Update fastsurfer.smk

greydongilmore · Feb 11, 2022 · e56ae97 · e56ae97
1 parent 240aeb9
commit e56ae97
Showing 1 changed file with 12 additions and 5 deletions.
diff --git a/workflow/rules/fastsurfer.smk b/workflow/rules/fastsurfer.smk
@@ -1,9 +1,17 @@
 def get_pre_t1_filename(wildcards):
-    files=glob(bids(root=join(config['out_dir'], 'bids'), subject=config['subject_prefix']+f'{wildcards.subject}', datatype='anat', session='pre', run='*', suffix='T1w.nii.gz'))
+    files=glob(bids(root=join(config['out_dir'], 'bids'), subject=config['subject_prefix']+f'{wildcards.subject}', datatype='anat', session='pre', acq=config['noncontrast_t1']['acq'], run='*', suffix='T1w.nii.gz'))
     if len(files) <=1:
-        file=expand(bids(root=join(config['out_dir'], 'bids'), subject=config['subject_prefix']+'{subject}', datatype='anat', session='pre', run='01', suffix='T1w.nii.gz'),subject=wildcards.subject)
+        file=expand(bids(root=join(config['out_dir'], 'bids'), subject=config['subject_prefix']+'{subject}', datatype='anat', session='pre', acq=config['noncontrast_t1']['acq'], run='01', suffix='T1w.nii.gz'),subject=wildcards.subject)
+        if len(file)==0:
+            file=expand(bids(root=join(config['out_dir'], 'bids'), subject=config['subject_prefix']+'{subject}', datatype='anat', session='pre', run='01', suffix='T1w.nii.gz'),subject=wildcards.subject)
     else:
+        files.sort(key=lambda f: int(re.sub('\D', '', f)))
         file=files[-1]
+    if file:
+        if not exists(file[0]):
+            file=expand(bids(root=join(config['out_dir'], 'bids'), subject=config['subject_prefix']+'{subject}', datatype='anat', session='pre', run='01', suffix='T1w.nii.gz'),subject=wildcards.subject)
+    if file:
+        print(f'Pre T1w non-contrast file: {basename(file[0])}')
     return file
 
 if config['fastsurfer']['seg_only']:
@@ -22,9 +30,8 @@ if config['fastsurfer']['seg_only']:
             touch_fastsurfer=touch(join(config['out_dir'], 'logs', 'sub-' + subject_id + "_fastsurfer.done")),
         threads:config['fastsurfer']['threads']
         shell:
-            "export FASTSURFER_HOME={params.fastsurfer_run} &&export PYTORCH_CUDA_ALLOC_CONF=max_split_size_mb:50&&{params.fastsurfer_run}/run_fastsurfer.sh \
---t1 {input.t1} --sd {output.fastsurfer_out} --sid {params.sid} --order {params.order} \
---py {params.py} --threads {params.threads} --parallel"
+            "export FASTSURFER_HOME={params.fastsurfer_run} &&PYTORCH_CUDA_ALLOC_CONF=max_split_size_mb:4096 {params.fastsurfer_run}/run_fastsurfer.sh \
+--t1 {input.t1} --sd {output.fastsurfer_out} --sid {params.sid} --order {params.order} --py {params.py} --run_viewagg_on cpu"
 else:
     rule fastsurfer_seg:
         input: