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Do you have the text "template_list" in your file template_list ? On 10 Feb 2014, at 16:11, Jacobs H (NP) <[log in to unmask]> wrote: > Hi Gwenaëlle, > > Thanks for your feedback. > This is the result of the ls command: > > CON_HJ_101_T1.nii.gz CON_HJ_120_T1.nii.gz MCI_HJ_215_T1.nii.gz > CON_HJ_103_T1.nii.gz CON_HJ_121_T1.nii.gz MCI_HJ_216_T1.nii.gz > CON_HJ_104_T1.nii.gz MCI_HJ_201_T1.nii.gz MCI_HJ_217_T1.nii.gz > CON_HJ_105_T1.nii.gz MCI_HJ_202_T1.nii.gz MCI_HJ_218_T1.nii.gz > CON_HJ_106_T1.nii.gz MCI_HJ_203_T1.nii.gz slicesdir > CON_HJ_107_T1.nii.gz MCI_HJ_204_T1.nii.gz struc > CON_HJ_108_T1.nii.gz MCI_HJ_205_T1.nii.gz template_list > CON_HJ_109_T1.nii.gz MCI_HJ_206_T1.nii.gz TwogroupsMCI.con > CON_HJ_110_T1.nii.gz MCI_HJ_207_T1.nii.gz TwogroupsMCI_cov.png > CON_HJ_112_T1.nii.gz MCI_HJ_208_T1.nii.gz TwogroupsMCI_cov.ppm > CON_HJ_113_T1.nii.gz MCI_HJ_209_T1.nii.gz TwogroupsMCI.fsf > CON_HJ_114_T1.nii.gz MCI_HJ_210_T1.nii.gz TwogroupsMCI.grp > CON_HJ_115_T1.nii.gz MCI_HJ_211_T1.nii.gz TwogroupsMCI.mat > CON_HJ_116_T1.nii.gz MCI_HJ_212_T1.nii.gz TwogroupsMCI.png > CON_HJ_117_T1.nii.gz MCI_HJ_213_T1.nii.gz TwogroupsMCI.ppm > CON_HJ_118_T1.nii.gz MCI_HJ_214_T1.nii.gz > > And this is the result van cat template_list: > [heidi@Heidihost my_fsl_vbm]$ cat template_list > CON_HJ_101_T1.nii.gz > CON_HJ_103_T1.nii.gz > CON_HJ_104_T1.nii.gz > CON_HJ_105_T1.nii.gz > CON_HJ_106_T1.nii.gz > CON_HJ_107_T1.nii.gz > CON_HJ_108_T1.nii.gz > CON_HJ_109_T1.nii.gz > CON_HJ_110_T1.nii.gz > CON_HJ_112_T1.nii.gz > CON_HJ_113_T1.nii.gz > CON_HJ_114_T1.nii.gz > CON_HJ_115_T1.nii.gz > CON_HJ_116_T1.nii.gz > CON_HJ_117_T1.nii.gz > CON_HJ_118_T1.nii.gz > CON_HJ_120_T1.nii.gz > CON_HJ_121_T1.nii.gz > MCI_HJ_201_T1.nii.gz > MCI_HJ_202_T1.nii.gz > MCI_HJ_203_T1.nii.gz > MCI_HJ_204_T1.nii.gz > MCI_HJ_205_T1.nii.gz > MCI_HJ_206_T1.nii.gz > MCI_HJ_207_T1.nii.gz > MCI_HJ_208_T1.nii.gz > MCI_HJ_209_T1.nii.gz > MCI_HJ_210_T1.nii.gz > MCI_HJ_211_T1.nii.gz > MCI_HJ_212_T1.nii.gz > MCI_HJ_213_T1.nii.gz > MCI_HJ_214_T1.nii.gz > MCI_HJ_215_T1.nii.gz > MCI_HJ_216_T1.nii.gz > MCI_HJ_217_T1.nii.gz > MCI_HJ_218_T1.nii.gz > template_list > > Hope this helps in finding what could be wrong. > Thanks > Heidi > > ================================================ > Dr. Heidi Jacobs > Postdoc researcher > Faculty of Health, Medicine and Life Sciences > School for Mental Health and Neurosciences > Division Cognitive Neuropsychiatry and Clinical Neurosciences > Alzheimer Center Limburg > [log in to unmask] > www.maastrichtuniversity.nl > www.heidijacobs.nl > > Dr. Tanslaan 12, 6229 ET Maastricht > P.O. Box 616, 6200 MD Maastricht, The Netherlands > T +31 43 38 84 090 F +31 43 38 84 092 > ================================================ > ________________________________________ > Van: FSL - FMRIB's Software Library [[log in to unmask]] namens Gwenaëlle DOUAUD [[log in to unmask]] > Verzonden: maandag 10 februari 2014 13:04 > Aan: [log in to unmask] > Onderwerp: Re: [FSL] fslvbm2 error with init > > Hi Heidi, > > it would seem that the problem comes from your template_list file. > > Could you please copy/paste the result of an 'ls' and of a 'cat template_list' in your my_fsl_vbm directory? > > Cheers, > Gwenaëlle > > ------------------------------------------------------------------------------------------------------------------------ > Gwenaëlle Douaud, PhD > University Research Lecturer & MRC Career Development Fellow > > FMRIB Centre, University of Oxford > John Radcliffe Hospital, Headington > OX3 9DU Oxford UK > Switchboard: +44 (0) 1865 222 493 > Fax: +44 (0) 1865 222 717 > > www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud > www.fmrib.ox.ac.uk/research/fmrib-interface-analysis-clinical-neuroscience-group<http://www.fmrib.ox.ac.uk/research/fmrib-interface-analysis-clinical-neuroscience-group> > ----------------------------------------------------------------------------------------------------------------------- > > ________________________________ > De : Jacobs H (NP) <[log in to unmask]> > À : [log in to unmask] > Envoyé le : Samedi 8 février 2014 18h45 > Objet : [FSL] fslvbm2 error with init > > Dear Fsl developers, > > I have tried to run fslvbm_2_template, but keep on getting the same error message. I have tried to run it on mac and linux, but I have the impression that it is not creating the init files to make the template. > This is the error message: > [heidi@Heidihost<mailto:heidi@Heidihost> my_fsl_vbm]$ fslvbm_2_template -n > CON_HJ_101_T1_struc > CON_HJ_103_T1_struc > CON_HJ_104_T1_struc > CON_HJ_105_T1_struc > CON_HJ_106_T1_struc > CON_HJ_107_T1_struc > CON_HJ_108_T1_struc > CON_HJ_109_T1_struc > CON_HJ_110_T1_struc > CON_HJ_112_T1_struc > CON_HJ_113_T1_struc > CON_HJ_114_T1_struc > CON_HJ_115_T1_struc > CON_HJ_116_T1_struc > CON_HJ_117_T1_struc > CON_HJ_118_T1_struc > CON_HJ_120_T1_struc > CON_HJ_121_T1_struc > MCI_HJ_201_T1_struc > MCI_HJ_202_T1_struc > MCI_HJ_203_T1_struc > MCI_HJ_204_T1_struc > MCI_HJ_205_T1_struc > MCI_HJ_206_T1_struc > MCI_HJ_207_T1_struc > MCI_HJ_208_T1_struc > MCI_HJ_209_T1_struc > MCI_HJ_210_T1_struc > MCI_HJ_211_T1_struc > MCI_HJ_212_T1_struc > MCI_HJ_213_T1_struc > MCI_HJ_214_T1_struc > MCI_HJ_215_T1_struc > MCI_HJ_216_T1_struc > MCI_HJ_217_T1_struc > MCI_HJ_218_T1_struc > Running segmentation: ID=6301 > Running initial registration: ID=8555 > Image Exception : #22 :: ERROR: Could not open image template_list_struc_GM_to_T > terminate called after throwing an instance of 'RBD_COMMON::BaseException' > ./fslvbm2c: line 13: 12270 Aborted (core dumped) $FSLDIR/bin/fslmerge -t template_4D_GM $mergelist > Cannot open volume template_4D_GM for reading! > ERROR: Could not open file > /home/heidi/Applications/fsl/bin/fslswapdim: line 106: [: =: unary operator expected > ERROR: Could not open file > /home/heidi/Applications/fsl/bin/fslswapdim: line 114: [: -gt: unary operator expected > ERROR: Could not open file > /home/heidi/Applications/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 /home/heidi/Applications/fsl/data/standard/tissuepriors/avg152T1_gray struc/template_GM > to check general alignment of mean GM template vs. original standard space template. > > Any idea what might have happened or how I can solve this? > For each subjects, the struc folder has the following files: > _struc_brain_mixeltype.nii.gz > _struc_cut.nii.gz > _struc_brain.nii.gz > _struc_GM.nii.gz > _struc_brain_pve_0.nii.gz > _struc_GM_to_T.mat > _struc_brain_pve_2.nii.gz > _struc_GM_to_T.nii.gz > _struc_brain_pveseg.nii.gz > _struc.nii.gz > _struc_brain_seg.nii.gz > > Thanks! > Heidi > > ================================================ > Dr. Heidi Jacobs > Postdoc researcher > Faculty of Health, Medicine and Life Sciences > School for Mental Health and Neurosciences > Division Cognitive Neuropsychiatry and Clinical Neurosciences > Alzheimer Center Limburg > [log in to unmask]<mailto:[log in to unmask]> > www.maastrichtuniversity.nl > www.heidijacobs.nl > > Dr. Tanslaan 12, 6229 ET Maastricht > P.O. Box 616, 6200 MD Maastricht, The Netherlands > T +31 43 38 84 090 F +31 43 38 84 092 > ================================================ --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet