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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
================================================