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Getting Error while running Groupwise_niftyreg_run.sh in ubuntu 16.04 #39

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ghost opened this issue Sep 7, 2018 · 0 comments
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ghost commented Sep 7, 2018

yubraj@Liverpool:~/niftyreg_install/bin$ more exp.sh
#!/bin/sh

############################################################################
###################### PARAMETERS THAT CAN BE CHANGED ######################
############################################################################

Array that contains the input images to create the atlas

export IMG_INPUT=(ls ~/AAD/*.nii.gz)
export IMG_INPUT_MASK= # leave empty to not use floating masks

template image to use to initialise the atlas creation

export TEMPLATE=(ls ~/temp/MNI152T1.nii.gz)
export TEMPLATE_MASK= # leave empty to not use a reference mask

folder where the result images will be saved

export RES_FOLDER=pwd/groupwise_result

argument to use for the affine (reg_aladin)

export AFFINE_args="-omp 4"

argument to use for the non-rigid registration (reg_f3d)

export NRR_args="-omp 4"

number of affine loop to perform - Note that the first step is always rigid

export AFF_IT_NUM=5

number of non-rigid loop to perform

export NRR_IT_NUM=10

grid engine arguments

export QSUB_CMD="qsub -l h_rt=05:00:00 -l tmem=0.9G -l h_vmem=0.9G -l vf=0.9G -l s_stack=10240 -j y -S /bin/csh -b y -cwd
-V -R y -pe smp 4"
############################################################################
yubraj@Liverpool:/niftyreg_install/bin$ sh ./groupwise_niftyreg_run.sh ./params.sh
./groupwise_niftyreg_run.sh: 23: .: Can't open ./params.sh
yubraj@Liverpool:
/niftyreg_install/bin$ sh ./groupwise_niftyreg_run.sh ./exp.sh
./groupwise_niftyreg_run.sh: 7: ./exp.sh: Syntax error: "(" unexpected
yubraj@Liverpool:/niftyreg_install/bin$ sh groupwise_niftyreg_run.sh exp.sh
groupwise_niftyreg_run.sh: 7: /home/yubraj/niftyreg_install/bin/exp.sh: Syntax error: "(" unexpected
yubraj@Liverpool:
/niftyreg_install/bin$

And, is there any way to run reg_aladin in the loop, because it's tedious to load image every time.

@mmodat mmodat self-assigned this Jul 14, 2022
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