When writing a shell script, I want to include some names of subdirectories to work-CodePudding

hello? The directory structure is as follows.

/image03

 /UM1234ABCD2R1_MRI

 /UM1234ABCD1R1_MRI

 /UM0120AABD1R1_DTI

 /UM0120AABC1R1_bold_reward

 /CU0112XCMF2R1_b0map_bold

 /CU1243XMDM1R1_b0map_dti
    .....

There are hundreds of such directories, and among each of these directories, we want to output the following sentence only for directories that do not containing 'b0map'.

dcm2bids -d (directory name) -p (first 6 letters of directory) -S (10th letter of directory) -c /image03/dcm2bids_config.json

To this end, I wrote and ran a shell script like this, but an error came up. Could you please tell me how to solve it?

#!/bin/bash

DICOM_DIR = /image03/*/

PARTICIPANT_ID = {DICOM_DIR:0:6}

SESSION_ID = {DICOM_DIR:10}

for /image03/*$PARTICIPANT_ID*[^b0map]*/

do echo dcm2bids -d $DICOM_DIR -p $PARTICIPANT_ID -S $SESSION_ID -c /image03/dcm2bids_config.json

done

Error message

(EMBARC) [drbong@node16 EMBARC]$ ./anatfuncdti
./anatfuncdti: line 3: DICOM_DIR: command not found
./anatfuncdti: line 4: PARTICIPANT_ID: command not found
./anatfuncdti: line 5: SESSION_ID: command not found
./anatfuncdti: line 9: `/image03/*$PARTICIPANT_ID*[^b0map]*/': not a valid identifier

Thank you for your help while you are busy.

CodePudding user response：

this is bash... no space between your variable name and the value

more like:

DICOM_DIR='/image03/*/'

CodePudding user response：

suggesting the following:

find . -type d -not -name "*b0map*" | awk '{printf("dcm2bids -d %s -p %s -S -c /image03/dcm2bids_config.json\n", $0, substr($0,1,6), substr($0,10,1));}'

CodePudding user response：

find /image03 -type d -print0 | 

{m,g}awk '($!NF=sprintf("%s -d %-35s -p %.6s -S %.1s -c /%s/%s_config.json;",
              _="dcm2bids",$ _,$NF, substr($NF,10), $(NF-1), _))^(/b0map/)' \
RS='\0' FS='[/]'

———————————————————————————

dcm2bids -d /image03/UM1234ABCD2R1_MRI          -p UM1234 -S D -c /image03/dcm2bids_config.json;
dcm2bids -d /image03/UM1234ABCD1R1_MRI          -p UM1234 -S D -c /image03/dcm2bids_config.json;

dcm2bids -d /image03/UM0120AABD1R1_DTI          -p UM0120 -S D -c /image03/dcm2bids_config.json;
dcm2bids -d /image03/UM0120AABC1R1_bold_reward  -p UM0120 -S C -c /image03/dcm2bids_config.json;