Dear All,
I want to run recon-all for multiple subjects.
I named my sbjects as SZ01.nii, SZ02.nii etc.
After setting the cd and environmanet variable, I ran using following for loop:
>for x in *
> do
>recon-all -i SZ*.nii -s $x -all
>done
I got the following error: WHAT MIGHT BE THE REASON FOR
Hi,
I too am facing the same problem as mentioned by Miklos Argyelan:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html
Jitesh
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Dear Marcos,
> 1- How do I save the combined 3D view I got as a surface?
Do you want a surface of the whole hippocampus? In that case I would
suggest adding up the probability volumes from all the subfields and
thresholding the resulting volume.
> 2-I know the hippo-subifields .mgz files are pr
Hi All,
I have a similar error, which I traced back (I think!) to bbregister
failing to write FLAIRraw.lta. My only solution was to download the subject
directories from our linux (RedHat) cluster and run the registration on an
OSX binary. This then creates the .lta file and I upload it back to th
Hi all!
I am almost ready to do my first longitudinal run with Tracula. I guess that
for the remaining insecurities it is probably best to stick with the
default options but I'd like to be more confident with it and just wanted
to ask which option to choose and why or why not:
My config file conta
Hi Nate
how much RAM is there, not disk space.
cheers
Bruce
On Wed, 17 Apr 2013, Nate Lee wrote:
Hello Bruce,
The iMac has 500GB capacity, and 425GB is not in use.
Best regards,
Nate
On Wed, Apr 17, 2013 at 12:06 PM, Bruce Fischl
wrote:
Hi Nate
how much memory do you have
Hello Bruce,
The iMac has 500GB capacity, and 425GB is not in use.
Best regards,
Nate
On Wed, Apr 17, 2013 at 12:06 PM, Bruce Fischl
wrote:
> Hi Nate
>
> how much memory do you have in the machine?
> Bruce
>
> On Wed, 17 Apr 2013, Nate Lee wrote:
>
> Hello everyone,
>> I'm using Freesurfer
Eduard,
Can you send the whole recon-all.log file? The error show below is a
strange one. It appears as if the string "ERROR: could not determine
file" is the input to mri_convert, and I'm not sure how that can happen.
Also double check (by viewing in freeview) that T2raw.mgz is a valid
file (i
Hi Nate
how much memory do you have in the machine?
Bruce
On Wed, 17 Apr 2013, Nate Lee
wrote:
Hello everyone,
I'm using Freesurfer from Texas Medical Center. I'm using an iMac, and am
experiencing regular
crashes during these several occasions:
1. Opening more than two volumes at once
2. W
Hello everyone,
I'm using Freesurfer from Texas Medical Center. I'm using an iMac, and am
experiencing regular crashes during these several occasions:
1. Opening more than two volumes at once
2. When one volume and one surface is open and:
a. switching back and forth between different exposé d
Yes but I don't want to create a registration template initialized with FS
template (fsaverage). That's why I followed the part "creating a
registration template from scratch" in this web page
http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
But for annotation I will have to use apa
I'd suggest running make_average_subject which will create tiffs for you
as well as other useful template-specific maps (like an annotation).
doug
On 04/17/2013 05:48 AM, Sophie Maingault wrote:
> Hi Experts,
>
> I'm creating a template from scratch. When I run mris_make_template is
> it enough
Hi,
On Wed, April 17, 2013 10:27 am, Bruce Fischl wrote:
> Hi Sophie
>
> the surface has to be a spherical one. Internally it will use the geometry
> for some other surfaces like smoothwm, but the command line has to be a
> spherical surfaces. Usually the first time with an individual subject you
Hi Sophie
the surface has to be a spherical one. Internally it will use the geometry
for some other surfaces like smoothwm, but the command line has to be a
spherical surfaces. Usually the first time with an individual subject you
can use sphere, but if you are using multiple ones it should be
Hi Sophie,
if you want the template to represent corresponding points across your
subjects you need to use sphere.reg
cheers
Bruce
On Wed, 17 Apr 2013, Sophie Maingault
wrote:
Hi Experts,
I'm creating a template from scratch. When I run mris_make_template is it
enough to
run mris_make_te
Hi Chikku
a 30,000 vertex defect means something is dramatically wrong - that's
about 1/4 of the whole cortex. Check your filled.mgz or lh.orig.nofix and
see if the skull is attached or the cerebellum or something. The
computational complexity of the topology fixing is quadratic in the
convex
Dear FreeSurfer experts,
First of all, congrats for this new 5.2 stable version.
My name is Eduard, and I'm trying to perform de T2 pial refinement in a
pre-processed subject with the B0 image from a DTI. I used that command:
recon-all -autorecon3 -T2pial -s ACC019/ -T2
/home/linux/Escritorio
Hi Experts,
I'm creating a template from scratch. When I run mris_make_template is it
enough to run mris_make_template ?h smoothwm my.temp0.tif ? My
question is about which sphere_name I have to put for argument ? I hope I
was clear.
Best regards.
Sophie
__
Hi All,
I am running recon-all on a set of Diff images since last 2 days
and it looks like FS stopped working.It says correcting defect 0 since
yesterday afternoon.
Any way to figure whats going on?
Many Thanks
Chikku
#@# Fix Topology lh Tue Apr 16 14:47:22 CEST 2013
\n cp ../surf/l
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