From 0a058bdad78189a5d61a8c422b4f76a43e9bdaa5 Mon Sep 17 00:00:00 2001 From: Neurodesk User Date: Wed, 22 Nov 2023 06:46:32 +0000 Subject: [PATCH 1/2] debugged issues with fileformats and some yaml specs --- .gitignore | 2 + nipype-auto-conv/specs/dot.yaml | 230 ++++++++++++++++---------------- 2 files changed, 117 insertions(+), 115 deletions(-) diff --git a/.gitignore b/.gitignore index b040690..2c1dc0b 100644 --- a/.gitignore +++ b/.gitignore @@ -143,3 +143,5 @@ dmypy.json /pydra/tasks/afni/auto /pydra/tasks/afni/_version.py + +_version.py diff --git a/nipype-auto-conv/specs/dot.yaml b/nipype-auto-conv/specs/dot.yaml index e8f783d..9f2eaeb 100644 --- a/nipype-auto-conv/specs/dot.yaml +++ b/nipype-auto-conv/specs/dot.yaml @@ -8,14 +8,14 @@ # Correlation coefficient between sub-brick pairs. # All datasets in in_files list will be concatenated. # You can use sub-brick selectors in the file specification. -# +# # .. warning:: -# +# # This program is not efficient when more than two subbricks are input. -# +# # For complete details, see the `3ddot Documentation. # `_ -# +# # >>> from nipype.interfaces import afni # >>> dot = afni.Dot() # >>> dot.inputs.in_files = ['functional.nii[0]', 'structural.nii'] @@ -24,8 +24,8 @@ # >>> dot.cmdline # '3dDot -dodice functional.nii[0] structural.nii |& tee out.mask_ae_dice.txt' # >>> res = copy3d.run() # doctest: +SKIP -# -# +# +# task_name: Dot nipype_name: Dot nipype_module: nipype.interfaces.afni.utils @@ -35,12 +35,12 @@ inputs: rename: # dict[str, str] - fields to rename in the Pydra interface types: - # dict[str, type] - override inferred types (use "mime-like" string for file-format types, - # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred - # from the nipype interface, but you may want to be more specific, particularly - # for file types, where specifying the format also specifies the file that will be - # passed to the field in the automatically generated unittests. - in_files: generic/file+list-of + # dict[str, type] - override inferred types (use "mime-like" string for file-format types, + # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred + # from the nipype interface, but you may want to be more specific, particularly + # for file types, where specifying the format also specifies the file that will be + # passed to the field in the automatically generated unittests. + in_files: medimage/nifti1+list-of # type=list|default=[]: list of input files, possibly with subbrick selectors mask: generic/file # type=file|default=: Use this dataset as a mask @@ -58,11 +58,11 @@ outputs: rename: # dict[str, str] - fields to rename in the Pydra interface types: - # dict[str, type] - override inferred types (use "mime-like" string for file-format types, - # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred - # from the nipype interface, but you may want to be more specific, particularly - # for file types, where specifying the format also specifies the file that will be - # passed to the field in the automatically generated unittests. + # dict[str, type] - override inferred types (use "mime-like" string for file-format types, + # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred + # from the nipype interface, but you may want to be more specific, particularly + # for file types, where specifying the format also specifies the file that will be + # passed to the field in the automatically generated unittests. out_file: text/text-file # type=file: output file # type=file|default=: collect output to a file @@ -74,102 +74,102 @@ outputs: requirements: # dict[str, list[str]] - input fields that are required to be provided for the output field to be present tests: -- inputs: - # dict[str, str] - values to provide to inputs fields in the task initialisation - # (if not specified, will try to choose a sensible value) - in_files: - # type=list|default=[]: list of input files, possibly with subbrick selectors - out_file: - # type=file: output file - # type=file|default=: collect output to a file - mask: - # type=file|default=: Use this dataset as a mask - mrange: - # type=tuple|default=(, ): Means to further restrict the voxels from 'mset' so thatonly those mask values within this range (inclusive) willbe used. - demean: - # type=bool|default=False: Remove the mean from each volume prior to computing the correlation - docor: - # type=bool|default=False: Return the correlation coefficient (default). - dodot: - # type=bool|default=False: Return the dot product (unscaled). - docoef: - # type=bool|default=False: Return the least square fit coefficients {{a,b}} so that dset2 is approximately a + b\*dset1 - dosums: - # type=bool|default=False: Return the 6 numbers xbar= ybar= <(x-xbar)^2> <(y-ybar)^2> <(x-xbar)(y-ybar)> and the correlation coefficient. - dodice: - # type=bool|default=False: Return the Dice coefficient (the Sorensen-Dice index). - doeta2: - # type=bool|default=False: Return eta-squared (Cohen, NeuroImage 2008). - full: - # type=bool|default=False: Compute the whole matrix. A waste of time, but handy for parsing. - show_labels: - # type=bool|default=False: Print sub-brick labels to help identify what is being correlated. This option is useful whenyou have more than 2 sub-bricks at input. - upper: - # type=bool|default=False: Compute upper triangular matrix - num_threads: - # type=int|default=1: set number of threads - outputtype: - # type=enum|default='AFNI'|allowed['AFNI','NIFTI','NIFTI_GZ']: AFNI output filetype - args: - # type=str|default='': Additional parameters to the command - environ: - # type=dict|default={}: Environment variables - imports: - # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item - # consisting of 'module', 'name', and optionally 'alias' keys - expected_outputs: - # dict[str, str] - expected values for selected outputs, noting that tests will typically - # be terminated before they complete for time-saving reasons, and therefore - # these values will be ignored, when running in CI - timeout: 10 - # int - the value to set for the timeout in the generated test, - # after which the test will be considered to have been initialised - # successfully. Set to 0 to disable the timeout (warning, this could - # lead to the unittests taking a very long time to complete) - xfail: true - # bool - whether the unittest is expected to fail or not. Set to false - # when you are satisfied with the edits you have made to this file -- inputs: - # dict[str, str] - values to provide to inputs fields in the task initialisation - # (if not specified, will try to choose a sensible value) - in_files: - # type=list|default=[]: list of input files, possibly with subbrick selectors - dodice: 'True' - # type=bool|default=False: Return the Dice coefficient (the Sorensen-Dice index). - out_file: '"out.mask_ae_dice.txt"' - # type=file: output file - # type=file|default=: collect output to a file - imports: - # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item - # consisting of 'module', 'name', and optionally 'alias' keys - expected_outputs: - # dict[str, str] - expected values for selected outputs, noting that tests will typically - # be terminated before they complete for time-saving reasons, and therefore - # these values will be ignored, when running in CI - timeout: 10 - # int - the value to set for the timeout in the generated test, - # after which the test will be considered to have been initialised - # successfully. Set to 0 to disable the timeout (warning, this could - # lead to the unittests taking a very long time to complete) - xfail: true - # bool - whether the unittest is expected to fail or not. Set to false - # when you are satisfied with the edits you have made to this file + - inputs: + # dict[str, str] - values to provide to inputs fields in the task initialisation + # (if not specified, will try to choose a sensible value) + in_files: + # type=list|default=[]: list of input files, possibly with subbrick selectors + out_file: + # type=file: output file + # type=file|default=: collect output to a file + mask: + # type=file|default=: Use this dataset as a mask + mrange: + # type=tuple|default=(, ): Means to further restrict the voxels from 'mset' so thatonly those mask values within this range (inclusive) willbe used. + demean: + # type=bool|default=False: Remove the mean from each volume prior to computing the correlation + docor: + # type=bool|default=False: Return the correlation coefficient (default). + dodot: + # type=bool|default=False: Return the dot product (unscaled). + docoef: + # type=bool|default=False: Return the least square fit coefficients {{a,b}} so that dset2 is approximately a + b\*dset1 + dosums: + # type=bool|default=False: Return the 6 numbers xbar= ybar= <(x-xbar)^2> <(y-ybar)^2> <(x-xbar)(y-ybar)> and the correlation coefficient. + dodice: + # type=bool|default=False: Return the Dice coefficient (the Sorensen-Dice index). + doeta2: + # type=bool|default=False: Return eta-squared (Cohen, NeuroImage 2008). + full: + # type=bool|default=False: Compute the whole matrix. A waste of time, but handy for parsing. + show_labels: + # type=bool|default=False: Print sub-brick labels to help identify what is being correlated. This option is useful whenyou have more than 2 sub-bricks at input. + upper: + # type=bool|default=False: Compute upper triangular matrix + num_threads: + # type=int|default=1: set number of threads + outputtype: + # type=enum|default='AFNI'|allowed['AFNI','NIFTI','NIFTI_GZ']: AFNI output filetype + args: + # type=str|default='': Additional parameters to the command + environ: + # type=dict|default={}: Environment variables + imports: + # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item + # consisting of 'module', 'name', and optionally 'alias' keys + expected_outputs: + # dict[str, str] - expected values for selected outputs, noting that tests will typically + # be terminated before they complete for time-saving reasons, and therefore + # these values will be ignored, when running in CI + timeout: 10 + # int - the value to set for the timeout in the generated test, + # after which the test will be considered to have been initialised + # successfully. Set to 0 to disable the timeout (warning, this could + # lead to the unittests taking a very long time to complete) + xfail: true + # bool - whether the unittest is expected to fail or not. Set to false + # when you are satisfied with the edits you have made to this file + - inputs: + # dict[str, str] - values to provide to inputs fields in the task initialisation + # (if not specified, will try to choose a sensible value) + in_files: + # type=list|default=[]: list of input files, possibly with subbrick selectors + dodice: "True" + # type=bool|default=False: Return the Dice coefficient (the Sorensen-Dice index). + out_file: '"out.mask_ae_dice.txt"' + # type=file: output file + # type=file|default=: collect output to a file + imports: + # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item + # consisting of 'module', 'name', and optionally 'alias' keys + expected_outputs: + # dict[str, str] - expected values for selected outputs, noting that tests will typically + # be terminated before they complete for time-saving reasons, and therefore + # these values will be ignored, when running in CI + timeout: 10 + # int - the value to set for the timeout in the generated test, + # after which the test will be considered to have been initialised + # successfully. Set to 0 to disable the timeout (warning, this could + # lead to the unittests taking a very long time to complete) + xfail: true + # bool - whether the unittest is expected to fail or not. Set to false + # when you are satisfied with the edits you have made to this file doctests: -- cmdline: 3dDot -dodice functional.nii[0] structural.nii |& tee out.mask_ae_dice.txt - # str - the expected cmdline output - inputs: - # dict[str, str] - name-value pairs for inputs to be provided to the doctest. - # If the field is of file-format type and the value is None, then the - # '.mock()' method of the corresponding class is used instead. - in_files: - # type=list|default=[]: list of input files, possibly with subbrick selectors - dodice: 'True' - # type=bool|default=False: Return the Dice coefficient (the Sorensen-Dice index). - out_file: '"out.mask_ae_dice.txt"' - # type=file: output file - # type=file|default=: collect output to a file - imports: - # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item - # consisting of 'module', 'name', and optionally 'alias' keys - directive: - # str - any doctest directive to place on the cmdline call, e.g. # doctest: +ELLIPSIS + - cmdline: 3dDot -dodice functional.nii[0] structural.nii |& tee out.mask_ae_dice.txt + # str - the expected cmdline output + inputs: + # dict[str, str] - name-value pairs for inputs to be provided to the doctest. + # If the field is of file-format type and the value is None, then the + # '.mock()' method of the corresponding class is used instead. + in_files: + # type=list|default=[]: list of input files, possibly with subbrick selectors + dodice: "True" + # type=bool|default=False: Return the Dice coefficient (the Sorensen-Dice index). + out_file: '"out.mask_ae_dice.txt"' + # type=file: output file + # type=file|default=: collect output to a file + imports: + # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item + # consisting of 'module', 'name', and optionally 'alias' keys + directive: + # str - any doctest directive to place on the cmdline call, e.g. # doctest: +ELLIPSIS From b9a191d291d49865a25bf88faee414166fb31f41 Mon Sep 17 00:00:00 2001 From: Neurodesk User Date: Thu, 23 Nov 2023 06:33:46 +0000 Subject: [PATCH 2/2] edited first 3 alphabetically yaml files aboverlap, afnitonifti, alignepianat. However proper test files were not used. --- nipype-auto-conv/specs/a_boverlap.yaml | 188 +++++++++--------- nipype-auto-conv/specs/afn_ito_nifti.yaml | 24 +-- nipype-auto-conv/specs/align_epi_anat_py.yaml | 24 ++- 3 files changed, 115 insertions(+), 121 deletions(-) diff --git a/nipype-auto-conv/specs/a_boverlap.yaml b/nipype-auto-conv/specs/a_boverlap.yaml index d36bb44..e34ed68 100644 --- a/nipype-auto-conv/specs/a_boverlap.yaml +++ b/nipype-auto-conv/specs/a_boverlap.yaml @@ -7,10 +7,10 @@ # ---- # Output (to screen) is a count of various things about how # the automasks of datasets A and B overlap or don't overlap. -# +# # For complete details, see the `3dABoverlap Documentation. # `_ -# +# # Examples # -------- # >>> from nipype.interfaces import afni @@ -21,8 +21,8 @@ # >>> aboverlap.cmdline # '3dABoverlap functional.nii structural.nii |& tee out.mask_ae_overlap.txt' # >>> res = aboverlap.run() # doctest: +SKIP -# -# +# +# task_name: ABoverlap nipype_name: ABoverlap nipype_module: nipype.interfaces.afni.utils @@ -32,11 +32,11 @@ inputs: rename: # dict[str, str] - fields to rename in the Pydra interface types: - # dict[str, type] - override inferred types (use "mime-like" string for file-format types, - # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred - # from the nipype interface, but you may want to be more specific, particularly - # for file types, where specifying the format also specifies the file that will be - # passed to the field in the automatically generated unittests. + # dict[str, type] - override inferred types (use "mime-like" string for file-format types, + # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred + # from the nipype interface, but you may want to be more specific, particularly + # for file types, where specifying the format also specifies the file that will be + # passed to the field in the automatically generated unittests. in_file_a: medimage/nifti1 # type=file|default=: input file A in_file_b: medimage/nifti1 @@ -55,11 +55,11 @@ outputs: rename: # dict[str, str] - fields to rename in the Pydra interface types: - # dict[str, type] - override inferred types (use "mime-like" string for file-format types, - # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred - # from the nipype interface, but you may want to be more specific, particularly - # for file types, where specifying the format also specifies the file that will be - # passed to the field in the automatically generated unittests. + # dict[str, type] - override inferred types (use "mime-like" string for file-format types, + # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred + # from the nipype interface, but you may want to be more specific, particularly + # for file types, where specifying the format also specifies the file that will be + # passed to the field in the automatically generated unittests. out_file: text/text-file # type=file: output file # type=file|default=: collect output to a file @@ -71,86 +71,82 @@ outputs: requirements: # dict[str, list[str]] - input fields that are required to be provided for the output field to be present tests: -- inputs: - # dict[str, str] - values to provide to inputs fields in the task initialisation - # (if not specified, will try to choose a sensible value) - in_file_a: - # type=file|default=: input file A - in_file_b: - # type=file|default=: input file B - out_file: - # type=file: output file - # type=file|default=: collect output to a file - no_automask: - # type=bool|default=False: consider input datasets as masks - quiet: - # type=bool|default=False: be as quiet as possible (without being entirely mute) - verb: - # type=bool|default=False: print out some progress reports (to stderr) - num_threads: - # type=int|default=1: set number of threads - outputtype: - # type=enum|default='AFNI'|allowed['AFNI','NIFTI','NIFTI_GZ']: AFNI output filetype - args: - # type=str|default='': Additional parameters to the command - environ: - # type=dict|default={}: Environment variables - imports: - # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item - # consisting of 'module', 'name', and optionally 'alias' keys - expected_outputs: - # dict[str, str] - expected values for selected outputs, noting that tests will typically - # be terminated before they complete for time-saving reasons, and therefore - # these values will be ignored, when running in CI - timeout: 10 - # int - the value to set for the timeout in the generated test, - # after which the test will be considered to have been initialised - # successfully. Set to 0 to disable the timeout (warning, this could - # lead to the unittests taking a very long time to complete) - xfail: true - # bool - whether the unittest is expected to fail or not. Set to false - # when you are satisfied with the edits you have made to this file -- inputs: - # dict[str, str] - values to provide to inputs fields in the task initialisation - # (if not specified, will try to choose a sensible value) - in_file_a: - # type=file|default=: input file A - in_file_b: - # type=file|default=: input file B - out_file: ' "out.mask_ae_overlap.txt"' - # type=file: output file - # type=file|default=: collect output to a file - imports: - # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item - # consisting of 'module', 'name', and optionally 'alias' keys - expected_outputs: - # dict[str, str] - expected values for selected outputs, noting that tests will typically - # be terminated before they complete for time-saving reasons, and therefore - # these values will be ignored, when running in CI - timeout: 10 - # int - the value to set for the timeout in the generated test, - # after which the test will be considered to have been initialised - # successfully. Set to 0 to disable the timeout (warning, this could - # lead to the unittests taking a very long time to complete) - xfail: true - # bool - whether the unittest is expected to fail or not. Set to false - # when you are satisfied with the edits you have made to this file + - inputs: + # dict[str, str] - values to provide to inputs fields in the task initialisation + # (if not specified, will try to choose a sensible value) + in_file_a: + # type=file|default=: input file A + in_file_b: + # type=file|default=: input file B + # out_file: + # type=file: output file + # type=file|default=: collect output to a file + no_automask: "False" + # type=bool|default=False: consider input datasets as masks + quiet: "False" + # type=bool|default=False: be as quiet as possible (without being entirely mute) + verb: "False" + # type=bool|default=False: print out some progress reports (to stderr) + num_threads: 1 + # type=int|default=1: set number of threads + outputtype: + # type=enum|default='AFNI'|allowed['AFNI','NIFTI','NIFTI_GZ']: AFNI output filetype + imports: + # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item + # consisting of 'module', 'name', and optionally 'alias' keys + expected_outputs: + # dict[str, str] - expected values for selected outputs, noting that tests will typically + # be terminated before they complete for time-saving reasons, and therefore + # these values will be ignored, when running in CI + timeout: 10 + # int - the value to set for the timeout in the generated test, + # after which the test will be considered to have been initialised + # successfully. Set to 0 to disable the timeout (warning, this could + # lead to the unittests taking a very long time to complete) + xfail: true + # bool - whether the unittest is expected to fail or not. Set to false + # when you are satisfied with the edits you have made to this file + - inputs: + # dict[str, str] - values to provide to inputs fields in the task initialisation + # (if not specified, will try to choose a sensible value) + in_file_a: + # type=file|default=: input file A + in_file_b: + # type=file|default=: input file B + # out_file: + # type=file: output file + # type=file|default=: collect output to a file + imports: + # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item + # consisting of 'module', 'name', and optionally 'alias' keys + expected_outputs: + # dict[str, str] - expected values for selected outputs, noting that tests will typically + # be terminated before they complete for time-saving reasons, and therefore + # these values will be ignored, when running in CI + timeout: 10 + # int - the value to set for the timeout in the generated test, + # after which the test will be considered to have been initialised + # successfully. Set to 0 to disable the timeout (warning, this could + # lead to the unittests taking a very long time to complete) + xfail: true + # bool - whether the unittest is expected to fail or not. Set to false + # when you are satisfied with the edits you have made to this file doctests: -- cmdline: 3dABoverlap functional.nii structural.nii |& tee out.mask_ae_overlap.txt - # str - the expected cmdline output - inputs: - # dict[str, str] - name-value pairs for inputs to be provided to the doctest. - # If the field is of file-format type and the value is None, then the - # '.mock()' method of the corresponding class is used instead. - in_file_a: - # type=file|default=: input file A - in_file_b: - # type=file|default=: input file B - out_file: ' "out.mask_ae_overlap.txt"' - # type=file: output file - # type=file|default=: collect output to a file - imports: - # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item - # consisting of 'module', 'name', and optionally 'alias' keys - directive: - # str - any doctest directive to place on the cmdline call, e.g. # doctest: +ELLIPSIS + - cmdline: 3dABoverlap functional.nii structural.nii |& tee out.mask_ae_overlap.txt + # str - the expected cmdline output + inputs: + # dict[str, str] - name-value pairs for inputs to be provided to the doctest. + # If the field is of file-format type and the value is None, then the + # '.mock()' method of the corresponding class is used instead. + in_file_a: + # type=file|default=: input file A + in_file_b: + # type=file|default=: input file B + out_file: ' "out.mask_ae_overlap.txt"' + # type=file: output file + # type=file|default=: collect output to a file + imports: + # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item + # consisting of 'module', 'name', and optionally 'alias' keys + directive: + # str - any doctest directive to place on the cmdline call, e.g. # doctest: +ELLIPSIS diff --git a/nipype-auto-conv/specs/afn_ito_nifti.yaml b/nipype-auto-conv/specs/afn_ito_nifti.yaml index a644af5..28aaabb 100644 --- a/nipype-auto-conv/specs/afn_ito_nifti.yaml +++ b/nipype-auto-conv/specs/afn_ito_nifti.yaml @@ -73,27 +73,23 @@ tests: # (if not specified, will try to choose a sensible value) in_file: # type=file|default=: input file to 3dAFNItoNIFTI - out_file: + #out_file: # type=file: output file # type=file|default=: output image file name - pure: + pure: "False" # type=bool|default=False: Do NOT write an AFNI extension field into the output file. Only use this option if needed. You can also use the 'nifti_tool' program to strip extensions from a file. - denote: + denote: "False" # type=bool|default=False: When writing the AFNI extension field, remove text notes that might contain subject identifying information. - oldid: + oldid: "False" # type=bool|default=False: Give the new dataset the input datasets AFNI ID code. - newid: + newid: "False" # type=bool|default=False: Give the new dataset a new AFNI ID code, to distinguish it from the input dataset. - num_threads: + num_threads: 1 # type=int|default=1: set number of threads - outputtype: + outputtype: "'NIFTI'" # type=enum|default='AFNI'|allowed['AFNI','NIFTI','NIFTI_GZ']: AFNI output filetype - args: - # type=str|default='': Additional parameters to the command - environ: - # type=dict|default={}: Environment variables imports: - # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item + # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item # consisting of 'module', 'name', and optionally 'alias' keys expected_outputs: # dict[str, str] - expected values for selected outputs, noting that tests will typically @@ -112,11 +108,11 @@ tests: # (if not specified, will try to choose a sensible value) in_file: # type=file|default=: input file to 3dAFNItoNIFTI - out_file: ' "afni_output.nii"' + #out_file: # type=file: output file # type=file|default=: output image file name imports: - # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item + # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item # consisting of 'module', 'name', and optionally 'alias' keys expected_outputs: # dict[str, str] - expected values for selected outputs, noting that tests will typically diff --git a/nipype-auto-conv/specs/align_epi_anat_py.yaml b/nipype-auto-conv/specs/align_epi_anat_py.yaml index 50367a8..34bdc6b 100644 --- a/nipype-auto-conv/specs/align_epi_anat_py.yaml +++ b/nipype-auto-conv/specs/align_epi_anat_py.yaml @@ -125,29 +125,31 @@ tests: # type=file|default=: EPI dataset to align anat: # type=file|default=: name of structural dataset - epi_base: + epi_base: + #Blank is mapped to None # type=traitcompound|default=None: the epi base used in alignmentshould be one of (0/mean/median/max/subbrick#) - anat2epi: + anat2epi: "False" # type=bool|default=False: align anatomical to EPI dataset (default) - epi2anat: + epi2anat: "False" # type=bool|default=False: align EPI to anatomical dataset save_skullstrip: # type=bool|default=False: save skull-stripped (not aligned) - suffix: + suffix: "'_al'" # type=str|default='_al': append suffix to the original anat/epi dataset to usein the resulting dataset names (default is "_al") - epi_strip: + epi_strip: "'3dSkullStrip'" # type=enum|default='3dSkullStrip'|allowed['3dAutomask','3dSkullStrip','None']: method to mask brain in EPI datashould be one of[3dSkullStrip]/3dAutomask/None) - volreg: + volreg: "'on'" # type=enum|default='on'|allowed['off','on']: do volume registration on EPI dataset before alignmentshould be 'on' or 'off', defaults to 'on' - tshift: + tshift: "'on'" # type=enum|default='on'|allowed['off','on']: do time shifting of EPI dataset before alignmentshould be 'on' or 'off', defaults to 'on' - outputtype: + outputtype: "'AFNI'" # type=enum|default='AFNI'|allowed['AFNI','NIFTI','NIFTI_GZ']: AFNI output filetype - py27_path: + ###delete the following 3:### + #py27_path: # type=traitcompound|default='python2': - args: + #args: # type=str|default='': Additional parameters to the command - environ: + #environ: # type=dict|default={}: Environment variables imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item