Hi Pedro
the instructions are at:
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
have you tried control points in the temporal wm? And what receive coil did
you use? You might be better off with something like 1.1mm isotropic if you
can change the acquisition
cheers
Bruce
On Fri,
if you mean topological defects, those are always there. If the output
looks good you should be all set.
cheers
Bruce
On Fri, 6 Mar 2015, pablo najt wrote:
Hello Bruce,
I run recon-all and open the output with tkmedit/freeview. The output looked
good but there seem to be defects in the recon-a
The 0 index is always "unknown". What problem does the other issue
cause? It may be that there are just some items in the color table that
are not represented in the annotation
doug
On 03/05/2015 09:05 PM, Octavian Lie wrote:
> Dear Bruce,
>
> Reading the doc for read_annotation, it suggests th
For some reason the spatial fwhm calculation is failing. This sometimes
happens if the mask is highly fractured. Can you look at
group.glm/mask.nii.gz and see if there are a bunch of isolated voxels?
On 03/05/2015 11:50 PM, Eiran Vadim Harel wrote:
>
>
>
>
> Hi Doug,
> Thanks for your reply.
>
Dear Doug,
I figured it out.
I wanted to relate a set of points on the pial surface to their
corresponding Desikan indices and label names.
If
[vertices, label, colortable] = read_annotation([some-path
'\rh.aparc.annot'], 0);
x=unique(label);
y=sort(colortable.table(:,5));
Points labeled with
Hi Doug,It seems ok, no isolated voxels.I attach it.Any other ideas?Thanks,Eiran
On Friday, March 6, 2015 6:22 PM, Douglas N Greve
wrote:
For some reason the spatial fwhm calculation is failing. This sometimes
happens if the mask is highly fractured. Can you look at
group.glm/mas
Can you upload the ces.nii.gz and cesvar.nii.gz files to our filedrop?f
On 03/06/2015 12:23 PM, Eiran Vadim Harel wrote:
> Hi Doug,
> It seems ok, no isolated voxels.
> I attach it.
> Any other ideas?
> Thanks,
> Eiran
>
>
>
> On Friday, March 6, 2015 6:22 PM, Douglas N Greve
> wrote:
>
>
>
> Fo
There appears to be a bug in the computation of the fwhm and it appears
that I fixed the bug somewhere between 5.3 and now. I've put a new
version of mri_glmfit here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit
see if that works for you
doug
On 03/06/2015 12:38 PM
Thanks
Xiaomin
On Mon, Mar 2, 2015 at 11:51 AM -0800, "Douglas N Greve"
wrote:
try this
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lta_convert
On 02/26/2015 12:48 PM, Xiaomin Yue wrote:
> Hi,
>
> Is it possible to download lta_convert?
>
> Thanks,
>
> Xiaomin
>
>
>
>
> O
Thanks. The new freeview can create correct register file
Xiaomin
On Mon, Mar 2, 2015 at 11:06 AM -0800, "Douglas N Greve"
wrote:
On 02/18/2015 09:54 PM, Xiaomin Yue wrote:
> Hi Doug,
>
> Thanks for your response. I did run bbregister to register the EPI to
> T1, but it did not resample t
Hi Doug,It is giving me this
error:[Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran%
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm
--nii.gz --surface fsaverage lh/Applications/freesurfer/bin/mri_glmfit: line 9:
syntax error near unexpected token `('
sorry, gave you a linux binary. Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit.mac
On 03/06/2015 02:25 PM, Eiran Vadim Harel wrote:
> Hi Doug,
> It is giving me this error:
> [Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran%
> mri_glmfi
Doug,It works well now,Many thanks!,Eiran
On Friday, March 6, 2015 9:28 PM, Douglas N Greve
wrote:
sorry, gave you a linux binary. Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit.mac
On 03/06/2015 02:25 PM, Eiran Vadim Harel wrote:
> Hi Doug,
Hi,
I am having trouble with the WM segmentation, several parts are excluded, its
due to the poor contrast. Is there a way i can change the contrast in
freesurfer?
Thanks,
SHaheen
UT Southwestern
Medical Center
The future of medicine, today.
Hi all,
I am new to Freesurfer and have run my participants’ data through the
longitudinal preprocessing stream and am now trying to assemble my data so
that they can be put into a linear mixed effect model analysis. While the
longitudinal tutorial with cortical thickness data is very helpful, I
Hi Shaheen
you can't change the contrast, but you can use the expert options in
recon-all to change what we expect in mri_segment and mris_make_surfaces.
cheers
Bruce
On Fri, 6 Mar 2015, Shaheen Ahmed wrote:
Hi, I am having trouble with the WM segmentation, several parts are
excluded, its
Hi Ping-Hong - The tracts are not registered, as opposed to a voxel-based
method. Here the measures are extracted in each subject's native space.
After tracula has derived the posterior probability distribution of the
path (in trac-all -path) it can find the maximum a posteriori (MAP) path,
i
Hi Alan - Your culprit is here:
WARN: Could not find
/data/alanf/FreeSurfer_5.3/diffusion_recons/105014/mri/aparc+aseg.mgz
WARN: You will not be able to complete TRACULA processing without it
You have to make sure your freesurfer recon is there, or define
SUBJECTS_DIR appropriately if it's el
Hi Eileen - It looks like there was a A-P flip introduced to your gradient
vectors. (See screenshot of the tensor eigenvectors. Because they look
right in the coronal view but wrong in the sagittal and axial views,
that's why I'm assuming the flip is in the A-P direction.) To fix this you
nee
Hi Anastasia,
Thank you very much for your answer, kindly I have one more question:
I wanted to use the path.pd for the corticospinal tract as an ROI in PET data.
What is the correct method to thrrashold the path.pd for the corticospinal
tract over the subjects. I.e in order to normalize all the
Hi Katherine - Did you specify the gradient table and b-value table in
your configuration file? I suspect that the issue is that it can't find
them.
a.y
On Tue, 3 Mar 2015, Katherine Damme wrote:
> Hello Freesurfers,
>
> I recently updated my Freesurfer version and now I am getting an error
Hi Emad - The error is:
dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib
Does the freesurfer build that you're using match the computer that you're
running it on?
a.y
On Wed, 4 Mar 2015, Emad Ahmadi wrote:
Hello Freesurfers!
I’m trying to use tracheal -prep, and I’m getting a
Hi Janosch - Each tract has been labeled manually in a set of training
subjects. Based on these manually labeled tracts and the aparc+aseg of the
same training subjects, TRACULA computes the probability of a tract going
through each aparc+aseg label, or next to each aparc+aseg label in the L,
Hi Mohamad - There's is no single correct way, but the default way that
the path.pd.nii.gz is used to get FA/MD/etc is after thresholding at 20%
or its max value.
a.y
On Sat, 7 Mar 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
Thank you very much for your answer, kindly I have one more q
Hi Anastasia,
if I want to do the same process. I.e thrrashold 20% of it is max value.
How do I calculate the max value for every tract ?
Mohamad
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Ye
Try fslstats -R.
On Sat, 7 Mar 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
if I want to do the same process. I.e thrrashold 20% of it is max value.
How do I calculate the max value for every tract ?
Mohamad
From: freesurfer-boun...@nmr.mgh.harvard.e
Thanks Anastasia:
Yes that helps. Have a great weekend!
Alan
On Fri, Mar 6, 2015 at 6:30 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Alan - Your culprit is here:
>
> WARN: Could not find /data/alanf/FreeSurfer_5.3/
> diffusion_recons/105014/mri/aparc+aseg.mgz
> WARN: You
Hi, Bruce.
I am currently putting the file (Well-C0-T1w-023-20050425_124.zip) - it will
take a while.
I was able to make it a lot better using the Topological Defect correction in
tkmedit. Is it suitable for this task? I have not tried adding control points.
This is an older data with a quite
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