I'll leave that for Nick, or one of the gcut developers.
cheers
Bruce
On Wed, 13 Apr
2011, Sarah Whittle wrote:
> Thanks for your reply. I guess it could be dura. Here's a picture pre
> FreeSurfer with skull on. This is a particularly bad image. No, it's
> not gado enhanced.
>
> gcut is automati
A little off-topic maybe, but:
I am working to load external data into analysis programs using .nii
format files. I have inplanes acquired at an ACPC orientation, as well
as data collected and specially pre-processed through a MATLAB pathway
that unfortunately strips away all orientation inform
Freesurfers --
This morning, I was trying to convert a 4 frame MPRAGE scan into a 1 frame RMS
image. I wrote my own matlab code to do it ...
function err = rms_mprage(old,new)
%convert 4-frame mprage into 1 frame mprage by taking RMS of voxels
old_hdr = load_nifti(old);
new_hdr = old_hdr;
new
Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School
Job Description
A postdoctoral position is available with the TRANSCEND Research Program
(www.transcendresearch.org) at the Martinos Center for Biomedical Imaging
in Charlestown, MA (www.martinos.org) which is affiliated
no worries, and I'm happy to take a look (although in general not as happy
as I am to blame Marty)
Bruce
On Tue, 12 Apr 2011, Fred Dick
wrote:
> Hi Bruce
>
> Believe it or not, we are running stable 5.0.0 (!). Since emailing I wised up
> and consulted recon all dev table for files - the firs
Hi Bruce
Believe it or not, we are running stable 5.0.0 (!). Since emailing I wised up
and consulted recon all dev table for files - the first sign of trouble is in
aseg.auto_noCCseg.mgz. The wm.seg.mgz is fine. I can upload a sub to incoming
if you want to take a look
Sorry didn't check
Hi Doug,
I read this on a previous email, and I already tried to run recon-all -make
all. I included it in my original email, but I'll copy it here:
"I then tried to perform recon-all -make all, but got this error:
*ERROR: mpr2mni305 failed, see transforms/talairach_avi.log*
In the .log, I got
It usually means that you have a subject whose surfaces are
out-of-synch. This usually happens when you've made edits, launched
recon-all, but then then recon-all does not finish for some reason.
Check the time stamps on that subject or try running recon-all -make all
-s subject
doug
btw, a "
Hi Fred,
do you want to send us an example set and we'll track it down? What
version are you running? I suspect there is some old piece of code that
Marty wrote that is at fault.
cheers,
Bruce
On Tue, 12 Apr 2011, Fred Dick wrote:
> Dear all
>
> we have had some odd behavior in 4 fairly high
Hi Roger,
you certainly don't need to remove all of it - only the pieces that are
erroneously retained within the pial surface.
As for gcut, it depends on what version you are using whether it is run
automatically.
cheers
Bruce
On Tue, 12 Apr 2011 roger@yale.edu wrote:
> Hi all,
>
> Sor
Dear all
we have had some odd behavior in 4 fairly high quality datasets that have been
very nicely normalized and deskulled with a good Talairach but then only half
filled in wm.mgz and all surfs (to various semi-planes). Orientation seems
correct in tkmedit as well. We were thinking that it m
Hi Bruce,
I mean the "mris_preproc" step.
Thanks,
Allie
(forgot to reply to all)
On Tue, Apr 12, 2011 at 11:35 AM, Bruce Fischl
wrote:
> Hi Allie,
>
> what do you mean by "trying to assemble my subjects into a single surface
> space"?
>
> thanks
> Bruce
>
> On Tue, 12 Apr 2011, Allie Rosen wro
Hi all,
Sorry for the newbie questions, but I was wondering if there were any general
guidelines on how much remaining DURA MATER and ARACHNOID MATER is acceptable
after running autorecon1.
In general, should dura be completely removed and arachnoid be left as is?
Also, is mri_gcut run automatic
Hi Allie,
what do you mean by "trying to assemble my subjects into a single surface
space"?
thanks
Bruce
On Tue, 12 Apr 2011, Allie Rosen wrote:
> Hi All,
>
> Upon trying to assembly my subjects into a single surface space, I got the
> following error:
>
> *ERROR: number of vertices in
> /media
Hi All,
Upon trying to assembly my subjects into a single surface space, I got the
following error:
*ERROR: number of vertices in
/media/AMMONIS/fsSubjects/AR_normals/C42/surf/lh.thickness does not match
surface (142271,140585)
ERROR: reading curvature file
*
I then tried to perform recon-all -ma
that looks like it is the right command-line. Can you send the terminal
output?
Saad Ramadan wrote:
> Hi freesurfer-ers:
>
> when you run something like:
>
>
> * bbregister --s MySubject --t1 --mov t1_svs.nii --init-fsl --reg
> t1.reg.dat *
> * *
> I expect to generate a file "t1.reg.dat"
Hi,
When I try to download an old version of freesurfer (4.3.1) from
http://www.freesurfer.net/pub/dist/freesurfer/4.3.1/ I get the following
error message:
The connection was reset
The connection to the server was reset while the page was loading.
I get the same error message with all version
wow, that is noisy. Looks like the bright ring is dura. This isn't
gado enhanced, is it? You could try using the gcut stuff
On Tue, 12 Apr 2011, Sarah Whittle wrote:
> Hi,
>
>
>
> I'm working with some poor quality images and having a lot of trouble
> with FreeSurfer segmentation. The main issue
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