Hi,
I recently install Freesurfer under ubuntu. I tested two own data. It works in
one our own case, but did not work for other cases. The problem is the
Freesurfer not found or unknown file type for file
/home/d4201z/Desktop/im_4/2000110815073505086.dcm when convert convert dcm
to mgz.
Anastasia,
Thanks for such a quick reply!
Please find my answers inline...
2012/7/26 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Hi Sergio - Thank you for your kind words, and also thank you for taking
the time to search the archives for answers!
The first problems you had with
Hi,
I would like to follow the workflow for the FreeSurfer TrackVis Transforms
(http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms) but I'm
not sure how to get started. The first step is to load the trk data and divide
the trk coordinates from the file by the voxel_size in
Hi Matthew
you could save the surfaces generated internally by mri_watershed with
the -surf surfname option, compute the volume of the interior of that
with mris_volume, then subtract out whatever other tissue classes you want
using the aseg.
cheers
Bruce
On Fri, 27 Jul 2012, Matthew
Hi Yawu
where did you get that dicom from? Does the file you are pointing to
exist?
cheers
Bruce
On Fri, 27 Jul 2012, Liu Yawu wrote:
Hi,
I recently install Freesurfer under ubuntu. I tested two own data. It works
in one our own case, but did not work for other cases. The problem is the
Dear All,
I want to use cingulate bundle as ROIs more exactly mask for fiber tracking.
Can someone explain please how I can use the JHU-WhiteMatter-labels-1mm.nii.gz
and their labels JHU-WhiteMatter-labels-1mm.txt to get a mask of my cingulate
bundle in my diffusion space for each
Hey experts,
Thank you very much for your advice!
So I guess my best guess would be to use recon-all with -nuintensitycor-3T
and add an expert option file for -b 20 and -n 5.
These flags belong to the mri_normalize binary?
Best regards
Thomas
On Thu, Jul 26, 2012 at 4:12 PM, Bruce Fischl
Steps 2 and 3 look ok. The first step will probably fail. You need a
registration between the JHU atlas and the individual. The people who
developed the JHU atlas can probably tell you how to do this.
doug
On 07/27/2012 10:39 AM, Antonella Kis wrote:
Dear All,
I want to use cingulate
What a coincide! Our teams have both chosen the same release cycle strategy
:P
I ran bedpostx_postproc and I've got so many errors that makes me think the
problem is before this step (see output in attached
n1-bedpostx-postproc.txt).
So, I ran again bedpostx on the dmri directory, which the
Hi Doug,
Sorry to bother with the same issue, I just remembered something. My DTI data
for each individual subjects is registered on the MNI152 using Flirt so I
wonder if I should first register the atlas to the MNI and then apply to my
subjects. Can I do this? Then do I need to run the
Can you send the result of
mri_probedicom --i
/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm
doug
On 07/27/2012 05:38 AM, Liu Yawu wrote:
Hi,
I recently install Freesurfer under ubuntu. I tested two own data. It works
in one our own case, but did not work
I don't know anything about the JHU atlas. If you have an anatomical in
line with the JHU atlas, then align your low b image directly to that.
You can then map the JHU atlas into the native diffusion space with
mri_label2vol.
doug
On 07/27/2012 12:08 PM, Antonella Kis wrote:
Hi Doug,
Sorry
The monitoring script that bedpostx runs and tells you if things have or
haven't finished properly can't always be trusted. So if that's the only
error message you see, I wouldn't worry about it. Have the *ph1* and *th1*
files appeared this time?
On Fri, 27 Jul 2012, Sergio Medina wrote:
Dear Experts,
I am occasionally noticing some 'pinching' on the inflated brain surfaces
around the temporal lobe pole. When I check the brainmask.mgz files, the raised
areas are due to a 'bubble' of pial surface forming on top of pial surface.
Upon checking white matter and grey matter
Hi Antonella, if you are using something from FSL, you should be posting
to the FSL list. As I said before, I don't know where the JHU atlas came
from or what space it is in. It does not appear that this application is
related to the FreeSurfer tools. I bet the FSL folks could answer your
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