Dear Douglas,
Thank you very much for your input.
1. I generated the ind matrix as per your script, but what I wanted is to
get a matrix with the RAS coordinates for the pixels indexed in ind. Is
there a way to do this?
Thank you,
Octavian
___
Freesur
Hi Gabriel
we find the mean of the label intensity in a region around the voxel in
question using voxels that don't border another label, then do the same
for the most common neighboring label that is different from the one in
question and compute the volume fraction assuming a linear mixing b
On 12/17/2012 05:56 PM, octavian lie wrote:
> Dear All,
>
> I have created a volume of interest in itksnap and imported it in FS
> as a .mgz volume filled binary mask. How can I:
> 1. export it from FS in matlab and generate a .mat array containing
> only the volume pixels within the volume (inten
Dear All,
I have created a volume of interest in itksnap and imported it in FS
as a .mgz volume filled binary mask. How can I:
1. export it from FS in matlab and generate a .mat array containing
only the volume pixels within the volume (intensity 1) ?
2. Is there a way to generate a 3D surface me
Sorry, I'll have to defer to Bruce, who wrote the code.
doug
On 12/17/2012 11:24 AM, Gabriel Gonzalez Escamilla wrote:
> OK the Doug,
>
> I know which are the voxels contained into a ROI. From all of them I
> know the norm.mgz and the brainmask.mgz values, because I'm assuming
> that FS always
Hi Deirdre
just copy the updated recon-all into $FREESURFER_HOME/bin and you should
be all set
cheers
Bruce
On Mon, 17 Dec 2012, Deirdre O Shea wrote:
Hi,
I have experienced this problem before also.So I have downloaded the script you
provided but as a non-programmer I am wondering
how I c
Hi,
I have experienced this problem before also.So I have downloaded the script
you provided but as a non-programmer I am wondering how I can incorporate
this script into my work using Linux. Can I simply copy and paste this into
the text editer and run it that way?
Thanks,
Deirdre
On Fri, Dec 1
Hello
I have one more problem. Some of the subjects completed step 1
(preprocessing) successfully according to the logs & there are no
error messages.
However, when I try to run the bedpost step on these subjects, I get
an error message saying there is no data.nii.gz file in the dmrirc
There is ho
Hello
I have been running trac-paths, and thought it finishes with a message
saying no errors,
I get an error saying ERROR: Degenerate spline segment in the
intermediate message logs
Also I looked at the result using this command:
freeview -v $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/dtifit_
OK the Doug, I know which are the voxels contained into a ROI. From all of them I know the norm.mgz and the brainmask.mgz values, because I'm assuming that FS always work with the brainmask.mgz to know the actual voxel intensity, as indicated when running mri_segstats.I can easily calculate the mea
Hi Fred
if you upload the data I'll take a look, although I don't think a bunch of
steps will work properly with .75mm data. Usually we resample to 1mm, then
recon and run a post-hoc surface deformation to match the .75mm data
cheers
Bruce
On Mon, 17 Dec 2012, Fred Dick
wrote:
> Dear all
>
>
Dear all
I have been trying to recon a high-res (.75 isotropic) volume, which goes
along fine until it hits a certain bit of mri_ca_normalize. I've run this
4 times and it always dies at the same point.
There was also a previous unanswered post about 8 months ago showing an
error at the same plac
Good Morning,
I would like to run deterministic global tracktography on 2 tracts for
which tract tracing techniques in animals have established white
matter connections. However, these tracts are not part of the 18
segmented in TRACULA. Because of crossing fibers, deterministic global
tract
The PV is done based on intensities. For each voxel an the boundary of
an ROI, the voxel intensity is assumed to be a weighted summation of the
the average intensities in each ROI. Knowing the average intensities in
the ROIs and the actual intensity of the voxel, the PV can be computed.
doug
O
Just use
mri_convert norm.mgz normInMNI.img --apply_transform
transforms/talairach.xfm -oc 0 0 0
no need for the other arguments
doug
On 12/15/2012 12:38 PM, Prasanna M wrote:
> I had one more question:
> What transform do I apply to get all the norm.mgz of all timepoints of
> a subject to get t
yes, it should
doug
On 12/14/2012 07:43 PM, octavian lie wrote:
> Dear Doug,
> Thank you for your suggestions,
> to be more clear, the original preresection volume was in old analyze
> format (hdr/img), and was already processed through freesurfer, so I
> have pre.mgz instead of pre.img. I do not
do you have a question?
doug
On 12/16/2012 05:15 PM, xiangbo_2010 wrote:
> Dear doug
> My roi was obtained by drawing after the analysis in freesurfer. Thanks!
>
> Bo Xiang
>
>
>
> At 2012-12-17 02:06:53,"Douglas Greve" wrote:
>
> Hi Bo, look at the multimodal integration tutorial on our wik
Hi,
Talairach.xfm is a text file which contains a transformation matrix.
Though there is small numerical difference between two transformation
matrix made using mritotal and the default Talairach registration. The
process of calculation the ICV may amplify this difference since it used
the det
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