<Screen Shot 2014-11-04 at 11.39.17 PM.png>Please also do what Steve suggests about showing example components. I would not expect field map correction to cause artifact around internal tissue boundaries away from the edges. Also, the field map being applied should be an entirely static effect (i.e. whether or not you apply a field map the motion related artifacts should not change).Are you concatenating across runs or anything like that?Peace,Matt.From: "David V. Smith" <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, November 4, 2014 at 10:47 PM
To: <[log in to unmask]>
Subject: Re: [FSL] noise components following B0 unwarpingSure. Our coverage is OK, but there’s definitely not much room to spare (37 slices; slice thickness = 3.3mm). Note the “artifact” also appears around tissue boundaries (e.g., ventricles and caudate); i.e., it’s not strictly limited to the top/bottom slices, although it is most notable there.Thanks,David<Screen Shot 2014-11-04 at 11.39.17 PM.png>On Nov 4, 2014, at 10:37 PM, Matt Glasser <[log in to unmask]> wrote:Can you post some images showing what kind of coverage you have? I’ve certainly never seen anything like this, but the data I’ve worked with cover the whole brain with room to spare and the only place where anything like this might occur would be in the lower brain stem.Peace,Matt.From: "David V. Smith" <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, November 4, 2014 at 8:54 PM
To: <[log in to unmask]>
Subject: Re: [FSL] noise components following B0 unwarpingSame issue without slice-timing correction. And it comes up (to approximately the same degree) in subjects who move a lot and in subjects who move a little.It also happens with a different sequence using a “regular up” slice acquisition instead of interleaved.The key variable seems to be the field map correction, which does a nice job of correcting spatial distortions but at the cost of introducing these noise components.Thanks,DavidOn Nov 4, 2014, at 8:56 PM, Matt Glasser <[log in to unmask]> wrote:What happens if you don’t do slice timing correction? Is your subject moving a lot when this happens?Peace,Matt.From: "David V. Smith" <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, November 4, 2014 at 1:52 PM
To: <[log in to unmask]>
Subject: Re: [FSL] noise components following B0 unwarpingHi Matt,I’m using the default order implemented in FEAT.So, motion correction matrices are estimated first:/usr/share/fsl/5.0/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile reg/unwarp/EF_D_example_func -rmsrel -rmsabsThose transforms are then applied during unwarping:/usr/share/fsl/5.0/bin/applywarp -i grot0000 -o grot0000 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0000 -w reg/example_func2highres_warp.nii.gz -r example_func --rel --postmat=reg/highres2example_func.matAnd slice-timing correction is performed after unwarping:/usr/share/fsl/5.0/bin/slicetimer -i prefiltered_func_data_unwarp --out=prefiltered_func_data_st -r 2.000000 --oddIs this default order optimal, especially given an interleaved slice acquisition? The MRC imaging wiki suggests that, for an interleaved slice acquisition, slice-timing correction should probably occur before motion correction.Thanks for any guidance!Cheers,DavidOn Nov 4, 2014, at 11:20 AM, Matt Glasser <[log in to unmask]> wrote:<t1.png>Are you doing motion correction before B0 unwarping?Peace,Matt.From: "David V. Smith" <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, November 4, 2014 at 9:58 AM
To: <[log in to unmask]>
Subject: [FSL] noise components following B0 unwarpingHi,I am planning to use FIX to denoise my data. I’ve noticed that I get very noisy components when I include B0 unwarping in my preprocessing. These components have a distinct time course (see attached), and they seem to load mostly on the top/bottom two slices and around tissue boundaries). These noise components are explaining up to 50% of the total variance in my data (according to the MELODIC output).Have other people seen this type of artifact following B0 unwarping? Are these components reflecting an interaction between head motion and the distortions?Thanks!David<t1.png>----------------------------------------------David V. Smith, Ph.D.
Postdoctoral Fellow, Delgado LabDepartment of PsychologyRutgers UniversityNewark, NJ 07102----------------------------------------------