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👔 Restore movement-parameters to outputs, but now as a TSV
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@shnizzedy
shnizzedy committed Oct 12, 2023
1 parent 31a2b8c commit 9650cbb
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Showing 3 changed files with 53 additions and 47 deletions.
2 changes: 1 addition & 1 deletion CPAC/func_preproc/func_motion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -699,7 +699,7 @@ def normalize_motion_parameters(in_file):
-motion_params[4, :]))
motion_params = np.transpose(motion_params)

out_file = os.path.join(os.getcwd(), 'motion_params.1D')
out_file = os.path.join(os.getcwd(), 'motion_params.tsv')
np.savetxt(out_file, motion_params)

return out_file
95 changes: 50 additions & 45 deletions CPAC/generate_motion_statistics/generate_motion_statistics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -268,13 +268,13 @@ def motion_power_statistics(name='motion_stats',
name='calc_motion_parameters')

get_all_motion_parameters = pe.Node(Function(input_names=[
'in_file_FDJ',
'in_file_FDP',
'in_file_maxdisp',
'in_file_motion',
'in_file_power',
'in_file_relsdisp',
'in_file_DVARS'],
'fdj',
'fdp',
'maxdisp',
'motion',
'power',
'relsdisp',
'dvars'],
output_names=[
'all_motion_val',
'summary_motion_power'],
Expand All @@ -283,16 +283,16 @@ def motion_power_statistics(name='motion_stats',
name='get_all_motion_parameters')

calc_motion_parameters.inputs.motion_correct_tool = motion_correct_tool
wf.connect(calculate_FDJ, 'fd', get_all_motion_parameters, 'in_file_FDJ')
wf.connect(calculate_FDP, 'fd', get_all_motion_parameters, 'in_file_FDP')
wf.connect(calculate_FDJ, 'fd', get_all_motion_parameters, 'fdj')
wf.connect(calculate_FDP, 'fd', get_all_motion_parameters, 'fdp')
wf.connect(calc_motion_parameters, 'maxdisp',
get_all_motion_parameters, 'in_file_maxdisp')
get_all_motion_parameters, 'maxdisp')
wf.connect(calc_motion_parameters, 'relsdisp',
get_all_motion_parameters, 'in_file_relsdisp')
get_all_motion_parameters, 'relsdisp')
wf.connect(calc_motion_parameters, 'info',
get_all_motion_parameters, 'in_file_motion')
get_all_motion_parameters, 'motion')
wf.connect(cal_DVARS_strip, 'DVARS_val',
get_all_motion_parameters, 'in_file_DVARS')
get_all_motion_parameters, 'dvars')
wf.connect(input_node, 'movement_parameters',
calc_motion_parameters, 'movement_parameters')
wf.connect(input_node, 'max_displacement',
Expand All @@ -317,7 +317,7 @@ def motion_power_statistics(name='motion_stats',

calc_power_parameters.inputs.motion_correct_tool = motion_correct_tool
wf.connect(calc_power_parameters, 'info',
get_all_motion_parameters, 'in_file_power')
get_all_motion_parameters, 'power')
wf.connect(cal_DVARS, 'out_file',
calc_power_parameters, 'dvars')

Expand Down Expand Up @@ -503,6 +503,7 @@ def gen_motion_parameters(movement_parameters, max_displacement,
max_displacement : string
path of file with maximum displacement (in mm) for brain voxels
in each volume
movement_parameters : string
path of 1D file containing six movement/motion parameters
(3 Translation, 3 Rotations) in different columns
Expand All @@ -512,14 +513,16 @@ def gen_motion_parameters(movement_parameters, max_displacement,
-------
out_file : string
path to csv file containing various motion parameters
info : text
contains information about motion parameters
maxdisp : array
max displacement value
relsdisp : array
rels displacement value
"""

mot = np.genfromtxt(movement_parameters).T

# Relative RMS of translation
Expand Down Expand Up @@ -756,49 +759,51 @@ def calculate_DVARS(func_brain, mask):
return out_file, dvars


def get_allmotion(in_file_FDJ, in_file_FDP, in_file_maxdisp, in_file_motion,
in_file_power, in_file_relsdisp=None, in_file_DVARS=None):
def get_allmotion(fdj, fdp, maxdisp, motion, power, relsdisp=None, dvars=None):
"""
Method to append all the motion and power parameters into 2 files
Parameters
----------
in_file_FDJ
file with framewise displacement Jenkinson
in_file_FDP
file with framewise displacement power
in_file_maxdisp
file with maximum displacement value
in_file_motion
file with motion values
in_file_power
file with power values
in_file_rels
file with rels displacement value
in_file_DVARS
file with DVARS value
fdj
framewise displacement (Jenkinson)
fdp
framewise displacement (Power)
maxdisp
maximum displacement value
motion
motion info
power
Power values
relsdisp
rels displacement value
dvars
DVARS value
Returns
-------
all_motion_val : string
all_motion_val : str
path to file containing all motion parameters appended
summary_motion_power
summary_motion_power : str
path to file containing all motion parameters appended
"""
all_motion_val = os.path.join(os.getcwd(), 'motion.tsv')
summary_motion_power = os.path.join(os.getcwd(), 'desc-summary_motion.tsv')

df_FDJ = pd.DataFrame(in_file_FDJ)
df_FDJ.columns = ['Framewise displacement Jenkinson']
df_FDP = pd.DataFrame(in_file_FDP)
df_FDP.columns = ['Framewise displacement Power']
df_DVARS = pd.DataFrame(in_file_DVARS)
df_DVARS.columns = ['DVARS']
df_maxdisp = pd.DataFrame(in_file_maxdisp)
df_fdj = pd.DataFrame(fdj)
df_fdj.columns = ['Framewise displacement Jenkinson']
df_fdp = pd.DataFrame(fdp)
df_fdp.columns = ['Framewise displacement Power']
df_dvars = pd.DataFrame(dvars)
df_dvars.columns = ['DVARS']
df_maxdisp = pd.DataFrame(maxdisp)
df_maxdisp.columns = ['Max Displacement']
df_relsdisp = pd.DataFrame(in_file_relsdisp)
df_relsdisp = pd.DataFrame(relsdisp)
df_maxdisp.columns = ['Rels Displacement']
data_frames = [df_FDJ, df_FDP, df_DVARS, df_maxdisp, df_relsdisp]
data_frames = [df_fdj, df_fdp, df_dvars, df_maxdisp, df_relsdisp]
all_motion_val_df = pd.concat(data_frames, axis=1)
#raise Exception(len(all_motion_val_df.columns))

if len(all_motion_val_df.columns) == 5:
np.savetxt(all_motion_val, all_motion_val_df, delimiter="\t",
header="Framewise displacement Jenkinson\tFramewise "
Expand All @@ -810,8 +815,8 @@ def get_allmotion(in_file_FDJ, in_file_FDP, in_file_maxdisp, in_file_motion,
"displacement power\tDVARS\tMax Displacement",
comments='')

df_motion = pd.DataFrame(in_file_motion)
df_power = pd.DataFrame(in_file_power)
df_motion = pd.DataFrame(motion)
df_power = pd.DataFrame(power)
data_frames_motionpower = [df_motion, df_power]
summary_motion_pow_df = pd.concat(data_frames_motionpower)
np.savetxt(summary_motion_power, summary_motion_pow_df, delimiter="\t",
Expand Down
3 changes: 2 additions & 1 deletion CPAC/resources/cpac_outputs.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,8 @@ space-template_res-derivative_desc-bold_mask mask template func NIfTI
motion motion func TSV
desc-summary_motion motion func TSV
motion-filter-plot motion func png
unfiltered-movement-parameters motion func 1D
movement-parameters motion func TSV
unfiltered-movement-parameters motion func TSV
label-CSF_probseg probseg T1w anat NIfTI
label-GM_probseg probseg T1w anat NIfTI
label-WM_probseg probseg T1w anat NIfTI
Expand Down

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