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| # Sphinx build info version 1 | ||
| # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. | ||
| config: f87de8b0c59005225db4e18afe44d67f | ||
| config: 07d27a37c07d9a0511eade0d8bbceda9 | ||
| tags: 645f666f9bcd5a90fca523b33c5a78b7 |
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| .. _reproin: | ||
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| reproin | ||
| ======= | ||
| This is the reproin heuristic, copied from `heudiconv <https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py>`_ | ||
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| .. code-block:: console | ||
| (AKA dbic-bids) Flexible heuristic to establish BIDS DataLad datasets hierarchy | ||
| Initially developed and deployed at Dartmouth Brain Imaging Center | ||
| (http://dbic.dartmouth.edu) using Siemens Prisma 3T under the umbrellas of the | ||
| Center of Reproducible Neuroimaging Computation (ReproNim, http://repronim.org) | ||
| and Center for Open Neuroscience (CON, http://centerforopenneuroscience.org). | ||
| ## Dataset ownership/location | ||
| Datasets will be arranged in a hierarchy similar to how study/exam cards are | ||
| arranged at the scanner console. You should have | ||
| - "region" defined per each PI, | ||
| - on the first level most probably as PI_StudentOrRA/ (e.g., Gobbini_Matteo) | ||
| - StudyID_StudyName/ (e.g. 1002_faceangles) | ||
| - Arbitrary name for the exam card -- it doesn't get into Study Description. | ||
| Selecting specific exam card would populate Study Description field using | ||
| aforementioned levels, which will be used by this heuristic to decide on the | ||
| location of the dataset. | ||
| In case of multiple sessions, it is recommended to generate separate "cards" | ||
| per each session. | ||
| ## Sequence naming on the scanner console | ||
| Sequence names on the scanner must follow this specification to avoid manual | ||
| conversion/handling: | ||
| [PREFIX:]<seqtype[-label]>[_ses-<SESID>][_task-<TASKID>][_acq-<ACQLABEL>][_run-<RUNID>][_dir-<DIR>][<more BIDS>][__<custom>] | ||
| where | ||
| [PREFIX:] - leading capital letters followed by : are stripped/ignored | ||
| <...> - value to be entered | ||
| [...] - optional -- might be nearly mandatory for some modalities (e.g., | ||
| run for functional) and very optional for others | ||
| *ID - alpha-numerical identifier (e.g. 01,02, pre, post, pre01) for a run, | ||
| task, session. Note that makes more sense to use numerical values for | ||
| RUNID (e.g., _run-01, _run-02) for obvious sorting and possibly | ||
| descriptive ones for e.g. SESID (_ses-movie, _ses-localizer) | ||
| <seqtype[-label]> | ||
| a known BIDS sequence type which is usually a name of the folder under | ||
| subject's directory. And (optional) label is specific per sequence type | ||
| (e.g. typical "bold" for func, or "T1w" for "anat"), which could often | ||
| (but not always) be deduced from DICOM. Known to BIDS modalities are: | ||
| anat - anatomical data. Might also be collected multiple times across | ||
| runs (e.g. if subject is taken out of magnet etc), so could | ||
| (optionally) have "_run" definition attached. For "standard anat" | ||
| labels, please consult to "8.3 Anatomy imaging data" but most | ||
| common are 'T1w', 'T2w', 'angio' | ||
| func - functional (AKA task, including resting state) data. | ||
| Typically contains multiple runs, and might have multiple different | ||
| tasks different per each run | ||
| (e.g. _task-memory_run-01, _task-oddball_run-02) | ||
| fmap - field maps | ||
| dwi - diffusion weighted imaging (also can as well have runs) | ||
| _ses-<SESID> (optional) | ||
| a session. Having a single sequence within a study would make that study | ||
| follow "multi-session" layout. A common practice to have a _ses specifier | ||
| within the scout sequence name. You can either specify explicit session | ||
| identifier (SESID) or just say to maintain, create (starts with 1). | ||
| You can also use _ses-{date} in case of scanning phantoms or non-human | ||
| subjects and wanting sessions to be coded by the acquisition date. | ||
| _task-<TASKID> (optional) | ||
| a short name for a task performed during that run. If not provided and it | ||
| is a func sequence, _task-UNKNOWN will be automatically added to comply with | ||
| BIDS. Consult http://www.cognitiveatlas.org/tasks on known tasks. | ||
| _acq-<ACQLABEL> (optional) | ||
| a short custom label to distinguish a different set of parameters used for | ||
| acquiring the same modality (e.g. _acq-highres, _acq-lowres etc) | ||
| _run-<RUNID> (optional) | ||
| a (typically functional) run. The same idea as with SESID. | ||
| _dir-[AP,PA,LR,RL,VD,DV] (optional) | ||
| to be used for fmap images, whenever a pair of the SE images is collected | ||
| to be used to estimate the fieldmap | ||
| <more BIDS> (optional) | ||
| any other fields (e.g. _acq-) from BIDS acquisition | ||
| __<custom> (optional) | ||
| after two underscores any arbitrary comment which will not matter to how | ||
| layout in BIDS. But that one theoretically should not be necessary, | ||
| and (ab)use of it would just signal lack of thought while preparing sequence | ||
| name to start with since everything could have been expressed in BIDS fields. | ||
| ## Last moment checks/FAQ: | ||
| - Functional runs should have _task-<TASKID> field defined | ||
| - Do not use "+", "_" or "-" within SESID, TASKID, ACQLABEL, RUNID, so we | ||
| could detect "canceled" runs. | ||
| - If run was canceled -- just copy canceled run (with the same index) and re-run | ||
| it. Files with overlapping name will be considered duplicate/canceled session | ||
| and only the last one would remain. The others would acquire | ||
| __dup0<number> suffix. | ||
| Although we still support "-" and "+" used within SESID and TASKID, their use is | ||
| not recommended, thus not listed here | ||
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| ============ | ||
| Usage | ||
| ============ | ||
| .. code-block:: console | ||
| usage: xnat_downloader [-h] [-c CONFIG] [-i INPUT_JSON] | ||
| xnat_downloader downloads xnat dicoms and saves them in BIDs compatible | ||
| directory format | ||
| optional arguments: | ||
| -h, --help show this help message and exit | ||
| -c CONFIG, --config CONFIG login file (contains user/pass info) | ||
| Required arguments: | ||
| -i INPUT_JSON, --input_json INPUT_JSON json file defining inputs for this script. | ||
| json format | ||
| ------------------- | ||
| The json file has multiple fields specifying where and how | ||
| the data are downloaded from xnat. | ||
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| * **destination**: string | ||
| (required) The absolute path to the | ||
| output base directory of the BIDS dataset | ||
| * **project**: string | ||
| (required) The name of the project on xnat | ||
| * **server**: string | ||
| (required) The base URL to the xnat server (e.g. "https://central.xnat.org") | ||
| * **subjects**: list | ||
| (optional) The subjects you wish to download from xnat. | ||
| Use the subject names as they are seen on xnat. | ||
| * **sub_dict**: dictionary | ||
| (optional) (non-BIDS) If you want to change the subject label | ||
| that is not represented in the xnat subject name | ||
| * **session_labels**: list | ||
| (optional) (non-BIDS) If you want to replace the names of the sessions | ||
| on xnat with your own list of scans. | ||
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| .. warning:: this will not behave as expected if the subject on xnat | ||
| has a missing "middle" session or an extra session. | ||
| * **scan_dict**: dictionary | ||
| (conditionally required) (non-BIDS) required if your dicoms are not stored | ||
| in a BIDS format on xnat. The keys to the dictionary are | ||
| scan names as they are seen on xnat (e.g. "SAG FSPGR BRAVO"), | ||
| and the values are the associated :ref:`reproin` (BIDS-ish) | ||
| name for the scan (e.g. "anat-T1w"). | ||
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| Once installed and the json file is configured, the final step is to call the command, like so: | ||
| example json | ||
| ************ | ||
| .. literalinclude:: ../tests/non_bids_test.json | ||
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| Once installed and the json file is configured, | ||
| the final step is to call the command. | ||
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| **locally installed:** (python2 only) | ||
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| .. code-block:: console | ||
| xnat_downloader -i /path/to/json/file.json | ||
| **via docker:** | ||
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| .. code-block:: console | ||
| docker run \ | ||
| -v /path/to/out:/out \ | ||
| -v /path/to/json/:/json \ | ||
| jdkent:xnat_downloader \ | ||
| -i /json/file.json | ||
| **Note**: when calling via docker, | ||
| the destination location should be specified | ||
| relative to where the path is in the docker | ||
| container, not on your machine. |
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