This example will create the necesary folders and scripts on the MURFI platform in order to synchronize and send real-time Network Based information to the rt-Psychopy Project to set up a neurofeedback experiment
please make sure you have installed and tested all these before continuing:
On your Ubuntu laptop where MURFI is installed (preferably with rt@rt as the rootname, if not some paths have to change on the scripts) folow these steps:
cd /home/rt/
git clone https://github.com/cccbauer/MURFI-user-manual.git
Move the rt-murfi-PyProject to your home directory
mv MURFI-user-manual/murfi-rt-PyProject/ .
cd murfi-rt-PyProject/scripts/
Ready, no we are able to setu up all necesary files to sart a test run:
1) Setup a subject folder folder with all relevant information to run the neurofeedback, this needs to happen for each new subject you will run:
source createxml.sh sub-test setup
This will show this message:
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
created all directories for sub-test
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
This means that all directories for "sub-test" were succesfully created
To check all the subfolders you can open a new terminal and navigate to:
/home/rt/murfi-rt-PyProject/subjects/sub-test
and in the created "sub-test" folder you will find :
fsfs img log mask rest ses-localizer ses-real ses-sham xfm xml
under xml you will find the script that MURFI will use to extract the neurofeedback information and send it to the rt-PsychoPy script.
under xfm you will receive/find the session_ref.nii images that will be used to register the ROI masks in MINI space to the current session images and Fields of View (FOV)
more info on this [here]
From the /home/rt/murfi-rt-PyProject/scripts folder we continue to prepare MURFI
source feedback.sh sub-test setup
this will show a message like:
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Wellcome to MURFI real-time Neurofeedback
+ running setup
+ subject ID: sub-test
+ working dir: /home/rt/murfi-rt-PyProject/subjects/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
checking the presence of scanner and stim computer
PING 192.168.2.1 (192.168.2.1) 56(84) bytes of data.
64 bytes from(192.168.2.1): icmp_seq=1 ttl=116 time=8.31 ms
64 bytes from(192.168.2.1): icmp_seq=2 ttl=116 time=10.4 ms
64 bytes from(192.168.2.1): icmp_seq=3 ttl=116 time=10.9 ms
--- 192.168.2.1 ping statistics ---
3 packets transmitted, 3 received, 0% packet loss, time 2028ms
PING 192.168.2.6 (192.168.2.6) 56(84) bytes of data.
64 bytes from(192.168.2.6): icmp_seq=1 ttl=116 time=8.31 ms
64 bytes from(192.168.2.6): icmp_seq=2 ttl=116 time=10.4 ms
64 bytes from(192.168.2.1): icmp_seq=3 ttl=116 time=10.9 ms
--- 192.168.2.6 ping statistics ---
3 packets transmitted, 3 received, 0% packet loss, time 2028ms
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
This sets up all connections to Scanner (192.168.2.1) and Stimmulus computer (192.168.2.6)
If there is any issue with the network connections you will see a note stating you need to revise the connections:
make sure Wi-Fi is off make sure you are Wired Connected to rt-fMR ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
From the /home/rt/murfi-rt-PyProject/scripts folder we continue to prepare MURFI
source feedback.sh sub-test ses-localizer run-01 resting_state
This will pop-up MURFI interface ready to receive 250 Resting State images from the Scanner like this:
Now you can start the Resting State scan on the scanner or alternatively run the Resting State simmulation like this:
Open a new terminal and from
/home/rt/murfi-rt-PyProject/scripts
start the Resting State as follows:
$ /home/rt/singularity-images/murfi2.sif ./servedata.sh 250vol
this will start sending images as if it ware a resting state for 250 volumes at 1.2 seconds TR:
1 using niiStem=img/img
2 using series=1
3 using numImgs=250
4 using firstImg=1
5 using numSlices=68
6 using tr=1200000
7 using port=15000
8 using host=localhost
loading nifti img/img-00001-00001.nii
made connection, loading image
sending img 1
sending info of size 616
sending img of size 2654208
loading nifti img/img-00001-00002.nii
made connection, loading image
sending img 2
etc. . .\
Once the Resting State has finished, close the MURFI terminal and start the network extraction pipeline as follows:
source feedback.sh sub-test ses-localizer run-01 extract_rs_networks
this will initialize the network extraction peline as follows:
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
compiling resting state run into analysis folder
calculating resting state networks this will take about 25 minutes
+ started at: Thu Jul 7 16:21:44 EDT 2022e\
and pop-up FSL MELODIC browser window:
Once the MELODIC ICA Resting State Network computation has finished we are ready to get the ROIs for our neurofeedback paradigm.
In the current setup we will compute:
a) Default Mode Network (dmn) b) Central Excecutive Network (cen) c) Somatomotor Cortex (smc)
source feedback.sh sub-test ses-localizer run-01 process_roi_masks
which will display:
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Generating DMN, CEN and SMC masks.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\
and when finished computing the ROI masks for DMN, CEN and SMC display them for QA in fsleyes:
If everything is succesfull we are ready to start the Neurofeedback Scans
If you ran the resting state network computation and mask creation between scans and are starting a new rea-time Neurofeedback scan or run, repeat setup as described in step (2).
Now we are ready for aquiring the updated field of view
source feedback.sh sub-test ses-nf1 run-01 2vol
This will pop-up MURFI interface ready to receive 2 volumes from the Scanner like this:
If you are doing a real scann, the 2vol sequence on the Scanner can be started
If you are doing a simmulation:
open a new terminal:
cd /home/rt/murfi-rt-PyProject/scripts
Start the simmulator MURFI singularity image with the 2vol flag to just send 2 images:
/home/rt/singularity-images/murfi2.sif ./servedata.sh 2vol
1 using niiStem=img/img
2 using series=1
3 using numImgs=2
4 using firstImg=1
5 using numSlices=68
6 using tr=1200000
7 using port=15000
8 using host=localhost
loading nifti img/img-00001-00001.nii
made connection, loading image
sending img 1
sending info of size 616
sending img of size 2654208
loading nifti img/img-00001-00002.nii
made connection, loading image
sending img 2
sending info of size 616
sending img of size 2654208
failed to connect
And on the MURFI interface you will see how the images are being received:
CONTROL-C to quit this MURFI interface if it not automatically quit.
source feedback.sh sub-test ses-nf1 run-01 register
This will start the registration of the masks created in stem (found in
/home/rt/murfi-rt-PyProject/subjects/sub-test/mask/mni
cen_mni.nii.gz dmn_mni.nii.gz smc_mni.nii.gz stg_mni.nii.gz
and will pop-up fsleyes to check the registration
Now you are ready to start the real-time neurofeecback scans
The order of this next step is important:
First: Start the Murfi interface to receive the feedback run:
source feedback.sh sub-test run-01 dmn
This will pop-up the interface to receive images similar to the 2vol one seen above with the difference that the lenth is 120 seconds and the regression to compute the beta values on murfi is continuous over the whole run.
On the stimulus computer:
Start PsychoPy
Run rt-network_feedback.py script
Read the instructions and go all the way to "waiting for scanner trigger"
if running a real subject, now the scan can begin and the triggers will start the experiment
If running a simulation you would neet to:
Press "t" at the same time than starting the simmulator on the second terminal:
Press "t" on the stimmulus computer
Hit enter after this line on the second termial:
/home/rt/singularity-images/murfi2.sif ./servedata.sh 120vol
This will start the feedback scann and you can see how the data is integrated and the feedback display on the stimulus computer is being updated:
