diff --git a/ruoyi-admin/src/main/resources/static/alignTemplate.ftl b/ruoyi-admin/src/main/resources/static/alignTemplate.ftl index 15332fe..baae160 100644 --- a/ruoyi-admin/src/main/resources/static/alignTemplate.ftl +++ b/ruoyi-admin/src/main/resources/static/alignTemplate.ftl @@ -2,21 +2,21 @@ import os # This script can align cpac output and AAL template to the same space temp_file = '/data/Atlas/AAL_61x73x61_YCG.nii' -fmri_file_mb = '${fmriFileMb}' -fmri_reg_out_file = '${fmriRegOutFile}' +fmri_file_mb = '/data/${fmriFileMb}' +fmri_reg_out_file = '/data/${fmriRegOutFile}' system_str_mb = f"flirt -ref {temp_file} -in {fmri_file_mb} -dof 6 -omat {fmri_reg_out_file}" print(system_str_mb) os.system(system_str_mb) -fmri_file_dpp = f"${fmriFileDpp}" -fmri_r2t1_out_file = "${fmriR2t1OutFile}" +fmri_file_dpp = f"/data/${fmriFileDpp}" +fmri_r2t1_out_file = "/data/${fmriR2t1OutFile}" system_str_dpp = f"applywarp -i {fmri_file_dpp} -r {temp_file} -o {fmri_r2t1_out_file} --premat={fmri_reg_out_file} --interp=spline" print(system_str_dpp) print("***Please wait for a moment***") os.system(system_str_dpp) -smri_file_mb = '${smriFileMb}' -smri_reg_out_file = '${smriOutFile}' +smri_file_mb = '/data/${smriFileMb}' +smri_reg_out_file = '/data/${smriOutFile}' system_str_mb = f"flirt -ref {temp_file} -in {smri_file_mb} -dof 12 -out {smri_reg_out_file} " print(system_str_mb) -os.system(system_str_mb) \ No newline at end of file +os.system(system_str_mb) diff --git a/ruoyi-admin/src/main/resources/static/cpacSh.ftl b/ruoyi-admin/src/main/resources/static/cpacSh.ftl index f325adf..1398f9c 100644 --- a/ruoyi-admin/src/main/resources/static/cpacSh.ftl +++ b/ruoyi-admin/src/main/resources/static/cpacSh.ftl @@ -1,9 +1,7 @@ #!/bin/bash echo "Hello, output-43207!" -cd /data - -python ${alignPath} +python /data/${alignPath} python /data/test2.py --sub_id ${subId} --TR ${tr} --root_dir ${fmriR2t1OutFile} --out_dir ${fmriOutPath} --anat_dir ${smriOutFile} diff --git a/ruoyi-admin/src/main/resources/static/dealData.ftl b/ruoyi-admin/src/main/resources/static/dealData.ftl index c02fc78..fde4dce 100644 --- a/ruoyi-admin/src/main/resources/static/dealData.ftl +++ b/ruoyi-admin/src/main/resources/static/dealData.ftl @@ -1,11 +1,9 @@ #!/bin/bash -cd /data -cd /data echo "执行源文件处理脚本" -python dealTest.py --base_dir ${playground} --output_dir ${playground}/BIDS_output --json_dir ${playground}/BIDS_output/sub-001/func/ -rm -rf ./${playground}/BIDS_output/config.json -cp ./README ${playground}/BIDS_output/ +python dealTest.py --base_dir cd /data/${playground} --output_dir /data/${playground}/BIDS_output --json_dir /data/${playground}/BIDS_output/sub-001/func/ +rm -rf /data/${playground}/BIDS_output/config.json +cp /data/README /data/${playground}/BIDS_output/ echo "通过源文件进行二次处理" docker run --rm -e DOCKER_VERSION_8395080871=27.3.1 -v /data/license.txt:/opt/freesurfer/license.txt:ro -v /data/${playground}/BIDS_output:/data:ro -v /data/${playground}/preprocessed:/out nipreps/fmriprep:23.2.3 /data /out participant --participant-label 001 --fs-no-reconall -python scriptAge.py --dicom_folder ${playground} +python scriptAge.py --dicom_folder /data/${playground}