Hello,
I was wondering if anyone has compiled the localGI code with the matlab runtime
& integrated with recon-all? We have a lot of data that we'd like to run
through the localGI stream, however we have a limited number of matlab
licenses. Are there other easy ways to "parallelize" this (i.e
Dear FreeSurfers,
I have a question regarding conversion from MNI152 coordinates to MNI305
coordinates. I want to take ROIs from a VBM study and use these exact same
ROIs in my vertexwise analysis. So I need to translate the x, y, z
coordinates from MNI152 space into MNI305 space. In previous post
Hi,
I am having trouble running qdec over an NX session. I downloaded a FreeSurfer
installation (5.3.0) to a network drive
(/cluster/neuromind/dwakeman/software/freesurfer/). The installation has no
trouble running recon-all; however, when I try to run qdec, I get vtk errors
(see below):
ERRO
Hi Doug, the Choi volume is in MNI152 space, not MNI305 space.
Hi Kathy, the correct command is "mri_vol2vol --mov $input --targ
$FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader --o
output1.nii.gz --no-save-reg --interp nearest"
Please note the use of the "--regheader" flag. The Choi
Hi,
I am using FS v5.3 and I had two questions regarding the calculation of
cortical thickness in the stats files:
1) Is the average cortical thickness of each structure (i.e. precuneus)
calculated by averaging the cortical thickness values of each location in
that structure?
2) Is the mean thic
Thanks. What do these files look like?
/export/data/brain1/RSTOM/TLR108/dmri/bvecs
/export/data/brain1/RSTOM/TLR108/dmri/bvals
These are the ones that the error message in trac-all.log is about, so
something probably goes wrong with the conversion from your original
files.
Also, I recommend ve
The problem is that your original TLR108.bvec file is still in 3 rows, not
3 columns. You need to transpose the rows into columns.
Yes, there's an example config file that comes with the 5.3 distribution
and it's as usual in $FREESURFER_HOME/bin/dmrirc.example. It's also
described on the wiki,
why not just invertthe matrix? The inverse is
1.00220.0071 -0.01770.0528
-0.01460.99900.0027 -1.5519
0.01290.00941.0027 -1.2012
0 0 01.
On 11/12/2013 09:59 AM, Anita van Loenhoud wrote:
> Dear FreeSurfers,
>
> I hav
On 11/12/2013 11:26 AM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi,
>
> I am using FS v5.3 and I had two questions regarding the calculation of
> cortical thickness in the stats files:
>
> 1) Is the average cortical thickness of each structure (i.e. precuneus)
> calculated by averaging the cortical t
Hi Ryan,
Sorry I have no experience with that. But two years ago someone from the
mailing list posted the following approach:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19239.html. Maybe
they can help you with that, or maybe someone else from the mailing list knows
better.
Hello FreeSurfer experts,
I have a question regarding group analysis and running of recon all group
wise.
For example I have group A, B, and C with several subjects in each group, if
want want to compare their cortical and subcortical measurements group wise,
how do I run the recon all.
Also c
Hi Doug,
Thanks for your response. In addition, as it it mentioned in the wiki page
the total white matter volume is volume inside the white surface minus
anything that is not WM. Would it be correct to say that even though the
total white matter volume calculation is based on a surface-based volu
yes
On 11/12/2013 03:21 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> Thanks for your response. In addition, as it it mentioned in the wiki page
> the total white matter volume is volume inside the white surface minus
> anything that is not WM. Would it be correct to say that even though
I don't know of a way to fully automate it, but once you have the single
vertex stored as a label you could run mri_label2label to do the dilation.
doug
On 11/08/2013 10:44 AM, Wesley Burge wrote:
> Dear Freesurfer experts,
>
> I am about to start an analysis where we will be drawing surface
Just put the name of the seed file, not its full path, i,e
-taskreg connect_FEF2FEF.txt
same for -nuisreg
doug
On 11/08/2013 12:34 AM, Scott Cameron Kolbe wrote:
> Hi there
> We are performing a connectivity analysis using a seed mask we have
> drawn from a label on the average surface in tk
each subject is run separately through recon-all regardless of group.
For group analysis, you will run mris_preproc, mris_surf2surf (to
smooth), then mri_glmfit (after creating an appropriate FSGD file). Look
at our group analysis tutorial and exmaple FSGD page
doug
On 11/12/2013 02:10 PM,
Great, thanks Doug!
Panos
>
> yes
>
>
> On 11/12/2013 03:21 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> Thanks for your response. In addition, as it it mentioned in the wiki
>> page
>> the total white matter volume is volume inside the white surface minus
>> anything that is not WM.
Hi Marcos, I have found and fixed the problem. As you suspected, the
orig surface was being loaded instead of the surface you need. The fix
is here (for centos6):
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_label2annot
Use the --surf option to specify your surface (witho
Dear All,
We use freesurfer in an automatic routine mainly for brain extraction/
parcellation schemes. I want to upgrade from 5.2 to 5.3 on a linux (ubuntu,
64bit) computer, but without surprises.
So:
1. When extracting files/installing freesurfer tar.gz, would the update
override the 5.2 files i
Hi Octavian
1. just untar it to a difference place and point FREESURFER_HOME there and
you should be fine without deleting 5.2.
2. Not sure. Zeke? Nick?
3. Andre (ccd) can point you at them. We find that the FLAIR version of
T2_SPACE is best, but it works without the inversion as well.
che
Hi Victor
yes, that's common. Above 5 I think things work pretty well. 2-5 takes
some work, and below 18 months or so is hard or impossible
cheers
Bruce
On Mon, 11 Nov
2013, Victor Kovac wrote:
> Hello Freesurfers,
> I am just wondering if there is a generally accepted lower age limit for
> ru
Thanks! What do you mean by my "original TLR108.bvec file"? I think the
issue may be that the bvec and bval files were originally created using
dcm2nii before we had decided to use Tracula. I am just having trouble
determining in which directory the original bvec and bval files were
created, becaus
No problem. By original I mean the file that you specify by "set bvecfile
= ..." in your config file. That one need to be in columns, not rows.
On Wed, 13 Nov 2013, Laura Christine Anderson wrote:
Thanks! What do you mean by my "original TLR108.bvec file"? I think the
issue may be that the b
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