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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>
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