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Tom Close tclose National Imaging Facility - University of Sydney Sydney, Australia

NrgXnat/xnat-docker-compose 32

Build an XNAT server configuration with Docker Compose

tclose/Diophantine 6

A Python implementation of an algorithm for solving systems of diophantine equations

tclose/banana 2

A collection of Arcana Study classes that implement neuroimaging analysis pipelines

tclose/FouTS 1

A toolset written in C++ for characterising white matter tracts from dMRI using Fourier Tract Sampling (FouTS)

MonashBI/xnat-eeg-upload 0

A simple interactive script for uploading EEG/COG data to XNAT

tclose/arcana 0

Archive-centric NeuroImaging processing architecture based on NiPype

tclose/CompareNest 0

A Mock NEST environment for debugging of generated model code

tclose/ctopy 0

Hacking on ESR's ctopy the C to Python conversion tool: http://www.catb.org/~esr/ctopy/

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Tom Close

commit sha d808bb5ca792d1300d7653837a28b40e9645ebc3

added radiologics mriqc command

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Tom Close

commit sha 8898db59766d631437877355f8c6acc40924d863

replaced old mriqc command with radiologics

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Tom Close

commit sha 1737b0651c4af0bda4041c868d71367ab003b173

made output spec of mergetuple general to avoid bug in nipype

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Tom Close

commit sha 909312e6fe426a45bfabe642bfe657672bfd47f2

implemented multi-shell tensor residual calculation

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create barnchAustralian-Imaging-Service/xnat-docker-compose

branch : config-scripts

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issue openedMonashBI/arcana

Construct "directory" formats from nested file formats

Should be able to specify file-group formats in rich manner such that the contents of the directory are specified as collections of their constituent file formats (analogous to the way you can build up complex types/traits)

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created tagAustralian-Imaging-Service/xnatutils

tag0.7.1

A collection of CLI scripts for conveniently up/downloading and listing data on/from XNAT repositories.

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created tagMonashBI/xnatutils

tag0.7.0

A collection of CLI scripts for conveniently up/downloading and listing data on/from XNAT repositories.

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commit sha 0a3e8dc2064a99386f7e5f45ce4ae656fd5f2835

Fixes bugs with generalisation of xnat-get/ls to arbitrary subject/session naming conventions

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branch : predicted_signal

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added residual calculation to the tensor

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commit sha 2c739a47dee0ad9c8b28e90820e5d0fcb7f0ed7d

fixed up handling of reprocessing of protected artefacts

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issue commentnipy/nipype

Nipype 2.0 Progress

I started a new discussion on the Pydra issue tracker above for anyone interested

dafrose

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issue openednipype/pydra

Comparisons between Pydra, Nipype v1 and CWL

<!-- For the Question, Include the following:

What are you trying to accomplish? What have you tried? -->

This discussion follows on from https://github.com/nipy/nipype/issues/3245#issuecomment-698512224.

Thanks for the explanation @djarecka. I get the benefits of caching now.

Looking at the generated input/output interfaces, am I right in saying that the main benefit you have over the CWL tool spec is the specification of available flags/parameters in the tool interface, and which are required for the other? I didn't quite follow where the specification fits with this, and how it will replace the _list_outputs functionality from in Nipype v1.

While we are on the topic of input specs, one of the things I find a bit unintuitive/verbose in Nipype v1 interfaces is having to define output files in the input spec as well as the output spec. I understand that this is because for most tools you need to supply the output filename in the command line args. However, I was thinking that you could just generate the command line str from a combination of the input and output specs. Would this work?

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Christopher J. Markiewicz

commit sha 6e18a80ce51186ef73f0c4441d75241b99948ef6

DOC: 1.1.8 changelog

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Christopher J. Markiewicz

commit sha ef077f98554ed9ad6b01f26ff3836a16f43039c3

MNT: Version 1.1.8

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Christopher J. Markiewicz

commit sha 4aed1e24c564a80f0d8fb0956c682785b4dd1344

MNT: Update .zenodo ordering

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Yaroslav Halchenko

commit sha 597c03f64f3d74cce0065ad33b45669766cf66ac

Merge remote-tracking branch 'origin/master' into bf-2847 * origin/master: (63 commits) Update nipype/interfaces/dipy/tracks.py Update nipype/interfaces/dipy/reconstruction.py MNT: Install numpy!=1.16.0 from conda in Docker Add FSL auto test remake specs Update nipype/interfaces/io.py Remove return type named tuple Update nipype/info.py STY: Whitespace, line length Remove out_ prefix from EddyQuad outputs Apply minor edits from code review Use os.path.basename for the fallback output_dir in EddyQuad._list_outputs() Add output_dir check to EddyQuad._list_outputs() Remove redundant out_avg_b_png lines Add glob stuff back in Edit in response to @effigies comments on PR #2825 Fix tests for EddyQuad in interfaces/fsl/epi.py Add name to .zenodo.json Add doctest for EddyQuad fix: made the outputdir be mandatory and use the default val ...

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Yaroslav Halchenko

commit sha d633a57ce001452e420341616a608563911de7bd

BF: provide chain of requires for LaplacianThickness Thanks @effigies. This should prevent incorrect specification` of parameters in the command line since for ants they are just positional ones, so all previous ones should be specified

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Horea Christian

commit sha 81670e4f540c29965e901856116fffcf9504c25e

BF: allowing bids_event_file as alternate input

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Christopher J. Markiewicz

commit sha 59a7c3df0e1bf35665e806844a3ed04afc7cc088

MAINT: Update .mailmap

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Christopher J. Markiewicz

commit sha 19a73be984d0423de05487ec06a891251fde55f8

Merge remote-tracking branch 'upstream/master' into rel/1.1.8

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Katrin Leinweber

commit sha 8d292cb526de82742e2aab22723134adde9c770d

Accept invitation as Zenodo release co-author (see #2864)

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Christopher J. Markiewicz

commit sha 2ef8ab154569b840a14b79ab01f8d2bccf41982d

MNT: Update .zenodo ordering

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MNT: Update .mailmap

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commit sha dabb674111bdb453ab0d5fbd01beb3a8146b2611

MNT: Add @feilong to .zenodo, update ordering

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Chris Markiewicz

commit sha 70add2941679146307a5bd0769358fc8bcdff17c

Merge pull request #2864 from nipy/rel/1.1.8 REL: 1.1.8

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Christopher J. Markiewicz

commit sha 0772cd3b935566ff87d2cfe967000651c083d9e1

MAINT: Bump dev version

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Christopher J. Markiewicz

commit sha f112c586f5682f57248d363dde24b76f0c62a6b2

Merge remote-tracking branch 'upstream/master' into dev/2.0

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Horea Christian

commit sha ae10cd457741ea7fcf0e02da23e3fbd0f5039a5c

BF: unambiguous conditions order If this is not done, condition order for orthogonalizarion is unpredictable.

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Christopher J. Markiewicz

commit sha ce65afba686dcea29194e03a4b57f5d05dee39dd

Revert "BF: unambiguous conditions order" This reverts commit ae10cd457741ea7fcf0e02da23e3fbd0f5039a5c.

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Joerg Stadler

commit sha ca3cf74d21a17f3c67dce38783fd05a742116aa3

camino: fix procstreamline raw streamline output, without outputroot as suggested by @effigies https://github.com/nipy/nipype/pull/2739

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Chris Markiewicz

commit sha 86a3ea3a1e80d965ee41ef358e61326853aa3ed0

Merge pull request #2739 from cni-md/master FIX: Ensure outputs can be listed in camino.ProcStreamlines by defining instance variable

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Horea Christian

commit sha 28a943a7a1e7d6b3a1b3844e72aac6175d4e5572

DOC: typos and spacing

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issue commentnipy/nipype

Nipype 2.0 Progress

@satra I have had the chance to look into Pydra a bit more, and I really like what you guys have done in streamlining the API.

Having the ability to quickly generate an interface for a new tool should save a lot of time but I didn't quite get where the wrappers for more complex uses are implemented in the new structure (i.e. what was often put in '_list_outputs').

(would it be better to ask such questions on a different forum?)

dafrose

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issue commentnipy/nipype

Nipype 2.0 Progress

@satra, thanks for the detailed explanation.

For context, I have been considering whether it would make sense to adapt Arcana so it can spit out CWL descriptions, which could then be run in a CWL engine (along with bioinformatics pipelines) integrated into the analysis platform we are building.

CWL is a specification and has two components: a workflow spec and a tool spec.

the CWL tool spec is really hard to use for many neuroimaging tools because many of the tools are like a leatherman tool - they do many things. in nipype we addressed this using python code, while for CWL you will need to write javascript code. hence it didn't make a whole lot of sense to adopt this. btw, this same limitation exists for boutiques as well. both of these are really good at capturing a specific use of tool, much less as a generic wrapper for an arbitrary command line tool. by using python both nipype/pydra can generate wrappers for more complex uses. for a specific example of such complexity see: https://github.com/nipy/nipype/blob/master/nipype/interfaces/fsl/preprocess.py#L893

I see. If you were so inclined, could you write the CWL tool spec to wrap the Nipype interface instead of the tool itself, or would you still run into the same limitations do you think?

as a workflow spec CWL is easier to map to, but the CWL workflow spec requires the corresponding CWL tool spec. so if you were creating a tool spec just for the specific instantiation of the tool you are using then CWL will be able to cover both the workflow and the tool. with nipype we wanted a general tool representation that can be re-instantiated for different use cases, since much of the neuroimaging world has created such tools.

conclusion: CWL can definitely be used for many neuroimaging workflows, but creating a common tool library is going to be harder.

Ok, I think I see the issue now. You would need multiple CWL tool specs for each slightly different use of the tool, do I have that right?

in pydra, we have evolved the status of a workflow as being synonymous with a task. so it can be cached just like an interface. this is true while still supporting nested workflows and supporting parameter sweeps over both workflows and tasks (interfaces). as far as i know this flexibility is harder to implement in CWL. leveraging python over any abstract DSL provides us much greater flexibility to construct the complex workflows that exist in neuroimaging.

I'm not quite sure I follow. What is the significance of caching a workflow like an interface?

Does this solve the problem of iterating over a variable number sub-nodes, the number of which are only known at runtime (i.e. determined by an upstream node of the pipeline)?

hope that helps.

Much appreciated :)

dafrose

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issue commentmathworks-ref-arch/matlab-dockerfile

Unable to locate the required files during docker build

Thanks @josmartin, I haven't had the chance to check this out but it sounds right

tclose

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Tom Close

commit sha 92e2e7a1a566dad815004e0c39f75d4ba5b10ac7

added scan id option

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Tom Close

commit sha fbf29280800fc0eafdb50e944ee5fd970a1709f1

fixed subject_id switch

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added project and subject ID to the argument parser for xnat-put

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upped version to 0.6.5

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issue openedmathworks-ref-arch/matlab-dockerfile

Unable to locate the required files during docker build

Hi,

I am trying to follow the installation instructions but not sure what I am doing wrong. The following is the directory structure of the repo

$ tree -L 2
.
├── Dockerfile
├── Dockerfile.R2019b
├── LICENSE.md
├── README.md
├── SECURITY.md
├── file-installation-key.txt
├── license.lic
├── matlab-install
│   ├── VersionInfo.xml
│   ├── archives
│   ├── bin
│   ├── cefclient
│   ├── help
│   ├── install
│   ├── installer_input.txt
│   ├── java
│   ├── license_agreement.txt
│   ├── mathworks_installation_help.pdf
│   ├── mathworks_installation_help_es.pdf
│   ├── mathworks_installation_help_ja_JP.pdf
│   ├── mathworks_installation_help_ko_KR.pdf
│   ├── mathworks_installation_help_zh_CN.pdf
│   ├── patents.txt
│   ├── readme.txt
│   ├── resources
│   ├── sys
│   ├── trademarks.txt
│   └── ui
├── matlab_installer_input.txt
└── startmatlab.sh

but I am getting the following error


(Sep 10, 2020 06:48:25) Reading from /matlab-install/archives
(Sep 10, 2020 06:48:25) Starting local product/component search in download directory
(Sep 10, 2020 06:48:25) Searching for archives...
(Sep 10, 2020 06:48:25) Reading /matlab-install/archives
(Sep 10, 2020 06:48:25) 2 files found in /matlab-install/archives
(Sep 10, 2020 06:48:25) Archive search complete.  2 total files found.
(Sep 10, 2020 06:48:25) Completed local product/component search
(Sep 10, 2020 06:48:25) Finished reading from/matlab-install/archives
(Sep 10, 2020 06:48:25) Missing Installation Files: Unable to locate the required files.

To use a File Installation Key, you must run the installer from a directory that contains the installation files.

For information on how to get the files, see this MATLAB Answer.
	at com.mathworks.install_core_common.MATLABInstallerExceptionUtil.getApplicationException(MATLABInstallerExceptionUtil.java:16)
	at com.mathworks.matlab_installer.services.MatlabInstallerServices.checkArchives(Unknown Source)
	at com.mathworks.installservicehandler.context.ExceptionInterceptor.invoke(ExceptionInterceptor.java:21)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.mathworks.installservicehandler.JsonPassThroughResponseWrapper.getData(JsonPassThroughResponseWrapper.java:24)
	at com.mathworks.installservicehandler.JsonPassThroughResponseWrapper.getData(JsonPassThroughResponseWrapper.java:10)
	at com.mathworks.installservicehandler.InstallServiceHandlerClient.executeService(InstallServiceHandlerClient.java:18)
	at com.mathworks.matlab_installer.MatlabInstallerClient$3.executeService(Unknown Source)
	at com.mathworks.installjscommon.InstallerClientUtility.executeGetNextStateInSequence(Unknown Source)
	at com.mathworks.matlab_installer.MatlabInstallerClient.clientMain(Unknown Source)
Caused by: java.lang.Exception: Installer Error: Unable to locate required installation files
	... 13 more

(Sep 10, 2020 06:48:25) Exiting with status -2
(Sep 10, 2020 06:48:25) End - Unsuccessful
The command '/bin/sh -c cd /matlab-install &&     chmod +x ./install &&     ./install -mode silent         -inputFile /matlab_installer_input.txt         -outputFile /tmp/mlinstall.log         -destinationFolder /usr/local/MATLAB     ; EXIT=$? && cat /tmp/mlinstall.log && test $EXIT -eq 0' returned a non-zero code: 1

Which installation files am I missing?

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branch : master

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issue commentnipy/nipype

Nipype 2.0 Progress

Hi @satra,

Nice to see the progress towards 2.0 👍

I remember you raised CWL in the discussion around potential directions for Nipype 2 at the BrainHack in Singapore. What are the main limitations of CWL w.r.t. neuroimaging workflows that made it an unattractive solution? Is its workflow branching/merging structures too inflexible for typical neuroimaging workflows.

Cheers,

Tom

dafrose

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issue closedMonashBI/xnat-docker-compose

Project License - License.md ?

Hi! Is this project also open-source like the rest of XNAT? Thanks!

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ktunallux

issue commentMonashBI/xnat-docker-compose

Project License - License.md ?

done

ktunallux

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issue commentkbrose/vsc-python-indent

Close parens on indented line

Thanks!

On Wed, 26 Aug 2020 at 14:39, Kevin Rose notifications@github.com wrote:

Hi @tclose https://github.com/tclose, there is a new option ( keepHangingBracketOnLine) available in v1.11.0 of the extension for this behavior. Please note that I bumped the required version of VSCode to the most recent, so you'll have to be on an up-to-date VSCode to update the extension.

If you have problems, please submit a new issue.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/kbrose/vsc-python-indent/issues/66#issuecomment-680600020, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIBRFTQ6MXD7MXDTQXBNB3SCSGXHANCNFSM4P5X77QA .

-- THOMAS G. CLOSE, PHD Imaging Informatics Officer

Monash Biomedical Imaging Monash University Room 139, 770 Blackburn Rd Clayton Campus, Clayton VIC 3800 Australia

T: +61 3 9902 9804 M: +61 491 141 390 E: tom.close@monash.edu mbi.monash.edu.au

tclose

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issue commentkbrose/vsc-python-indent

Close parens on indented line

Re your first comment, yes, that would be my preference.

Re #65, I would consider them separate issues personally. Solving #65 would be nice, but isn't a big deal to my mind as you just need to enter another tab when starting to define the function arguments.

tclose

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issue commentMonashBI/xnat-docker-compose

Project License - License.md ?

Hi,

Yes, it should be licenced under the MIT licence. I will add in the licence file.

Cheers,

Tom

On Tue, 25 Aug 2020 at 09:27, ktunallux notifications@github.com wrote:

Hi! Is this project also open-source like the rest of XNAT? Thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/MonashBI/xnat-docker-compose/issues/21, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIBRFSQOAB57AVFFOYTTILSCLZP7ANCNFSM4QKATRYA .

-- THOMAS G. CLOSE, PHD Imaging Informatics Officer

Monash Biomedical Imaging Monash University Room 139, 770 Blackburn Rd Clayton Campus, Clayton VIC 3800 Australia

T: +61 3 9902 9804 M: +61 491 141 390 E: tom.close@monash.edu mbi.monash.edu.au

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issue openedkbrose/vsc-python-indent

Close parens on indented line

Just a matter of taste but I prefer to close parens at the end of the indented line instead of putting them on a new line, i.e.

variable = function(
    |)

instead of


variable = function(
    |
)

It seems like it should be fairly easy to add a config setting to specify this (I could have a crack at it myself although I am not familiar with TS). Would this be desirable?

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A Python module for use with Elsevier's APIs: Scopus, ScienceDirect, others.

http://api.elsevier.com

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Scripts to aid NIF reporting

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Merge pull request #3 from MonashBI/down-xml added ability to download from xml files (downloaded from the XNAT UI)

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PR merged MonashBI/xnatutils

added ability to download from xml files (downloaded from the XNAT UI)

Ups version to 0.5.8 and adds functionality to download as specified from XML files downloaded from XNAT UI

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added ability to download from xml files (downloaded from the XNAT UI)

Ups version to 0.5.8 and adds functionality to download as specified from XML files downloaded from XNAT UI

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