more crescents: with sequence variations

Back in January I posted about the "crescent" artifacts that show up in the PA runs of some people. (In a few people reversed crescents appear in the AP runs as well.) The working hypothesis is still that these are N/2 ghosts and perhaps related to insufficient fat suppression. I am still extremely interested in any advice people have for avoiding these, especially as I now have evidence that task signal is noticeably reduced in the "crescent" areas (details soon, hopefully).

We have begun a set of pilot scans to see if some parameter combinations produce better subcortical and frontal signal in a reward task. So far all scans have been on a Siemens Prisma, 64 32 channel head coil, CMRR MB4 sequences; we'll be doing the tests on a Siemens Vida as well in a few weeks. So far, scans are acquired with 2.4 or 3.0 mm isotropic voxels, either "flat" (AC-PC aligned as usual) or "tilted" (30 degrees off AC-PC); more acquisition details below the jump.

Of the two pilot people (so far), one has the crescent artifact and the other does not, and the appearance of the crescents in the different acquisitions is interesting. All of these images are voxelwise standard deviation, calculated over the entire run (no censoring, but extremely low motion), and on raw images (preprocessing is in progress).

First, here are sagittal views of a flat (left, scan 15) and tilted (right, scan 37) 2.4 mm isotropic run. The crescent artifact is visible in both; I marked the approximate ends with green arrows (click to enlarge). The multiband slice boundary is visible in both a fourth of the way up the image (red arrows).

Here are axial slices of the set of runs we have so far for this person. All are with the same color scaling (0 to 200); brighter is higher standard deviation. These are raw images, so the slice appearance varies quite a bit between the "flat" and "tilted" runs.

The "crescents" are visible in all PA runs, though perhaps easiest to spot with the 2p4 (2.4 mm isotropic) voxels. The slices in which the crescents appear varies between the tilted and flat acquisitions (e.g., k=31-46 for run 15_2p4flat_PA; 22-31 for run 37_2p4tilt_PA). It will be easier to compare the crescent locations after preprocessing.

The 3p0 (3.0 mm isotropic voxels) images are generally more uniform and dark than the 2p4 runs, likely reflecting improved signal-to-noise, particularly in the middle of the brain. While the large vessels are brightest in all runs (as they should be), the runs with 2.4 mm voxels (2p4) generally have a "starburst" type effect (brighter in the center, darker towards the edges), which is worrying, particularly since we want good signal in reward areas.

I will share other observations on this blog as the piloting and analyses progress. Please contact me if you'd like to run your own analyses; we'd be happy to share and are very interested in others' thoughts.

UPDATE 18 April 2018: I've wondered before if head size was a factor in which people have the crescent artifact, using the total intracranial volume measurement produced by freesurfer as a proxy. I don't have those measurements yet, but they kindly allowed me to measure their heads as if fitting them for hats, and they were nearly identical: about 58 cm for the person without the crescent artifact, and about 57 for the person shown in this person (with the artifact). Both people have a normal healthy body size; the person without the artifact was a bit shorter (around 5'2") than the other (around 5'7"). So, at least for these two pilots, external head size doesn't seem to matter for the artifact.

more acquisition parameters below the jump

Here are some of the parameters for the functional runs. We collected SBRef and SpinEchoFieldMaps for each as well; let me know if you'd like me to list additional parameters.

2p4flat scans:

CMRR_fMRI_TASK_AP_2.4mm_368meas
Image Type ORIGINAL\PRIMARY\M\MB\ND\NORM\MOSAIC
Vox. Res. 2.3958332538605, 2.3958332538605, 2.4000000953674
FOV 768 x 768
TR 1200.0
TE 30.0
Flip 52
Sequence epfid2d1_96

2p4tilt scans:

Series Desc CMRR_fMRI_TASK_AP_30degree_2.4mm_368meas
Image Type ORIGINAL\PRIMARY\M\MB\ND\NORM\MOSAIC
Vox. Res. 2.3958332538605, 2.3958332538605, 2.4000000953674
FOV 768 x 768
TR 1200.0
TE 30.0
Flip 52
Sequence epfid2d1_96

3p0flat scans:

Series Desc CMRR_fMRI_TASK_AP_3mm_442meas
Image Type ORIGINAL\PRIMARY\M\MB\ND\NORM\MOSAIC
Vox. Res. 3.0, 3.0, 3.0
FOV 608 x 608
TR 1000.0
TE 30.0
Flip 52
Sequence epfid2d1_76

3p4tilt scans:

Series Desc CMRR_fMRI_TASK_AP_30degree_3mm_442meas.
Image Type ORIGINAL\PRIMARY\M\MB\ND\NORM\MOSAIC
Vox. Res. 3.0, 3.0, 3.0
FOV 608 x 608
TR 1000.0
TE 30.0
Flip 52
Sequence epfid2d1_76