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Hi Carina,

it looks like the segmentation has not run or has not worked, as you should have a file called A_P10_T1_struc_GM.nii.gz. There should be an error in the related log (fslvbm2a.e*), could you please copy/paste it?

Cheers,
Gwenaëlle
 
------------------------------------------------------------------------------------------------
Gwenaëlle Douaud, PhD
MRC Career Development Fellow

FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington
OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523
Fax: +44 (0) 1865 222 717

www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud
-----------------------------------------------------------------------------------------------

De : Carina Mendes <[log in to unmask]>
À : [log in to unmask]
Envoyé le : Lundi 5 août 2013 23h21
Objet : Re: [FSL] Error running fslvbm_2_template

Hi,

As you suggested Mark I looked up into the logs and there was no error associated with the registration.

Gwenaëlle, the template_list contents are the following:

$ cat template_list
A_P10_T1.nii.gz
A_P11_T1.nii.gz
A_P1_T1.nii.gz
A_P2_T1.nii.gz
A_P3_T1.nii.gz
A_P4_T1.nii.gz
A_P5_T1.nii.gz
A_P6_T1.nii.gz
A_P7_T1.nii.gz
A_P8_T1.nii.gz
A_P9_T1.nii.gz
B_P12_T1.nii.gz
B_P13_T1.nii.gz
B_P14_T1.nii.gz
B_P15_T1.nii.gz
B_P16_T1.nii.gz
B_P17_T1.nii.gz
B_P19_T1.nii.gz
B_P20_T1.nii.gz
B_P21_T1.nii.gz
B_P22_T1.nii.gz

and the ls A_P10_T1* on struct directory gives:

$ ls A_P10_T1*
A_P10_T1_struc_brain.nii.gz  A_P10_T1_struc_cut.nii.gz  A_P10_T1_struc.nii.gz


Any suggestion?

Thank you for your help,
Carina


On Mon, Aug 5, 2013 at 11:45 AM, Gwenaëlle DOUAUD <[log in to unmask]> wrote:
Hi Carina,

to add to what MJ said this morning, could you also please copy/paste the result of an ls A_P10_T1* in your struc/ directory and the content of your template_list file?

Cheers,
Gwenaëlle
 
------------------------------------------------------------------------------------------------
Gwenaëlle Douaud, PhD
MRC Career Development Fellow

FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington
OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523
Fax: +44 (0) 1865 222 717

www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud
-----------------------------------------------------------------------------------------------

De : Carina Mendes <[log in to unmask]>
À : [log in to unmask]
Envoyé le : Jeudi 1 août 2013 15h39
Objet : [FSL] Error running fslvbm_2_template

Hello,

I was following the user guide provided on FSL-VBM page, and encountered an error when I tried the command:

fslvbm_2_template -n

the output was:
"...
Running segmentation: ID=9108
Running initial registration: ID=10273
Cannot open volume A_P10_T1_struc_GM_to_T for reading!
Cannot open volume template_4D_GM for reading!
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 106: [: =: unary operator expected
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 114: [: -gt: unary operator expected
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 116: [: -gt: unary operator expected
Cannot open volume template_GM for reading!
Cannot open volume template_GM for reading!
Creating first-pass template: ID=
/bin/sh: line 1: 30: command not found
Running registration to first-pass template: ID=
/bin/sh: line 1: 15: command not found
Creating second-pass template: ID=
Study-specific template will be created, when complete, check results with:
fslview struc/template_4D_GM
and turn on the movie loop to check all subjects, then run:
fslview  /usr/local/fsl/data/standard/tissuepriors/avg152T1_gray  struc/template_GM
to check general alignment of mean GM template vs. original standard space template."