[{"_1":2,"_169":-5,"_170":-5},"loaderData",{"_3":4,"_13":14,"_21":22,"_144":145},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","routes/_layout",{"_15":-5,"_16":17,"_18":17,"_19":11,"_20":11},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_23":24,"_25":-5,"_26":11,"_27":11,"_28":29,"_30":31,"_32":-5,"_33":11,"_34":35,"_84":-5,"_85":86,"_135":-5,"_136":11,"_137":17,"_138":11,"_139":-5,"_140":11,"_141":-5,"_142":143},"canonicalUrl","https://hub.docker.com/r/cbinyu/pipelines/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","cbinyu","reponame","pipelines","cloudBuildSource","isAutobuildsAvailable","repo",{"_36":37,"_38":39,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":51,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":58,"_60":61,"_62":-5,"_63":64,"_65":66,"_67":11,"_68":29,"_69":70,"_75":17,"_76":77,"_81":29,"_82":83},"categories",[],"content_types",[40],"image","date_registered","2018-10-30T16:56:04.212215Z","description","Docker image of the CBI version of the HCP Pipelines (v.3.4)","is_private","last_updated","2019-06-20T19:26:24.012955Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[52],"application/vnd.docker.container.image.v1+json","name","pull_count",23201,"repository_type","star_count",1,"status","status_description","active","source","collaborator_count",0,"full_description","# HCP Pipelines \n\nThe HCP Pipelines product is a set of tools (primarily, but not exclusively,\nshell scripts) for processing MRI images for the [Human Connectome Project][HCP]. \nAmong other things, these tools implement the Minimal Preprocessing Pipeline \n(MPP) described in [Glasser et al. 2013][GlasserEtAl]\n\n-----\n\n## Table of Contents\n\n* [Release notes](#release-notes)\n* [Prerequisities](#prerequisites)\n* [Notes on gradient nonlinearity correction](#notes-on-gradient-nonlinearity-correction)\n* [Installation](#installation)\n* [Getting example data](#getting-example-data)\n* [Running the HCP Pipelines on example data](#running-the-hcp-pipelines-on-example-data)\n * [Structural Preprocessing](#structural-preprocessing)\n * [Diffusion Preprocessing](#diffusion-preprocessing)\n * [Functional Preprocessing](#functional-preprocessing)\n * [Task Analysis](#task-analysis)\n* [The ICA FIX pipeline](#the-ica-fix-pipeline)\n* [A note about resource requirements](#a-note-about-resource-requirements)\n* [Hint for detected Out of Memory conditions](#hint-for-detecting-out-of-memory-conditions)\n* [I still have questions](#i-still-have-questions)\n\n-----\n\n\n## Release notes\n\n\n1. The HCP Pipelines scripts are being released in essentially the form that they were \n successfully used for processing data provided in the [Human Connectome Project][HCP] \n *500 Subjects Data Release*. That processing was done using 64-bit Red Hat Linux version 5.\n\n2. Some improvements to the documentation have been made since they were used for that release.\n\n3. One known difference between these scripts as they were used for the \n *500 Subjects Data Release* and their currently released form is the version of the \n `wb_command` from the [Connectome Workbench][Connectome-Workbench] that is used.\n\n When these scripts were being used for the *500 Subjects Data Release*, Connectome\n Workbench had not reached its 1.0 release level. Therefore, we used an earlier\n version of the `wb_command` for processing data for the data release. Distributing \n that older version of the `wb_command` binary as part of this product is less than \n ideal because that embedded binary is platform specific and is not\n part of an official Connectome Workbench release.\n\n If needed, the Red Hat/CentOS specific version of the `wb_command` binary and it\n associated libraries used are available in older, tagged, pre-release versions of this\n project.\n\n4. We have begun the process of making the scripts more robust, well-documented, and \n usable in other environments (other versions of operating systems, other queueing \n systems, other versions of prerequisite tools, etc.) But that process is not complete.\n Therefore, we cannot guarantee that you will not have to make modifications to the \n scripts for them to be used successfully in your environment.\n\n5. A significant part of the value of the open source model of software development\n is the ability to improve software based on source code level feedback from the \n community of users. Along those lines, if you find that you do need to make changes\n to the source code to use the tools successfully, we would welcome feedback and \n improvement suggestions. (If you have to change something in the scripts to make\n them work for you, let us know and we'll evaluate how/if to incorporate those\n changes into the released product.)\n\n Discussion of HCP Pipeline usage and improvements can be posted to the \n hcp-users discussion list. Sign up for hcp-users at \n [http://humanconnectome.org/contact/#subscribe](http://humanconnectome.org/contact/#subscribe)\n\n6. For the HCP 500 Subjects Data Release, FSL version 5.0.6 was used with these \n scripts. There is a known issue with using FSL 5.0.7 for the Task fMRI Analysis \n Pipeline. See the [Prerequisites](#prerequisites) section below for further information.\n\n7. Improvements to the internal documentation of these scripts are planned.\n\n8. Validation tests to ensure that your installation is working correctly with at \n least the sample data are also planned but not yet available. \n\n-----\n\n\n## Prerequisites\n\n\nThe HCP Pipelines have the following software requirements:\n\n1. A 64-bit Linux Operating System\n\n2. The [FMRIB Software Library][FSL] (a.k.a. [FSL][FSL]) version \n 5.0.6 installed and configuration file properly sourced. \n\n **NB: This version of the HCP Pipelines requires version 5.0.6 of FSL, not version\n 5.0.6 or greater. This version of the HCP Pipelines is not fully tested with the\n any version of FSL other than version 5.0.6. Preliminary testing has detected that\n there is a difference in behavior between version 5.0.6 of FSL and version 5.0.7 \n of FSL which, while it is an intentional improvement to FSL, is known to cause \n the Task Analysis pipeline in particular to fail.**\n\n There is currently a separate branch in this repository named `fsl-5.0.7-changes`.\n That branch is not yet included in a released version of the code, but it contains \n changes to the Task Analysis pipeline that we expect will fix that pipeline \n so that it works with version 5.0.7 of FSL. These changes are not fully tested, \n but they are available to anyone who wants to run the Task Analysis pipeline\n and use FSL 5.0.7.\n\n3. [FreeSurfer][FreeSurfer] version 5.3.0-HCP available at \n [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP](ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP)\n\n **NB: You *must* create and install a license file for FreeSurfer by\n visiting and submitting the \n [FreeSurfer registration form](https://surfer.nmr.mgh.harvard.edu/registration.html).**\n\n **NB: The version of FreeSurfer used is a special release of FreeSurfer which is not \n part of the normal release cycle. The 5.3.0-HCP version of FreeSurfer contains a \n slightly different version of the `mris_make_surfaces` program than is part\n of the standard FreeSurfer 5.3.0 release.**\n\n4. [Connectome Workbench][Connectome-Workbench] version 1.0\n\n The HCP Pipelines scripts use the `wb_command` which is part of the Connectome Workbench.\n They locate the `wb_command` using an environment variable. Instructions for setting\n this environment variable are provided below in the \n [Running the HCP Pipelines on example data](#running-the-hcp-pipelines-on-example-data) section.\n\n5. The [HCP version of gradunwarp][HCP-gradunwarp] version 1.0.2 (if gradient nonlinearity correction is to be done.)\n\n-----\n\n\n## Notes on gradient nonlinearity correction\n\n\n1. Gradient Nonlinearity Correct is sometimes also referred to as Gradient Distortion Correction\n or GDC\n\n2. As is true of the other prerequisite pieces of software, the HCP version of \n gradunwarp has its own set of prerequisites. See the HCP gradunwarp \n [README](https://github.com/Washington-University/gradunwarp/blob/master/README.md) \n file for those prerequisites. \n\n3. In order to run HCP gradunwarp, you will need a gradient coefficients file to \n use as an input to the gradient distortion correction process. Please\n see questions 7 and 8 in the \n [HCP Pipelines FAQ](https://github.com/Washington-University/Pipelines/blob/master/FAQ.md) \n for further information about gradient nonlinearity correction and obtaining a\n gradient coefficients file.\n\n4. The HCP Pipelines scripts expect to be able to find the main module of the \n gradunwarp tool (gradient_unwarp.py) within a directory specified in the \n `PATH` environment variable. \n\n5. As distributed, the examples scripts that serve as templates for running\n various types of pipeline processing are set to *not* run gradient \n distortion correction. Commented out portions of those scripts illustrate\n how to change the variable settings to perform gradient distortion correction.\n These commented out portions assume that you have placed the gradient \n coefficients file in the standard configuration directory for your\n installation of HCP Pipelines (the `global/config` directory within \n your HCP Pipelines installation directory.\n\n-----\n\n\n## Installation\n\n\n1. Install the listed [prerequisites](#prerequisites) first.\n\n * Installation Notes for FSL\n\n * Once you have installed FSL, verify that you have the correct version of FSL\n by simply running the `$ fsl` command. The FSL window that shows\n up should identify the version of FSL you are running in its title bar. \n\n * Sometimes FSL is installed without the separate documentation package, it is \n most likely worth the extra effort to install the FSL documentation package.\n\n * Ubuntu Installation Notes for FreeSurfer\n\n * For Linux, FreeSurfer is distributed in gzipped tarballs for CentOS 4 and CentOS 6.\n\n * The instructions [here](http://simnibs.de/installation/installfsandfsl) provide\n guidance for installing FreeSurfer on Ubuntu. If following the instructions\n there, be sure to download version 5.3.0-HCP of FreeSurfer and not version\n 5.1.0 as those instructions indicate.\n\n * Ubuntu (at least starting with version 12.04 and running through version 14.04 LTS)\n is missing a library that is used by some parts of FreeSurfer. To install\n that library enter `$ sudo apt-get install libjpeg62`.\n\n2. Download the necessary compressed tar file (.tar.gz) for the \n [HCP Pipelines release][HCP-pipelines-release].\n\n3. Move the compressed tar file that you download to the directory in which you want\n the HCP Pipelines to be installed, e.g.\n \n $ mv Pipelines-3.4.0.tar.gz ~/projects\n\n4. Extract the files from the compressed tar file, e.g.\n\n $ cd ~/projects\n $ tar xvf Pipelines-3.4.0.tar.gz\n\n5. This will create a directory containing the HCP Pipelines, e.g.\n\n $ cd ~/projects/Pipelines-3.4.0\n $ ls -F\n DiffusionPreprocessing/ fMRIVolume/ PostFreeSurfer/ TaskfMRIAnalysis/\n Examples/ FreeSurfer/ PreFreeSurfer/ tfMRI/\n FAQ.md global/ product.txt VersionHistory.md*\n fMRISurface/ LICENSE.md* README.md version.txt\n $\n\n6. This newly created directory is your *HCP Pipelines Directory*. \n\n In this documentation, in documentation within the script files themselves,\n and elsewhere, we will use the terminology *HCP Pipelines Directory* \n interchangably with `HCPPIPEDIR`, `$HCPPIPEDIR`, or `${HCPPIPEDIR}`.\n\n More specifically, `$HCPPIPEDIR` and `${HCPPIPEDIR}` refer to an environment \n variable that will be set to contain the path to your *HCP Pipelines Directory*.\n\n-----\n\n\n## Getting example data\n\n\nExample data for becoming familiar with the process of running the HCP Pipelines\nand testing your installation is available from the Human Connectome Project.\n\nIf you already have (or will be obtaining) the gradient coefficients file\nfor the Connectome Skyra scanner used to collect the sample data and want \nto run the pipelines including the steps which perform gradient distortion \ncorrection, you can download a zip file containing example data \n[here](https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources&resource=SampleData&filePath=HcpPipelinesExampleDataNonGDC.zip).\n\nIn that case, you will need to place the obtained gradient coefficients \nfile (`coeff_SC72C_Skyra.grad`) in the `global/config` directory within \nyour HCP Pipelines Directory.\n\nIf you do not have and are not planning to obtain the gradient coefficients \nfile for the Connectome Skyra scanner used to collect the sample data and \nwant to run the pipelines on files on which gradient distortion correction\nhas already been performed, you should should download a zip file containing \nexample data [here](https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources&resource=SampleData&filePath=HcpPipelinesExampleDataGDC.zip).\n\nThe remainder of these instructions assume you have extracted the example data\ninto the directory `~/projects/Pipelines_ExampleData`. You will need to \nmodify the instructions accordingly if you have extracted the example data\nelsewhere.\n\n-----\n\n\n## Running the HCP Pipelines on example data\n\n\n\n### Structural preprocessing\n\n\nStructural preprocessing is subdivided into 3 parts (Pre-FreeSurfer processing, \nFreeSurfer processing, and Post-FreeSurfer processing). These 3 steps should\nbe excuted in the order specified, and each of these 3 parts is implemented\nas a separate `bash` script.\n\n#### Pre-FreeSurfer processing\n\nIn the `${HCPPIPEDIR}/Examples/Scripts` directory, you will find \na shell script for running a batch of subject data through the \nPre-FreeSurfer part of structural preprocessing. This shell script is \nnamed: `PreFreeSurferPipelineBatch.sh`. You should review and possibly \nedit that script file to run the example data through the \nPre-FreeSurfer processing.\n\n*StudyFolder*\n\nThe setting of the `StudyFolder` variable near the top of this script\nshould be verified or edited. This variable should contain the path to a \ndirectory that will contain data for all subjects in subdirectories named \nfor each of the subject IDs.\n\nAs distributed, this variable is set with the assumption that you have\nextracted the sample data into a directory named `projects/Pipelines_ExampleData`\nwithin your login or \"home\" directory.\n\n StudyFolder=\"${HOME}/projects/Pipelines_ExampleData\"\n\nYou should either verify that your example data is extracted to that\nlocation or modify the variable setting accordingly.\n\n*Subjlist*\n\nThe setting of the `Subjlist` variable, which comes immediately\nafter the setting of the `StudyFolder` variable, should also be \nverified or edited. This variable should contain a space delimited \nlist of the subject IDs for which you want the Pre-FreeSurfer processing\nto run. \n\nAs distributed, this variable is set with the assumption that you will\nrun the processing only for the single example subject, which has a\nsubject ID of `100307`. \n\n Subjlist=\"100307\"\n\nUsing this value in conjunction with the value of the `StudyFolder` variable,\nthe script will look for a directory named `100307` within the directory \n`${HOME}/projects/Pipelines_ExampleData`. This is where it will expect to \nfind the data it is to process.\n\nYou should either verify that your example data is in that location\nor modify the variable setting accordingly.\n\n*EnvironmentScript*\n\nThe `EnvironmentScript` variable should contain the path to a \nscript that sets up the environment variables that are necessary \nfor running the Pipeline scripts. \n\nAs distributed, this variable is set with the assumption that you\nhave installed the HCP Pipelines in the directory \n`${HOME}/projects/Pipelines` (i.e. that your HCP Pipelines directory\nis `${HOME}/projects/Pipelines`) and that you will use the \nexample environment setup provided in the \n`Examples/Scripts/SetUpHCPPipeline.sh` script.\n\nYou may need to update the setting of the `EnvironmentScript` \nvariable to reflect where you have installed the HCP Pipelines.\n\n*GradientDistortionCoeffs*\n\nFurther down in the script, the `GradientDistortionCoeffs` variable\nis set. This variable should be set to contain either the path to \nthe gradient coefficients file to be used for gradient distortion \ncorrection or the value `NONE` to skip over the gradient distortion\ncorrection step.\n\nAs distributed, the script sets the variable to skip the gradient \ndistortion correction step. \n\nYou will need to update the setting of this variable if you have\na gradient coefficients file to use and want to perform the\ngradient distortion correction\n\n*`HCPPIPEDIR` and the `SetUpHCPPipeline.sh` script*\n\nThe script file referenced by the `EnvironmentScript` variable \nin the `PreFreeSurferPipelineBatch.sh` file (by default the \n`SetUpHCPPipeline.sh` file in the Examples\\Scripts folder)\ndoes nothing but establish values for all the environment\nvariables that will be needed by various pipeline scripts.\n\nMany of the environment variables set in the `SetUpHCPPipeline.sh`\nscript are set relative to the `HCPPIPEDIR` environment variable.\n\nAs distributed, the setting of the `HCPPIPEDIR` environment \nvariable assumes that you have installed the HCP Pipelines\nin the `${HOME}/projects/Pipelines` directory. You may \nneed to change this to reflect your actual installation\ndirectory. \n\nAs distributed, the `SetUpHCPPipeline.sh` script assumes \nthat you have: \n\n* properly installed FSL\n* set the FSLDIR environment variable\n* sourced the FSL configuration script\n* properly installed FreeSurfer\n* set the FREESURFER_HOME environment variable\n* sourced the FreeSurfer setup script\n\nExample statements for setting FSLDIR, sourcing the \nFSL configuration script, setting FREESURFER_HOME,\nand sourcing the FreeSurfer setup script are provided\nbut commented out in the `SetUpHCPPipeline.sh` script\nprior to setting `HCPPIPEDIR`.\n\n*`CARET7DIR` in the `SetUpHCPPipeline.sh` script*\n\nThe `CARET7DIR` variable must provide the path to the directory \nin which to find the Connectome Workbench `wb_command`. As \ndistributed, the `CARET7DIR` is set with the assumption that \nthe necessary `wb_command` binary is installed in the \n`${HOME}/workbench/bin_linux64` directory.\n\nIt is very likely that you will need to change the value of the \n`CARET7DIR` environment variable to indicate the location of your \ninstalled version of the `wb_command`.\n\n*Running the Pre-FreeSurfer processing after editing the setup script*\n\nOnce you have made any necessary edits as described above,\nPre-FreeSurfer processing can be invoked by commands\nsimilar to:\n\n $ cd ~/projects/Pipelines/Examples/Scripts\n $ ./PreFreeSurferPipelineBatch.sh\n This script must be SOURCED to correctly setup the environment \n prior to running any of the other HCP scripts contained here\n\n 100307\n Found 1 T1w Images for subject 100307\n Found 1 T2w Images for subject 100307\n About to use fsl_sub to queue or run /home/user/projects/Pipelines/PreFreeSurfer/PreFreeSurferPipeline.sh\n\nAfter reporting the number of T1w and T2w images found, the \n`PreFreeSurferPipelineBatch.sh` script uses the FSL command `fsl_sub` \nto submit a processing job which ultimately runs the `PreFreeSurferPipeline.sh` \npipeline script.\n\nIf your system is configured to run jobs via an Oracle Grid Engine cluster \n(previously known as a Sun Grid Engine (SGE) cluster), then `fsl_sub` will \nsubmit a job to run the `PreFreeSurferPipeline.sh` script on the\ncluster and then return you to your system prompt. You can check on the\nstatus of your running cluster job using the `qstat` command. See the\ndocumentation of the `qstat` command for further information. \n\nThe standard output (stdout) and standard error (stderr) for the job\nsubmitted to the cluster will be redirected to files in the directory\nfrom which you invoked the batch script. Those files will be named\n`PreFreeSurferPipeline.sh.o` and \n`PreFreeSurferPipeline.sh.e` respectively, where\n`` is the cluster job ID. You can monitor the progress\nof the processing with a command like:\n\n $ tail -f PreFreeSurferPipeline.sh.o1434030\n\nwhere 1434030 is the cluster job ID.\n\nIf your system is not configured to run jobs via an Oracle Grid Engine\ncluster, `fsl_sub` will run the `PreFreeSurferPipeline.sh` script\ndirectly on the system from which you launched the batch script.\nYour invocation of the batch script will appear to reach a point\nat which \"nothing is happening.\" However, the `PreFreeSurferPipeline.sh`\nscript will be launched in a separate process and the \nstandard output (stdout) and standard error (stderr) will have\nbeen redirected to files in the directory from which you invoked\nthe batch script. The files will be named \n`PreFreeSurferPipeline.sh.o` and \n`PreFreeSurferPipeline.sh.e' respectively, where\n`` is the operating system assigned unique process\nID for the running process.\n\nA similar `tail` command to the one above will allow you to monitor\nthe progress of the processing.\n\nKeep in mind that depending upon your processor speed and whether or not \nyou are performing gradient distortion correction, the Pre-FreeSurfer\nphase of processing can take several hours.\n\n#### FreeSurfer processing\n\nIn the `${HCPPIPEDIR}/Examples/Scripts` directory, you will find\na shell script for running a batch of subject data through the \nFreeSurfer part of structural preprocessing. This shell script is\nnamed: `FreeSurferPipelineBatch.sh`. You should review and possibly\nedit that script file to run the example data through the \nFreeSurfer processing.\n\nThe `StudyFolder`, `Subjlist`, and `EnvironmentScript` variables\nare set near the top of the script and should be verified and edited\nas indicated above in the discussion of Pre-FreeSurfer processing.\n\nYour environment script (`SetUpHCPPipeline.sh`) will need to have\nthe same environment variables set as for the Pre-FreeSurfer \nprocessing.\n\nOnce you have made any necessary edits as described above\nand the Pre-FreeSurfer processing has completed, then invoking \nFreeSurfer processing is quite similar to invoking Pre-FreeSurfer \nprocessing. The command will be similar to:\n\n $ cd ~/projects/Pipelines/Examples/Scripts\n\t$ ./FreeSurferPipelineBatch.sh\n This script must be SOURCED to correctly setup the environment \n prior to running any of the other HCP scripts contained here\n\n\t100307\n\tAbout to use fsl_sub to queue or run /home/user/projects/Pipelines/FreeSurfer/FreeSurferPipeline.sh\n\nAs above, the `fsl_sub` command will either start a new process on the current \nsystem or submit a job to an Oracle Grid Engine cluster. Also as above, you can \nmonitor the progress by viewing the generated standard output and standard error \nfiles.\n\n#### Post-FreeSurfer processing\n\nIn the `${HCPPIPEDIR}/Examples/Scripts` directory, you will find\na shell script for running a batch of subject data through the \nPost-FreeSurfer part of structural preprocessing. This shell script\nis named: `PostFreeSurferPipelineBatch.sh`. This script follows\nthe same pattern as the batch scripts to run Pre-FreeSurfer and\nFreeSurfer processing do. That is, you will need to verify/edit\nthe `StudyFolder`, `Subjlist`, and `EnvironmentScript` variables\nthat are set at the top of the script, and your environment \nscript (`SetUpHCPPipeline.sh`) will need to set environment variables\nappropriately.\n\nThere is an additional variable in the `PostFreeSurferPipelineBatch.sh`\nscript that needs to be considered. The `RegName` variable tells\nthe pipeline whether to use MSMSulc for surface alignment. (See\nthe [FAQ][FAQ] for further information about MSMSulc.) As distributed,\nthe `PostFreeSurferPipelineBatch.sh` script assumes that you do *not*\nhave access to the `msm` binary to use for surface alignment. Therefore,\nthe `RegName` variable is set to `\"FS\"`. \n\nIf you *do* have access to the `msm` binary and wish to use it, you \ncan change this variable's value to `\"MSMSulc\"`. If you do so, then \nyour environment script (e.g. `SetUpHCPPipeline.sh`) will need to set \nan additional environment variable which is used by the pipeline \nscripts to locate the `msm` binary. That environment variable is\n`MSMBin` and it is set in the distributed example `SetUpHCPPipeline.sh` \nfile as follows:\n\n export MSMBin=${HCPPIPEDIR}/MSMBinaries\n\nYou will need to either place your `msm` executable binary file \nin the `${HCPPIPEDIR}/MSMBinaries` directory or modify the\nvalue given to the `MSMBin` environment variable so that it\ncontains the path to the directory in which you have placed\nyour copy of the `msm` executable.\n\nOnce those things are taken care of and FreeSurfer processing \nis completed, commands like the following can be issued:\n\n $ cd ~/projects/Pipelines/Examples/Scripts\n $ ./PostFreeSurferPipelineBatch.sh\n\tThis script must be SOURCED to correctly setup the environment\n\tprior to running any of the other HCP scripts contained here\n\n\t100307\n\tAbout to use fsl_sub to queue or run /home/user/projects/Pipelines/PostFreeSurfer/PostFreeSurferPipeline.sh\n\nThe `fsl_sub` command used in the batch script will behave as described \nabove and monitoring the progress of the run can be done as described\nabove.\n\n\n### Diffusion Preprocessing\n\n\nDiffusion Preprocessing depends on the outputs generated by Structural \nPreprocessing. So Diffusion Preprocessing should not be attempted on\ndata sets for which Structural Preprocessing is not yet complete.\n\nThe `DiffusionPreprocessingBatch.sh` script in the `${HCPPIPEDIR}/Examples/Scripts`\ndirectory is much like the example scripts for the 3 phases of Structural \nP","has_starred","hub_user","immutable_tags_settings",{"_71":11,"_72":73},"enabled","rules",[74],".*","is_automated","permissions",{"_78":17,"_79":11,"_80":11},"read","write","admin","user","storage_size",39717231559,"orgData","recentTags",[87,125],{"_88":40,"_89":90,"_91":92,"_93":94,"_95":96,"_46":114,"_115":90,"_116":29,"_117":52,"_53":118,"_119":120,"_121":105,"_122":114,"_123":61,"_124":17},"content_type","creator",2979839,"full_size",2714999880,"id",38925289,"images",[97],{"_98":99,"_100":101,"_102":103,"_104":105,"_106":107,"_108":109,"_110":103,"_111":-5,"_112":92,"_59":61,"_113":-5},"architecture","amd64","digest","sha256:d99116094554e4875d8a05f326c1fd6d855fbebecb5d7f57a0e472d282c9de5f","features","","last_pulled","2026-09-23T11:16:15.980108095Z","last_pushed","2019-06-20T19:26:24Z","os","linux","os_features","os_version","size","variant","2019-06-20T19:26:23.674774Z","last_updater","last_updater_username","media_type","latest","repository",6221751,"tag_last_pulled","tag_last_pushed","tag_status","v2",{"_88":40,"_89":90,"_91":126,"_93":127,"_95":128,"_46":133,"_115":90,"_116":29,"_117":52,"_53":134,"_119":120,"_121":131,"_122":133,"_123":61,"_124":17},2708068568,38922165,[129],{"_98":99,"_100":130,"_102":103,"_104":131,"_106":132,"_108":109,"_110":103,"_111":-5,"_112":126,"_59":61,"_113":-5},"sha256:ab53d1b8b2cfa3467b50612d76ebb5cb252f1a465dd7b3808ecd2fc87154f039","2026-09-21T09:42:04.389284212Z","2019-06-20T18:46:14Z","2019-06-20T18:46:13.723043Z","v3.4","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_34":146,"_153":154,"_142":167,"_168":11},{"_36":147,"_38":148,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":149,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":58,"_60":61,"_62":-5,"_63":64,"_65":66,"_67":11,"_68":29,"_69":150,"_75":17,"_76":152,"_81":29,"_82":83},[],[40],[52],{"_71":11,"_72":151},[74],{"_78":17,"_79":11,"_80":11},"tags",{"_155":156,"_157":-5,"_158":-5,"_159":160},"count",2,"next","previous","results",[161,164],{"_88":40,"_89":90,"_91":92,"_93":94,"_95":162,"_46":114,"_115":90,"_116":29,"_117":52,"_53":118,"_119":120,"_121":105,"_122":114,"_123":61,"_124":17},[163],{"_98":99,"_100":101,"_102":103,"_104":105,"_106":107,"_108":109,"_110":103,"_111":-5,"_112":92,"_59":61,"_113":-5},{"_88":40,"_89":90,"_91":126,"_93":127,"_95":165,"_46":133,"_115":90,"_116":29,"_117":52,"_53":134,"_119":120,"_121":131,"_122":133,"_123":61,"_124":17},[166],{"_98":99,"_100":130,"_102":103,"_104":131,"_106":132,"_108":109,"_110":103,"_111":-5,"_112":126,"_59":61,"_113":-5},[],"canDeleteTags","actionData","errors"]

cbinyu/pipelines

Tags for cbinyu/pipelines