Thank you Nick, this one works fine.
Ed
On 3 Oct 2011, at 17:53, Nick Schmansky wrote:
> i've posted mri_morphology for the mac here:
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-
> leopard-intel
>
> n.
>
>
> On Mon, 2011-10-03 at 11:01 -0400, Bruce Fischl wrote:
>> the d
Hi
I have processed several subjects using recon-all. However there is problem
with non-brain matter being labels as cortex around the eye ball. Are there any
automatically methods to correct mislabeling of eye socket as cortex? I am
having problem with mislabeling in ctx-lh-lateral orbital an
Can you please tell me if the cerebellum is included in Freesurfer 5.1's total
subcortical gray and/or total gray matter volumes? Also, what exactly is
included in the total subcortical gray (everything that's produced in the aseg
volumes)?
Thanks so much,
Heather
_
Hi,
I'd like to convert a subject's aparc+aseg.mgz to mni305 (2mm) space.
So, I ran the following commands (FS 5.1):
(from subject's mri directory)
mri_vol2vol --mov orig.mgz --tal --s $SUBNAME --o orig.mni2mm.mgz
mri_label2vol --seg aparc+aseg.mgz --o aparc+aseg.mni2mm.nii.gz --reg
orig.mni2mm.
Hi Freesurfers,
I've run reg-feat2anat to register my FSL FEAT data to the freesurfer
anatomical data.
And for most subjects the registration needs a little manual editing (which
sometimes includes stretching).
But for a few subjects, registration is terrible, e.g. coronal is switched
with horizont
just completing this thread. our sysadmin found a solution that works well
for us:
you can see glxgears working in NX if you type:
export LIBGL_ALWAYS_INDIRECT=yes
in the terminal before running glxgears. it's not fast, but it works. i
think the same holds true for VNC.
-matt
cheers,
satra
On
Can you check that the subjectname file is correct? In some cases, it
looks like it is using subject sj12, in others it looks like it is using
subject ld12.
doug
Michelle Umali wrote:
> Hi Doug,
> I re-ran from preproc-sess using the -force flag, and I still get the
> same dimension mismatch e
You can an asynchrony between your fmri data and the anatomical:
Anatomical: num vertices: 146530
fMRI: 158944 vertices
re-run the fMRI starting from preproc-sess. You will need to make sure that
preproc-sess actually re-runs at least the sample-to-surface. By default, it
just looks to see if th
Thanks! I'll try that!
Andreia
Citando Nick Schmansky :
> you can try:
>
> -talairach -use-mritotal
>
> which will use an alternate talarairch alignment scheme (from the MNI).
> it sometimes works better.
>
> you should also probably add:
>
> -nuintensitycor-3T
>
> to the end of your recon-al
On Mon, Oct 3, 2011 at 12:22 PM, Spencer Boucher wrote:
> New to Freesurfer here, but I was wondering if there is any viability to the
> idea of parallelizing freesurfer for running on multiple servers so as to
> reduce the time required to run recon-all on a single subject. Is there an
> aspec
Hi:
There exist any paper related to the subcortical volume in children
(below 15 years old)?... any image database ?...
Sincerely,
Gonzalo Rojas Costa
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Hi Doug,
I've attached the mri_info output on the eccen and polar images as well as
the mris_info on the lh.sphere surface
Thanks.
Michelle
On Mon, Oct 3, 2011 at 2:38 PM, Douglas N Greve
wrote:
> Can you send me the result of running mri_info on
> eccen/real.nii
> eccen/imag.nii
> polar/real
I figured out it is so, and now rectified the error, thanks to you both for the
time and patience!
On 03/10/2011 19:28, "Nick Schmansky" wrote:
addendum:
these dmri_* replacements are for snow lepard (10.6.0) only. if
installed on leopard (10.5.*), you will get the 'load command' error.
the
Hi Anita, you need to check the math on your design. You have 86
stimuli. Each stimulus requires 0.5s for presentation and 2 sec for null
means 215sec total (minimum). But you have TR=2 and Ntp=86 meaning a run
of only 172 sec. You will need to increase the number of TRs or
decrease the number
Thank you very much Bruce!
Have a nice day/night.
2011/10/3 Bruce Fischl
> The stuff outside the pial surface won't affect things, which is one of the
> reasons we prefer the surface-based measured of cortical morphometry.
>
> Similarly, we don't use the surface-based stuff in the hippocampus,
addendum:
these dmri_* replacements are for snow lepard (10.6.0) only. if
installed on leopard (10.5.*), you will get the 'load command' error.
the dmri_* utils included with the leopard freesurfer release should
work.
n.
On Mon, 2011-10-03 at 14:12 -0400, Nick Schmansky wrote:
> i think those
Hi everyone, I'm using optseq2 and a tnullmin of 2 seconds to force 2 seconds
between each event for my paradigm, but I get a "segmentation fault" error.
Here's my command line below. I didn't specify a tnullmax, so that I would
avoid any errors by specifying both. I tried other values for tnull
i think those are found here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
to install:
cd /Applications/freesurfer/bin
sudo tar zxvf /dmri_5.1_snow_leopard.tar.gz
sudo chmod a+x dmri*
n.
On Mon, 2011-10-03 at 00:25 -0400, Anas
you can try:
-talairach -use-mritotal
which will use an alternate talarairch alignment scheme (from the MNI).
it sometimes works better.
you should also probably add:
-nuintensitycor-3T
to the end of your recon-all command, which will run the nu_correct
stage optimized for 3T. it wont help yo
Hi Doug,
I've attached the output from running fieldsign-sess.
Thanks for all your help.
Michelle
On Mon, Oct 3, 2011 at 12:59 PM, Douglas N Greve
wrote:
> Michelle, before you do that, can you run the offending program with -debug
> and send me the (copious) terminal output? Your anat should no
Michelle, before you do that, can you run the offending program with
-debug and send me the (copious) terminal output? Your anat should not
have to be re-run.
doug
Michelle Umali wrote:
> Hi Bruce,
> Will this undo my wm and pial edits?
>
> Thanks.
> Michelle
>
> On Sat, Oct 1, 2011 at 3:37 PM,
no, it shouldn't, but make a backup of your data before running it for
sure
On Mon, 3 Oct 2011, Michelle Umali wrote:
Hi Bruce,
Will this undo my wm and pial edits?
Thanks.
Michelle
On Sat, Oct 1, 2011 at 3:37 PM, Bruce Fischl
wrote:
try running
recon-all -s subject -make all
Hi Bruce,
Will this undo my wm and pial edits?
Thanks.
Michelle
On Sat, Oct 1, 2011 at 3:37 PM, Bruce Fischl wrote:
> try running
>
>
> recon-all -s subject -make all
>
> and leave the -dontrun off. It should bring everything up to date
>
> Bruce
>
>
>
> On Sat, 1 Oct 2011, Michelle Umali wrote
You can also parallelize by hemisphere by running a single job up to the
tessellation stage (about 8 hours), then two jobs (one for each hemi).
In serial these 2nd steps take about 8 hours, so you could in theory
save 4 hours.
doug
Bruce Fischl wrote:
> Hi Spencer,
>
> the easy answer is that w
Hi Spencer,
the easy answer is that we have a GPU implementation of several binaries
that speed things up. The parallelization ranges from easy to impossible,
but we are working on it. We don't have any generic (e.g. MPI)
parallization at the moment, just some CUDA code.
cheers
Bruce
On Mon,
New to Freesurfer here, but I was wondering if there is any viability to the
idea of parallelizing freesurfer for running on multiple servers so as to
reduce the time required to run recon-all on a single subject. Is there an
aspect of the algorithm that makes this inherently infeasible?
Spence
i've posted mri_morphology for the mac here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel
n.
On Mon, 2011-10-03 at 11:01 -0400, Bruce Fischl wrote:
> the dev build probably didn't complete. Nick?
> On Mon, 3 Oct 2011, Ed
> Gronenschild wrote:
>
> > Hi Bruce,
>
what pial edits to you want to undo specifically? Was it just edits to the
brain.finalsurfs.mgz volume?
On Mon, 3 Oct 2011, Torsten Ruest wrote:
> Hi there,
>
> I think there is an option to remove all edits that have been
> incorporated using recon2 -clean.
>
> Is there a chance that I can sel
The stuff outside the pial surface won't affect things, which is one of
the reasons we prefer the surface-based measured of cortical morphometry.
Similarly, we don't use the surface-based stuff in the hippocampus, so you
should be all set (since many of the cortical assumptions aren't valid
th
the dev build probably didn't complete. Nick?
On Mon, 3 Oct 2011, Ed
Gronenschild wrote:
> Hi Bruce,
>
> I've grabbed the dev version
>
> freesurfer-Darwin-leopard-i686-dev.tar.gz (date 2 Oct 2011, 13:10)
> at
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
>
> and tried
>
> mri_morph
Hi all,
I have the same problem. I'm also working with 3T, and I need to
stretch the movable template with tkregister2 in almost every subject.
It would be nice if this wasn't necessary, is there a workaround?
Thanks,
Andreia
Citando Maria Felber :
> Dear Ms. Kakunoori,
>
> sorry to bother
Hi there,
I think there is an option to remove all edits that have been
incorporated using recon2 -clean.
Is there a chance that I can selectively undo all incorporated pial
edits (ie that have been incorporated by running "recon-all -subject
TEST -autorecon2 > TEST-2.log")?
Thanks very much in
Hi Bruce,
I've grabbed the dev version
freesurfer-Darwin-leopard-i686-dev.tar.gz (date 2 Oct 2011, 13:10)
at
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
and tried
mri_morphology fill_holes 26
but got the message that the operation "fill_holes"
is not supported.
Ed
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