Hi Doug,
OK, just one last question! I've decided I'd rather use the smaller masks
(generated by resampling aparc+aseg.mgz to functional space, as in my Method
1), since the difference is small (~2%), but there's absolutely no overlap
in this case. Thus it's both the most conservative approach and
Hi Nick:
I uncompress fscudabins-linux-centos4.tgz, but I continue to get the error:
"mri_em_register_cuda -skull nu.mgz
/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca
transforms/talairach_with_skull.lta
Acquiring CUDA device
Using default device
CUDA Error in file 'devicemanage
Thanks Doug.
I'll do it!
TK
On Fri, Aug 20, 2010 at 7:08 PM, Douglas N Greve
wrote:
> The ICV is not computed based on a sum of the volumes of individual
> structures. It is a summary measure computed from the registration to
> talairach space. See the wiki and Randy Buckner's paper for more
The ICV is not computed based on a sum of the volumes of individual
structures. It is a summary measure computed from the registration to
talairach space. See the wiki and Randy Buckner's paper for more info.
As for combining across field strengths, that would not be highly
recommended. If you
Hi FS,
I have two important doubts...
Is it the CSF volume included in the ICV volume (aseg.stats)?
Is it possible include in the same group patient acquired from 1.5T and
3.0T? Do you have an article about this topic?
TK
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i've just posted the file 'fscudabins-linux-centos4.tgz' here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4/
note that we have recently discovered a new problem with running
mri_em_register_cuda on brains with skull: the results are off compared
to the cpu version. so
you can play around with the fill threshold
doug
Timothy Vickery wrote:
> I see, thanks for the quick clarification. So in the Method 2 there is
> a chance that some voxels will show up in multiple ROIs, right? Is
> there a modification of Method 2 that maximizes that number of labeled
> voxel
I see, thanks for the quick clarification. So in the Method 2 there is a
chance that some voxels will show up in multiple ROIs, right? Is there a
modification of Method 2 that maximizes that number of labeled voxels while
ensuring that they will not show up in multiple ROIs?
Thanks again,
Tim
On
Hi, fsurfer team,
I am just asking if there is any coming release of fs5.0 for ia64 cpu
architecture? Thank you!
Best,
--
Xinian Zuo, Ph.D
Associate Research Scientist
Institute for Pediatric Neuroscience
NYU Child Study Center
215 Lexington Ave., 14th Floor
New York, NY 10016
Phone: (212) 263 2
The difference is the partial volume correction is different if there
are a bunch of other labels there (aparc+aseg) vs only one label
doug
Timothy Vickery wrote:
> Hi all,
>
> I'm creating binary mask volumes in a subject's native functional
> space from the segmented brain in aparc+aseg.mgz (
If the source is the FSL standard brain, then use
$FREESURFER_HOME/average/mni152.register.dat as the registration. See if
that works at stage 4.
Lena Palaniyappan wrote:
> Doug, thanks
> So, is this a correct sequence:
>
> Im extracting thickness measures from VBM contrasts generated by FSL
>
Hi all,
I'm creating binary mask volumes in a subject's native functional space from
the segmented brain in aparc+aseg.mgz (FS v 4.5). I have found that doing
this two different ways produces different results, and I'm wondering if
anyone can illuminate why this might occur and which method is mor
Doug, thanks
So, is this a correct sequence:
Im extracting thickness measures from VBM contrasts generated by FSL VBM
analysis (this is 2X2X2):
1. To convert VBM contrast file to a binary mask:
mri_binarize --i vbmcontrast.nii.gz --o vbmmask.nii --min 0.95 --max 1 (for
fsl vbm generated corrp
Hi:
Any solution for the 32 bit version ?...
Sincerely,
Gonzalo Rojas Costa
> Message: 6
> Date: Fri, 20 Aug 2010 15:55:39 -0400
> From: Nick Schmansky
> Subject: Re: [Freesurfer] CUDA Error - all CUDA-capable devices are
> busyor unavailable
> To: Daniel Guellmar
> Cc: f
CUDA users,
The problem with the _cuda binaries (message: CUDA Error in file
'devicemanagement.cu'...) has been fixed, and new binaries are available
for download from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/
download the file 'fscudabins-linux-centos
You'll have to sample that mask onto the surface using mri_vol2surf with
the --interp nearest option. You will also have to have a registration
matrix, which will depend on where the volume came from.
doug
Lena Palaniyappan wrote:
> I have a mask file which I need to overlay on the individual i
I have a mask file which I need to overlay on the individual images of a
group of subjects to extract thickness values within ht mask. But the mask
is of dimension 2X2X2, will this be an issue?
Thanks
Lena
___
Lena Palaniyappan
Clinical Lecture
no, it's very, very old. Mona: you should definitely rerun everything
On
Fri, 20 Aug 2010, Pedro Paulo de Magalhães Oliveira Junior wrote:
FreeSurferAlpha? Is this a new product?
On Fri, Aug 20, 2010 at 15:08, Mona wrote:
Hello,
I'd like to extract hippocampal and PHC volumes from files
r
FreeSurferAlpha? Is this a new product?
On Fri, Aug 20, 2010 at 15:08, Mona wrote:
> Hello,
>
> I'd like to extract hippocampal and PHC volumes from files
> reconstructed with FreeSurferAlpha.
> Is there a command for this or would you recommend re-reconstructing
> to obtain label volumes?
>
> T
Hello,
I'd like to extract hippocampal and PHC volumes from files
reconstructed with FreeSurferAlpha.
Is there a command for this or would you recommend re-reconstructing
to obtain label volumes?
Thank you,
Mona
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Freesurfe
You don't have to specify a threshold at all. In that case it will
average over the entire structural ROI. What you have below will average
only over the positive values. What about the current stream is not
streamlined? Or, how could it be improved?
doug
Adam Nitenson wrote:
> Hello Freesu
This does not work too well as the left hemi is registered to the right
hemi atlas. This can create systematic LR differences that don't really
exist. We are working on a symmetric template (and have been for a while).
doug
johanna feiler wrote:
> Hello FreeSurfers,
>
> I wonder if it is possi
That warning in and of itself is not critical, but it does suggest that
the initial registration failed. I assume the registration still looks
bad? Does this happen on a bunch of data sets or just this one? There
are a couple of more steps. First, you can run with --init-fsl and check
the initi
Thanks for the suggestions. It is whole-brain epi data. Unfortunately, it was
not acquired at the same time as the anatomical. Just for the heck of it I
tried substituting --init-header for --init-fsl anyway, and got the same
warning about negative G-W contrast.
-Kathleen
On 8/19/10 2:39 PM
Hello FreeSurfers,
I wonder if it is possible to mirror my complete data, so that the right
hemisphere will be the left one and the other way round. I was thinking about
using this command:
fslswapdim z -x -y https://produkte.web.de/go/demail02
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