Hello,
I´m working with FSL for DTI data analysis.
I wanted to use TBSS on my data set. Here are some information about my data:
Subjects: 68 in 3 groups (26;26;16)
Age rage: 11 to 17 years old
diffusion weighting: 1
b-value: 1300 s/mm²
diffusion directions: 36
Phase encoding direction: p-a
As on your webpage only offers a template for adults to use in TBSS I wanted to create my own template with the following command: TBSS_2_reg-n.
As this step will take some time we wanted to use our batch submission systemto parallelize this process and asked our service desk to edit
$FSLDIR/bin/fsl_sub to setup FSL fort he cluster environment It is a HPC with a SLURM workload manager and bash system (https://doc.zih.tu-dresden.de/hpc-wiki/bin/view/Compendium/HardwareTaurus) and we use the FSL version 5.0.11.
Our service desk made some adjustments but when we started tbss_2_reg we got the following error:
“sw/installed/FSL/5.0.11-foss-2018b/fsl/bin/tbss_2_reg: line 130:
> /sw/installed/FSL/5.0.11-foss-2018b/fsl/bin/imglob: No such file or directory”
We did some research and asked the service desk to reinstall FSL because of the following instruction on your page:
“If, after installing and using FSL (5.0.11 or later), you encounter errors such as imcp: No such file or directory (or similar errors referring to imglob or immv), then this means that the installation did not complete successfully. To fix this, follow these steps (you may need administrative privileges to perform them):
1. Check to see if a directory called $FSLDIR/fslpython exists. If it does, delete it.
2. Run $FSLDIR/etc/fslconf/fslpython_install.sh -f $FSLDIR to re-install the missing components.
Note that this will cause a large amount of data to be downloaded - a fast and reliable internet connection is necessary in order for the installation to complete successfully.”
They did this and claimed the installation was successful but the conda environment was not build properly so the symlink “fslpython” is broken and the “imglob” file is also missing.
Since I have no administrative privileges and our service desk said they don’t have time right now to debug this themselves do you have any idea how to approach this problem?
Also, do you know of a template for children in this age rage (11-17 years old) that we can use to do the tbss_2_reg-t step?
Thanks you so much for your help!
Greetings from Germany,
Franziska
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