cmind.pipeline.cmind_T1map_preprocess¶
Functions
cmind_T1map_preprocess (output_dir, ...[, ...]) |
T1EST preprocessing prior to fitting T1 values |
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cmind.pipeline.cmind_T1map_preprocess.
cmind_T1map_preprocess
(output_dir, T1EST_nii_folder, T1EST_glob='', ANTS_bias_cmd=None, do_motion_cor=True, generate_figures=True, ForceUpdate=False, verbose=False, logger=None)[source]¶ T1EST preprocessing prior to fitting T1 values
Parameters: output_dir : str
directory in which to store the output
T1EST_nii_folder : str or list of str or list of tuple
folder containing all of the T1EST NIFTI-GZ files or a list of tuples where the first element of the tuple is a filename and the second is the corresponding TI value. If a text file is provided instead it must be formatted withe one comma separated filename and TI value per line. TI values should be specified in ms.
T1EST_glob : str, optional
if this string is not empty, use this as the file pattern to match within T1EST_nii_folder (e.g. T1EST_glob=’T1EST.nii.gz’). The filenames will be required to have TI values stored within them as _TI%d_. For general filenames, use csv file input as described above under T1EST_nii_folder.
ANTS_bias_cmd : str, optional
path to the ANTs bias correction binary
do_motion_cor : bool, optional
coregister the images from the different TI times
generate_figures : bool, optional
if true, generate additional summary images
ForceUpdate : bool,optional
if True, rerun and overwrite any previously existing results
verbose : bool, optional
print additional output (to terminal and log)
logger : logging.Logger or str, optional
logging.Logger object (or string of a filename to log to)
Returns: T1concat_mcf : str
concatenated T1EST images after (optional) motion correction
TIvals_file : str
text file containing the TI values
T1concat_mean_N4 : str
output volume containing mean over T1concat_mcf
T1concat_mean_N4_brain : str
T1concat_mean_N4 after brain extraction
T1concat_mean_N4_mask : str
mask corresponding to T1concat_mean_N4_brain
Notes
combines separate 3D T1EST images into a single 4D timeseries optionally coregisters the separate T1EST images as well
For the CMIND study, the T1EST_TI.nii.gz files for a given subject can be stored in a folder and the files will be found and have the TI values extracted automatically. For more general inputs, see the documentation of the T1EST_nii_folder input.