; 1) MG17
> > 2) recon-all -i
> > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
> > MG17_SurferOutput
> > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
> > 3) ERROR: Flag
> > /autofs/space/huygens_001/users/mia/s
It was initially in the wrong folder, but now it in the mri folder.
ls -l
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz
-rw-rw-r-- 1 miaborz acqcash 15954217 Jan 20 16:16
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz
Still unabl
does
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz
exist?
On 01/20/2015 03:40 PM, Borzello, Mia wrote:
> Okay, cool, I just tried with the full path to the .nii file and it worked.
> However, when I tried to load the ct.anat.mgz using tkmedit i get an error in
>
Okay, cool, I just tried with the full path to the .nii file and it worked.
However, when I tried to load the ct.anat.mgz using tkmedit i get an error in
loading the volume.
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
I was able to convert your file without problem. When you run mri_convert, you
have to give a path to a file that exists. Below, the error says that it cannot
find /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii
Does this file exist? It is different than the one you have below, ie
/auto
use my email
On 01/20/2015 02:29 PM, Borzello, Mia wrote:
> yes, definitely. I just tried to upload to this email:
> freesurfer@nmr.mgh.harvard.edu
> and it says "Server Error! User 'freesurfer' is not a valid NMR Account
> holder"
> I have a feeling this is a user error- sorry about that.
>
> T
yes, definitely. I just tried to upload to this email:
freesurfer@nmr.mgh.harvard.edu
and it says "Server Error! User 'freesurfer' is not a valid NMR Account holder"
I have a feeling this is a user error- sorry about that.
Thanks,
m
From: freesurfer-boun
Hi guys,
full command line: mri_convert ct.anat.nii ct.anat.mgz
command line: ls -l
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
-rw-rw-r-- 1 miaborz acqcash 32506208 Jan 19 22:12
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
Can you put this on our file drop?
On 01/20/2015 11:26 AM, mborze...@partners.org wrote:
> *
> You have received 1 secure file from mborze...@partners.org.
> *
> Use the secure link below to download.
> Here is the ct.anat.nii file
> Secure File Downloads:
> Available until: **30 January 2015**
Hi Mia,
try to change the name of the nifti file from ct.ana.nii to ctana.nii.
Azeez
> Date: Tue, 20 Jan 2015 11:09:07 -0500
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] converting .nii to .mgz
>
> Does that file exist?
>
> On 01/19/2015 11
You have received 1 secure file from mborze...@partners.org.
Use the secure link below to download.
Here is the ct.anat.nii file
Secure File Downloads:
Available until: 30 January 2015
Click link to download:
ct.anat.nii ,31,744.34 KB
https://transfer.partners.org/seos/1000/mpd/ui31012015928325bc
If that is the model you want, then you will have to create your own
design matrix. The FSGD format does not allow for some covariates
(Score) to have interaction terms and others (Age) to not.
doug
On 01/18/2015 04:08 PM, lindsay hanford wrote:
> Dear Freesurfer Community,
>
> I'm running in
Use View->Configure->Overlay
On 01/20/2015 08:48 AM, Worker, Amanda wrote:
> Hi Bruce,
>
> Thanks for your help. Is there a way that I can now change the colour bar,
> it's currently red to yellow meaning pretty much the whole brain is red. I'd
> like several different colours to illustrate di
Does that file exist?
On 01/19/2015 11:30 PM, Borzello, Mia wrote:
> Hi Bruce,
>
> Thanks for getting back to me so quickly!
> I just tried that and got the following error:
> reading from ct.anat.nii...
> niiRead(): error opening file
> /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii
>
Hi Bruce,
Thanks for your help. Is there a way that I can now change the colour bar, it's
currently red to yellow meaning pretty much the whole brain is red. I'd like
several different colours to illustrate different thickness'.
I don't seem to be able to edit Mid or Slope.
Thanks,
Amanda
__
Hi Amanda,
click the "truncate" button.
cheers
Bruce
On Tue, 20 Jan 2015, Worker, Amanda wrote:
> My command line was "tksurfer mean.lh.thick_age.thickness.10.mgh lh inflate"
> d- which is when I got the error.
>
> I have now tried loading fsaverage first with "tksurfer fsaverage lh
> inflated"
Hi Muhammad
can you really run 40 subjects at the same time? Usually that means you
have a processor farm and it has some mechanism for submitting jobs and
load balancing and such (like qsub).
cheers
Bruce
On Tue, 20 Jan 2015, Muhammad Naveed
Iqbal Qureshi wrote:
Can we apply recon-all on
Hi Mia
can you please send us the full command line? And also do an ls -l of
that file and include it?
thanks
Bruce
On Tue, 20 Jan 2015, Borzello, Mia wrote:
> Hi Bruce,
>
> Thanks for getting back to me so quickly!
> I just tried that and got the following error:
> reading from ct.anat.nii...
Dear Freesurfer experts,After I added the Tracula update at
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula, I have been unable to use
mri_onvert. Since I have Ubuntu 14.04, I used the Centos 6 x86_64 version found
at this link. However, when I tried to use mri_convert it segement fault. I
My command line was "tksurfer mean.lh.thick_age.thickness.10.mgh lh inflate" d-
which is when I got the error.
I have now tried loading fsaverage first with "tksurfer fsaverage lh inflated"
and it seems to be working fine.
The problem now is changing the colour scale to display only positive va
*Dear Colleagues,*
I am sorry if my question is a bit out-of-topic...
I wonder if there is a an opportunity to find a community affiliation
vector estimated using any of the large-scale datasets (like the Human
Connectome Project, for example).. I was just thinking that having
independently estima
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