Hello
I am trying to analyse my retinotopic data with freesurfer FS-FAST.
Regarding the workflow, I found very helpful information on the
freesurfer WIKI, except one preprocessing issue:
Instead of smoothing my data in the volume I want to to smooth the
retinotopic data on the surface before st
Hi Yuanchao,
Please find the answers below:
Quoting Zhangyuanchao :
> Hi,Marie
>
> In the paper "A surface based approach to quantify local
> gyrification" on TMI. There is a discussion the relation between lGI
> and curvature-based method. I noticed the following discussion:
> "In the c
Hi all,
I've tried running mri_label2vol on a few different computers now and keep
encountering the same memory error. Can anyone provide suggestions as to how
to get around this problem? I've included the output from a run using linux
on a dual 3.05 GHz Xeon with 8GB ram below.
Thanks for your hel
Hi,
I have a Siemens DTI dataset which I am converting with mri_convert
(freesurfer) from dicom to nifti and then fitting the tensors with FSL.
Since mri_convert outputs my data in Neurological orientation, despite of
fsl's warnings about flipping, I have to do fslswapdim and
fslorient -swapori
Mike Harms tried to explain that to me, but I was missing how the
resampling affected the i term. Thanks, Tom, for spelling it out for me. ;-)
Fortunately, John Harwell has less noise in his neural network than I
do, so Caret does the right thing. (Just checked.)
On 10/17/2009 10:29 AM, Doug Gr
I believe that the FreeSurfer version is also doing the right thing. Do
you have reason to believe otherwise?
thanks
doug
Donna Dierker wrote:
> Mike Harms tried to explain that to me, but I was missing how the
> resampling affected the i term. Thanks, Tom, for spelling it out for me. ;-)
>
>
Nope, sorry. You can use our dt_recon program to do the tensor fit, but
it might not be compatible with higher level FSL routines.
Alina Jurcoane wrote:
> Hi,
>
> I have a Siemens DTI dataset which I am converting with mri_convert
> (freesurfer) from dicom to nifti and then fitting the tensors w
No, Doug. I think I was the only one mis-interpreting the FDR steps,
and I'm considerably closer to the Caret source than the Freesurfer
source. ;-)
On 10/19/2009 11:18 AM, Douglas N Greve wrote:
> I believe that the FreeSurfer version is also doing the right thing.
> Do you have reason to bel
good, just checking!
Donna Dierker wrote:
> No, Doug. I think I was the only one mis-interpreting the FDR steps,
> and I'm considerably closer to the Caret source than the Freesurfer
> source. ;-)
>
> On 10/19/2009 11:18 AM, Douglas N Greve wrote:
>> I believe that the FreeSurfer version is als
how many labels are in that annot? The way that mri_label2vol works is
to create a multi-frame volume with the number of frames equal to the
number of labels in the annotation. It then counts the number of times
each voxel "sees" a given label. It then assigns that voxel to the most
frequently
Alex,
Can you send me the orig.mgz and .annot file used as input to this? To
the file drop:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Nick
On Mon, 2009-10-19 at 13:38 +0100, Alex Fornito wrote:
> Hi all,
> I've tried running mri_label2vol on a few different computers now an
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