To fix in main_surface.sh

ins-amu / scripts

prepare data for TVB

MIT License

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To fix in main_surface.sh #12

Closed pausz closed 10 years ago

pausz commented 10 years ago

Line 31

lmax = 6 --> lmax=6

Line 34

recon-all is searching for T1.nii in ~data/T1/T1.nii

but

mrconvert is placing this file in ~data/T1.nii

timpx commented 10 years ago

exact, thanks for the notice, I fixed the errors.

pausz commented 10 years ago

Also to avoid un/commenting the mrconvert command:

file="$PRD/data/T1/T1.nii"

if [ ! -e $file ] 
then 
        echo "Generating NIFTI T1 ..."
        mrconvert $PRD/data/T1/ $PRD/data/T1/T1.nii
fi

Something similar could be done for the recon-all part, like checking if the subjects folder exists in $FREESURFER_HOME

I'm not doing a pull request because my main_surface.sh will have my own configuration parameters. Having said that, maybe all those params like PRD, exports and aliases could be in a separate file and we source it before running main_surface.sh.

timpx commented 10 years ago

Yes I was planning to do that.

I plan to have the following structure:

a SCRIPTS clone you can put whereever you want
a root with:
- config with options like verbose or not mode, error or not, etc. But this file can actually be wherever you want.
- data/
- T1/
- DWI

then you do something like:

sh main_surface.sh -config /home/user/my_config/config

you can do a pull request, it's not important if you parameters are commited.

I update for a separate config file very soon.

timpx commented 10 years ago

done