Given the answer by Niels Bergsland, it's most likely a lot easier (and cleaner) to simply install FSL 5.0.10 than to compile this yourself.

In a publication, you could also simply state that you used FSL 5.0.10, and would not have to mention v 5.0.9 and a modified cluster command.

That being said, if you insist on trying to compile, read on:

> On December 18, 2018 at 12:33 PM Carlotta Fabris <[log in to unmask]> wrote:
>    I had some problems doing the things you suggested:
    1) couldn't copy some of the directories in my FSLDIR. for example the bin directories that contains cluster


Why? Did you get any error message? You could do something like:

mkdir ~/fsl_modified
cp -r /path/to/your/FSL ~/fsl_modified

Replace the /path/to/your/FSL with your install path, of course.

>    2) couldn't replace the FSL source files in the 3 dirs under src/ with files from the repo because I didn't find any src folder

If you do not have the it, you do not have the source distribution of FSL and will have to download it FSL first. (And only use the copy command from step 1 afterwards, of course.)

>   3) I downloaded the content of the github repository, and I wnent into the cluster folder, but when I did make, it gave me an error telling no make file found.

This is expected if you do not have the source distribution of FSL. The 'make' command uses a file named 'Makefile' in that dir. The file is part of the FSL source distribution and this NOT included in the github repo.


As I wrote above, I would recommend to simply install FSL 5.0.10: you may run into more trouble when running make even after completing these steps.


>    Maybe I am doing something wrong, I also noticed that in the fsl shell setup they say to do FSLDIR=/usr/local/fsl, but my FSLDIR is different. /usr/share/fsl/5.0
    Could it have something to do with me not being able to run this new cluster version?

No. The FSLDIR environment variable must point at your installation directory. You can install to where ever you want as long as you have it point there. I think the reason for not being able to run the command is that your FSL version is too old.

> On December 18, 2018 at 12:33 PM Carlotta Fabris <[log in to unmask]> wrote:
>
>
> Thank you for your answer!
>
> I had some problems doing the things you suggested:
> 1) couldn't copy some of the directories in my FSLDIR. for example the bin directories that contains cluster
> 2) couldn't replace the FSL source files in the 3 dirs under src/ with files from the repo because I didn't find any src folder
> 3) I downloaded the content of the github repository, and I wnent into the cluster folder, but when I did make, it gave me an error telling no make file found.
>
> Maybe I am doing something wrong, I also noticed that in the fsl shell setup they say to do FSLDIR=/usr/local/fsl, but my FSLDIR is different. /usr/share/fsl/5.0
> Could it have something to do with me not being able to run this new cluster version?
>
> Sorry to bother you with this,
> Thank you,
> Carlotta.
>
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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