######################################################## ARCHIVED - CFMRI GE MR750 Imaging Protocol Documentation ######################################################## ARCHIVED - CFMRI Multiband Protocol #1 ====================================== Protocol Location and Receiver Coil Info ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The ABCD protocol requires the use of the Nova Medical 32 channel head coil The ABCD protocol can be found on both the 3T West and 3T East scanners under: * Adult >Template-> C_CFMRI_ABCD_Scan_Session1_v22 Pre-Scan Preparation ^^^^^^^^^^^^^^^^^^^^ * Place the 32channel coil on the scanner table and plug it in * Make sure the coil is recognized by the scanner by checking on the iROC monitor above the patient bed * Setup peripheral equipment such as the projector, screen, stimulus laptop, etc. * Setup the subject (blanket, emergency communication device, mirror, etc.) on the scanner patient bed * Setup physiological monitoring if needed * Register the subject and “Start Exam” Data Acquisition: EPI & Topup Distortion Correction ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ CFMRI fwd ABCD (~17 sec) """""""""""""""""""""""" * Magnetic susceptibility and geometric distortion artifacts can be addressed by acquiring two short sequences with opposite phase encoding directions (1. Forward: Anterior-->Posterior, 2. Reverse: Posterior-->Anterior), followed by preprocessing using FSL topup https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup * The ABCD topup scans should have 60 slices * The topup scans do not utilize multiband acceleration * The number of slices you see in the Rx reflects the total acquisition coverage * Center the slices over the desired location in the brain .. image:: images/abcd/abcd1.png :width: 1000 * Save Rx-->Scan * There may be a long (20 sec) pause before the topup scan begins CFMRI rvs ABCD (~17 sec) """""""""""""""""""""""" * To run the second (rvs) topup scan you will need to copy the Rx from the previous topup scan (fwd) * Use the Graphic Rx Toolbar * Select the previous topup (fwd) scan Rx .. image:: images/abcd/abcd2.png :width: 1000 * Save Rx-->Scan rsfMRI_Run_#(1-4) (~5.5 min each) """""""""""""""""""""""""""""""""" * The multiband ABCD fMRI sequence acquires 60 total slices using a multiband factor of 6. * Using the current GE MR750 software available on CFMRI scanners, only 10 of the 60 slices are visible during the final Rx setup phase .. image:: images/abcd/abcd3.png :width: 1000 * Erase the default Rx (10 visible slices) and copy the full (60 slice) Rx from the CFMRI fwd ABCD series .. image:: images/abcd/abcd4.png :width: 1000 * Copying this Rx will keep the location consistent across topup and fMRI scans, which is critical for the success of your imaging session * After the slice coverage is successfully copied from the topup scan, reduce the number of visible slices to the original parameter setting (10 slices) * The duration of your fMRI scan can be adjusted using Phases per Location on the console (Multi-Phase tab) * The total scan time for your scan is calculated by TR x number of Phases per Location * IMPORTANT: The first 2 x Multiband Factor ( 2 x 6 (ABCD MB factor) = 12) reps will not be included in your final dataset. These volumes are internal calibration images used as reference images for the reconstruction (https://cni.stanford.edu/wiki/MUX_EPI). * 12 reps x 1000 ms (TR) = 9.6 seconds of data not included in the final dataset * The timing of your stimulus presentation must be designed with this in mind .. image:: images/abcd/abcd5.png :width: 1000 * When you are ready to save the Rx, check the scan time to ensure it is an accurate reflection of the expected acquisition time (TR x Phases per location) * Save Rx-->Scan Data Acquisition: Diffusion Tensor Imaging (DTI) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ DTI pe0 (7:27) """""""""""""" * The multiband ABCD DTI sequence acquires 81 total slices using a multiband factor of 3 * Using the current GE MR750 software only 27 of the 81 slices are visible during the final Rx setup phase .. image:: images/abcd/abcd6.png :width: 1000 * It is easier to set the Rx and ensure proper anatomical coverage if you can see all of the slices that you will acquire * This will require temporarily setting the number of slices to 81 * Before changing the number of slices to 81 (total number of slices collected) you must increase the TR dramatically to account for the length of time required to image a larger number of slices (ex: from 4,100 ms to 1,4100 ms) .. image:: images/abcd/abcd7.png :width: 1000 * Increase TR (4,100 --> 14,100) * Set the number of slices to 81 (total number of slices collected) * If you do not change the TR before editing the number of slices you will receive an advisory error indicating that you have exceeded the maximum number of slices that can be acquired within the current TR * Center the slices over the desired coverage area of the brain * Return # of slices to the original value (27) * Change TR back to 4,100 ms * If you do not return the number of slices to 27 before editing the TR you will receive an advisory error indicating that you have exceeded the maximum number of slices that can be acquired within the current TR .. image:: images/abcd/abcd8.png :width: 1000 * If the scan time has returned to normal (7:27), you are ready to begin .. image:: images/abcd/abcd9.png :width: 1000 DTI Distortion Correction Acquisition Option #1: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ DTI pe1 (7:27) """""""""""""" * To run the second (pe1) DTI scan you will need to copy the Rx from the previous DTI scan * Use the Graphic Rx Toolbar .. image:: images/abcd/abcd10.png :width: 1000 * Select the previous DTI scan Rx * Save Rx-->Scan DTI Distortion Correction Acquisition Option #2: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ DTI_fieldmap (pe1) (~0:50) """""""""""""""""""""""""" * The official ABCD protocol uses an Rx matched, 50 second, reverse phase encoded DTI acquisition to perform distortion correction on the full (7:27) forward (pe0) acquisition * Pros: Reduces total scan session time by ~6 min * Cons: All resulting diffusion analyses are based on one ~7 minute acquisition * The process of running the DTI_fieldmap is identical to the instructions above (DTI pe1) ARCHIVED - CFMRI Multiband Protocol #2 ====================================== Protocol Location and Receiver Coil Info ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The CFMRI Multiband Protocol #2 (HCP Lifespan Based) requires the use of the Nova Medical 32 channel head coil The MB Protocol #2 can be found on both the 3T West and 3T East scanners under: * Adult >Template-> C_CFMRI_HCP_LIFESPAN Pre-Scan Preparation ^^^^^^^^^^^^^^^^^^^^ * Place the 32channel coil on the scanner table and plug it in * Make sure the coil is recognized by the scanner by checking on the iROC monitor above the patient bed * Setup peripheral equipment such as the projector, screen, stimulus laptop, etc. * Setup the subject (blanket, emergency communication device, mirror, etc.) on the scanner patient bed * Setup physiological monitoring if needed * Register the subject and “Start Exam” Data Acquisition: EPI & Topup Distortion Correction ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ CFMRI fwd HCP-L (~17 sec) """"""""""""""""""""""""" * Magnetic susceptibility and geometric distortion artifacts can be addressed by acquiring two short sequences with opposite phase encoding directions (1. Forward: Anterior-->Posterior, 2. Reverse: Posterior-->Anterior), followed by preprocessing using FSL topup https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup * The HCP-L topup scans should have 72 slices * The topup scans do not utilize multiband acceleration * The number of slices you see in the Rx reflects the total acquisition coverage * Center the slices over the desired location in the brain .. image:: images/hcp/hcp1.png :width: 1000 * Save Rx-->Scan * There may be a long (20 sec) pause before the topup scan begins CFMRI rvs HCP-L (~17 sec) """"""""""""""""""""""""" * To run the second (rvs) topup scan you will need to copy the Rx from the previous topup scan (fwd) * Use the Graphic Rx Toolbar * Select the previous topup (fwd) scan Rx .. image:: images/hcp/hcp2.png :width: 1000 * Save Rx-->Scan rsfMRI_Run_#(1-4) HCP-L (~5.5 min each) """""""""""""""""""""""""""""""""""""""" * The multiband HCP-L fMRI sequence acquires 72 total slices using a multiband factor of 8. * Using the current GE MR750 software available on CFMRI scanners, only 9 of the 72 slices are visible during the final Rx setup phase .. image:: images/hcp/hcp3.png :width: 1000 * Erase the default Rx (9 visible slices) and copy the full (72 slice) Rx from the CFMRI fwd ABCD series .. image:: images/hcp/hcp4.png :width: 1000 * Copying this Rx will keep the location consistent across topup and fMRI scans, which is critical for the success of your imaging session * After the slice coverage is successfully copied from the topup scan, reduce the number of visible slices to the original parameter setting (10 slices) * The duration of your fMRI scan can be adjusted using Phases per Location on the console (Multi-Phase tab) * The total scan time for your scan is calculated by TR x number of Phases per Location * IMPORTANT: The first 2 x Multiband Factor ( 2 x 6 (ABCD MB factor) = 12) reps will not be included in your final dataset * 12 reps x 1000 ms (TR) = 9.6 seconds of data not included in the final dataset * The timing of your stimulus presentation must be designed with this in mind .. image:: images/hcp/hcp5.png :width: 1000 * When you are ready to save the Rx, check the scan time to ensure it is an accurate reflection of the expected acquisition time (TR x Phases per location) * Save Rx-->Scan