If you are running freeview on a Mac, you can ignore those “Invalid drawable”
messages. Can you post a screenshot of the whole freeview window with the color
bar issue?
Best,
Ruopeng
On Jul 20, 2014, at 11:34 PM, 郝磊 wrote:
> Dear experts
>
> when I open freeview, it report that "2014-07-
Hello FreeSurfers,
during the course of my diploma thesis i wrote a few R functions around
FreeSurfer, mainly for group analysis of FreeSurfer surface data in R. I
thought i'd just contribute the code here, on the off chance that
someone may find it useful, and despite the code quality (i wrote th
Hi Andreas:
Very kind of you to share your code. I am sure many of us will benefit from
this.
thanks,
Alan Francis
On Mon, Jul 21, 2014 at 9:12 AM, Andreas Berger <
n0642...@students.meduniwien.ac.at> wrote:
> Hello FreeSurfers,
>
> during the course of my diploma thesis i wrote a few R funct
What date type is your volume? Is it uchar? If so, a value of 570 would
overflow.
Ruopeng
On 07/20/2014 12:25 PM, Tracy Riggins wrote:
Hello Freesurfer experts
I am trying to edit an aseg file. I want to set my brush value to a
value that does not exist in the default lookup table (e.g,. 5
Hello Anastasia,
I ran Tracula on Freesurfer 5.3 but without the 2013 Tracula updates. Now, I
would like to use the command "dwi_motion" on my data. I have installed the
updates, but will I have to completely reprocess my data inducing steps
trac-all -prep, trace-all -bedp, and trac-all path i
Dear FreeSurfers,
In the training that I attended in May, I believe it was demonstrated by
Allison that you could fix multiple problems at the same time. I
understand how to make the edits at the same time, but am unsure what
command to run to integrate all of these changes concurrently.
Since
Hi Angela,
Have you tried that:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html ?
You can look also in the release notes
(http://freesurfer.net/fswiki/ReleaseNotes), under LGI issue when using Matlab
2013.
The issue will be corrected in the next FreeSurfer release.
Hi Melly,
The LGI has the same format as the thickness files, so you can extract them
using mris_anatomical_stats (providing you have your own annotation). The
command will look something like:
mris_anatomical_stats -a $SUBJ/label/YOUR_ANNOT -t $SUBJ/surf/?h.pial_lgi -f
$SUBJ/stats/OUTPUT_F
Dear freesurfer experts,
For diffusion analysis in freesurfer - I want to know which gradient matrix
freesurfer expects.
The thing is - when I look at the gradient matrix created using a MATLAB
script that reads the directions from the dicom header - I get one table,
but the bvecs file created in
FS uses FSL tools under the hood, so you want to use the bvecs that are rotated into the axes of the scan.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School
Hello Doug,
Ideally, I am trying to take subject tstat maps from FsFast (stable3
environment) and register these native structural space maps to the
MNI152_2mm standard brain.
The t_000.bfloat file is what was generated relative to my contrast that
was set up in FsFast stable3. There are a series
Hi Jacob
Doug is on vacation for a couple of weeks, so you should probably repost
in early August.
cheers
Bruce
On Mon, 21 Jul 2014, jaco...@nmr.mgh.harvard.edu wrote:
> Hello Doug,
>
> Ideally, I am trying to take subject tstat maps from FsFast (stable3
> environment) and register these native
hi freesurfer experts
I am compiling the FA segment stats for several subject
I used
mri_vol2vol --mov fa.nii --reg register.dat --fstarg ../mri/orig.mgz --interp
nearest --o fa.anat.mgh
then I used:
mri_segstats --seg mri/wmparc.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --i dti/fa
Hi Cat - Just install the update and run trac-all -qa. This will produce
the motion measures. Check the tutorial for where to find the output.
a.y
On Mon, 21 Jul 2014, Cat Chong wrote:
Hello Anastasia,
I ran Tracula on Freesurfer 5.3 but without the 2013 Tracula updates. Now,
I would like
Thank you for the heads up Bruce.
> Hi Jacob
>
> Doug is on vacation for a couple of weeks, so you should probably repost
> in early August.
>
> cheers
> Bruce
> On Mon, 21 Jul 2014, jaco...@nmr.mgh.harvard.edu wrote:
>
>> Hello Doug,
>>
>> Ideally, I am trying to take subject tstat maps from FsFa
Dear Real-Time Functional Neuroimaging Community,
It is our pleasure to announce the conference on real-time Functional
Imaging and Neurofeedback (rtFIN) in Gainesville, Florida on February
12-13, 2015 at the University of Florida, hosted by Prof. Ranganatha
(Ranga) Sitaram.
This conference is the
thank you Marie!
>
> Hi Angela,
>
> Have you tried that:
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html ?
>
> You can look also in the release notes
> (http://freesurfer.net/fswiki/ReleaseNotes), under LGI issue when using
> Matlab 2013.
>
> The issue will be corrected
It'd be nice if things were that simple, but!
Although the pre-processing is done with FSL tools, tractography is done
with locally written code. Some gradient sets may appear to work with FSL,
but they won't work for us. For example, some dicom converters may perform
a L-R flip as preparatio
Hi FS experts,
Is the DtiMap software (www.kennedykrieger.org) compatible with
Freesurfer/Tracula?
Thanks
Shantanu
--
Shantanu Ghosh, Ph.D.
Harvard Medical School & Massachusetts General Hospital
Martinos Center for Biomedical Imaging
--
Not only is the universe stranger than we think, it is s
Hi Bastian,
yes, lta are the (here rigid) transformations (dat files are deprecated).
you can use mri_convert -at
or mri_vol2vol for mapping images.
I think, however, you are not interested in mapping images, but in ROI's
on the surface.
You can do the following:
- draw/create the ROI in the
Hi Sal,
(please send to freesurfer list).
Take a look at the cross sectional qdec file. Years will be the average
of 0 and 0.1 (= 0.05) for all subjects, so that may be the reason why it
fails as a co-variate.
Age is also not time-varying, it is the average age per subject. The
analysis at th
Dear Wang
Ok. The sceenshot of the whole freeeview window was in the attachment. I
cann't send the screenshot to freesurferATnmr.mgh.harvard.edu.
Thank you
2014-07-21 20:36 GMT+08:00 Ruopeng Wang :
> If you are running freeview on a Mac, you can ignore those “Invalid
> drawable” messages.
Hi Shantanu - What do you mean by compatible? Are you trying to import an
output from the other software into tracula or vice versa?
a.y
On Mon, 21 Jul 2014, Shantanu Ghosh wrote:
> Hi FS experts,
>
> Is the DtiMap software (www.kennedykrieger.org) compatible with
> Freesurfer/Tracula?
>
> Tha
Sounds great, will try that!
Again, thank you very much for your help!
Bastian.
On 22 July 2014 01:53, Martin Reuter wrote:
> Hi Bastian,
>
> yes, lta are the (here rigid) transformations (dat files are deprecated).
>
> you can use mri_convert -at
>
> or mri_vol2vol for mapping images.
>
> I thi
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