def tracks_gen(self,params):
import tractography
self.tracks = tractography.plot_fancily(params.track_file,
figure=self.scene.mayavi_scene)
tractography.apply_affines_carefully(self.tracks, params.b0_volume,
params.track_file, params.subject, params.subjects_dir,
fsenvsrc=params.fs_setup)
tractography.fix_skewing(self.tracks, use_fsavg5=False,
lhsurf=self.syrf_lh, rhsurf=self.syrf_rh)
def tracks_gen(self, params):
import tractography
self.tracks = tractography.plot_fancily(params.track_file,
figure=self.scene.mayavi_scene)
tractography.apply_affines_carefully(self.tracks,
params.b0_volume,
params.track_file,
params.subject,
params.subjects_dir,
fsenvsrc=params.fs_setup)
tractography.fix_skewing(self.tracks,
use_fsavg5=False,
lhsurf=self.syrf_lh,
rhsurf=self.syrf_rh)
import tractography import os truff='/local_mount/space/truffles/1/users/rlaplant/' trk=os.path.join(truff,'data/qbi/hcps030/tracts20k.trk') b0=os.path.join(truff,'data/qbi/hcps030/dset/b0.nii.gz') subj='hcps030_FS' subjects_dir=os.path.join(truff,'data/hcpnmr/') fs_script='/usr/local/freesurfer/nmr-stable53-env' self.tark = tark = tractography.plot_fancily(trk) tractography.apply_affines_carefully(tark, b0, trk, subj, subjects_dir, fsenvsrc=fs_script) tractography.fix_skewing(tark)
import tractography
import os
truff = '/local_mount/space/truffles/1/users/rlaplant/'
trk = os.path.join(truff, 'data/qbi/hcps030/tracts20k.trk')
b0 = os.path.join(truff, 'data/qbi/hcps030/dset/b0.nii.gz')
subj = 'hcps030_FS'
subjects_dir = os.path.join(truff, 'data/hcpnmr/')
fs_script = '/usr/local/freesurfer/nmr-stable53-env'
self.tark = tark = tractography.plot_fancily(trk)
tractography.apply_affines_carefully(tark,
b0,
trk,
subj,
subjects_dir,
fsenvsrc=fs_script)
tractography.fix_skewing(tark)
truff='/local_mount/space/truffles/1/users/rlaplant/' s='hcps026' subj='%s_FS'%s subjects_dir=os.path.join(truff,'data/hcpnmr/') pcp = self.parcellation_chooser_window.ctl pcp.subjects_dir = subjects_dir pcp.subject = subj pcp.parcellation_name = 'aparc' pcp.labelnames_file = 'orders/aparc_cmp.txt' pcp.surface_type = 'pial' self.parcellation_chooser_window.finished=True self.parcellation_chooser_window.notify=True trk=os.path.join(truff,'data/qbi/%s/tracts20k.trk'%s) b0=os.path.join(truff,'data/qbi/%s/dset/b0.nii.gz'%s) fs_script='/usr/local/freesurfer/nmr-stable53-env' self.tark = tark = tractography.plot_fancily(trk) tractography.apply_affines_carefully(tark, b0, trk, subj, subjects_dir, fsenvsrc=fs_script) ds = self.controller.ds_orig tractography.fix_skewing(tark,use_fsavg5=False, lhsurf=ds.dv_3d.syrf_lh, rhsurf=ds.dv_3d.syrf_rh)