general_convert_cifti#

qx_mri.general.general_convert_cifti(fin, fout, output_format, atlas, parcel_method, verbose)#

general_convert_cifti(fin, fout, output_format, atlas, parcel_method, verbose)

Perform smoothing using img_smooth() method and use img_find_peaks method to define peak ROI using a watershed algorithm to grow regions from peaks.

Parameters

--fin (str):

The input cifti file path to be converted.

--fout (str):

Output cifti file path.

--output_format (str):

The desired output format:

  • 'dense' ... dense cifti image

  • 'parcellated ... parcellated cifti image

  • 'label' ... label cifti image

--atlas (str, default ''):

The parcellated atlas image. Only required for dense to parcellated conversion.

--parcel_method (str, default 'mean'):

The metod to use to compute the values for parcels.

Options are:

  • 'mean' ... average value of the ROI

  • 'median' ... median value across the ROI

    • 'max' ... maximum value across the ROI

    • 'min' ... minimum value across the ROI

  • 'pca' ... first eigenvariate of the ROI

  • 'threshold' ... average of all voxels above threshold

  • 'maxn' ... average of highest n voxels

  • 'weighted' ... weighted average across ROI voxels

  • 'all' ... all voxels within a ROI

--verbose (bool, default false):

Whether to be verbose.

Output files

The script saves the resulting converted file under the specified filename.

Notes

The function is a wrapper to the nimage.img_convert_cifti method and is used to convert cifti files from between dense, parcellated and label formats. Please see the method documentation for specifics about the parameters.

Examples

Dense to parcellated conversion:

To convert a dtseries image to a parcellated ptseries object using a dlabel atlas with the defined parcels use:

qunex general_convert_cifti \
    --fin='bold.dtseries.nii' \
    --fout='bold.ptseries.nii' \
    --output_format='parcellated' \
    --atlas='atlas.dlabel.nii' \
    --parcel_method='mean' \
    --verbose=1
Parcellated to dense conversion:

To convert (expand) a ptseries image to a dtseries object use:

qunex general_convert_cifti \
    --fin='bold.ptseries.nii' \
    --fout='bold.dtseries.nii' \
    --output_format='dense' \
    --verbose=1
Parcellated to label conversion:

To convert a ptseries image to a label image use:

qunex general_convert_cifti \
    --fin='bold.ptseries.nii' \
    --fout='bold.label.nii' \
    --output_format='label' \
    --verbose=1
Dense to label conversion:

To convert a dtseries image to a label image use:

qunex general_convert_cifti \
    --fin='bold.dtseries.nii' \
    --fout='bold.label.nii' \
    --output_format='label' \
    --verbose=1