Hello FSL experts,
I am attempting to run a VBM analysis following the steps in the VBM practical provided by FSL. I was able to run the practical without error. However, with my own data, I get the following error when I run 'fslvbm_2_template -n'. The current directory when running this line was the 'VBMAnalysis' folder.
Cannot open volume . . . VBMAnalysis/Con_BARTON_PP_S14_1006_1_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 107: [: =: unary operator expected
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 115: [: -gt: unary operator expected
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 117: [: -gt: unary operator expected
Cannot open volume template_GM for reading!
Cannot open volume template_GM for reading!
Creating first-pass template: ID=
Running registration to first-pass template: ID=The command you have requested cannot be found or is not executable
/bin/sh: line 1: you: 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.
It seems the function is looking for the GM_to_T files in the VBManalysis folder, but those files were auto created in the struc folder when I ran fslvbm_2_template, not the VBManalysis folder.
Any suggestions? Based on looking through the archives, I'm guessing you might want to see the ls for these folders.
Best,
Sherryse
ls VBMAnalysis #the origdata folder was made manually by me, based on the FSL practical. I thought that might be the issue.
Con_BARTON_PP_S14_1006_1.nii.gz Pat_P218_Structural.nii.gz
Con_BARTON_PP_S15_1006_1.nii.gz Pat_P219_Structural.nii.gz
Con_BARTON_PP_S16_1007_1.nii.gz Pat_P221_Structural.nii.gz
Con_BARTON_PP_S17_1006_1.nii.gz Pat_P222_Structural.nii.gz
Con_BARTON_PP_S18_1006_1.nii.gz Pat_P224_Structural.nii.gz
Con_BARTON_WORD_S17_9_1.nii.gz README_StepByStepNotes.rtf
Con_BARTON_WORD_S18_8_1.nii.gz design.con
Con_BARTON_WORD_S19_8_1.nii.gz design.fsf
Con_BARTON_WORD_S20_8_1.nii.gz design.grp
Con_BARTON_WORD_S21_8_1.nii.gz design.mat
Con_BARTON_WORD_S23_8_1.nii.gz design.png
Con_BARTON_WORD_S25_8_1.nii.gz design.ppm
Con_BARTON_WORD_S26_8_1.nii.gz design_cov.png
Con_BARTON_WORD_S27_8_1.nii.gz design_cov.ppm
Con_BARTON_WORD_S28_8_1.nii.gz origdata
Con_BARTON_WORD_S29_8_1.nii.gz struc
Pat_P206_Structural.nii.gz template_list
ls struc
Con_BARTON_PP_S14_1006_1_struc.nii.gz
Con_BARTON_PP_S14_1006_1_struc_GM.nii.gz
Con_BARTON_PP_S14_1006_1_struc_GM_to_T.mat
Con_BARTON_PP_S14_1006_1_struc_GM_to_T.nii.gz
Con_BARTON_PP_S14_1006_1_struc_brain.nii.gz
Con_BARTON_PP_S14_1006_1_struc_brain_mixeltype.nii.gz
Con_BARTON_PP_S14_1006_1_struc_brain_pve_0.nii.gz
Con_BARTON_PP_S14_1006_1_struc_brain_pve_2.nii.gz
Con_BARTON_PP_S14_1006_1_struc_brain_pveseg.nii.gz
Con_BARTON_PP_S14_1006_1_struc_brain_seg.nii.gz
Con_BARTON_PP_S14_1006_1_struc_cut.nii.gz
Con_BARTON_PP_S15_1006_1_struc.nii.gz
Con_BARTON_PP_S15_1006_1_struc_GM.nii.gz
Con_BARTON_PP_S15_1006_1_struc_GM_to_T.mat
Con_BARTON_PP_S15_1006_1_struc_GM_to_T.nii.gz
Con_BARTON_PP_S15_1006_1_struc_brain.nii.gz
Con_BARTON_PP_S15_1006_1_struc_brain_mixeltype.nii.gz
Con_BARTON_PP_S15_1006_1_struc_brain_pve_0.nii.gz
Con_BARTON_PP_S15_1006_1_struc_brain_pve_2.nii.gz
Con_BARTON_PP_S15_1006_1_struc_brain_pveseg.nii.gz
Con_BARTON_PP_S15_1006_1_struc_brain_seg.nii.gz
Con_BARTON_PP_S15_1006_1_struc_cut.nii.gz
Con_BARTON_PP_S16_1007_1_struc.nii.gz
Con_BARTON_PP_S16_1007_1_struc_GM.nii.gz
Con_BARTON_PP_S16_1007_1_struc_GM_to_T.mat
Con_BARTON_PP_S16_1007_1_struc_GM_to_T.nii.gz
Con_BARTON_PP_S16_1007_1_struc_brain.nii.gz
Con_BARTON_PP_S16_1007_1_struc_brain_mixeltype.nii.gz
Con_BARTON_PP_S16_1007_1_struc_brain_pve_0.nii.gz
Con_BARTON_PP_S16_1007_1_struc_brain_pve_2.nii.gz
Con_BARTON_PP_S16_1007_1_struc_brain_pveseg.nii.gz
Con_BARTON_PP_S16_1007_1_struc_brain_seg.nii.gz
Con_BARTON_PP_S16_1007_1_struc_cut.nii.gz
Con_BARTON_PP_S17_1006_1_struc.nii.gz
Con_BARTON_PP_S17_1006_1_struc_GM.nii.gz
Con_BARTON_PP_S17_1006_1_struc_GM_to_T.mat
Con_BARTON_PP_S17_1006_1_struc_GM_to_T.nii.gz
Con_BARTON_PP_S17_1006_1_struc_brain.nii.gz
Con_BARTON_PP_S17_1006_1_struc_brain_mixeltype.nii.gz
Con_BARTON_PP_S17_1006_1_struc_brain_pve_0.nii.gz
Con_BARTON_PP_S17_1006_1_struc_brain_pve_2.nii.gz
Con_BARTON_PP_S17_1006_1_struc_brain_pveseg.nii.gz
Con_BARTON_PP_S17_1006_1_struc_brain_seg.nii.gz
Con_BARTON_PP_S17_1006_1_struc_cut.nii.gz
Con_BARTON_PP_S18_1006_1_struc.nii.gz
Con_BARTON_PP_S18_1006_1_struc_GM.nii.gz
Con_BARTON_PP_S18_1006_1_struc_GM_to_T.mat
Con_BARTON_PP_S18_1006_1_struc_GM_to_T.nii.gz
Con_BARTON_PP_S18_1006_1_struc_brain.nii.gz
Con_BARTON_PP_S18_1006_1_struc_brain_mixeltype.nii.gz
Con_BARTON_PP_S18_1006_1_struc_brain_pve_0.nii.gz
Con_BARTON_PP_S18_1006_1_struc_brain_pve_2.nii.gz
Con_BARTON_PP_S18_1006_1_struc_brain_pveseg.nii.gz
Con_BARTON_PP_S18_1006_1_struc_brain_seg.nii.gz
Con_BARTON_PP_S18_1006_1_struc_cut.nii.gz
Con_BARTON_WORD_S17_9_1_struc.nii.gz
Con_BARTON_WORD_S17_9_1_struc_GM.nii.gz
Con_BARTON_WORD_S17_9_1_struc_GM_to_T.mat
Con_BARTON_WORD_S17_9_1_struc_GM_to_T.nii.gz
Con_BARTON_WORD_S17_9_1_struc_brain.nii.gz
Con_BARTON_WORD_S17_9_1_struc_brain_mixeltype.nii.gz
Con_BARTON_WORD_S17_9_1_struc_brain_pve_0.nii.gz
Con_BARTON_WORD_S17_9_1_struc_brain_pve_2.nii.gz
Con_BARTON_WORD_S17_9_1_struc_brain_pveseg.nii.gz
Con_BARTON_WORD_S17_9_1_struc_brain_seg.nii.gz
Con_BARTON_WORD_S17_9_1_struc_cut.nii.gz
Con_BARTON_WORD_S18_8_1_struc.nii.gz
Con_BARTON_WORD_S18_8_1_struc_GM.nii.gz
Con_BARTON_WORD_S18_8_1_struc_GM_to_T.mat
Con_BARTON_WORD_S18_8_1_struc_GM_to_T.nii.gz
Con_BARTON_WORD_S18_8_1_struc_brain.nii.gz
Con_BARTON_WORD_S18_8_1_struc_brain_mixeltype.nii.gz
Con_BARTON_WORD_S18_8_1_struc_brain_pve_0.nii.gz
Con_BARTON_WORD_S18_8_1_struc_brain_pve_2.nii.gz
Con_BARTON_WORD_S18_8_1_struc_brain_pveseg.nii.gz
Con_BARTON_WORD_S18_8_1_struc_brain_seg.nii.gz
Con_BARTON_WORD_S18_8_1_struc_cut.nii.gz
Con_BARTON_WORD_S19_8_1_struc.nii.gz
Con_BARTON_WORD_S19_8_1_struc_GM.nii.gz
Con_BARTON_WORD_S19_8_1_struc_GM_to_T.mat
Con_BARTON_WORD_S19_8_1_struc_GM_to_T.nii.gz
Con_BARTON_WORD_S19_8_1_struc_brain.nii.gz
Con_BARTON_WORD_S19_8_1_struc_brain_mixeltype.nii.gz
Con_BARTON_WORD_S19_8_1_struc_brain_pve_0.nii.gz
Con_BARTON_WORD_S19_8_1_struc_brain_pve_2.nii.gz
Con_BARTON_WORD_S19_8_1_struc_brain_pveseg.nii.gz
Con_BARTON_WORD_S19_8_1_struc_brain_seg.nii.gz
Con_BARTON_WORD_S19_8_1_struc_cut.nii.gz
Con_BARTON_WORD_S20_8_1_struc.nii.gz
Con_BARTON_WORD_S20_8_1_struc_GM.nii.gz
Con_BARTON_WORD_S20_8_1_struc_GM_to_T.mat
Con_BARTON_WORD_S20_8_1_struc_GM_to_T.nii.gz
Con_BARTON_WORD_S20_8_1_struc_brain.nii.gz
Con_BARTON_WORD_S20_8_1_struc_brain_mixeltype.nii.gz
Con_BARTON_WORD_S20_8_1_struc_brain_pve_0.nii.gz
Con_BARTON_WORD_S20_8_1_struc_brain_pve_2.nii.gz
Con_BARTON_WORD_S20_8_1_struc_brain_pveseg.nii.gz
Con_BARTON_WORD_S20_8_1_struc_brain_seg.nii.gz
Con_BARTON_WORD_S20_8_1_struc_cut.nii.gz
Con_BARTON_WORD_S21_8_1_struc.nii.gz
Con_BARTON_WORD_S21_8_1_struc_GM.nii.gz
Con_BARTON_WORD_S21_8_1_struc_GM_to_T.mat
Con_BARTON_WORD_S21_8_1_struc_GM_to_T.nii.gz
Con_BARTON_WORD_S21_8_1_struc_brain.nii.gz
Con_BARTON_WORD_S21_8_1_struc_brain_mixeltype.nii.gz
Con_BARTON_WORD_S21_8_1_struc_brain_pve_0.nii.gz
Con_BARTON_WORD_S21_8_1_struc_brain_pve_2.nii.gz
Con_BARTON_WORD_S21_8_1_struc_brain_pveseg.nii.gz
Con_BARTON_WORD_S21_8_1_struc_brain_seg.nii.gz
Con_BARTON_WORD_S21_8_1_struc_cut.nii.gz
Con_BARTON_WORD_S23_8_1_struc.nii.gz
Con_BARTON_WORD_S23_8_1_struc_GM.nii.gz
Con_BARTON_WORD_S23_8_1_struc_GM_to_T.mat
Con_BARTON_WORD_S23_8_1_struc_GM_to_T.nii.gz
Con_BARTON_WORD_S23_8_1_struc_brain.nii.gz
Con_BARTON_WORD_S23_8_1_struc_brain_mixeltype.nii.gz
Con_BARTON_WORD_S23_8_1_struc_brain_pve_0.nii.gz
Con_BARTON_WORD_S23_8_1_struc_brain_pve_2.nii.gz
Con_BARTON_WORD_S23_8_1_struc_brain_pveseg.nii.gz
Con_BARTON_WORD_S23_8_1_struc_brain_seg.nii.gz
Con_BARTON_WORD_S23_8_1_struc_cut.nii.gz
Con_BARTON_WORD_S25_8_1_struc.nii.gz
Con_BARTON_WORD_S25_8_1_struc_GM.nii.gz
Con_BARTON_WORD_S25_8_1_struc_GM_to_T.mat
Con_BARTON_WORD_S25_8_1_struc_GM_to_T.nii.gz
Con_BARTON_WORD_S25_8_1_struc_brain.nii.gz
Con_BARTON_WORD_S25_8_1_struc_brain_mixeltype.nii.gz
Con_BARTON_WORD_S25_8_1_struc_brain_pve_0.nii.gz
Con_BARTON_WORD_S25_8_1_struc_brain_pve_2.nii.gz
Con_BARTON_WORD_S25_8_1_struc_brain_pveseg.nii.gz
Con_BARTON_WORD_S25_8_1_struc_brain_seg.nii.gz
Con_BARTON_WORD_S25_8_1_struc_cut.nii.gz
Con_BARTON_WORD_S26_8_1_struc.nii.gz
Con_BARTON_WORD_S26_8_1_struc_GM.nii.gz
Con_BARTON_WORD_S26_8_1_struc_GM_to_T.mat
Con_BARTON_WORD_S26_8_1_struc_GM_to_T.nii.gz
Con_BARTON_WORD_S26_8_1_struc_brain.nii.gz
Con_BARTON_WORD_S26_8_1_struc_brain_mixeltype.nii.gz
Con_BARTON_WORD_S26_8_1_struc_brain_pve_0.nii.gz
Con_BARTON_WORD_S26_8_1_struc_brain_pve_2.nii.gz
Con_BARTON_WORD_S26_8_1_struc_brain_pveseg.nii.gz
Con_BARTON_WORD_S26_8_1_struc_brain_seg.nii.gz
Con_BARTON_WORD_S26_8_1_struc_cut.nii.gz
Con_BARTON_WORD_S27_8_1_struc.nii.gz
Con_BARTON_WORD_S27_8_1_struc_GM.nii.gz
Con_BARTON_WORD_S27_8_1_struc_GM_to_T.mat
Con_BARTON_WORD_S27_8_1_struc_GM_to_T.nii.gz
Con_BARTON_WORD_S27_8_1_struc_brain.nii.gz
Con_BARTON_WORD_S27_8_1_struc_brain_mixeltype.nii.gz
Con_BARTON_WORD_S27_8_1_struc_brain_pve_0.nii.gz
Con_BARTON_WORD_S27_8_1_struc_brain_pve_2.nii.gz
Con_BARTON_WORD_S27_8_1_struc_brain_pveseg.nii.gz
Con_BARTON_WORD_S27_8_1_struc_brain_seg.nii.gz
Con_BARTON_WORD_S27_8_1_struc_cut.nii.gz
Con_BARTON_WORD_S28_8_1_struc.nii.gz
Con_BARTON_WORD_S28_8_1_struc_GM.nii.gz
Con_BARTON_WORD_S28_8_1_struc_GM_to_T.mat
Con_BARTON_WORD_S28_8_1_struc_GM_to_T.nii.gz
Con_BARTON_WORD_S28_8_1_struc_brain.nii.gz
Con_BARTON_WORD_S28_8_1_struc_brain_mixeltype.nii.gz
Con_BARTON_WORD_S28_8_1_struc_brain_pve_0.nii.gz
Con_BARTON_WORD_S28_8_1_struc_brain_pve_2.nii.gz
Con_BARTON_WORD_S28_8_1_struc_brain_pveseg.nii.gz
Con_BARTON_WORD_S28_8_1_struc_brain_seg.nii.gz
Con_BARTON_WORD_S28_8_1_struc_cut.nii.gz
Con_BARTON_WORD_S29_8_1_struc.nii.gz
Con_BARTON_WORD_S29_8_1_struc_GM.nii.gz
Con_BARTON_WORD_S29_8_1_struc_GM_to_T.mat
Con_BARTON_WORD_S29_8_1_struc_GM_to_T.nii.gz
Con_BARTON_WORD_S29_8_1_struc_brain.nii.gz
Con_BARTON_WORD_S29_8_1_struc_brain_mixeltype.nii.gz
Con_BARTON_WORD_S29_8_1_struc_brain_pve_0.nii.gz
Con_BARTON_WORD_S29_8_1_struc_brain_pve_2.nii.gz
Con_BARTON_WORD_S29_8_1_struc_brain_pveseg.nii.gz
Con_BARTON_WORD_S29_8_1_struc_brain_seg.nii.gz
Con_BARTON_WORD_S29_8_1_struc_cut.nii.gz
Pat_P206_Structural_struc.nii.gz
Pat_P206_Structural_struc_GM.nii.gz
Pat_P206_Structural_struc_GM_to_T.mat
Pat_P206_Structural_struc_GM_to_T.nii.gz
Pat_P206_Structural_struc_brain.nii.gz
Pat_P206_Structural_struc_brain_mixeltype.nii.gz
Pat_P206_Structural_struc_brain_pve_0.nii.gz
Pat_P206_Structural_struc_brain_pve_2.nii.gz
Pat_P206_Structural_struc_brain_pveseg.nii.gz
Pat_P206_Structural_struc_brain_seg.nii.gz
Pat_P206_Structural_struc_cut.nii.gz
Pat_P218_Structural_struc.nii.gz
Pat_P218_Structural_struc_GM.nii.gz
Pat_P218_Structural_struc_GM_to_T.mat
Pat_P218_Structural_struc_GM_to_T.nii.gz
Pat_P218_Structural_struc_brain.nii.gz
Pat_P218_Structural_struc_brain_mixeltype.nii.gz
Pat_P218_Structural_struc_brain_pve_0.nii.gz
Pat_P218_Structural_struc_brain_pve_2.nii.gz
Pat_P218_Structural_struc_brain_pveseg.nii.gz
Pat_P218_Structural_struc_brain_seg.nii.gz
Pat_P218_Structural_struc_cut.nii.gz
Pat_P219_Structural_struc.nii.gz
Pat_P219_Structural_struc_GM.nii.gz
Pat_P219_Structural_struc_GM_to_T.mat
Pat_P219_Structural_struc_GM_to_T.nii.gz
Pat_P219_Structural_struc_brain.nii.gz
Pat_P219_Structural_struc_brain_mixeltype.nii.gz
Pat_P219_Structural_struc_brain_pve_0.nii.gz
Pat_P219_Structural_struc_brain_pve_2.nii.gz
Pat_P219_Structural_struc_brain_pveseg.nii.gz
Pat_P219_Structural_struc_brain_seg.nii.gz
Pat_P219_Structural_struc_cut.nii.gz
Pat_P221_Structural_struc.nii.gz
Pat_P221_Structural_struc_GM.nii.gz
Pat_P221_Structural_struc_GM_to_T.mat
Pat_P221_Structural_struc_GM_to_T.nii.gz
Pat_P221_Structural_struc_brain.nii.gz
Pat_P221_Structural_struc_brain_mixeltype.nii.gz
Pat_P221_Structural_struc_brain_pve_0.nii.gz
Pat_P221_Structural_struc_brain_pve_2.nii.gz
Pat_P221_Structural_struc_brain_pveseg.nii.gz
Pat_P221_Structural_struc_brain_seg.nii.gz
Pat_P221_Structural_struc_cut.nii.gz
Pat_P222_Structural_struc.nii.gz
Pat_P222_Structural_struc_GM.nii.gz
Pat_P222_Structural_struc_GM_to_T.mat
Pat_P222_Structural_struc_GM_to_T.nii.gz
Pat_P222_Structural_struc_brain.nii.gz
Pat_P222_Structural_struc_brain_mixeltype.nii.gz
Pat_P222_Structural_struc_brain_pve_0.nii.gz
Pat_P222_Structural_struc_brain_pve_2.nii.gz
Pat_P222_Structural_struc_brain_pveseg.nii.gz
Pat_P222_Structural_struc_brain_seg.nii.gz
Pat_P222_Structural_struc_cut.nii.gz
Pat_P224_Structural_struc.nii.gz
Pat_P224_Structural_struc_GM.nii.gz
Pat_P224_Structural_struc_GM_to_T.mat
Pat_P224_Structural_struc_GM_to_T.nii.gz
Pat_P224_Structural_struc_brain.nii.gz
Pat_P224_Structural_struc_brain_mixeltype.nii.gz
Pat_P224_Structural_struc_brain_pve_0.nii.gz
Pat_P224_Structural_struc_brain_pve_2.nii.gz
Pat_P224_Structural_struc_brain_pveseg.nii.gz
Pat_P224_Structural_struc_brain_seg.nii.gz
Pat_P224_Structural_struc_cut.nii.gz
command.e47087
command.o47087
fslvbm2a
fslvbm2a.e43614.1
fslvbm2a.e43614.10
fslvbm2a.e43614.11
fslvbm2a.e43614.12
fslvbm2a.e43614.13
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fslvbm2a.e43614.2
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fslvbm2a.e43614.7
fslvbm2a.e43614.8
fslvbm2a.e43614.9
fslvbm2a.o43614.1
fslvbm2a.o43614.10
fslvbm2a.o43614.11
fslvbm2a.o43614.12
fslvbm2a.o43614.13
fslvbm2a.o43614.14
fslvbm2a.o43614.15
fslvbm2a.o43614.16
fslvbm2a.o43614.17
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fslvbm2a.o43614.2
fslvbm2a.o43614.20
fslvbm2a.o43614.21
fslvbm2a.o43614.22
fslvbm2a.o43614.3
fslvbm2a.o43614.4
fslvbm2a.o43614.5
fslvbm2a.o43614.6
fslvbm2a.o43614.7
fslvbm2a.o43614.8
fslvbm2a.o43614.9
fslvbm2b
fslvbm2b.e45071.1
fslvbm2b.e45071.10
fslvbm2b.e45071.11
fslvbm2b.e45071.12
fslvbm2b.e45071.13
fslvbm2b.e45071.14
fslvbm2b.e45071.15
fslvbm2b.e45071.16
fslvbm2b.e45071.17
fslvbm2b.e45071.18
fslvbm2b.e45071.19
fslvbm2b.e45071.2
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