Several bugs when processing

[HenkMutsaerts]

Description

In some functions we check for a comma ',' as a comma in the extension should be removed: this occurs with spm paths in the format:

dir/filename.nii(.gz),1
dir/filename.nii(.gz),2
dir/filename.nii(.gz),n

for different volumes in a 4D NIfTI file.

When there is a comma in a path (e.g. when mounting), it is useful if we don't have to move data to avoid having to resync it.

Example for me now:

'/Users/hjmutsaerts/surfdrive - Mutsaerts, H.J.M.M. (Henk-Jan)@surfdrive.surf.nl/HolidayPics/studyName'

Matlab otherwise works fine with this path, so spaces, commas, @ don't seem to be a problem in the foldername.

When converting csv to tsv, the comma is converted to a tab, creating another column. The number of columns will be inconsistent and csvtotsv will crash.
We can do two things (or both):

1. Not put the directory name in a stats/tsv file
2. Recognize when something is a path and ignore any delimiters in a path (this is perhaps more tricky)

Note that this is only valid for directory names, not for filenames. BIDS subject & visit names should not include illegal chars.

Tasks

• Extend xASL_fileparts that it detects ,1 as well as .nii(.gz)
• Check for other potential path problems
• Minor bug fix in xASL_adm_DeleteManyTempFiles, for xASL_TrackProgress, and speeding up by removing recursive file searching where not needed
• xASL_qc_SortBySpatialCoV: Print warnings only once. We still repeat the fprintf for the scans that may need checking, but avoid repeating warnings for huge verbosity.
• xASL_stat_PrintStats: bugfixes empty end of list. When scans are missing, they are not included but the rest should still be reported, filling empties with 'n/a'. Did didn't happen with empties at the end of the list, because the list was shorter than expected, this function crashed. Now fixed.
• ps_LST_tlv: avoid listing the path, which avoids seeing a comma in a path as delimiter
• xASL_qc_CollectQC_Structural & xASL_stat_GetVolumeStatistics: correct indices for not having a path in the tsv-files
• xASL_wrp_GetVolumetrics: revamp (accordingly)
• xASL_adm_GzipAllFiles: UNIX bugfix

How to test

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Release notes

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