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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." > >