding on a few (say, 100) iterations to see if it
completes? Then try with backgrounding (problem may be backgrounding)
On 08/25/2016 01
Something strange is going on in your data. You are using fsaverage, but
the size of the data in PDvsMCI_lh_thickness_10mm/y.mgh does not match
(it has 148278 vertices, not 163842 of fsaverage). This is causing the
processes to die, but the backgrounding software does not know that the
process
Hi all,
This is the subcortical mask for a subject's functional data overlaid on
top of $FREESURFER/average/mni305.cor.mgz: https://imgur.com/XQPwGVT
The mask was produced with
preproc-sess -s $SESS -fsd bold -nostc -per-session -fwhm 5 -mni305
Is the spread beyond the anatomical boundaries a
Hi Vasudev
those areas are definied in the aseg.mgz (and the wmparc.mgz), so you
should be able to get them from either of those volumes.
cheers
Bruce
On Thu, 25 Aug
2016, Dev vasu wrote:
Dear all,
After running through recon-all ,I have obtained wmparc parcellation file (see
the at
Hi Doug,
Thanks for the help! I think I figured out the issue based on your
response.
1) I created a template to use for this group and named it fsaverage
(including creating monte carlo simulations) for simplicity of integrating
with freesurfer as I am newer to it. This is why the sizes didn'
That is basically expected. I created a slightly liberal mask so as to
not exclude any regions. Having said that, you should check the
talairach.xfm transform of your subjects. Sometimes the scaling can be a
little off.
On 08/25/2016 04:40 PM, Christopher J Markiewicz wrote:
> Hi all,
>
> This
On 08/25/2016 05:13 PM, Ajay Kurani wrote:
> Hi Doug,
>Thanks for the help! I think I figured out the issue based on your
> response.
> 1) I created a template to use for this group and named it fsaverage
> (including creating monte carlo simulations) for simplicity of
> integrating with
Hi,
You might want to check out FSL’s PALM tool, which has a bit more sophisticated permutation framework, and allows for permutation in the context of non-orthogonal covariates.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Hi Doug,
No that file does not exist.I am using freesurfer
-Linux-centos6_x86_64-dev-20160617-428ca78
Thanks
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Friday, 26 August 2016 12:20 A
Thanks again Douglas! Your time and help is greatly appreciated!
Best, Silas
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
Sent: Thursday, August 25, 2016 4:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] I rece
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