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update readme
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hlpureboy committed Nov 24, 2021
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -26,10 +26,10 @@ class fMRI_Prep_Job:
fmri_work="/share/fmri_work"
# freesurfer_license
freesurfer_license = "/share/user_data/public/fanq_ocd/license.txt"
# contianer id fmriprep
contianer_id = "d7235efbbd3c"
# image id fmriprep
image_id = "d7235efbbd3c"
# fmriprep cmd
cmd ="docker run -it --rm -v {bids_data_path}:/data -v {freesurfer_license}:/opt/freesurfer/license.txt -v {bids_output_path}:/out -v {fmri_work}:/work {contianer_id} /data /out --skip_bids_validation --ignore slicetiming fieldmaps -w /work --omp-nthreads {thread} --fs-no-reconall --resource-monitor participant --participant-label {subject_ids}"
cmd ="docker run -it --rm -v {bids_data_path}:/data -v {freesurfer_license}:/opt/freesurfer/license.txt -v {bids_output_path}:/out -v {fmri_work}:/work {image_id} /data /out --skip_bids_validation --ignore slicetiming fieldmaps -w /work --omp-nthreads {thread} --fs-no-reconall --resource-monitor participant --participant-label {subject_ids}"
```
## 2. fmriprep post preocess
这一步的操作主要依赖于`fmribrant`,主要作用是回归掉白质信号、脑脊液信号、全脑信号、头动信息、并进行滤波(可选),将其处理后的文件放存在`prcoessed/post-precoss/<un>fliter/clean_imgs`中,`<un>`可选表示是否进行滤波。该配置中不建议修改`dataset_path`,`store_path`
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