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SPM xASL Functions

CorrClusTh.m

Format:

function [k,Pc] = CorrClusTh(SPM,u,alpha,guess)

Description:

Finds the corrected cluster size (spatial extent) threshold for a given cluster defining threshold u and FWE-corrected level alpha.

xASL_Copy.m

Format:

xASL_Copy(SrxASL_SysCopyath, DstPath[, bOverwrite, bVerbose)])

Description:

Copies a file to a file or a directory to a directory. For a file, it zips it in the end if the destination path contains nii.gz. It also makes sure that only one of .nii and .nii.gz exists in the destination directory. It is faster than the default Matlab function, and runs on multiple OSes.

NB: This function calls xASL_SysMove for the actual copying. Run xASL_SysMove instead of xASL_Move if you don't want the .nii|.nii.gz management/checking

xASL_Move.m

Format:

xASL_Move(SrcPath, DstPath[, bOverwrite, bVerbose])

Description:

Moves a file to a file, a file to a directory, or a directory to a directory. It manages the unzipping or zipping according to the extension after the move. And it makes sure that only one of .nii and .nii.gz exists in the destination directory. Bypass inefficient Matlab stuff on Linux and Windows, but can only move on the same file system.

NB: This function calls xASL_SysMove for the actual moving. Run xASL_SysMove instead of xASL_Move if you don't want the .nii|.nii.gz management/checking

xASL_SysCopy.m

Format:

xASL_SysCopy(SrcPath, DstPath, bOverwrite, bVerbose)

Description:

Copies a file to a file or a directory to a directory. Bypass inefficient matlab stuff on linux and windows, but can only move on the same file system.

xASL_SysMove.m

Format:

xASL_SysMove(SrcPath, DstPath[, bForce, bSourceCheck])

Description:

Moves a file to a file, a file to a directory, or a directory to a directory. SBypass inefficient matlab stuff on linux and windows, but can only move on same file system!

xASL_TrackProgress.m

Format:

xASL_TrackProgress(iCurrent[, iMax])

Description:

Counts the percentage of the work done and display on the screen. Either iCurrent of iMax are given. Or only the percentages are given.

xASL_adm_ConvertSeconds2TimeString.m

Format:

TimeString = xASL_adm_ConvertSeconds2TimeString(Seconds)

Description:

Converts number to time input hh (with minutes in fractions/floating point) -> output hhmm Inverse from xASL_adm_ConvertTime2Nr.

xASL_adm_ConvertSlash.m

Format:

[newString] = xASL_adm_ConvertSlash( StringOriginal,ForceUnix)

Description:

Converts Windows forward slashes to backward slashes Prevents confusion file separation & regular expression forward slashes in Windows.

xASL_adm_CreateDir.m

Format:

status = xASL_adm_CreateDir(strPath)                  create all missing subdirs
status = xASL_adm_CreateDir(strPath, strBranch)       create strBranch (if missing) under existing strPath
status = xASL_adm_CreateDir(strPath, nMaxNewDirs)     impose limit on the number of new directories

Description:

Recursively creates missing directories at the given path or for given subdirectories, with an option to limit the number of newly created directories.

xASL_adm_DeleteFileList.m

Format:

filepaths = xASL_adm_DeleteFileList(strDirectory, strRegEx[, bRecurse, nRequired])
xASL_adm_DeleteFileList(strDirectory, strRegEx[, bRecurse, nRequired])

Description:

Delete the files that match regular expression STRREGEXP in the given directory STRDIRECTORY. Deletes recursively if specified in BRECURSE. Deletes all files unless the number is specified by NREQUIRED, if the number is not met, then does not delete anything and throws an error.

xASL_adm_GetFileList.m

Format:

filepaths = xASL_adm_GetFileList(strDirectory[, strRegEx, mode, nRequired, bGetDirNames])

Description:

List files or directories from a given path. And optionally uses regular expressions to filter the result with option to set a minimal requirement on the number of results.

xASL_adm_GzipNifti.m

Format:

pathOut = xASL_adm_GzipNifti(pathIn [,bOverwrite])

Description:

Take the input file, zips it, overwriting any existing zipped file and return the path of the zipped file.

xASL_adm_ManageMoCoMat.m

Format:

xASL_adm_ManageMoCoMat(PathIn)

Description:

This function manages the orientation matrices that SPM puts in an external .mat sidecar file if there are more than 1 volumes. The first volume should be equal to the orientation header of the NIfTI, if not, we assume that the NIfTI header is correct. This function performs several checks & corrects if necessary, combined with throwing a warning:

  • A) the nVolumes in .mat & .nii image should be equal, if not, delete sidecar
  • B) .mat should have more than one volume, if not delete sidecar
  • C) If there are illegal numbers in the diagonal of the .mat orientation matrices (here only checked for zeros or non finite values) then the .mat is removed
  • D) If this is true for the first volume only, the .mat is retained but the first volume orientation is overwritten with a zero matrix

xASL_adm_UnixPath.m

Format:

[PathIs] = xASL_adm_UnixPath(PathIs[, bTryWSL])

Description:

This function performs the following steps to convert a path to a path that is compatible with the Unix-filesystem as used in e.g. Linux/MacOS. It also has special support for Windows Subsystem for Linux (WSL), though this should only be activated specifically for WSL calls.

Note that we want to use this function for most Unix calls (to fix paths), but in the case of WSL only for some calls, where Matlab in Windows calls Linux-code through WSL (e.g. for FSL) - these have to be explicitly specified by the bTryWSL option.

  1. Skip this function without Unix-filesystem
  2. Trim whitespace
  3. Selectively convert forward to backward slashes (ignore already escaped whitespace)
  4. Escape characters and residual whitespaces (ignore already escaped whitespaces)
  5. If WSL: add mounting prefix

xASL_adm_UnzipNifti.m

Format:

pathOut = xASL_adm_UnzipNifti(pathIn[, bOverwrite])

Description:

Takes the input file, unzips if needed, delete the zipped file and return the path to the unzipped file. If the input is already unzipped, then does nothing, but returns the original filename - so it can be run just to be sure a file is unzipped without much overhead. Returns error if more than one file is in the archive, if the filename does not exist, is a directory etc. If there's a NII and NII.GZ already existing, then return error, or just overwrite in case overwrite is set to 1

xASL_adm_ZipFileNameHandling.m

Format:

[srcOut, dstOut] = xASL_adm_ZipFileNameHandling(srcIn, dstIn)

Description:

Adjusts the source and destination filenames of a nifti file to reflect if NII or NII.GZ exist on the input. If either .nii or .nii.gz is corrupt, it automatically deletes the corrupt one and keeps the healthy one, while reporting a warning. This happens when you restart the pipeline after it crashed, if it crashed while unzipping.

xASL_bids_csv2tsvReadWrite.m

Format:

[PathTSV, CellContents] = xASL_bids_csv2tsvReadWrite(PathIn[, bDeleteCSV, bWriteTSV])

Description:

This function PathIn and loads it, also trying CSV or TSV extensions if these exist. It outputs the contents to a cell array. If a CSV file exists but not a TSV file, it converts and replaces the CSV to TSV file, per BIDS. This function has the following parts:

  1. Read the CSV or TSV file
  2. Write the TSV file (if requested)
  3. Delete the CSV file (if requested)

xASL_csvRead.m

Format:

[CellContents] = xASL_csvRead(PathCSV)

Description:

This function loads a comma-separated value (csv) file - which is the format that BIDS prefers - and outputs it to a cell array.

xASL_csvWrite.m

Format:

xASL_csvWrite(InputCell, PathCSV, bOverwrite)

Description:

Rudimentary function, please use xASL_tsvWrite instead. For usage, type help xASL_tsvWrite. This function will still work though.

xASL_delete.m

Format:

xASL_delete(InputPath)

Description:

Delete the file in the given path. If a NIFTI file with extension '.nii' or '.nii.gz' is given, Then delete both the .nii and .nii.gz files.

xASL_exist.m

Format:

xASL_exist(PathIn[,Type])

Description:

Check if the given path exists, wrapper around the Matlab exist function, to allow checking for either .nii or .nii.gz Otherwise, exist is used normally.

xASL_fileparts.m

Format:

[Fpath, Ffile, Fext] = xASL_fileparts(InputPath)

Description:

Returns the path, file name, and file extension for InputPath using the fileparts.m function. If a file ending at nii.gz is given, then the whole nii.gz is returned as the extension. Does not verify the existence of the file, or existence of .nii or .nii.gz

xASL_im_ConvertMap2Mask.m

Format:

[IMout] = xASL_im_ConvertMap2Mask(IMin)

Description:

Provides a robust way of conversion of a continuous map to a binary mask, which can be used for lesions, ROIs, or tissue probability maps. Based on the assumption that a map should be thresholded at 50% to form a map, which is often the case for automatic segmentations.

xASL_im_DistanceTransform.m

Format:

[dist, x, y, z] = xASL_im_DistanceTransform(im)

Description:

Calculates the distance transform in a binary image Uses Borgefors Chamfers computation of Euclidean distance in 3D using a 5x5x5 window.

xASL_im_FillNaNs.m

Format:

xASL_im_FillNaNs(InputPath[, UseMethod, bQuality])

Description:

This function fills any NaNs in an image. In SPM, any voxels outside the boundary box/field of view are filled by NaNs when resampling. These NaNs can confuse some algorithms, hence it doesn't hurt replacing them in some cases (e.g. for flowfields). Also, smoothing restricted in a mask is done in ExploreASL with the function xASL_im_ndnanfilter, after first setting all voxels outside the mask to NaN. In this case, this functon can be useful to extrapolate the smoothed image to avoid any division artifact near brain edges (e.g. for reducing the M0 image to a smooth biasfield). This function performs the following 3 steps:

  1. Load image
  2. Replace NaNs
  3. Save image

xASL_im_LesionRemoval4CAT.m

Format:

[Ycls, LesionImOut] = xASL_im_LesionRemoval4CAT(Ycls, PathIn)

Description:

For all lesion masks in the anatomical directory, remove them from the current segmentations.

xASL_im_ResampleIM.m

Format:

[imOut] = xASL_im_ResampleIM(imIn, matIn, matOut, dimOut[, interpolationType])

Description:

Resamples an input image imIn oriented according to the homogeneous matrix matIn to and output image imOut that has dimension dimOut and matrix matOut. This allows to resample images between two spaces with different orientation and matrix sizes. It uses the Matlab interp3 function and the interpolation method used by this method can be chosen. Note that the recommended use of this function is resampling between space with similar resolution or upsampling. For downsampling, simple interpolation does not delivery correct results respecting the point-spread-function and a combination of xASL_im_PreSmooth and xASL_spm_reslice should be used instead.

xASL_im_SaveOriginal4CAT.m

Format:

xASL_im_SaveOriginal4CAT(Ycls, PathIn)

Description:

Save the segmentation before lesion masking.

xASL_im_conv3Dsep.m

Format:

[imConv] = xASL_mex_conv3Dsep(im,kX,[kY,kZ])

Description:

3D separable convolution with a supplied kernel It converts the results to double Returned is the convoluted image The wrapper makes sure that kX are Nx1 format, removes nan, and removes excessive zeros at the ends.

xASL_im_ndnanfilter.m

Format:

[Y,fil] = xASL_im_ndnanfilter(X,filterType,F,WNAN)

Description:

This function applies a 3-dimensional convolution of X with given kernel. NaNs elements are taken into account (ignored).

By default, edges are not padded and one-sided filter is used at the image edges.

Notes:

  • * Accepts empty value for any input. When X is empty, the program can be used as a N-dimensional window generator.
  • * NaNs elements surrounded by no-NaNs elements (which will depend on window width) are the ones that will be interpolated. The others are leaved untouched.
  • * When WNAN=2, the programs acts like an NAN-interpolat/GAP-filling, leaving untouched the no-NaNs elements but the filtering is perfomed anyway. I recommend the default behaviour (WNAN=0) in order to keep the filtered data in the workspace, and then use the code at the end of this function to get/remove the interpolated NaNs
  • * To achieve similar results as ndnanfilter previously, use same F as with the 'rect' filter.
  • * Note that the FWHM of Gaussian is given in VOXELS, not in mm

  • * For the Gaussian filter, use (previous N, new FWHM)

  • N= 1 ~ FWHM 0.94

  • N= 2 ~ FWHM 1.885
  • N= 4 ~ FWHM 3.76
  • N= 6 ~ FWHM 5.652
  • N= 8 ~ FWHM 7.536
  • N=10 ~ FWHM 9.42
  • N=12 ~ FWHM 11.3
  • N=16 ~ FWHM 15.07
  • N=20 ~ FWHM 18.84
  • N=10/2.355 ~ FWHM 4
  • Basically divide by 1.06

xASL_io_Nifti2Im.m

Format:

imOut = xASL_io_Nifti2Im(niftiIn [, ImageSize])

Description:

This function loads a NIfTI image matrix with flexible input (as explained under INPUT: niftiIn). It does the following.

  1. Try to load a NIfTI
  2. If NIfTI successfully loaded, try to load the NIfTI image
  3. If the above didnt work, try to create a dummy image
  4. Convert to single precision data format
  5. Also able to load NIfTI as .nii.mat format

xASL_io_ReadNifti.m

Format:

[NiftiObject, pathIn] = xASL_io_ReadNifti(pathIn)

Description:

Read Nifti file given by the path. Return the NII object. And also return the actual path to the loaded Nifti if by any reason the name changed during the function runtime (e.g. unzipping).

xASL_io_SaveNifti.m

Format:

xASL_io_SaveNifti(pathOrigNifti, pathNewNifti, imNew[, nBits, bGZip, newMat])

Description:

It loads the pathOrigNifti, takes all the parameters from it, and creates a new Nifti file with these parameters, but new image matrix from imNew. It saves the result in pathNewNifti. It runs the following steps:

  1. Unzipping and manage name input file
  2. Determine the bit precision
  3. Create new NIfTI
  4. Remove redundant .mat orientation files
  5. Delete any pre-existing NIfTI files with the same name

xASL_round.m

Format:

[OutputN] = xASL_round(InputN[, PrecisionN])

Description:

Recent Matlab versions support a second input that specifies that number of decimals to round at, but earlier Matlab versions do not support this. For backward compatibility, use this wrapper instead of round.

xASL_spm_admin.m

Format:

xASL_spm_admin(pathIn[, bPadComma1])

Description:

This SPM admin function takes a NIfTI path and does a few checks to make this valid to SPM. It accepts both .nii and .nii.gz. It runs the following steps: 1. Unzip .nii.gz 2. Convert char to cell 3. Add ',1' suffix

xASL_spm_reslice.m

Format:

xASL_spm_reslice(refPath, srcPath[, srcAffinePath, bInvAffine, bQuality, NewName, InterpolationPar])

Description:

This wrapper runs SPM's reslice function (a.k.a. coregister: reslice) which resamples a source image into the space of a reference image, taking into account any orientation differences between the two images that are defined in the orientation matrix in the NIfTI header. When the source image contains multiple volumes, they are all resampled. The source image will get the same orientation matrix as the reference image, as it is now in the same space as the reference image. This can be useful when two images are to be compared voxel-by-voxel, e.g. when overlaying a CBF image over a structural image, or when wanting to use a mask from a different space. When after running this function, the reference and source images are not in alignment, they need to be registered first (i.e. xASL_spm_register). Resampling/reslicing needs an interpolation method to know from which voxels of the source image, a voxel in the new image will be computed. A simplistic explanation is that this determines the number of surrounding neighborhood voxels it uses to determine the new voxel value. The example syntax below would reslice/resample the CBF image to the T1w space (assuming the Affine was done to register CBF to T1w) It also works with the external .mat file of the source file that has the same name as the source file. It also can optionally take a _sn.mat containing the affine transformation information.

xASL_spm_smooth.m

Format:

xASL_spm_smooth(pathIn, fwhmSmooth, pathNew])

Description:

This SPM wrapper runs SPM's smooth function, which spatially smooths the input image with a Gaussian kernel. In the case of multiple volumes (i.e. a 4D NIfTI), each 3D volume is spatially smoothed separately. Note that smoothnesses combine with Pythagoras' rule (i.e. sum quadratically)

xASL_stat_MeanNan.m

Format:

y = xASL_stat_MeanNan(x[,dim])

Description:

It calculates the sum using the SUM functions and divides by the number of values but ignoring NaNs.

xASL_stat_MedianNan.m

Format:

y = xASL_stat_MedianNan(x[,dim])

Description:

It calculates the MEDIAN along the given dimension, but it sets all the NaNs to zero before calling it.

xASL_tsvRead.m

Format:

[CellContents] = xASL_tsvRead(PathTSV[, bStruct])

Description:

This function loads a tab-separated value (TSV) file - which is the format that BIDS prefers - and outputs it to a cell array.

xASL_tsvWrite.m

Format:

xASL_tsvWrite(InputCell, PathTSV[, bOverwrite, bCSV])

Description:

This function loads a cell array and prints it to a tab-separated value (TSV) file, which is the format that BIDS prefers.

xASL_wrp_DARTELSaveIntermedTrans.m

Format:

xASL_wrp_DARTELSaveIntermedTrans(Yy, u, odim, rdim, idim, Mar, mat, M0, M1, nameOut, numIteration)

Description:

This function is called from the CAT12 segmentation function to save the intermediate results of the DARTEL transformation. Normally, the registration only saves the final results - the final transformation field. This function enables to save also the intermediate transformation field. It takes all the internal variables from the transformation and save the field to a sub-directory 'mri' that normally contains all the intermediate results of the CAT12 segmentation. It adds a 'y_' prefix and adds the specified iteration number as postfix.

xASL_wrp_GSSaveIntermedTrans.m

Format:

xASL_wrp_GSSaveIntermedTrans(y, idim, odim, rdim, M0, M1, R, M1t, M1r, nameOut, numIteration)

Description:

This function is called from the CAT12 segmentation function to save the intermediate results of the Geodesic shooting transformation. Normally, the registration only saves the final results - the final transformation field. This function enables to save also the intermediate transformation field. It takes all the internal variables from the transformation and save the field to a sub-directory 'mri' that normally contains all the intermediate results of the CAT12 segmentation. It adds a 'y_' prefix and adds the specified iteration number as postfix.