If you have the script in your working directory, you should run it like this:
./easythresh_conj.sh -s ...
(The first dot represents the current directory.) You should be able to have the shell auto-complete the file name while typing by pressing the <tab> key, by the way. It's less typing, prevents typos and you notice when the file does not exist in the current directory or is not executable: in both cases, auto-complete will not work.
If the script is somewhere else, you have to add that directory to your PATH environment variable. After you did that, you should run it like this:
easythresh_conj.sh -s ...
I hope that helps.
Tim
> On September 24, 2018 at 8:54 PM Navot Naor <[log in to unmask]> wrote:
>
>
> Hey,
>
> I am trying to run the easythresh_conj.sh script in th following way:
>
> easythresh_conj -s /a/ha-nfs-2-ib/export/data/bswift-1/nnaor/PhD/group_analysis/ICA/TASK/FLAME_prpnrp_31.gfeat/cope1.feat/stats/smoothness /a/ha-nfs-2-ib/export/data/bswift-1/nnaor/PhD/group_analysis/ICA/TASK/flame_pewpnewp.gfeat/cope1.feat/stats/zstat1.nii.gz /a/ha-nfs-2-ib/export/data/bswift-1/nnaor/PhD/group_analysis/ICA/TASK/FLAME_prpnrp_31.gfeat/cope1.feat/stats/zstat1.nii.gz 3.1 0.01 /a/ha-nfs-2-ib/export/data/bswift-1/nnaor/PhD/group_analysis/ICA/TASK/FLAME_prpnrp_31.gfeat/cope1.feat/mask.nii.gz out
>
> but i keep getting - easythresh_conj: Command not found.
>
> I have used chmod to make it executable and tried running it with ./ and without
>
>
> What am i doing wrong?
>
>
> Thank you
>
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Forschung - Klinische Bildgebung
Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters
Universitätsklinikum Frankfurt / Haus 93, Raum A 305
Deutschordenstr. 50, 60528 Frankfurt am Main
Email: [log in to unmask] Tel.: +49 (0)69 6301 85832
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