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Add Dim Check #32

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Add Dim Check #32

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2a6c33a
Add dim check
saigerutherford Nov 6, 2018
88b9372
Add dim check
saigerutherford Nov 6, 2018
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24 changes: 13 additions & 11 deletions ICA_AROMA_functions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -157,13 +157,15 @@ def register2MNI(fslDir, inFile, outFile, affmat, warp):

# If the no affmat- or warp-file has been specified, assume that the data is already in MNI152 space. In that case only check if resampling to 2mm is needed
if (len(affmat) == 0) and (len(warp) == 0):
# Get 3D voxel size
# Get 3D voxel size & bounding box
pixdim1 = float(subprocess.getoutput('%sfslinfo %s | grep pixdim1 | awk \'{print $2}\'' % (fslDir, inFile)))
pixdim2 = float(subprocess.getoutput('%sfslinfo %s | grep pixdim2 | awk \'{print $2}\'' % (fslDir, inFile)))
pixdim3 = float(subprocess.getoutput('%sfslinfo %s | grep pixdim3 | awk \'{print $2}\'' % (fslDir, inFile)))

# If voxel size is not 2mm isotropic, resample the data, otherwise copy the file
if (pixdim1 != 2) or (pixdim2 != 2) or (pixdim3 != 2):
dim1 = float(subprocess.getoutput('%sfslinfo %s | grep "^dim1" | awk \'{print $2}\'' % (fslDir, inFile)))
dim2 = float(subprocess.getoutput('%sfslinfo %s | grep "^dim2" | awk \'{print $2}\'' % (fslDir, inFile)))
dim3 = float(subprocess.getoutput('%sfslinfo %s | grep "^dim3" | awk \'{print $2}\'' % (fslDir, inFile)))
# Check if data is 2mm isotropic voxel size and check that the bounding box dimensions match, if they don't then resample the data
if (pixdim1 != 2) or (pixdim2 != 2) or (pixdim3 != 2) or (dim1 != 91) or (dim2 != 109) or (dim3 != 91) :
os.system(' '.join([os.path.join(fslDir, 'flirt'),
' -ref ' + ref,
' -in ' + inFile,
Expand Down Expand Up @@ -211,7 +213,7 @@ def cross_correlation(a, b):


def feature_time_series(melmix, mc):
""" This function extracts the maximum RP correlation feature scores.
""" This function extracts the maximum RP correlation feature scores.
It determines the maximum robust correlation of each component time-series
with a model of 72 realignment parameters.

Expand Down Expand Up @@ -342,7 +344,7 @@ def feature_spatial(fslDir, tempDir, aromaDir, melIC):
---------------------------------------------------------------------------------
fslDir: Full path of the bin-directory of FSL
tempDir: Full path of a directory where temporary files can be stored (called 'temp_IC.nii.gz')
aromaDir: Full path of the ICA-AROMA directory, containing the mask-files (mask_edge.nii.gz, mask_csf.nii.gz & mask_out.nii.gz)
aromaDir: Full path of the ICA-AROMA directory, containing the mask-files (mask_edge.nii.gz, mask_csf.nii.gz & mask_out.nii.gz)
melIC: Full path of the nii.gz file containing mixture-modeled threholded (p>0.5) Z-maps, registered to the MNI152 2mm template

Returns
Expand Down Expand Up @@ -455,8 +457,8 @@ def feature_spatial(fslDir, tempDir, aromaDir, melIC):


def classification(outDir, maxRPcorr, edgeFract, HFC, csfFract):
""" This function classifies a set of components into motion and
non-motion components based on four features;
""" This function classifies a set of components into motion and
non-motion components based on four features;
maximum RP correlation, high-frequency content, edge-fraction and CSF-fraction

Parameters
Expand Down Expand Up @@ -499,7 +501,7 @@ def classification(outDir, maxRPcorr, edgeFract, HFC, csfFract):

# Put the indices of motion-classified ICs in a text file
txt = open(os.path.join(outDir, 'classified_motion_ICs.txt'), 'w')
if motionICs.size > 1: # and len(motionICs) != 0: if motionICs is not None and
if motionICs.size > 1: # and len(motionICs) != 0: if motionICs is not None and
txt.write(','.join(['{:.0f}'.format(num) for num in (motionICs + 1)]))
elif motionICs.size == 1:
txt.write('{:.0f}'.format(motionICs + 1))
Expand Down Expand Up @@ -532,7 +534,7 @@ def classification(outDir, maxRPcorr, edgeFract, HFC, csfFract):


def denoising(fslDir, inFile, outDir, melmix, denType, denIdx):
""" This function classifies the ICs based on the four features;
""" This function classifies the ICs based on the four features;
maximum RP correlation, high-frequency content, edge-fraction and CSF-fraction

Parameters
Expand All @@ -541,7 +543,7 @@ def denoising(fslDir, inFile, outDir, melmix, denType, denIdx):
inFile: Full path to the data file (nii.gz) which has to be denoised
outDir: Full path of the output directory
melmix: Full path of the melodic_mix text file
denType: Type of requested denoising ('aggr': aggressive, 'nonaggr': non-aggressive, 'both': both aggressive and non-aggressive
denType: Type of requested denoising ('aggr': aggressive, 'nonaggr': non-aggressive, 'both': both aggressive and non-aggressive
denIdx: Indices of the components that should be regressed out

Output (within the requested output directory)
Expand Down