It worked, thanks. I tried to invert it but the coordinates didn't fully
correspond; I must have made an error. Thanks for helping me out!
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Hi Doug,
Thanks for the code, this works. Nevertheless, I am a bit unsure about
whether the masks that are used as input into this command are correct. I
like to check all the stages of the process and when I open the mask.mgh
file within the appropriate glm folder, the segmentation is totally
Hello,
I have a question regarding nifti (.nii) input files. I have .nii image
files, which are aligned to AC-PC with SPM. The actual (original) data in
this file is not changed, but the transformation matrix is saved in the
.nii file.
When displaying the freesurfer reconstructed results with
Hi Krista:
You may want to update tcsh. You can do this by using SUDO and 'yum update'.
best,
Alan
On Thu, Nov 14, 2013 at 10:42 AM, krista kelly krista.kell...@gmail.comwrote:
Hello,
I'm running freesurfer's recon-all using Linux and the past few subjects
I've run, recon-all has exited
Hello,
I'm running freesurfer's recon-all using Linux and the past few subjects
I've run, recon-all has exited with errors. I've ran a few subjects so far
with no problems, and now all of a sudden there's an issue and I can't
figure out why. I have been able to run these problem' subjects using
Thank you. Can I then use
aparcstats2table --subjects --hemi lh --meas thickness --parc
lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the
values in 1 tablefile or should I use other command?
On Wed, Nov 13, 2013 at 6:59 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
To fix the second problem, why not reorient the T2w image so the image axes
are oriented in the way that FreeSurfer expects?
Peace,
Matt.
From: Martijn Steenwijk martijnsteenw...@gmail.com
Date: Thursday, November 14, 2013 8:13 AM
To: freesurfer freesurfer@nmr.mgh.harvard.edu
Cc: Veronica
Hi Martijn
we can print warning and errors if FSLDIR is not set, but the registration
errros seem to be mostly a flirt issue, no? Have you posted on the FSL
list?
Bruce
On Thu, 14 Nov 2013,
Martijn Steenwijk wrote:
Dear all,
There seem to be some serious issues with the T2pial /
Hi Matt, Bruce,
The problems are indeed a flirt issue, but given that it's programmed with
--init-fsl there is not much flexibility.
However, from a FS point of view, it might be a better and more robust
approach to first register FLAIRraw.mgz to raw.mgz, and then concatenate
the resulting
I think you can do it with mri_convert rl. I don't think it makes sense to
expect FLIRT to get the registration right reliably if the axes are off (in
the HCP Pipelines we definitely don't expect this and make sure all images
are RPI before processing them).
Peace,
Matt.
From: Martijn
Hi Matt
hopefully Doug will chime in, but I don't see why that is the case. We
preserve all the RAS information when we conform, so the info should be
there for flirt
cheers
Bruce
On Thu, 14 Nov 2013, Matt Glasser wrote:
I think you can do it with mri_convert ?rl. I don't think it makes
I think it would be
--parc aparc.pial_lgi
doug
On 11/14/2013 11:27 AM, Anna Jonsson wrote:
Thank you. Can I then use
aparcstats2table --subjects --hemi lh --meas thickness --parc
lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values in
1 tablefile or should I
The non-gui verion is to run mri_glmfit from the command line:)
doug
On 11/13/2013 05:23 PM, dgw wrote:
Hello,
I sent the message below yesterday. I can confirm that I am also having
problems visualizing with qdec using the standard nmr center install over nx.
Everytime I click generate
What is your tkmedit command used to view the segmentation?
doug
On 11/14/2013 07:10 AM, Suzanne Oosterwijk wrote:
Hi Doug,
Thanks for the code, this works. Nevertheless, I am a bit unsure about
whether the masks that are used as input into this command are
correct. I like to check all the
There are two matrices in the nifti file (qform and sform). By default
we use the qform. The qform is 6 dof and so is probably not appropriate
for your talairach transform. Bottom line is that the sform is probably
being ignored.
doug
On 11/14/2013 07:18 AM, c...@uos.de wrote:
Hello,
I
you will see some differences due to reslicing and interpolation. These
differences should be somewhat random, so they might be difficult to
detect in a group analysis. But in general, you should treat all your
data the same.
On 11/14/2013 03:40 PM, c...@uos.de wrote:
thanks, that was
Hi,
My interest is in cortical thickness measurements for longitudinal Alzheimer
data, namely the ADNI dataset.
My understanding is that recon-all can be used to generate cortical thicknesses.
I am trying to understand how the default parameter values used in recon-all
were arrived at.
Are
Dear All,
I was would like to double check the order of edits for longitudinal data. I
did edits for my cross-sectional data, and for my base data, I did the
following:
1. skull strips edits (if necessary) 2. control points edits 3. white matter
edits 4. pial edits 5.brain final surfs edits.
I
Dear all,
In CentOS5,which freesurfer5.3 version(centos4 or centos6?) can be compatible?
Thanks!
All the best.
2013-11-15
Rujing Zha___
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Dear All,
I need to export a T1.mgz and N points (Nx3 coordinates .mat file) of the
same volume in SPM12b. N are actually intracranial electrodes.
For this, I save T1.mgz as .nii prior to import into SPM.
Should I use volume index, volume RAS or surface RAS coordinates for N?
What other
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