@[toc](Contents) # Overview Our goal in this project is to understand how different scanning parameters (e.g., voxel size, temporal resolution, multiband, etc.) influence image quality and subcortical signal. We collected four subjects, each of whom performed a motor task (blocks of finger tapping) and reward task (reward learning or monetary incentive delay) under different scanning parameters (see below). We have not analyzed the the task-based responses yet, but we have conducted preprocessing using [FMRIPREP][4] and quality control with [MRIQC][3]. The outputs of these programs are stored in the OSF Storage folders named MRIQC and FMRIPPEP. In addition, all of our code can be found in the GitHub repository linked to this project. # Scanning parameters We evaluated four primary sets of parameters on our new 3T Siemens Prisma. The basic 1. **epi-3mm-slow**: Standard EPI with no acceleration, 3mm spatial resolution, and 2s TR. 2. **sms-3mm-slow**: Multiband EPI with acceleration factor of 3, 3mm spatial resolution, and 2s TR. 3. **sms-2mm-slow**: Multiband EPI with acceleration factor of 3, 2mm spatial resolution, and 2s TR. 4. **sms-2mm-fast**: Multiband EPI with acceleration factor of 3, 2mm spatial resolution, and 1.24s TR. The details of the scanning parameters for each subject can be found under the OSF Storage folder named ScanningProtocols. # Interim summary The whole-brain outputs of MRIQC are not particularly surprising. As you decrease voxel size or include acceleration, you see a drop in tSNR. This is just one metric, though; and we hope to look at others soon. # Next steps 1. Extract tSNR values and other image quality metrics (IQMs) from different nuclei within the striatum. 2. Run basic activation analyses and extract z-scores or effect sizes from within regions of interest. 3. Assess effects of prescan normalization on preprocessing. Currently, masking in FMRIPREP is [buggy][masking-bug] when prescan normalization is turned on. 4. Test multi-echo fMRI? Not sure if this will happen any time soon. # Relevant links 1. NeuroStars [Discussion][neurostars] (links to Twitter discussion) 2. relevant paper: "In the Range of 20 to 35 ms, an Echo-time of 20 ms is Preferred for 3-tesla Functional Magnetic Resonance Imaging" [ResearchGate][ResearchGate] 3. relevant paper: "What are normal relaxation times of tissues at 3 T?" [pubmed][pubmed2] 4. relevant paper: "A comprehensive evaluation of increasing temporal resolution with multiband-accelerated protocols and effects on statistical outcome measures in fMRI." [pubmed][pubmed1] 5. relevant paper: "Multi-echo fMRI: A review of applications in fMRI denoising and analysis of BOLD signals." [pubmed][pubmed3] 6. NIH page on [Multi-echo FMRI][multi-echo] [neurostars]: https://neurostars.org/t/advice-for-optimizing-subcortical-signal-with-phased-array-head-coils/1504 [multi-echo]: https://fim.nimh.nih.gov/projects/multi-echo-fmri [pubmed1]: https://www.ncbi.nlm.nih.gov/pubmed/29738911 [pubmed2]: https://www.ncbi.nlm.nih.gov/pubmed/27594531 [pubmed3]: https://www.ncbi.nlm.nih.gov/pubmed/28363836 [ResearchGate]: https://www.researchgate.net/profile/Hiroshi_Nagahama/publication/272261147_In_the_Range_of_20_to_35ms_an_Echo-time_of_20ms_is_Preferred_for_3-tesla_Functional_Magnetic_Resonance_Imaging/links/5508167c0cf26ff55f7fe8e1/In-the-Range-of-20-to-35ms-an-Echo-time-of-20ms-is-Preferred-for-3-tesla-Functional-Magnetic-Resonance-Imaging.pdf [masking-bug]: https://neurostars.org/t/ica-aroma-error-in-fmriprep-mask-and-image-must-be-the-same-size/1605/4?u=dvsmith [3]: https://mriqc.readthedocs.io/en/latest/about.html [4]: http://fmriprep.readthedocs.io/en/latest/index.html