ore the recon-all process exits with errors.
On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote:
In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and
find the relevant files. But I would expect the first step to take nifti just
fine. Can you send the command yo
In short, the answer is yes. The 2nd and 3rd steps will take the subject
ID and find the relevant files. But I would expect the first step to take
nifti just fine. Can you send the command you are running?
On Mon, 8 Jul 2013, Jonathan Holt wrote:
> As I'm having trouble importing nifti files in
That's correct.
On Thu, 14 Mar 2013, Mehul Sampat wrote:
Hi Folks,I was looking at the autorecon2-cp, autorecon-pial and autorecon-wm
flags in recon-all help and also here
http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags
My interpretation is when I use autorecon-pial, I only need the
Hi Kev,
For the two scenarios you mentioned, here are my best estimates. I assume
a healthy, adult population scanned with our recommended sequences. Any
other type of dataset (pediatric, one with some type of pathology, one
acquired long ago using a less than optimal sequence or coil, etc.) wo
dicoms, and make that my last resort since it
> takes a day to complete.
> Thanks,
> m
> ________
> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
> Sent: Monday, May 14, 2012 3:16 PM
> To: Borzello, Mia
> Cc: freesurfer@nmr.m
n't open rh.orig.nofix and lh.orig.nofix. On the popup
> image, it doesn't look like the skull is present, but it does look like the
> cerebellum is.
> ____________
> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
> Sent: Monday, May 14,
freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
> Sent: Monday, May 14, 2012 1:37 PM
> To: Allison Stevens Player
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] "cannot allocate memory" issue
>
> I
coms then?
>
> thanks,
> Mia
> ____________
> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
> Sent: Monday, May 14, 2012 1:02 PM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] "cannot alloc
Hi Cat,
You'll need to rerun those subjects with 5.1 to be able to use the
longitudinal analysis in 5.1.
You can also find a detailed explanation on how to go about edits here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
Allison
On Wed, 18 Apr 2012, Cat Chong wrote:
Dear F
Hi Jordan,
I'm not sure I understand your question. If you run -make all, it will run
recon-all again starting at the earliest step in which there are files that
were changed that affect that step. It will run all the way through to the end
as each step affects the next one. This will change you
Anthony,
Depending on what version of FreeSurfer you are running, you would have to
run the command it would normally run to create the aseg but substitute in
your atlas.
For example, in v5.1:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1
You can see the step next to -cala
You can make a copy of the LUT and remove all regions from it you don't want to
see. Then when you load you volume, specify you want to use this new LUT and
you will only see the ROIs in it.
Allison
On Apr 12, 2012, at 11:40 PM, Adil Javed wrote:
> Hi,
> is there any way to overlay only certai
Julia, could you send a snapshot of the area in question?
On Apr 2, 2012, at 5:33 AM, "Richter, Julia"
wrote:
> Dear freesurfer experts,
>
> I have several subjects whose cortical grey matter isn't included in the pial
> surface. Is there any possibility to correct the pial surface? I added
Hi Darshan,
There are instructions on how to do this here:
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F
Allison
On Tue, 27 Mar 2012, Darshan P wrote:
I have an MRI volume dataset, which is deskulled beforehand .
Is
Hi everyone,
We had a last minute drop-out from our Boston FreeSurfer course which
takes place April 2nd through the 4th. If anyone is interested in taking
this spot, please let me know.
Details about the course content, the registration fee, and other
logistics can be found here:
http://surfer
Hi everyone,
The Department of Radiology at VU University Medical Center in Amsterdam,
Netherlands is hosting a FreeSurfer Course on June 27th through June 29th.
Registration is now open. You can find details about course as well as the
registration form on the following website:
http://www.free
Although the white surface finds its place based on intensity, it's starting
point is the wm.mgz. So if there are no voxels in the wm.mgz in the area you
mention, drawing in some voxels combined with the intensity changes that come
from the control points may help.
Allison
On Mar 12, 2012, at 6
> recon-all -s P102_corr exited with ERRORS at Fri Mar 2 14:23:15 CET 2012
>
> For more details, see the log file
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> Best,
> Martijn
>
> On Fri, Mar 2, 2012 at 2:15 PM, Allison Stevens P
Hi Martijn,
autorecon-cp is correct, we start the process a bit earlier now. But even
better, regardless of what edits you make, you can rerun with "recon-all -make
all" and it will start at the earliest needed step. (Although running from
autorecon2 after the skullstrip fix is correct as well).
g volume to the MNI305 atlas, so the spatial
> normalization in FreeSurfer is still done in volume space but not in surface
> space, right?
>
> Best,
> Xiangyu
>
> On Fri, Feb 24, 2012 at 5:20 AM, Allison Stevens Player
> wrote:
> Maybe you can apply the tran
Maybe you can apply the transform using mri_convert or mri_vol2vol created
during autorecon1. Is that what you are looking for?
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
On Feb 22, 2012, at 11:26 AM, Long wrote:
> Dear all,
>
> I had EPI images and T1 image and the EPI images
Vincent,
Some may look like holes but as you mention are just sulci being cut through by
that plane.
A way to check if it is the above is to put the cursor on the surface that
creates this hole and then toggle to the other views (sagittal, axial,
coronal). It will become clearer whether it is
I don't think there is any other way. Is the talairach really that bad in all
of your data? It won't recon without fixing it?
On Feb 22, 2012, at 6:17 PM, cloud.c...@me.com wrote:
> After reading the tutorial at
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach, I understand
> th
23 matches
Mail list logo
