cmind_T1map_preprocess(output_dir, ...[, ...]) T1EST preprocessing prior to fitting T1 values
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


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)


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


combines separate 3D T1EST images into a single 4D timeseries optionally coregisters the separate T1EST images as well


Coregistered images magnitude images for each of the TI times

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.