Hi Anastasia,
Yes. I tried to run bedpostx on a stand-alone computer but it is very
slow although it can work well.
Regarding the b-values, we do have some subjects which were scanned in
different protocols a few years ago. If it is possible, please add the
option to the new version of Tracu
Hi Reza
can you use freeview for what you want instead? tksurfer and tkmedit are
deprecated
cheers
Bruce
On Thu, 11 Jun 2015, Reza Rajimehr wrote:
Hi,
Is there any plan by the Freesurfer team to address this well-known bug?
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35
Hi,
Is there any plan by the Freesurfer team to address this well-known bug?
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35938.html
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36193.html
For now the only workaround is to enter values through command-line.
Hello All,
I ran the freesurfer longitudinal stream for a subject with three time
points and found that the /stats/lh.BA.stats has remained constant across
all time points where as aseg.stats showed variations.
Sorry if this question is too nieve.
Thanks,
Pradeep
Do you not have the image in something other than analyze? If not, then
just keep playing with the letters (ie, PIR) until you get it right.
Note that you will not know what is left and right unless you have a
fiducial on the subject
doug
On 06/11/2015 04:19 PM, Kriegel, Jennifer Lynn Sarai wr
I'll need more information before I can help you. Please review our bug
reporting page to see what kind of info is needed:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On 06/11/2015 02:44 PM, Park, Jung Mi wrote:
> Hello Freesurfer team
>
> When I ran preprc-sess of dementia patient's fmri, f
I used the following command to convert a sagittal slice from analyze to mgz
format. The original was acquired in an anterior to posterior/right to left
angle of slices. However, while it is converting to an mgz properly, it seems
to be giving me a flip upside down, and reverting to transverse o
Hi Kate,
I am having trouble viewing the image. Could you send it as an attachment?
When you say main surface, are you referring to the pial or white surface?
-Allison
On 06/11/2015 03:07 PM, McLaughlin, Katie wrote:
Hello Freesurfer Experts,
I'm trying to troubleshoot a problem where the ma
Hello Freesurfer Experts,
I'm trying to troubleshoot a problem where the main surface in our brains is
not adjusting following white matter edits using Freesurfer 5.3. To be clear,
the procedure here is:
1) Make edits to wm.mgz
2) Run recon-all -3T -mprage -autorecon2-wm -autorecon3
Following
Dear Freesurfer team,
I had read a paper a while ago (see attached) on the effects of changing
workstation type across data.
I was wondering if that is still an issue.
I have a situation where a set of data were processed on a Mac with this
version of freesurfer:
freesurfer-i386-apple-darwin11
Research Study Assistant job available at Northwestern University’s
Cognitive Neurology and Alzheimer’s Disease Center in Chicago, IL.
The research assistant will be responsible for analysis of neuroimaging
datasets, in order to contribute to neuroscientific studies of normal aging
and pathologi
Hello Freesurfer team
When I ran preprc-sess of dementia patient's fmri, fmcpr.nii. files and
register.dof6.dat were not created automatically after preproc-sess. Thus I had
to bbregister in two dementia patients manually.
However recently I did preproc-sess in the another patient, fmcpr.nii and
The easy fix is to edit rawfunc2surf-sess and remove the --cortex flag.
Alternatively, you could run mri_vol2surf yourself from a script that
you write. I've fixed this in version 6 to allow turning off the use of
--cortex.
doug
On 06/09/2015 05:53 PM, Jackie Lam wrote:
> Hi all,
>
> I’ve rec
and can you load the same volume into freeview?
On Wed, 10 Jun 2015, dgw wrote:
> What command did you type?
>
>
> On Wed, Jun 10, 2015 at 5:32 PM, Mohammed Goryawala wrote:
>> Hello All,
>>
>> I am trying to read .mgz files into matlab on MacOSX using the MRIread
>> command.
>>
>> It returns me
Hi,
On Thu, Jun 11, 2015 at 2:09 AM, Jalmar Teeuw wrote:
> Hi Matthew,
>
> Thanks for getting back at this. We only process data for our users, so I
> don't have permission to share a sample with you. But I'll ask around to see
> if I can get a scan for you.
>
> To be honest, we aren't quite su
No, sorry. You can run tkregister-sess and it will show each one
sequentially. This is a good idea and it may be possible with the
transition to freeview.
doug
On 6/10/15 7:16 PM, sabin khadka wrote:
Hi all- Is there a command we can have screenshots (similar to one
employed in fsl) of fucnti
Hi Stefani
are the axes also flipped if you view in freeview?
cheers
Bruce
On Thu, 11 Jun 2015,
Stefani O'Donoghue wrote:
Hi Freesurfer, We've carried out the mri_label2vol step for ROIs in one
hemisphere. When opening in ITKsnap the orientations appeared flipped, with
the axial ROIs overlay
Hi Carl,
the use of quantifyHippocampalSubfields.sh is:
quantifyHippocampalSubfields.sh suffix outputFile [subjectsDirectory]
Simply run
quantifyHippocampalSubfields.sh T1 test_no-T1.txt
or
quantifyHippocampalSubfields.sh T1 test_no-T1.txt
/Applications/freesurfer/subjects/RBrain
and everythi
Hi Freesurfer,
We've carried out the mri_label2vol step for ROIs in one hemisphere. When
opening in ITKsnap the orientations appeared flipped, with the axial ROIs
overlayed onto the coronal orientation, and coronal over the axial, and the
sagittal plane appeared rotated.
Can anyone help us fix thi
Hi,
I was trying to compile freesurfer on an arm machine and I worked my way
through quite a few obstacles. But when I am compiling the package
mri_robust_register, I came across an error which stated that there is a
function zgees_(*) in MyMatrix.cpp being undeclared.
I wonder if anyone knows wh
Hi Matthew,
Thanks for getting back at this. We only process data for our users, so I don't
have permission to share a sample with you. But I'll ask around to see if I can
get a scan for you.
To be honest, we aren't quite sure if the problem is with nibabel (v1.3.0). I
tried to reproduce the p
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