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Thank you so so so much I thought I had try everything but no thanks for existing folks!!! You answer really quick and that is appreciated. > On 5 Sep 2019, at 16:27, paul mccarthy <[log in to unmask]> wrote: > > Hi Renew, > > You are escaping the double-quotes around the $line variable, so each word in the atlas name is being passed as a separate argument, rather than the atlas name being passed as one (multi-word) argument. Remove the backslashes before the double quotes. > > Pauk > > On Thu, 5 Sep 2019 at 15:17, Renew Andrade <[log in to unmask] <mailto:[log in to unmask]>> wrote: > Dear experts: > I’m trying to interpret MNI coordinates with a bash script I have no clue why the error that it says. The idea is to analyse all the atlases for each coordinate of the array “xyz”. > > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1> > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1> > > Terminal output is like this and it goes until it finishes. Thanks for all the help you can provide! > > > > MacBook-Air:interpretacion andraderenew$ sh /Volumes/FREESURFER/FSL/my_fsl_vbm/stats/interpretacion/loop > 42,40,38 > FSL atlasq 1.12.0 > > usage: atlasq [-h] command [options] > atlasq: error: unrecognized arguments: Atlas in MNI152 space after normalization with FLIRT" > FSL atlasq 1.12.0 > > usage: atlasq [-h] command [options] > atlasq: error: unrecognized arguments: Atlas in MNI152 space after normalization with FNIRT" > FSL atlasq 1.12.0 > > usage: atlasq [-h] command [options] > atlasq: error: unrecognized arguments: Cortical Structural Atlas" > FSL atlasq 1.12.0 > > usage: atlasq [-h] command [options] > atlasq: error: unrecognized arguments: Subcortical Structural Atlas" > FSL atlasq 1.12.0 > > usage: atlasq [-h] command [options] > atlasq: error: unrecognized arguments: Sensorimotor Tracts Labels" > FSL atlasq 1.12.0 > > usage: atlasq [-h] command [options] > atlasq: error: unrecognized arguments: ICBM-DTI-81 White-Matter Labels" > FSL atlasq 1.12.0 > > usage: atlasq [-h] command [options] > atlasq: error: unrecognized arguments: White-Matter Tractography Atlas" > FSL atlasq 1.12.0 > > usage: atlasq [-h] command [options] > atlasq: error: unrecognized arguments: Histological Atlas" > FSL atlasq 1.12.0 > > usage: atlasq [-h] command [options] > atlasq: error: unrecognized arguments: Structural Atlas" > FSL atlasq 1.12.0 > > usage: atlasq [-h] command [options] > atlasq: error: unrecognized arguments: Parietal connectivity-based parcellation" > ^Z > [1]+ Stopped sh /Volumes/FREESURFER/FSL/my_fsl_vbm/stats/interpretacion/loop > MacBook-Air:interpretacion andraderenew$ > > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1> > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1> ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1