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]> 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”. 


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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$ 


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