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Speed-up BA exvivo labels projection with python #183

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merged 12 commits into from
Sep 1, 2022
Merged

Speed-up BA exvivo labels projection with python #183

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0487785
typo and comment
m-reuter Aug 24, 2022
f9d372a
added: register based on segmentation centroids
m-reuter Aug 24, 2022
d7f2c6d
added code to map labels and combine into annotation
m-reuter Aug 28, 2022
e184c21
update dependency to python 3.8
m-reuter Aug 31, 2022
9ccb506
fix print and comment
m-reuter Aug 31, 2022
3dde9b2
update to append and modular main function
m-reuter Aug 31, 2022
4ccdee9
use our balabels mapping instead of slow recon-all
m-reuter Aug 31, 2022
7e91139
fix typo
m-reuter Aug 31, 2022
b148b79
added scikit-learn, needed for ba-labels python scripts
m-reuter Sep 1, 2022
7f04d44
fix missing -
m-reuter Sep 1, 2022
556a011
use fsaverage from FREESURFER_HOME
m-reuter Sep 1, 2022
7744916
fix output file name exvivo
m-reuter Sep 1, 2022
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use fsaverage from FREESURFER_HOME
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@m-reuter
m-reuter committed Sep 1, 2022
commit 556a0116719d45a3318605af49f85c7c566dbc47
14 changes: 5 additions & 9 deletions recon_surf/fs_balabels.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@
h_sid = 'subject id (name of directory within the subject directory)'
h_sd = 'subject directory path'
h_hemi = 'optioal: "lh" or "rh" (default run both hemispheres)'
h_fsaverage = 'optional: path to fsaverage (default is subject_dir/fsaverage)'
h_fsaverage = 'optional: path to fsaverage (default is $FREESURFER_HOME/subjects/fsaverage)'


def options_parse():
Expand All @@ -79,8 +79,6 @@ def options_parse():

if options.sid is None or options.sd is None:
sys.exit('\nERROR: Please specify --sid and --sd !\n Use --help to see all options.\n')
if options.fsaverage is None:
options.fsaverage=options.sd+"/fsaverage"
if options.hemi is None:
options.hemi = ["lh","rh"]
else:
Expand Down Expand Up @@ -134,7 +132,10 @@ def read_colortables(colnames,colappend,drop_unknown=True):
if sdir != options.sd:
print("WARNING environment $SUBJECTS_DIR is set differently to --sd !")
os.environ['SUBJECTS_DIR'] = options.sd

if options.fsaverage is None:
options.fsaverage=os.path.join(fshome,"subjects","fsaverage")


# read and stack colortable labels
ba = os.path.join(fshome,"average","colortable_BA.txt")
vpnl = os.path.join(fshome,"average","colortable_vpnl.txt")
Expand Down Expand Up @@ -188,8 +189,3 @@ def read_colortables(colnames,colappend,drop_unknown=True):

print("...done\n")