From ecfbf73e50c449648fd9b5bf1d206cd697117398 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Wed, 6 Mar 2019 12:18:21 +0100 Subject: [PATCH 1/2] =?UTF-8?q?dcm2nii=20=E2=86=92=20dcm2niix?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Change dicom converter recommendation from obsolete dcm2nii to modern dcm2niix. --- src/02-common-principles.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/02-common-principles.md b/src/02-common-principles.md index 2138fe03b6..bbe754ea61 100644 --- a/src/02-common-principles.md +++ b/src/02-common-principles.md @@ -206,7 +206,7 @@ possible. Since the NIfTI standard offers limited support for the various image acquisition parameters available in DICOM files, we RECOMMEND that users provide additional meta information extracted from DICOM files in a sidecar JSON file (with the same filename as the `.nii[.gz]` file, but with a `.json` extension). -Extraction of BIDS compatible metadata can be performed using [dcm2nii](https://www.nitrc.org/projects/dcm2nii/) +Extraction of BIDS compatible metadata can be performed using [dcm2niix](https://www.nitrc.org/projects/dcm2nii/) and [dicm2nii](http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter/content/dicm2nii.m) DICOM to NIfTI converters. A provided [validator](https://github.com/bids-standard/bids-validator) From 5ad238bb0566c735188f1c877683130251634a24 Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Wed, 6 Mar 2019 08:26:31 -0800 Subject: [PATCH 2/2] updated link to dcm2niix --- src/02-common-principles.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/02-common-principles.md b/src/02-common-principles.md index bbe754ea61..ecaf302dc4 100644 --- a/src/02-common-principles.md +++ b/src/02-common-principles.md @@ -206,7 +206,7 @@ possible. Since the NIfTI standard offers limited support for the various image acquisition parameters available in DICOM files, we RECOMMEND that users provide additional meta information extracted from DICOM files in a sidecar JSON file (with the same filename as the `.nii[.gz]` file, but with a `.json` extension). -Extraction of BIDS compatible metadata can be performed using [dcm2niix](https://www.nitrc.org/projects/dcm2nii/) +Extraction of BIDS compatible metadata can be performed using [dcm2niix](https://github.com/rordenlab/dcm2niix) and [dicm2nii](http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter/content/dicm2nii.m) DICOM to NIfTI converters. A provided [validator](https://github.com/bids-standard/bids-validator)