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.
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 maskstemplate 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 maskfolder where the result images will be saved
export RES_FOLDER=
pwd
/groupwise_resultargument 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.