# get pons normed globstr = '%s/nonan-ponsnormed*fdg**nii*' % (pth) dat = pp.find_single_file(globstr) if dat is None: logging.error('%s missing, skipping' % (globstr)) continue # get raparc corgdir = os.path.join(pth, 'roi_data') globstr = '%s/rB*aparc_aseg.nii*' % (corgdir) raparc = pp.find_single_file(globstr) if raparc is None: logging.error('%s missing, skipping ' % (globstr)) continue data = pp.nibabel.load(dat).get_data() meand = pp.mean_from_labels(roid, raparc, data) alld[subid] = meand ###write to file _, roifname = os.path.split(roifile) outf = os.path.join(root, 'roivalues_%s_%s_%s' % (tracer, cleantime, roifname)) fid = open(outf, 'w+') fid.write('SUBID,') rois = sorted(meand.keys()) roiss = ','.join(rois) fid.write(roiss) fid.write(',\n') for subid in sorted(alld.keys()): fid.write('%s,' % (subid)) for r in rois:
cstrokem = bg.copy_file(strokem, roidir) globstr = '%s/coreg/*.mat*' % pth xfm = pp.find_single_file(globstr) if xfm is None: logging.error('NO transform for %s' % globstr) continue stroke_mask = transform_vol(cstrokem, xfm, dat) # get raparc globstr = '%s/coreg/rB*aparc_aseg.nii*' % (pth) raparc = pp.find_single_file(globstr) if raparc is None: logging.error('Missing %s, SKIPPING' % globstr) continue data = pp.nibabel.load(dat).get_data() meand = pp.mean_from_labels(roid, raparc, data, othermask=stroke_mask) alld[subid] = meand ###write to file _, roifname = os.path.split(roifile) outf = os.path.join( userhome, 'roivalues_strokemasked_%s_%s_%s' % (tracer, cleantime, roifname)) fid = open(outf, 'w+') fid.write('SUBID,') rois = sorted(meand.keys()) roiss = ','.join(rois) fid.write(roiss) fid.write(',\n') for subid in sorted(alld.keys()): fid.write('%s,' % (subid))
continue # get pvc dvr globstr = '%s/pvcfs_DVR-%s*nii*'%(pvcdir,subid) dvr = pp.find_single_file(globstr) if dvr is None: logging.error('%s missing, skipping'%(globstr)) continue # get raparc corgdir = os.path.join(pth, 'coreg') globstr = '%s/rB*aparc_aseg.nii'%(corgdir) raparc = pp.find_single_file(globstr) if raparc is None: logging.error('%s missing, skipping '%(globstr)) continue dvr_data = pp.nibabel.load(dvr).get_data() meand = pp.mean_from_labels(roid, raparc, dvr_data) #csvfile = os.path.join(dvrdir, 'PIBINDEX_%s_%s.csv'%(subid,cleantime)) #pp.meand_to_file(meand, csvfile) alld[subid] = meand ###write to file fid =open('pvc_metzler_OLD_PIBINDEX_%s'%(cleantime), 'w+') fid.write('SUBID,') rois = sorted(meand.keys()) roiss = ','.join(rois) fid.write(roiss) fid.write(',\n') for subid in sorted(alld.keys()): fid.write('%s,'%(subid)) for r in rois: fid.write('%f,'%(alld[subid][r][0]))
else: exists = True if not exists: #last chance # find aparcaseg globstr = '%s/anatomy/*aparc_aseg.nii*'%sub aparc = glob(globstr) if not len(aparc)>0: logging.error('NO aparcaseg for %s'%globstr) continue aparc = aparc[0] caparc = bg.copy_file(aparc, roidir) raparc = transform_vol(caparc, xfm, dat) data = pp.nibabel.load(dat).get_data() meand = pp.mean_from_labels(roid, raparc, data, othermask=stroke_mask) alld[subid] = meand ###write to file _, roifname = os.path.split(roifile) outf = os.path.join(userhome, 'roivalues_strokemasked_%s_%s_%s'%(tracer, cleantime, roifname)) fid =open(outf, 'w+') fid.write('SUBID,') rois = sorted(meand.keys()) roiss = ','.join(rois) fid.write(roiss) fid.write(',\n') for subid in sorted(alld.keys()): fid.write('%s,'%(subid))