Re: [HCP-Users] Minimal Preprocessing Pipeline (on my own data): Flipped EPI (AP)

Mon, 20 Apr 2015 16:14:08 -0700

Perhaps there are some typos in the arguments (e.g. if it isn’t a typo I’m not familiar with the syntax in  ${PhaseInputName}), and it looks like you modified how the task list and phase encoding directions are called, so you’ll need to be sure that’s all correct.   

Not having an SBRef saved when using multi-band is definitely not recommended (MB has much lower anatomical contrast and this may pose problems for EPI to T1w registration).  

Also, a low resolution T2w image is problematic (minimum tested is 1mm isotropic and we know some things don’t work well when it gets worse than 1mm though that is probably not the source of the current issue).  

It is possible that because this data doesn’t meet the minimum acquisition requirements (at least 1mm isotropic T1w and T2w, field map, fMRI—if using MB then saving SBRef) you’ll have to hack the pipelines somehow to get them to work more robustly.  You’ll need to look into what is happening in the EPI to T1w registration, focusing on the files output by this module:


Especially focusing on line 255 (check that the inputs to epi_reg look okay and the outputs).  epi_reg is an FSL script, but you might have to either hack it or improve its inputs to get it to work.  These days, we recommend using spin echo phase reversed images that match your fMRI acquisition’s geometry and echo spacing to compute field maps (they are faster to acquire) and you don’t have to rely as much on epi_reg to handle everything in a black box.  

The files in question end up in this folder:

${StudyFolder}/${Subject}/${fMRIName}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased

Of course, we definitely recommend users ask about their MRI protocols on the HCP Users list before acquiring them, so we can prevent these kind of issues ahead of time.  

Peace,

Matt.

From: Julien Dubois <[email protected]>
Date: Monday, April 20, 2015 at 4:55 PM
To: Matt Glasser <[email protected]>
Cc: "[email protected]" <[email protected]>
Subject: Re: [HCP-Users] Minimal Preprocessing Pipeline (on my own data): Flipped EPI (AP)

Hi Matt

I uploaded the scripts that I use to this folder [https://caltech.box.com/s/u6bqsq6itv99k5pbf1n7lifmtz4eqjih] (I call VolumeProcessingPipelineBatch.sh, which calls GenericfMRIVolumeProcessingPipeline_mcflirt.sh, which calls among others MotionCorrection_MCFLIRTbased.sh -- recall that I made small alterations to the preprocessing pipeline to do MC with MCFLIRT). 

I also uploaded some data for one problematic subject: the unprocessed volumes (subfolder "unprocessed"), and the processed folder for one resting-state run ("rsBOLDMB1"). The EPI data is 2.5mm isotropic, 1s TR, multiband acceleration factor 4 -- the protocol is also uploaded ("rsBOLD_MB.pdf"). 

Thanks for any insights,
- Julien

PS1: You'll notice that the T2 for that subject is very low res (we were not yet acquiring a high res T2) - I imagine this is suboptimal for the pipeline, but that is what I have to work with (hopefully it does not completely throw things off)
PS2: If you have other comments on the outputs of the preprocessing, other than the AP flip which is obviously problematic, let me know. I personally find that the MNI warped EPIs look quite noisy... and also there are weird bumps in the FNIRT MNI registration of the structural scans. I could of course wait for the HCP course to discuss all this in person, but since I have your attention now...



Julien Dubois
Postdoctoral Scholar
California Institute of Technology, Pasadena, CA

http://www.emotion.caltech.edu/~jdubois


On Fri, Apr 17, 2015 at 4:19 PM, Glasser, Matthew <[email protected]> wrote:
Can you give us more details on the data you are feeding into the pipelines and how you called fMRIVolume?  We have not experienced this issue with HCP data or the non-HCP data we have tried the pipelines with.  

Peace,

Matt.

From: Julien Dubois <[email protected]>
Date: Friday, April 17, 2015 at 4:13 PM
To: "[email protected]" <[email protected]>
Subject: [HCP-Users] Minimal Preprocessing Pipeline (on my own data): Flipped EPI (AP)

Dear developers

I ran the minimal preprocessing pipeline on a number of my own subjects, and recently noticed that there was a rather unfortunate AP flip of the EPI during registration for ~30% of the subjects (explaining some rather odd results that I have been trying to track down for a couple of days).

The first volume in which I can notice this AP flip is the "Scout_gdc_undistorted_fieldmap2str.nii.gz" in "${SUBJECT_DIR}/${RUN}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/" (that the first first showing the incorrect AP orientation, according to `ls -lat`) . I'm having a hard time tracking down in the code (DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh) where this volume is created/used, and hence how to remedy the bug.

Let me know if you can help. Thanks!
- Julien

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