hi Corey-
There's many ways to do this, but here's how I would:
1.transform the talairach coordinates to RAS (using some transform you have
already determined), that's what the surface vertices are in. You probably
want to use the pial surface.
[vert_coords]=read_surf(SURFFILE);
2.for each elect
Sorry, I don't know anyone who can help with that. As you note, people
do it, so there must be people around who can extract the relevant
information out of the header. The information you need are the
direction cosines and RAS of the corner of the voxel. You can feed this
into mri_volsynth.
T
Hi Jonathan,
if you load the filled.mgz you should be able to see whether the cerebellum is
still attached, if so you might want to either edit the wm.mgz, the brainmask,
or make sure pons and cc were properly detected. For my non-human subjects I
have to always check the filled.mgz before runn
Hi Aga, that does sound strange. mri_concat does no processing at all,
so if that subject looks ok before you run mri_concat, it should look
fine afterwards. Try running just that subject through mri_concat (so
there's no real concatenation). Also, make sure that the bad subject in
the mri_co
Hi Andreia, I've done this before using information in the spectroscopy
header, then synthesizing an MRI "volume" with one voxel that covers the
size of your spectroscopy voxel, then registering that to the FS
anatomical, then computing the partial volume fractions from the
anatomical. The har
Hi Jonathan
usually that means there is a giant defect that will not be corrected
properly (e.g. cerebellum or skull attached). Did you check the
?h.inflated.nofix or ?h.orig.nofix surfaces?
cheers
Bruce
On Tue, 19 Jul 2011, Jonathan
McDaniel wrote:
Hi,
I have been running a surface re
Hi,
I have been running a surface reconstruction for over 19 days now, and it is
still in the process of correcting defects. Based on how long it took to do
one hemisphere (it is now on the second) it appears it will be done
hopefully within 3 days. I have been concurrently running other subject
This is the proposed workflow and some latter parts
are done with Matlab.
I assist is masses of Matlab jobs using compiled Matlab
and run thousands of jobs both in on center, on our campus
and out in to other resources in the GRID.
My problem is not how to run a compiled Matlab job, but
how to in
Hi Bill,
you want to look at mcc
(http://www.mathworks.com/help/toolbox/compiler/mcc.html
)
Usually what works for me is something like:
mcc -m -v matlab_file.m
This will generate a console executable "matlab_file"
--Thomas
On Jul 19, 2011, at 3:02 PM, Bill Taylor wrote:
> So I peaked in a
Hi Bill,
what portions are you talking about? recon-all shouldn't use any matlab.
cheers
Bruce
On
Tue, 19 Jul 2011, Bill Taylor wrote:
> So I peaked in archive and did not get a hit.
>
> The situation is that the University of Wisconsin
> Madison site license prohibits us running Matlab
> in a c
So I peaked in archive and did not get a hit.
The situation is that the University of Wisconsin
Madison site license prohibits us running Matlab
in a cluster unless it is compiled.
I am assisting a Neurology lab with having a Condor
workflow which this time round will do both Matlab
and FSL post
what format are the files in the archive in? They don't have an extension
On
Tue, 19 Jul 2011, Carolina Valencia wrote:
I hope this attachement works.I also noticed that some heterotopias are
classified as WM, other as GM and sometimes are outlined by the yellow line and
sometimes are not.
Hi Antonella,
you need to save the edits in the file wm.mgz, not rename it, otherwise
recon-all won't be able to find it. Then run recon-all with -autorecon2-wm
and autorecon3, but without the -i.
cheers
Bruce
On Tue, 19 Jul 2011, Antonella Kis
wrote:
Hi Bruce,
Based on your last suggest
Hi Carolina,
can you gzip it or use compression? Usually people can send a few images
to the list.
cheers
Bruce
On Tue, 19 Jul 2011, Carolina Valencia wrote:
Dear FS experts,
I'm trying to analyse a case of cortical dysplasia, but after recon-all I see
some errors in tkmedit that I don't kn
Hi Riccardo,
I don't understand what 4) is. A couple of points:
1. if you give mri_convert .nii.gz as an output extension it will do the
gzipping for you.
2. If you give mri_convert the flag -rl it will reslice
the input volume "like" the template.
not sure if that solves your problem. Can y
Hi Carolina,
To correct the red surface (pial surface), you can follow this tutorial
here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits
If some WM is labeled as GM, then most likely you'll need to do some white
matter edits by adding more wm voxels to the wm.mgz to extend the
Hi Antonella,
When saving wm edits, you don't need to save it as a different file.
FreeSurfer will recognize your edits under wm.mgz. You then can run
recon-all -autorecon2-wm -autorecon3 -s NPI001
If you want to save a copy of the original wm.mgz, you can rename that
(i.e. wm_orig.mgz).
-
Hi Bruce,
Based on your last suggestion, after running the recon-all on my NPI001 subject:
recon-all -s NPI001 -i
/usr/local/freesurfer/subjects/june2011/_orig_/NPI001.nii.gz -qcache -all
and editing the wm, I saved all my edits (using the tool box menu as Save
Volume As) under wm_edits_befor
Dear list,
I am performing single-voxel and multivoxel spectroscopy analysis and I need to
do partial volume correction. I found a thread on the list of someone asking if
it possible to achieve this using Freesurfer (see below), but there is no
answer saying how it is done. My question is how c
Dear FS experts,
I'm trying to analyse a case of cortical dysplasia, but after recon-all I
see some errors in tkmedit that I don't know what to edit. I found some
errors in cortical and subcortical segmentation, I don't find in the failure
mode presentation a way to solve this.
I saw the pial surf
Hi FS expert.
I need to port my T1 and a couple of ROIs from mgz to nii.gz. The same
for many subjects. The issue's about dimensions. When I use fslview,
it respond me that "All overlays must have same dimensions as the base
image!". Indeed T1's 256x256x256 with voxel sizee 1mm3, ROIs are
d
Dear all,
We are preprocessed our data to perform a longitudinal study using
longitudinal pipeline of Freesurfer 4.5. However, when we try to do the
group-analysis using qdec (Freesurfer 5.1), we obtain the following error:
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
ninp
Dear all,
We are preprocessed our data to perform a longitudinal study using
longitudinal pipeline of Freesurfer 4.5. However, when we try to do the
group-analysis using qdec (Freesurfer 5.1), we obtain the following error:
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
ninp
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