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--- neuroimagen:mri_deface [2020/05/14 08:32]
osotolongo created
+++ neuroimagen:mri_deface [2020/12/03 15:55] (current)
osotolongo
@@ Line 1: / Line 1: @@
 ====== mri deface ======
+===== Prueba =====
 https://surfer.nmr.mgh.harvard.edu/fswiki/AutomatedDefacingTools
@@ Line 38: / Line 40: @@
 ....
 ....
+anonymizing volume...
+using wm = 107.0, gm = 93.4
+wm covar:
+.39935;
+gm covar:
+.34979;
+.........................
+1058443 face voxels erased, 250588 ambiguous voxels retained
+resampling to original coordinate system...
+writing anonymized volume to deface/sub-0001_T1w_defaced.nii.gz...
+deidentification took 2 minutes and 54 seconds.
+</code>
+{{ :neuroimagen:2020-05-14-103453_grim.png |}}
+===== en paralelo =====
+<code python deface.py>
+#!/usr/bin/env python2
+import subprocess
+import re
+import os
+from slurm import send_sbatch
+defacer = '/nas/usr/local/bin/mri_deface_linux'
+def_dir = '/nas/usr/local/share/mri_deface/'
+tal_gca = def_dir+'talairach_mixed_with_skull.gca'
+face_gca = def_dir+'face.gca'
+finder = 'find /nas/data/facehbi/bids/sub-* -name "*.nii.gz"'
+outdir = '/nas/data/facehbi/defaced/'
+time = '2:0:0'
+cpus = 4
+wdir = os.environ.get('PWD')
+if not os.path.isdir(outdir): os.mkdir(outdir)
+ifiles = subprocess.check_output('find /nas/data/facehbi/bids/sub-* -name "*.nii.gz"', shell=True).split('\n')
+for ifile in ifiles:
+  if os.path.exists(ifile):
+    cdata = {'time':time, 'cpus':4, 'job_name':'deface'}
+    ofile = re.sub('bids','defaced/bids',ifile)
+    dst_dir = os.path.dirname(ofile)
+    if not os.path.isdir(dst_dir): os.makedirs(dst_dir)
+    order1 = defacer+' '+ifile+' '+tal_gca+' '+face_gca+' '+ofile
+    jfile = re.sub('\.nii\.gz','.json',ifile)
+    ojfile = re.sub('\.nii\.gz','.json',ofile)
+    order2 = 'cp '+jfile+' '+ojfile
+    name = os.path.basename(ifile).split('.')[0]
+    cdata['filename'] = wdir+'/deface_'+name+'.sh'
+    cdata['output'] = wdir+'/deface_'+name+'.out'
+    cdata['command'] = order1+'\n'+order2+'\n'
+    send_sbatch(cdata)
+mdata = {'job_name':'deface', 'filename':wdir+'/deface_end.sh', 'output':wdir+'/deface_end.log', 'dependency':'singleton'}
+send_sbatch(mdata)
 </code>

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