Is there a way to only get the stats from the -aseg file that we edited without
rebuilding everything? For example, I edited a subject yesterday and ran the
-make all option, but the reconstruction changed everything in -aseg so
cerebellum is marked as grey and white matter (see attached). Do
Dear Freesurfer users,
I would like to know what is the level of smooth recommanded to use for
surface-based group analysis?
Thank you,
All the best,
Charlotte
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Hi Jordan
That's pretty bad and means something's went radically wrong pretty early in
the process. Have you checked the talairach.lta?
Cheers
Bruce
On Apr 17, 2012, at 8:31 AM, Jordan Pierce wrote:
> Is there a way to only get the stats from the -aseg file that we edited
> without rebuild
Hi Nick,
It does not work properly, it only produces an error message,
even with no option at all:
'nknown option: '-
Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ...].
Ed
On 17 Apr 2012, at 16:28, Nick Schmansky wrote:
> a modified recon-all is attached. it will run nu_correct prior to the
>
It will replace it.
doug
On 04/14/2012 09:52 AM, Michelle Umali wrote:
> Hi Freesurfers,
> I ran reg-feat2anat and am now checking registration. For some
> subjects I had to edit the registration of feat to standard space.
> So, do I have to replace the example_func2standard.mat fsl's
> example_f
Have you tried using mri_label2vol with the aparc as the input instead
of the aseg?
doug
On 04/14/2012 12:06 PM, Bruce Fischl wrote:
> mris_calc should do what you want (although the aseg is not zero in
> the cortex, so you will change the cortical labels)
>
> cheers
> Bruce
> On Sat, 14 Apr 201
Just run
cp $FeatDir/reg/freesurfer/example_func2standard.mat
$FeatDir/reg/example_func2standard.mat
doug
On 04/14/2012 10:04 PM, Michelle Umali wrote:
> Hi Freesurfers,
> I ran reg-feat2anat to register freesurfer data to FSL feat in order
> to generate some binary masks.
> Afterwards I ed
There's not one level of smoothing that will fit all situations. I
usually use 5mm-15mm.
doug
On 04/17/2012 09:17 AM, Charlotte Bernard wrote:
> Dear Freesurfer users,
>
> I would like to know what is the level of smooth recommanded to use
> for surface-based group analysis?
> Thank you,
> Al
Can you run the following?
mri_surf2vol --mkmask --hemi rh --fillribbon --identity sub01 --template
subj01/mri/orig.mgz --o surf-mask.nii
tkmedit sub01 orig.mgz -overlay surf-mask.nii -fthresh .5
this should just create a mask of the rh surface in the volume. If this
fails, then there's somethi
It should not have changed the WM volume. Did you happen to see the
thread about a bug in mri_segstats? It could be causing this. You can
get a new version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux
The only thing that we have that comes close to quan
There should be an ocn.dat file that corresponds to the CSD base name
that you passed to mri_glmfit-sim. The cache just uses a pre-computed
table. The computations are pretty simple. It synthesizes white gaussian
noise on the surface, smooths it by a certain amount, then finds
clusters at vario
What should I be looking for in the talairach.lta?
Jordan Pierce
Graduate Student
Behavioral and Brain Sciences Program
Psychology Department
The University of Georgia
From: Bruce Fischl
To: Jordan Pierce
Cc: Allison Stevens Player ; Freesurfer Support
You can check it with:
cd $SUBJECTS_DIR/$subject/mri
tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca --targ
brainmask.mgz --lta-inv transforms/talairach.lta --reg junk.reg.dat
--s $subject
don't try to edit it though. If it is off, get back to us.
doug
On 04/17/2012 12:08 PM
no, you'll have to do it in some other tool (matlab, eg)
On 04/17/2012 02:50 AM, zhang mingxia wrote:
> Dear Freesurfer experts,
>
> Recently, I was creating ROI. But I just knew how to create it
> manually as this website introduce:
> http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit.
Hi Anastasia,
My mistake with the expiration date.
Please try with this link:
https://transfert.inria.fr/fichiers/0b1013b5de0fc0cc9e8dd2d6101a054b/testData.tar.gz
Thanks!
Viviana Siless
--
Parietal Team, INRIA Saclay
Neurospin, Centre CEA de Saclay
91191 Gif sur Yvette – FRANCE
On Tue, Apr 17,
Hi Sarina - You'll have to specify the list of gradient directions
(bvecfile) and b-values (bvalfile), see here for more info:
http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
Please send email to the freesurfer list and not to me directly. Emails
sent to the freesurfer list are saved
Hi Charlotte,
If the skull/neck that's left off is not affecting the surfaces, it should
be okay. Skull strip looks okay too but it's hard to tell from one slice.
Sita.
On Tue, 17 Apr 2012, Charlotte Bernard wrote:
>
> From: chak...@live.fr
> To: freesurfer@nmr.mgh.harvard.edu
> Subject:
> D
howdy brain imagers,
we are trying to put together a vocabulary of DICOM terms and their
definitions related to brain imaging. unfortunately, a lot of the useful
info is often in private tags and these differ from sequence to sequence
and from scanner to scanner.
to help us get at these tags, thi
Hi,
I have bias-corrected and co-registered longitudinal images, and I'm
interested to use Freesurfer to construct unbiased within-subject templates
(to be used in SPM). Using mri_roubust_template, I get the following error
message on some (not all) of the subjects. I was wondering whether I could
Hi All,
I thought I'd share my recent experiences with the newest Freesurfer v.
5.10 and subcortical segmentation.
I ran a large sample of brains using the default stream of Freesurfer v.
5.10. The resulting hippocampal segmentations were extremely poor, yet on
the same sample of brains Freesurfe
Hi Joshua:
What version of FS 4 did you use?
best,
Alan
On Tue, Apr 17, 2012 at 2:56 PM, Joshua Lee wrote:
> Hi All,
>
> I thought I'd share my recent experiences with the newest Freesurfer v.
> 5.10 and subcortical segmentation.
>
> I ran a large sample of brains using the default stream of
It was version 4.50. I had to walk over to the other room to find out. ;)
In any case, I achieved good results by including the use-mritotal flag on
the current version.
Josh
On Tue, Apr 17, 2012 at 12:00 PM, Alan Francis wrote:
> Hi Joshua:
>
> What version of FS 4 did you use?
>
> best,
>
I was told to use this recon-all flag and my talairach problem went away:
-use-mritotal
-
Josh
On Tue, Apr 17, 2012 at 7:51 AM, Nick Schmansky
wrote:
> Ed,
>
> email probably trounced it. recon-all is a text file. attached is a
> gzipped version. use gunzip to unpack it.
>
> N.
>
>
>
> On Tue,
wait it was Nick that told me to use this a while back when I had tal-check
failures...I just posted about my current issues where I discuss my recent
experiences with a high rate of talairach failures in the current version.
-
Josh
On Tue, Apr 17, 2012 at 12:49 PM, Joshua Lee wrote:
> I was to
Hi Viviana - I suspect it may be b/c you're using the 2mm-resolution MNI
template brain, and our atlas was built using the 1mm one. From your
dmrirc file:
# MNI template (the only option for inter-subject registration in this
version)
# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii
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