I see. Call recon-all once for each image with a different subject I'd
On Dec 1, 2012, at 3:58 PM, "Assaf B. Spanier" wrote:
>
>
>
>
> On Sat, Dec 1, 2012 at 10:47 PM, Bruce Fischl
> wrote:
> are they different time points or from the same session?
>
>
> Those are different time points
Thank you for your reply, Bruce. I'm running FreeSurfer using a VMWare
virtual machine on Windows 7. I've set the settings of the VM to use 2 CPUs
and 6GB ram. Here is the specifications of my computer hardware:
OS: Windows 7 professional
Processor: Intel Core i7-3770 CPU @ 3.40 GHz
RAM: 8 GB
Syste
Bo Xiang got the following Error Message. Attached are the mtx and
fsgd file. Does anyone what caused the error?
>
>On Fri, Nov 30, 2012 at 8:28 AM, xiangbo_2010 wrote:
>> Dear Donald McLaren
>>
>>I used the contrast to run, but the error is appear:
>>
>> mri_glmfit --y lh.gender_age.thic
On Sat, Dec 1, 2012 at 10:47 PM, Bruce Fischl wrote:
> are they different time points or from the same session?
Those are different time points in the same session (10 minute interval
between each acquisition)
> What are you trying to achieve?
What I would like to achieve ?
I would like t
are they different time points or from the same session? What are you
trying to achieve?
On Sat, 1 Dec 2012, Assaf B. Spanier wrote:
This is exactly the command I've used.
However, as I mentioned my subject has about six or seven T1-MRI images and
I have added all of them via the ""recon-all -
This is exactly the command I've used.
However, as I mentioned my subject has about six or seven T1-MRI
images andI have added all of them via the ""
recon-all -i image1 -i image2 etc'" command. I can even see those images
in the "mri/orig" directory. see:
~~
| |-- orig
| | |-- 001-
what different brain images do you mean? You can view them with the
surfaces via:
tkmedit norm.mgz lh.white -segmentation aparc+aseg.mgz
or
tkmedit norm.mgz lh.white -segmentation aparc2009s+aseg.mgz
the tools will be part of FS 5.2 when it comes out in the next month or so.
If you really
Can you please point me to those "tools" ? A link to the relevant website
will be highly appreciated. Thanks!
On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl wrote:
> Hi Spanier
>
> definitely don't invoke recon-all with the FLAIR image. We have some tools
> in 5.2 for this, but you would call it
Many thanks for the quick response - I would take a look on your
suggestion!
How about my first question ? About viewing the segmentation results of my
first trial ( without the Flair images)
[Please forgive my English :) ]
On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl wrote:
> Hi Spanier
>
> d
Hi Spanier
definitely don't invoke recon-all with the FLAIR image. We have some
tools in 5.2 for this, but you would call it as a postprocessing step with
a different command line in any case. Instead, you can use bbregister to
register the flair to the surfaces and resample it.
cheers
Bruce
can you check to see how much you actually have free? You are definitely
running out of memory, so something else is using it. What is your
hardware/software environment?
On Sat, 1 Dec 2012,
Negar Memarian wrote:
No, I tried running just one recon and I only have one xterm window open.
Anyt
Hi@all,
I have a dataset of several MRI T1 images and one Flair. All images of the
same subject and were taken in the same session. My goal is to register
and segment all those MRI images.
*= A =*
In my first try I have used, "recon-all -i image1 -i image2 etc'" for all
T1 images (here, I didn'
No, I tried running just one recon and I only have one xterm window open.
Anything I can do to fix this?
On Sat, Dec 1, 2012 at 11:11 AM, Bruce Fischl wrote:
> 6G should be plenty. Do you have anything else running? Maybe another
> recon at the same time?
> On Fri, 30 Nov 2012, Negar Memarian w
6G should be plenty. Do you have anything else running? Maybe another
recon at the same time?
On Fri, 30 Nov 2012, Negar Memarian wrote:
> Hi Bruce,
> I have 8 GB ram and have assigned 6GB of it to FreeSurfer. Shall I increase
> it to 8? Would that be enough or still too low?
>
> Thank you,
> Ne
what happens if you do
ls -l $SUBJECTS_DIR/us03.nii.gz
and
mri_info $SUBJECTS_DIR/us03.nii.gz
On Sun, 2 Dec 2012, aini ismafairus wrote:
Hi,
Have been tried that but still exited with errors.
is it because of iMac doesn't enable freesurfer to create the subject files
without security pa
you must change the subject directory outside the application
Azeez Adebimpe
Date: Sun, 2 Dec 2012 00:40:28 +0800
From: aini_ismafai...@yahoo.com.my
To: j.haen...@psychologie.uzh.ch; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all error
Hi,
Have been tried that but stil
Hi,
Have been tried that but still exited with errors.
is it because of iMac doesn't enable freesurfer to create the subject files
without security password?
do anybody know how to settle this problems?
Thank you.
Best,
Isma
From: Jürgen Hänggi
To: ain
Dear Aina
Unzip us03.nii.gz and try it again
Cheers
Jürgen
On [DATE], "aini ismafairus" <[ADDRESS]> wrote:
> Hello,
>
> I still new in using freesurfer.
> the freesurfer was successfully installed.
> but when i tried to run recon-all it give an error.
>
>
> [Ainis-iMac:~] ismafairus% setenv
Hello,
I still new in using freesurfer.
the freesurfer was successfully installed.
but when i tried to run recon-all it give an error.
[Ainis-iMac:~] ismafairus% setenv FREESURFER_HOME Applications/freesurfer
[Ainis-iMac:~] ismafairus% source $FREESURFER_HOME/SetUpFreeSurfer.csh
freesu
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