romainVala / matvol

batch scripting files for neuroimaging

Apache License 2.0

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Dev job obj #24

Closed benoitberanger closed 5 years ago

benoitberanger commented 5 years ago

job_* enhacements

@volume object can be used as input + more help :

job_do_segment
job_do_segmentCAT12
job_apply_normalize
do_topup_unwarp_4D
job_coregister
job_realign
job_slice_timing
job_smooth

Can skip if exist :

job_first_level_specify
job_first_level_estimate

job_do_segmentCAT12 : possibility to ask for wp (like wc) warped probability (compartment) maps

job_meicaafni : added the export of timeseriesoptimalycombined volume (tsoc_nogs.nii ). This is important in case of crash of the TEDANA part.

Output of dofsl* are columns, instead of lines :

do_fsl_add
do_fsl_mult

QC / analyze series

new @serie/seq2str
new @exam/regroupSeries, similar to @exam/countSeries, but using @serie.sequence to make groups, depending on the list of parameters you want.
@exam/analyzeCountSeries -> @exam/analyzeSeries
@exam/compareOrientation : upgrade, more robust

mvObject

cellstr2regex : can now ask for "exactly" the expression you need -> ^expr$
@exam/getExam can now use a cellstr as input, to ask for "exactly" (^expr$)
new @mvObject/toStruct
new @mvObject/unique
new str2char

Other

get_sequence_param_from_json : more robust, some new fields, updated fields
auto_import_obj : better dwi support, with better bvals bvect and INTERRUPT flag