If there is white matter that is being excluded from the white surface,
then if that is fixed, the pial surface will grow out further and may
include the gray matter originally excluded.
On Thu, 13 Oct 2011, Jordan Pierce wrote:
We're trying to reconstruct pial and white matter surfaces for c
I believe if you go to the View menu you can select "Edited voxels" which
will show what you edited in that session in blue.
If you run:
recon-all -show-edits -s subjid
this will show you white matter and brainmask edits you have made I
belive.
We don't print a log of the manual correections b
Can you send me a snapshot of a few slices where you see this?
On Thu, 13 Oct 2011, Jordan Pierce wrote:
> We can get that step to work when there's white matter, but there are areas
> of only gray matter that are still being excluded.
>
>
___
Freesurf
Yes, it looks like amygdala.
Here are instructions for uploading the case:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
Allison
On Fri, 14 Oct 2011, Bruce Fischl wrote:
Hi Jordan,
it's hard to tell from a single slice but it looks like that might be
amygdala, in which case you
There isn't a way to have the new or old results automatically saved under
a different name. I would suggest making copies of the files before edits
and after edits but before rerunning if you want to keep track of the
changes. Depending on what you are making edits to, you would likely need
to
You can copy your edited brainmask.mgz to brain.finalsurfs.manedit.mgz
then rerun the case from the beginning using:
recon-all -all -clean-bm -s subjid
This will recreate the brainmask.mgz so no chunks of cerebellum are
missing (and therefore cerebellum volume estimates won't be off). If you
d
Antonella,
Please refer to this website for help with group analysis:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
On Wed, 30 Nov 2011, Antonella Kis wrote:
Dear FS experts,
1) From dt_recon --help I found that:
Registration of lowb to same-subject anatomical using FSLs
-i needs to point to the first dicom (or whichever format your scanner
data is in) in the series.
Allison
On Mon, 19 Dec 2011, LAOUCHEDI MAKHLOUF wrote:
hi eveyone
i ru the command recon-all of the 5.1 version of
freesurfer on some subjects using the following arguments : rec
Hi Lara,
The biggest consideration is that someone editing data run with v4.5 will
probably have a lot more edits to do than if the same case was run with
5.0 or 5.1. It's probably best to rerun with 5.0 before editing if that's
the version that you are going to work with. For your longitudinal
Laouchedi,
The log says the file name is too long perhaps because of the tmp dir file
names.
Allison
On Mon, 2 Jan 2012, LAOUCHEDI MAKHLOUF wrote:
hi everyone
i run recon-all on 200 subjects on a cloud system and i
had the following message :
mp
Holger,
What we often do here is create a script that contains all the subjects
that looks something like this:
set SUBJECTS = (001 002 003 004)
setenv SUBJECTS "$SUBJECTS"
And then you can do a foreach loop after sourcing that script:
foreach s ($SUBJECTS)
mris_anatomical_stats -mgz -f stats/
Hi Catherine,
We hope to have a course in Boston in April.
Allison
On Wed, 4 Jan 2012, Cat Chong wrote:
Hi all,
Just checking.. is the Freesurfer course in New Zealand this May the only
course offered this year, or are there others?
would love to go but New Zealand may be a stretch...
chee
.
Allison
On Wed, 4 Jan 2012, Cat Chong wrote:
> Hi Allison,
> that would be great, is there a website I can check to register?
> Cat
>
> ____
> From: Allison Player
> To: Cat Chong
> Cc: "freesurfer
Hi Paolo,
I think you'll find this tutorial has what you are looking for:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion#ResamplingStructuralDataintheDiffusionSpace
Allison
On Tue, 10 Jan 2012, paolo wrote:
> Hi, i have a problem:
>
> i have a file aseg+aparc.mgz, generated by fre
Hi Vy,
I'm not sure why that only seems to be working sometimes. Can you send me
a case it did work on and a case it didn't work on?
Allison
On Thu, 12 Jan 2012, Vy Dinh wrote:
Dear Freesurfer experts,
We are about to do a mass reprocessing in our lab to update our FS 5.0 data
to the FS 5.1 a
Medical Center
> Phone: (312) 563-3853
> Fax: (312) 563-4660
> Email: vy_d...@rush.edu
>
>
> From: Allison Player [astev...@nmr.mgh.harvard.edu]
> Sent: Thursday, January 12, 2012 3:18 PM
> To: Vy Dinh
> Cc: freesurfer@nmr.mgh.harvard.edu; jennifer.g.gold...@gmail
The Freesurfer group will be offering a three-day Freesurfer Tutorial and
Workshop, April 2-4 at the Martinos Center in Charlestown, MA.
A description of the course, the tentative schedule, and the link to the
registration website can be found here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Cours
Please forward to anyone you think may be interested:
Position involves working in a fast-paced Computational Neuroimaging Lab.
The lab develops and maintains software for MR image analysis and works
primarily in a UNIX environment. The lab is also responsible for several
in vivo and ex vivo (h
It might be SupraTentorial depending on what you are looking for. They are
all explained on this wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
On Thu, 16 Feb 2012, Dana W. Moore wrote:
Hi everyone,
Previous versions of FreeSurfer had a whole brain measure in the aseg.stats
n the wiki that SupraTentorial
includes Cortex + CorticalWhiteMatter + SubCortGray. I notice that
subcortical white matter is not mentioned. Does this mean the corpus
callosum and internal capusle is left out? Also, am I correct that
Supratentorial does not include cerebellum?
On 02/16/12, Alli
Total gray matter includes all voxels between the pial and white surface +
subcortical gray matter which are labeled by the aseg.mgz.
Allison
On Thu, 23 Feb 2012, Yolanda Vives wrote:
Dear Freesurfer experts,
In Freesurfer v5.1, aseg.stats files give the value of total gray matter
volume. Is
It works like this:
setenv SUBJECTS_DIR /path/to/your/data
setenv FREESURFER_HOME /path/to/freesurfer
The primer Doug is referring to can be found on this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/April2012CourseSchedule
The Unix slides, online practice, and "Processing your own d
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
Hi Caterina,
This previous post to the mailing list may be helpful:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21491.html
Allison
On Thu, 15 Mar 2012, Catarina Duarte wrote:
Hi all,
I am trying to export the hippocampal subfields generated in Freesurfer 5.1.
To do that I us
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