In the first command, you need to tell recon-all to do something. Eg, if
you add -all, it tells it to analyze everything (keeping any manual
edits you might have made). You can also try "-make all" and it will
attempt to update the results (so it will not re-run any steps if it
thinks that re-r
What kind of remote access are you using?
Bruce
On Nov 8, 2012, at 3:04 PM, "Li, Hua" wrote:
>
>
> Hello,
>
> We recently installed freesurfer on an Ubuntu 12.04 workstation for doctors
> in Emergency room which will be used for CT scan analysis. In such case,
> remote access is require
Did you already try the suggestions on?:
http://surfer.nmr.mgh.harvard.edu/fswiki/RemoteAccess
Dan
On Thu, Nov 8, 2012 at 3:04 PM, Li, Hua wrote:
>
>
>
>
> Hello,
>
>
>
> We recently installed freesurfer on an Ubuntu 12.04 workstation for doctors
> in Emergency room which will be used for CT sc
Hello,
We recently installed freesurfer on an Ubuntu 12.04 workstation for doctors in
Emergency room which will be used for CT scan analysis. In such case, remote
access is required for multiple users.
No difficulty was encountered when we tested tkmedit bert orig.mgz locally.
However, it s
Hello,
I am having trouble with the pre-processing step. When I enter the recon-all
command I get an error:
[Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# recon-all -s ms_018
ERROR: nothing to do
When I enter 'recon-all -s ms_018 -qcache' I get a long list of output but I
don't thi
Can you send me the aseg.stats file for a single subject where you are
seeing this effect?
doug
On 11/08/2012 03:45 AM, Zheng Hui wrote:
> Hi Doug, I sum all structures except ventricle, CSF, cerebellum and
> brainstem in order to compare with SubCortGrayVol. Even the former
> includes some
On 10/25/2012 04:25 PM, Shigetoshi Takaya wrote:
> Dear Freesurfer experts,
>
> I would like to have your help.
>
> I have a volume data of a certain parameter on white/grey matter boundary
> (X.nii). What I want to do are as follows:
> Step 1: I want to register it onto a standard space using su
Hi Chris, the problem is that you do not have FSLDIR defined. Assuming
you have FSL installed, then setenv FSLDIR /place/where/fsl/is/installed
doug
On 11/06/2012 09:09 PM, Chris McNorgan wrote:
> Hi Doug,
>
> Attached are two plain-text files: fslog2.txt contains the redirected
> terminal outp
This could be a number of things. Did you restore the tkregister2 to the
original? The tkregister2.bin command was compiled under Redhat OS5.
What OS are you using?
doug
On 11/07/2012 06:15 PM, Eric Cunningham wrote:
> i tried replacing this file in tktools with the new tkregister2.bin,
> an
Thanks Bruce,I am currently using 4GB ram and i5 intel processor.
On 8 November 2012 15:08, Bruce Fischl wrote:
> how much RAM does the VM have?
>
> On Thu, 8 Nov 2012, Varghese Chikku wrote:
>
> Dear all,
>> I am trying to run recon all and FS will either exists with
>> this child pro
how much RAM does the VM have?
On Thu, 8 Nov 2012, Varghese Chikku wrote:
Dear all,
I am trying to run recon all and FS will either exists with
this child process exited abnormally...or just a blank window
appears with leaving the system to freeze.So i have to power off the VM
a
Dear all,
I am trying to run recon all and FS will either exists with this *
child process exited abnormally*...or just a blank window appears with
leaving the system to freeze.So i have to power off the VM and start
all over again.
Does it have to do with the system requirements
Thanks for the reply Nick,
Yes mris_info does return information I would need.
volume geometry:
extent : (256, 256, 256)
voxel : ( 1., 1., 1.)
x_(ras) : (-1., 0., 0.)
y_(ras) : ( 0., 0., -1.)
z_(ras) : ( 0., 1., 0.)
c_(ras) : ( 5.8612, -8.
Hi Doug, I sum all structures except ventricle, CSF, cerebellum and brainstem in order to compare with SubCortGrayVol. Even the former includes some white matter structures and all subcortical structures, it is smaller compared to SubCortGrayVol. My original question is about calculating the total
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