KCL-BMEIS / niftyreg

This project contains command line tools to perform rigid, affine and non-linear registration of nifti or analyse images as well as utilities
BSD 3-Clause "New" or "Revised" License
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Getting Error while running Groupwise_niftyreg_run.sh in ubuntu 16.04 #39

Open ghost opened 6 years ago

ghost commented 6 years ago

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.