Hi all,
I tried posting this on the FSL message board in January and have not gotten a response. Is anyone able to assist?
I’m trying to run fslVBM, and when I run fslvbm_2_template I get the following errors.
-------- freesurfer-darwin-macOS-7.3.2-20220804-6354275 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR /usr/local/fsl
[Deannas-iMac:~] deannaaghbashian% /var/folders/yg/zb215k6s6slgm38pzdvw8yn40000gn/T/com.barebones.bbedit/VBM_SSD_TD-694975564.585.sh.command ; exit;
chmod: fslvbm2a: No such file or directory
Error submitting job - Array task definition file fault: Unable to read './fslvbm2a'
Running segmentation: ID=
chmod: fslvbm2b: No such file or directory
usage: fsl_sub [-h] [-a ARCH] [-c COPROCESSOR]
[--coprocessor_multi COPROCESSOR_MULTI]
[--coprocessor_class COPROCESSOR_CLASS]
[--coprocessor_class_strict]
[--coprocessor_toolkit COPROCESSOR_TOOLKIT] [-F] [-j JOBHOLD]
[--not_requeueable] [--array_hold ARRAY_HOLD] [-l LOGDIR]
[-m MAILOPTIONS] [-M MAILTO] [-n] [-N NAME] [-p PRIORITY]
[-q QUEUE] [-r RESOURCE] [--delete_job DELETE_JOB]
[--extra EXTRA] [-R GB] [-s PARALLELENV,THREADS]
[-t ARRAY_TASK] [--array_native ARRAY_NATIVE] [-x NUMBER]
[--keep_jobscript] [--has_coprocessor COPROCESSOR_NAME]
[--has_queues] [--project PROJECT] [-S] [-T MINUTES]
[--show_config] [-v] [-V] [-z file]
...
fsl_sub: error: argument -j/--jobhold: expected one argument
Running initial registration: ID=
usage: fsl_sub [-h] [-a ARCH] [-c COPROCESSOR]
[--coprocessor_multi COPROCESSOR_MULTI]
[--coprocessor_class COPROCESSOR_CLASS]
[--coprocessor_class_strict]
[--coprocessor_toolkit COPROCESSOR_TOOLKIT] [-F] [-j JOBHOLD]
[--not_requeueable] [--array_hold ARRAY_HOLD] [-l LOGDIR]
[-m MAILOPTIONS] [-M MAILTO] [-n] [-N NAME] [-p PRIORITY]
[-q QUEUE] [-r RESOURCE] [--delete_job DELETE_JOB]
[--extra EXTRA] [-R GB] [-s PARALLELENV,THREADS]
[-t ARRAY_TASK] [--array_native ARRAY_NATIVE] [-x NUMBER]
[--keep_jobscript] [--has_coprocessor COPROCESSOR_NAME]
[--has_queues] [--project PROJECT] [-S] [-T MINUTES]
[--show_config] [-v] [-V] [-z file]
...
fsl_sub: error: argument -j/--jobhold: expected one argument
Creating first-pass template: ID=
chmod: fslvbm2d: No such file or directory
usage: fsl_sub [-h] [-a ARCH] [-c COPROCESSOR]
[--coprocessor_multi COPROCESSOR_MULTI]
[--coprocessor_class COPROCESSOR_CLASS]
[--coprocessor_class_strict]
[--coprocessor_toolkit COPROCESSOR_TOOLKIT] [-F] [-j JOBHOLD]
[--not_requeueable] [--array_hold ARRAY_HOLD] [-l LOGDIR]
[-m MAILOPTIONS] [-M MAILTO] [-n] [-N NAME] [-p PRIORITY]
[-q QUEUE] [-r RESOURCE] [--delete_job DELETE_JOB]
[--extra EXTRA] [-R GB] [-s PARALLELENV,THREADS]
[-t ARRAY_TASK] [--array_native ARRAY_NATIVE] [-x NUMBER]
[--keep_jobscript] [--has_coprocessor COPROCESSOR_NAME]
[--has_queues] [--project PROJECT] [-S] [-T MINUTES]
[--show_config] [-v] [-V] [-z file]
...
fsl_sub: error: argument -j/--jobhold: expected one argument
Running registration to first-pass template: ID=
usage: fsl_sub [-h] [-a ARCH] [-c COPROCESSOR]
[--coprocessor_multi COPROCESSOR_MULTI]
[--coprocessor_class COPROCESSOR_CLASS]
[--coprocessor_class_strict]
[--coprocessor_toolkit COPROCESSOR_TOOLKIT] [-F] [-j JOBHOLD]
[--not_requeueable] [--array_hold ARRAY_HOLD] [-l LOGDIR]
[-m MAILOPTIONS] [-M MAILTO] [-n] [-N NAME] [-p PRIORITY]
[-q QUEUE] [-r RESOURCE] [--delete_job DELETE_JOB]
[--extra EXTRA] [-R GB] [-s PARALLELENV,THREADS]
[-t ARRAY_TASK] [--array_native ARRAY_NATIVE] [-x NUMBER]
[--keep_jobscript] [--has_coprocessor COPROCESSOR_NAME]
[--has_queues] [--project PROJECT] [-S] [-T MINUTES]
[--show_config] [-v] [-V] [-z file]
...
fsl_sub: error: argument -j/--jobhold: expected one argument
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.
logout
I am running the script in the same directory. Below is the script, which I have also cc’d on this email
SCRIPT
#!/bin/bash
set subjectsDirectory = /Users/deannaaghbashian/Desktop/K99/
mkdir my_fsl_vbm
### copy into FSL-VBM directory all of subjects T1 images, giving each subject's T1 image a different name###
### create template need to use same ## from each group###
for g in SSD70990_anat.nii.gz SSD71030_anat.nii.gz SSD71060_anat.nii.gz SSD71090_anat.nii.gz SSD71110_anat.nii.gz SSD71130_anat.nii.gz SSD71140_anat.nii.gz SSD71210_anat.nii.gz SSD71260_anat.nii.gz SSD71270_anat.nii.gz SSD71280_anat.nii.gz SSD71300_anat.nii.gz SSD71330_anat.nii.gz SSD71390_anat.nii.gz SSD71410_anat.nii.gz SSD71420_anat.nii.gz SSD71520_anat.nii.gz SSD71530_anat.nii.gz SSD71540_anat.nii.gz SSD71560_anat.nii.gz SSD71590_anat.nii.gz SSD71610_anat.nii.gz \
#TD106E_anat.nii.gz TD163C_anat.nii.gz TD42003_anat.nii.gz TD42004_anat.nii.gz TD42007_anat.nii.gz TD42008_anat.nii.gz TD42009_anat.nii.gz TD42010_anat.nii.gz TD42013_anat.nii.gz TD42015_anat.nii.gz TD42016_anat.nii.gz TD42019_anat.nii.gz TD42022_anat.nii.gz TD42023_anat.nii.gz TD42027_anat.nii.gz TD42029_anat.nii.gz TD42030_anat.nii.gz TD42031_anat.nii.gz TD42033_anat.nii.gz TD42035_anat.nii.gz TD42036_anat.nii.gz TD42038_anat.nii.gz; do
echo $g >> template_list
done
##check if subjs structural what expected##
#slicesdir `imglob *`
### create your design.mat and design.con in your FSL-VBM directory###
###The first FSL-VBM script moves all your input images into a new struc subdirectory (and adding "_struc" to the end of each filename). It then runs brain extraction on the images.
#fslvbm_1_bet -b
#fslvbm_2_template –n
###fslvbm_2_template –a
#fslvbm_3_proc
Anyone have any ideas?
Deanna