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 off
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 tkm
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 wrote:
> 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
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
Dear all,
There seem to be some serious issues with the T2pial / FLAIRpial processing
options provided in the latest versions of FreeSurfer.
First of all, although not clearly documented, T2pial / FLAIRpial
processing does require the FSLDIR to be set (in order to use bbregister
with --init-fsl).
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
wrote:
> yes and yes
>
>
> On 1
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
Date: Thursday, November 14, 2013 8:13 AM
To: freesurfer
Cc: Veronica Popescu , Hugo Vrenken
Subject: [Freesurfer] T2pial/FLAI
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 / FLAIRpia
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 regist
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 Steenwi
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 make
So the T2w image is already having the axes realigned to RAS with
mri_convert in FreeSurfer prior to running -init-fsl? If that is the
case, FLIRT should work well enough assuming the input orientation
information in the T2w and T1w NIFTI headers was accurate. I suppose you
could also restrict th
It should not make a difference. We compute an initial registration
based on the header and pass that to FLIRT. Can you verify that this
initial registration is correct? You can do that with
tkregister2 --mov FLAIRraw.mgz --targ orig.mgz --regheader --reg junk
If that looks ok, then it is poss
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
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 genera
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
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
Hmmm, I can't replicate this error. This is 5.3 I assume?
doug
On 11/12/2013 06:02 PM, Michael Waskom wrote:
> sorry, unclear why the original email wasn't included in the reply.
> copied here:
>
>
> I'm running into a strange seg fault when trying to use mri_segstats
> (it's actually ocurrin
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 alre
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 th
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 transform
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