The error message has changed, now the script is actually being called.
From looking at that message, what's still wrong is that your call is missing the <brain_mask> parameter. Supply the path to the brain mask file before the <cluster_z_thresh> parameter and you should be fine.
Best,
Tim
> On September 25, 2018 at 2:45 AM Navot Naor <[log in to unmask]> wrote:
>
>
> 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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> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
> >
>
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>
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--
Tim
0176 84273709
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