... | ... | @@ -23,27 +23,27 @@ As specified in the context [tutorial](configuring-context-config) page, this co |
|
|
|
|
|
*If the area contains the correct information already, proceed to the following section.*
|
|
|
|
|
|
Begin by clicking the **Load context configuration** button on the GUI. You should be presented with a file chooser. Either navigate to your personally saved configuration or navigate to `/bids/derivatives/lossless/code/config` and select `contextconfig.cfg`. This will load some default options assuming the graham cluster's specifications. From this point you will need to modify the options as they only contain sample paths. For an in depth explanation of what needs to be modified, see the [tutorial](configuring-context-config).
|
|
|
Begin by clicking the **Load context configuration** button on the GUI. You should be presented with a file chooser. Either navigate to your personally saved configuration or navigate to `derivatives/lossless/code/config` and select `contextconfig.cfg`. This will load some default options assuming the graham cluster's specifications. From this point you will need to modify the options as they only contain sample paths. For an in depth explanation of what needs to be modified, see the [tutorial](configuring-context-config).
|
|
|
|
|
|
# 2. Batch Configuration
|
|
|
The next step is to load the configuration files that specify how the scripts will interact with the cluster and its scheduler. First, click **Load batch config**. A small GUI should be presented. Click **Batch configuration file** to open a file chooser. Either navigate to your own personalized scripts, or navigate to `/bids/derivatives/lossless/code/config/remote-sbatch`. Select all files beginning with the **c** prefix and press **open**. Selection of multiple files can typically be done by holding down the ctrl key. The lower text area of the small GUI should now have entries in it corresponding to the selected filed. Press **ok** to load these configurations into Matlab.
|
|
|
The next step is to load the configuration files that specify how the scripts will interact with the cluster and its scheduler. First, click **Load batch config**. A small GUI should be presented. Click **Batch configuration file** to open a file chooser. Either navigate to your own personalized configuration files, or navigate to `derivatives/lossless/code/config/remote-sbatch/`. Select all files beginning with the **c** prefix and press **open**. Selection of multiple files can typically be done by holding down the ctrl key. The lower text area of the small GUI should now have entries in it corresponding to the selected filed. Press **ok** to load these configurations into Matlab.
|
|
|
|
|
|
The batch configuration area should now be filled with texts.
|
|
|
The batch configuration area should now be filled with text.
|
|
|
|
|
|
**NOTE:** Users will **need** to modify the 'submit_options' field. Instead of '--acount=def-desjardins', it should be updated to be '--account=USERGROUP' for **all** configurations.
|
|
|
**NOTE:** Users will **need** to modify the 'submit_options' field. Instead of `--account=def-bucanl`, it should be updated to be `--account=groupname` for **all** batch configurations, where `groupname` is the name of the desired group. Alternatively, this field may be left empty if the user submitting the job(s) is only a member of one group. In this case, the user's default group will be used.
|
|
|
|
|
|
**NOTE:** These configurations assume your testing session is of average length. Increasing various parameters can cause a **major** increase in queue time. See the batch configuration [page](tuning-pipeline-configs) on how to customize memory and time parameters safely.
|
|
|
|
|
|
# 3. History and script files
|
|
|
These files specify what the pipeline actually does and how to accomplish it. For an in depth breakdown of what each section of the pipeline does, see [here](pipeline-scripts).
|
|
|
|
|
|
To select the pipeline's history files, click **History file** and navigate to `/bids/derivatives/lossless/code/scripts/` and select all files beginning with **s** and press **open**. Selection of multiple files can be done by holding down the ctrl key.
|
|
|
To select the pipeline's history files, click **History file** and navigate to `derivatives/lossless/code/scripts/` and select all files beginning with **s** and press **open** (currently, s01 - s05). Selection of multiple files can be done by holding down the ctrl key.
|
|
|
|
|
|
# 4. Data files
|
|
|
|
|
|
As this is the [BIDS](http://bids.neuroimaging.io/) lossless pipeline, if your data is stored BIDS compliant, begin importing by clicking the **Bids Import** button. Navigate to whichever stage of BIDS compliant subject structure you would like the pipeline to run on. Enter the directory so that all subject folders are visible in the file chooser. Click **open** in the file chooser. All subject files should now be imported into the text field. If not all subject files are currently desired, manually editing the text box and removing the line specifying participant files is the suggested method.
|
|
|
|
|
|
**Note:** The path field after BIDS importing should remain blank.
|
|
|
**Note:** The `path` field after BIDS importing should remain blank. Instead, the `file` field should now include the file path along with the filename.
|
|
|
|
|
|
If you wish to import data files not in BIDS format, you may select the **Data files import** button and navigate to your files this way. Note that the path field may no longer be empty and as such should be validated to be correct.
|
|
|
|
... | ... | @@ -63,7 +63,7 @@ The Matlab Command Window will detail the process of submitting the job and disp |
|
|
|
|
|
Below is an example of a completely filled in GUI with two participants files:
|
|
|
|
|
|
![historyFilled](/uploads/601c9bf8819fe1d7f008dc01450dfb36/historyFilled.png)
|
|
|
![pop_runhtb_filledin](/uploads/dedcfa9395b03845bc225eb76d6a4845/pop_runhtb_filledin.png)
|
|
|
|
|
|
***
|
|
|
[ :arrow_right: **Next Step**](tuning-pipeline-configs)
|
... | ... | |