From d47e96660600e170689a8499069ea8c6ddd846d6 Mon Sep 17 00:00:00 2001 From: Bogdan Petre Date: Fri, 31 May 2024 23:19:44 -0400 Subject: [PATCH 1/4] FILMGLS gifti output support for surface mode --- nipype/interfaces/fsl/base.py | 5 +++-- nipype/interfaces/fsl/model.py | 8 ++++++++ 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/nipype/interfaces/fsl/base.py b/nipype/interfaces/fsl/base.py index 7be822e4f2..ca3a9ba486 100644 --- a/nipype/interfaces/fsl/base.py +++ b/nipype/interfaces/fsl/base.py @@ -57,6 +57,7 @@ class Info(PackageInfo): "NIFTI_PAIR": ".img", "NIFTI_GZ": ".nii.gz", "NIFTI_PAIR_GZ": ".img.gz", + "GIFTI": ".func.gii" } if os.getenv("FSLDIR"): @@ -72,8 +73,8 @@ def output_type_to_ext(cls, output_type): Parameters ---------- - output_type : {'NIFTI', 'NIFTI_GZ', 'NIFTI_PAIR', 'NIFTI_PAIR_GZ'} - String specifying the output type. + output_type : {'NIFTI', 'NIFTI_GZ', 'NIFTI_PAIR', 'NIFTI_PAIR_GZ', 'GIFTI'} + String specifying the output type. Note: limited GIFTI support. Returns ------- diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py index 60057d69db..2a148025f5 100644 --- a/nipype/interfaces/fsl/model.py +++ b/nipype/interfaces/fsl/model.py @@ -812,12 +812,20 @@ class FILMGLS(FSLCommand): _cmd = "film_gls" input_spec = FILMGLSInputSpec output_spec = FILMGLSOutputSpec + if Info.version() and LooseVersion(Info.version()) > LooseVersion("5.0.6"): input_spec = FILMGLSInputSpec507 output_spec = FILMGLSOutputSpec507 elif Info.version() and LooseVersion(Info.version()) > LooseVersion("5.0.4"): input_spec = FILMGLSInputSpec505 + def __init__(self, **inputs): + super(FILMGLS, self).__init__(**inputs) + if Info.version() and LooseVersion(Info.version()) > LooseVersion("5.0.6"): + if 'output_type' not in inputs: + if isdefined(self.inputs.mode) and self.inputs.mode == 'surface': + self.inputs.output_type = 'GIFTI' + def _get_pe_files(self, cwd): files = None if isdefined(self.inputs.design_file): From cd9dbdab6c33524bdf14683ef198e1fe08de5a5d Mon Sep 17 00:00:00 2001 From: Bogdan Petre Date: Fri, 31 May 2024 23:24:56 -0400 Subject: [PATCH 2/4] addition to contributor list --- .zenodo.json | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.zenodo.json b/.zenodo.json index d01d2409e3..013012a5bf 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -924,7 +924,12 @@ "affiliation": "MIT, HMS", "name": "Ghosh, Satrajit", "orcid": "0000-0002-5312-6729" - } + }, + { + "affiliation": "Department of Psychological and Brain Sciences, Dartmouth College", + "name": "Petre, Bogdan", + "orcid": "0000-0002-8437-168X" + }, ], "keywords": [ "neuroimaging", From a2f78c89b61eb3cbe726d354cd8261d759546ae2 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Sun, 6 Oct 2024 12:49:53 -0400 Subject: [PATCH 3/4] Update nipype/interfaces/fsl/base.py --- nipype/interfaces/fsl/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/fsl/base.py b/nipype/interfaces/fsl/base.py index ca3a9ba486..61010ee9a0 100644 --- a/nipype/interfaces/fsl/base.py +++ b/nipype/interfaces/fsl/base.py @@ -57,7 +57,7 @@ class Info(PackageInfo): "NIFTI_PAIR": ".img", "NIFTI_GZ": ".nii.gz", "NIFTI_PAIR_GZ": ".img.gz", - "GIFTI": ".func.gii" + "GIFTI": ".func.gii", } if os.getenv("FSLDIR"): From 101945574d3088fb89df78404134bfa435244740 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Sun, 6 Oct 2024 12:50:20 -0400 Subject: [PATCH 4/4] Update .zenodo.json --- .zenodo.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.zenodo.json b/.zenodo.json index 013012a5bf..a0823fef52 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -929,7 +929,7 @@ "affiliation": "Department of Psychological and Brain Sciences, Dartmouth College", "name": "Petre, Bogdan", "orcid": "0000-0002-8437-168X" - }, + } ], "keywords": [ "neuroimaging",