brc_pipeline - v1.7.2

• The IDP extraction pipeline has been updated to include the Freesurfer IDPs.

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Published by Alirezamnk 6 months ago

brc_pipeline - v1.7.1

• A bug is fixed in the multi-channel tissue segmentation in the structural preprocessing pipeline.

- Shell
Published by Alirezamnk 9 months ago

brc_pipeline - v1.7.0

• An option is added to the dMRI processing pipeline to perform ringing artefact removal.
• The interpolation option in EDDY for the dMRI pipeline has been changed from trilinear to spline.
• New QC IDPs have been added to the IDP extraction pipeline.
• Bug fixed and performance improved.

- Shell
Published by Alirezamnk over 1 year ago

brc_pipeline - v1.6.9

• Option --alps is added to the diffusion pipeline to perform ALPS processing.
• Option --skip_preproc is added to the diffusion pipeline to skip the pre-processing of the data and just add new post-processing features to the existing processed data.
• A bug has been fixed in the functional processing pipeline.

- Shell
Published by Alirezamnk over 1 year ago

brc_pipeline - v1.6.8

• Fixed perfusion pipeline to deal with both .nii (NIFTI) and .nii.gz (NIFTI_GZ) file configurations of FSL

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Published by stefanpsz over 1 year ago

brc_pipeline - v1.6.7

• Modified perfusion pipeline to work with single-TI difference and calibration images separately and perform the quantification

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Published by stefanpsz over 1 year ago

brc_pipeline - v1.6.6

• Performance improved in all the pipelines.
• Cuda version has been updated for functional and diffusion pipelines.
• The Freesurfer and Fastsurfer versions have been updated.
• The FSL version has been updated.

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Published by Alirezamnk over 1 year ago

brc_pipeline - v1.6.5

• The diffusion_pipeline has been modified to be compatible with FSL6.0.6

- Shell
Published by Alirezamnk almost 2 years ago

brc_pipeline - v1.6.4

• The cuda version of the eddy (for diffusion pipeline) is updated to cuda9.1
• The cuda version of cuDIMOT updated to cuda12.2.2
• The IDP extraction pipeline has been updated to fix some problems

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Published by Alirezamnk almost 2 years ago

brc_pipeline - v1.6.3

• A new option (--dki) is added to the diffusion pipeline to produce microstructural maps using the diffusion kurtosis model.
• A new option (--wmti) is added to the diffusion pipeline to generate microstructural maps using the white matter tract integrity model.
• A new option (-mppca) is added to the diffusion pipeline, performing denoising using Marcenko-Pastur PCA.
• A new option (--use_topup) is added to the diffusion pipeline, ignoring the TOPUP step and using the previously provided files for the TOPUP step.

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Published by Alirezamnk over 2 years ago

brc_pipeline - v1.6.2

• The --dtimaxshell argument is added to the Diffusion Pipeline to specify the maximum bval in multishell data.
• The DTI model uses this maximum bval to calculate the microstructural maps.
• The cuDIMOT code has been modified to be compatible with the new option.

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Published by Alirezamnk about 3 years ago

brc_pipeline - v1.6.1

• The IDP_extraction pipeline has been updated to add the new microstructural IDPs added to the FSL 6.0.5

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Published by Alirezamnk about 3 years ago

brc_pipeline - v1.6.0

• reorient the T1 data to the standard orientation.
• A bug fixed in the IDP extraction pipeline.

- Shell
Published by Alirezamnk over 3 years ago

brc_pipeline - v1.5.9

• Bug fixed in Diffusion Pipeline for TBSS and NODDI analysis.
• Performance improved.

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Published by Alirezamnk over 3 years ago

brc_pipeline - v1.5.8

• List of the IDPs has been updated

- Shell
Published by Alirezamnk over 3 years ago

brc_pipeline - v1.5.7

• The --noddi option is added to the diffusion pipeline.
• The --tbss option is added to the diffusion pipeline.
• The IDP extraction pipeline has been updated to extract the diffusion IDPs like TBSS of FA, MD, MO, ICVF, and so on.
• Some bugs fixed and performance improvements in the diffsuion pipeline.

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Published by Alirezamnk over 3 years ago

brc_pipeline - v1.5.6

• Bug fixed and performance improved
• dataisshelled is added to the diffusion pipeline, internally (EDDY).
• --delvolumes is added to the functional processing pipeline to delete the first N volumes of the input 4D fMRI data.
• Now the users can run the pipeline on any path and no longer need to be in the pipeline path.

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Published by Alirezamnk over 3 years ago

brc_pipeline -

• For high-quality data, the time limit in the diffusion preprocessing pipeline is modified.
• A new option ("--clean") is added to the fMRI processing pipeline to clean middle steps generated files.
• A new type of registration is added to the structural preprocessing pipeline. The new feature (--regtype 3) uses ANTs to transform T1 and T2 data into the standard space.
• Improving the performance of the structural preprocessing pipeline.

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Published by Alirezamnk over 4 years ago

brc_pipeline - v1.5.4

Improvement to the ASL pipeline: Use BBR for registration between T1 and ASL image

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Published by stefanpsz over 4 years ago

brc_pipeline - v1.5.3

• Bug fixes and performance improvements in the IDP extractor pipeline.
• --t2lesion is added to the structural processing pipeline. This option takes a labeled lesion mask in t2 space as an input and will register it into T1 space.

- Shell
Published by Alirezamnk over 4 years ago

brc_pipeline - v1.5.2

• The structural pipeline has been updated to improve its performance and to be more compatible with the IDP extractor.
• The IDP extractor pipeline now can be run on the HPC.

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Published by Alirezamnk over 4 years ago

brc_pipeline - v1.5.1

• The 1st version of the IDP extractor is released to extract the Imaging Derived Phenotypes (IDPs) of T1 and T2 images.
• Two steps are added to the processing of the anatomical MRI data; SIENAX for T1 data and BIANCA for T2 data.

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Published by Alirezamnk almost 5 years ago

brc_pipeline - v1.5.0

• A bug is fixed in the pre-processing of high-resolution dMRI data.
• The procedure of pre-processing of T1/T2w data when (RegType = 1) is modified.

- Shell
Published by Alirezamnk almost 5 years ago

brc_pipeline - v1.4.9

• A bug is fixed on the registration of T2w images to the MNI space.
• A --hires option is added to the dMRI pre-processing pipeline to increase the time limits and the amount of memory that the pipeline needs to process the high resoloution data.

- Shell
Published by Alirezamnk about 5 years ago

brc_pipeline - v1.4.8

• A bug is fixed on the fMRI pre-processing pipeline to call EDDY on the cluster mode.

- Shell
Published by Alirezamnk about 5 years ago

brc_pipeline - v1.4.7

• Fixed bug with perfusion pipeline when partial volume correction method is set to NONE.
• On the 'BRCstructuralpipeline' an option is added to just apply a linear registration for the registration of the T1/T2 data to standard space.

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Published by stefanpsz about 5 years ago

brc_pipeline - V1.4.6

• In the functional pre-processing pipeline, EDDY has been modified to support the new versions of FSL.
• Some SetUpBRCPipeline.sh file is added to the repository as an example file to setup the pipeline in our internal clusters like Chilli, Pepper, and Augusta.
• A bug is fixed in the diffusion pre-processing pipeline when you use FSL 6.0.3.

- Shell
Published by Alirezamnk about 5 years ago

brc_pipeline - v1.4.5

• Added cluster support on perfusion pipeline

- Shell
Published by stefanpsz about 5 years ago

brc_pipeline - V1.4.4

• option --nofr2z is added to the fmri_group_analysis.sh pipeline to do not convert the correlation values to Fisher's Z values.
• performance improvement in the fmri_group_analysis.sh pipeline.

- Shell
Published by Alirezamnk over 5 years ago

brc_pipeline - v1.4.3

• an option (--gmroi) is added to the BRC_func_group_analysis to add the whole GM as an extra ROI to the functional connectivity analysis.

- Shell
Published by Alirezamnk over 5 years ago

brc_pipeline - v1.4.2

Bugfixes in mLTS PVC

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Published by stefanpsz over 5 years ago

brc_pipeline - v1.4.1

• mLTS partial volume correction
  • Bugfixes
  • Incorporated weighted GM+WM output

- Shell
Published by stefanpsz over 5 years ago

brc_pipeline - v1.4.0

• First version of the Perfusion pipeline has been incorporated
  • Modified partial least squares based partial volume correction

- Shell
Published by stefanpsz over 5 years ago

brc_pipeline - 05-May-2020

• In the diffusion preprocessing pipeline an option is added which accounts the --estimate_move_by_susceptibility option recently added to the Eddy pipeline.

- Shell
Published by Alirezamnk almost 6 years ago

brc_pipeline - 13-Feb-2020

• Bugs are fixed in all the pipelines. Most of them were about the required time to finish the jobs in the clusters.

- Shell
Published by Alirezamnk about 6 years ago

brc_pipeline - 22-Jan-2020

• in this version, a DOI is added to the BRC_Pipeline.

- Shell
Published by Alirezamnk about 6 years ago

brc_pipeline - 22-Jul-2019

• In the fMRIgroupanalysis pipeline, now the users can specify their own atlas for the functional analysis.
• Some bugs are modified.

- Shell
Published by Alirezamnk over 6 years ago

brc_pipeline - 17-Jul-2019

• The new version of the pipeline can run on the HPC clusters. The users cannot see any differences between the usage of the pipelines between the current version and the previous versions and everything managed internally.

- Shell
Published by Alirezamnk over 6 years ago

brc_pipeline - 21-May-2019

• Quality control of fMRI data based on DVARS is added to the pipeline.
• Some minor improvements on the output images and motion parameters of Eddy in the fMRI processing project.
• Some minor improvements on the outputs of MCFLIRT are added to the fMRI processing project.

- Shell
Published by Alirezamnk almost 7 years ago

brc_pipeline - 10-May-2019

• Some minor bugs are fixed in the BRCfuncgroup_analysis project.

- Shell
Published by Alirezamnk almost 7 years ago

brc_pipeline - 19-Feb-2019

• Some improvements in the fmri_group_analysis project.
• An option is added to the fMRI_preprocproject that the user can specify the output folder path for the functional analysis.

- Shell
Published by Alirezamnk about 7 years ago

brc_pipeline - 30-Jan-2019

• AAL atlas is added to BRC_func_group_analysis project

- Shell
Published by Alirezamnk about 7 years ago

brc_pipeline - 22-Jan-2019

• some improvements in the registration of diffusion data to structural and standard space in BRC_diffusion_pipeline project.
• The output files in the reg folder of BRC_diffusion_pipeline project are reorganized and all of them are in the processed folder.

- Shell
Published by Alirezamnk about 7 years ago

brc_pipeline - 14-Jan-2019

• Some minor bugs are fixed in the fmri_group_analysis project.

- Shell
Published by Alirezamnk about 7 years ago

brc_pipeline - 07-Jan-2019

• A minor bug is fixed in the linear registration in the BRC_structural_pipeline project.
• A minor bug is fixed in the GLM analysis of the BRC_func_group_pipeline project.
• Some input/output names are changed in the BRC_functional_pipeline project.

- Shell
Published by Alirezamnk about 7 years ago

brc_pipeline - 21-Dec-2018

• A bug fixed in the diffusion linear registration in the BRC_diffusion_pipeline project.
• Some options flag are revised to be consistent within all the preprocessing pipeline.
• An option is added to turn off AROMA in the BRC_functional_pipeline project.

- Shell
Published by Alirezamnk about 7 years ago

brc_pipeline - 18-Dec-2018

• The skull stripping procedure is completely revised in the struc_preproc.sh pipeline and it can affect the results of fMRI and dMRI pre-processing.
• the defacing option is added to the struc_preproc.sh pipeline.
• Preprocessing of T1w data using Freesurfer is updated and it can use T2w data to enhance the results of T1w pre-processing.

- Shell
Published by Alirezamnk about 7 years ago

brc_pipeline - 12-Dec-2018

• The BRC_func_group_analysis pipeline is added to the BRC_Pipeline.
• Some reference network maps are added to the global folder.

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Published by Alirezamnk about 7 years ago

brc_pipeline - 05-Dec-2018

• TOPUP config file is updated to support dMRI data with an odd number of slices in dMRI_preproc.sh project.
• A minor bug is solved to create AROMA folder in fMRI_preproc.sh project.

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Published by Alirezamnk about 7 years ago

brc_pipeline - 04-Dec-2018

• motion correction using MCFLIRT is updated to support MCFLIRT with 6 and 12 degrees of freedom in fMRI_preproc.sh pipeline.
• Intensity normalization and bias filed removal procedure is refined in fMRI_preproc.sh pipeline.
• Some minor bugs are fixed in fMRI_preproc.sh pipeline.

- Shell
Published by Alirezamnk about 7 years ago

brc_pipeline - 27-Nov-2018

• Data logging compatibility commands are added to the fMRI_preproc.sh project.
• The output files/folders are completely redesigned in the fMRI_preproc.sh project.
• The registration folder files for T1w and T2w data are revised in struct_preproc.sh project.
• A data2std folder is added to the struct_preproc.sh project.
• Data logging compatibility commands are added to the dMRI_preproc.sh project.
• The output files/folders are completely redesigned in the dMRI_preproc.sh project.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 24-Nov-2018

• Command logging is added to the `struc_preproc.sh' pipeline.
• Output folders and files are renamed and reorganized in struc_preproc.sh project.
• Cropping of the T1w images is edited and an option is added to skip the cropping in struc_preproc.sh project.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 16-Nov-2019

• The default value for Combined match is added to the dMRI_preproc.sh.
• The extension of eddy_combine is changed in the dMRI_preproc.sh.
• The eddy post processing is updated to solve a bug when we do not have SE data in the dMRI_preproc.sh.
• An option is added to have different echo spacing for SE and fMRI data in the fMRI_preproc.sh.
• Eddy is updated to support different Echo spacing for fMRI and SE in the fMRI_preproc.sh.
• TOPUP config is updated to run for the datasets with an odd number of slices.
• TOPUP updated to support an odd number of slices

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 05-Nov-2019

• Cuda setup path is added to the SetUpBRCPipeline.sh.
• A bug fixed with those data sets that have more than volume for the SE positive and negative phase encoding in BRC_functional_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 30-Oct-2018

• The spatial smoothing, intensity normalization, and temporal filtering procedure are modified in BRC_functional_pipeline.
  • A bug fixed in cropping the T1w images is fixed in BRC_structural_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 29-Oct-2018

• SetUpBRCPipeline.sh file is modified to automatically set up FSL and FreeSurfer.
• Spatial smoothing procedure is modified in the BRC_functional_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 27-Oct-2018

• Show version function is modified in all of the preprocessing pipelines.
• A bug fixed in cropping the head bottom in some T1w images in BRC_structural_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 25-Oct-2018

• The Bias field correction strategy is modified in the BRC_structural_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 24-Oct-2018

• Bug fixed in the Eddy processing when you do not choose TOPUP as an EPI distortion correction in BRC_functional_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 23-Oct-2018

• Name of the functional processing pipeline is changed to BRC_functional_pipeline.
• Structoral2functional transformation is generated and added to the reg folder in the BRC_functional_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 16-Oct-2018

• Minor bug fixed in generation of brain mask in functional space in BRC_functional_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 15-Oct-2018

• The order of the pipeline is modified and One Step Resampling is moved to the last step in BRC_functional_pipeline.
• The output files are modified BRC_functional_pipeline.
• One Step Resampling strategy, inputs and outputs are modified BRC_functional_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 12-Oct-2018

• Spatial smoothing strategy is midified in BRC_functional_pipeline.
• Bug fixed in One-Step-Resampling in BRC_functional_pipeline.
• Bug fixed in Eddy in BRC_functional_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 11-Oct-2018

• Eddy inputs and outputs are modified in BRC_functional_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 10-Oct-2018

• Bug fixed in input of intensity normalization in BRC_functional_pipeline.
• T1 Bias correction is modified in BRC_structural_pipeline.
• Temporal Filtering is added as an option to the BRC_diffusion_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 09-Oct-2018

• Bug fixed in Data organization inputs.
• Bug fixed in Intensity Normalization inputs.
• Run Time is added to the BRC_functional_pipeline and BRC_diffusion_pipeline.
• Bug fixed in Eddy processing in BRC_functional_pipeline project.
• Extracting TR from the data. Option --tr in BRC_functional_pipeline project is deleted.
• The output results of functional processing are organized in BRC_functional_pipeline project.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 08-Oct-2018

• Bug fixed in running Freesurfer and saving the outputs in BRC_structural_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 04-Oct-2018

• Minor bug to create IntensityNorm folder is fixed in `fMRIpreproc.shfunction in theBRCfunctionapipeline`.
• Minor bug fixed in One_Step_Resampling function in the BRC_functional_pipeline.
• To reduce the ambiguity, version of the software is added to all pipelines.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 03-Oct-2018

• Spatial smoothing and physiological noise removal inputs are updated in the BRC_functiona_pipeline.
• Using --slspec option, the BRC_functional_pipeline can extract SliceTiming information from the fMRI DICOM file.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 02-Oct-2018

• Intensity Normasization is added to BRC_functional_pipeline.

- Shell
Published by Alirezamnk over 7 years ago

brc_pipeline - 17-Oct-2018

• New Slice Timing Correction methods based on the FSL are added to the BRCfunctionalpipeline
• Slice to volume movement correction is added to the BRCdiffusionpipeline.
• Using --slspec option, the BRCdiffusionpipeline, the pipeline can extract SliceTiming information from the dMRI DICOM file.

- Shell
Published by Alirezamnk over 7 years ago