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Hey Tim,

Thank you for your replay, but that is what i am doing, all i get is the help message about how to call the function. What am i missing?

./easythreshconj.sh -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 grot

Provides conjuction thresholding outside of feat. IF, however, relevant feat
directory is available, specify the smoothness estimate with -s option
to get more accurate P-values.

Usage: easythresh_conj [-s SmoothEst] <raw_zstat1> <raw_zstat2> <brain_mask> <cluster_z_thresh> <cluster_prob_thresh> <background_image> <output_root> [--mm]

e.g.: easythresh_conj stats/zstat1 stats/zstat2 mask 2.3 0.01 example_func grot
or, more accurately,
easythresh_conj -s stats/smoothness stats/zstat1 stats/zstat2 mask 2.3 0.01 example_func grot

Or: easythresh_conj <stat1> <stat2> <stat_thresh> <background_image> <output_root>
e.g.: easythresh_conj stats/zstat1 stats/zstat2 2.3 example_func grot

On Mon, Sep 24, 2018 at 3:44 PM Tim Schäfer <[log in to unmask]> wrote:

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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