Hi Franziska,
It's not a guarantee, but to increase the chances that the FSL
installation will succeed, you could suggest to your administrators
that they add these lines to the fslpython_install.sh script, before
the "Create fslpython environment" section, before running it:
"${miniconda_bin_dir}/conda" config --file
"${miniconda_root_dir}"/.condarc --set remote_read_timeout_secs 240
"${miniconda_bin_dir}/conda" config --file
"${miniconda_root_dir}"/.condarc --set remote_connect_timeout_secs 20
"${miniconda_bin_dir}/conda" config --file
"${miniconda_root_dir}"/.condarc --set remote_max_retries 10
Paul
On 01/08/2019, Franziska baer <[log in to unmask]> wrote:
> 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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