How can I specify fMRIprep to use the MEMPRAGE RMS T1w scan for reconstruction, and not the multiple echoes?
We collect one MEMPRAGE scan per subject, and extract it with heudiconv. The Siemens console automatically generates a root mean square (RMS) average of the 4 echoes. Doug Greve suggested using just the RMS scan for FreeSurfer recon-all:
From: Douglas Greve
Date: Thu, May 9, 2013 at 8:44 PM
Subject: Re: [Freesurfer] Working with MEMPRAGE
To: freesurfer at nmr.mgh.harvard.edu
the dcmunpack command is right. You should make sure to analyze only the
RMS in recon-all (ie , that is the only volume that goes into mri/orig
Heudiconv produces these five files in the
sub-MOB1023_ses-01_acq-MEMPRAGE_run-1_echo-1_T1w.nii.gz sub-MOB1023_ses-01_acq-MEMPRAGE_run-1_echo-2_T1w.nii.gz sub-MOB1023_ses-01_acq-MEMPRAGE_run-1_echo-3_T1w.nii.gz sub-MOB1023_ses-01_acq-MEMPRAGE_run-1_echo-4_T1w.nii.gz sub-MOB1023_ses-01_acq-MEMPRAGErms_run-1_T1w.nii.gz
(I noticed the RMS JSON has copied the echo time of the first echo, but that’s an issue for another day.)
By default, fMRIprep uses all 5 MEMPRAGE scans. How can I specify it to just use the RMS for reconstruction?
Even longer version:
The multiple echoes can be used to remove dura and improve the cortical surface reconstruction, using the -dura flag:
Bruce Fischl Fri, 10 May 2013 09:42:02 -0700
did you run recon-all -all all the way through? you should name your echoes something different like echo1.mgz, echo2.mgz… then specify -dura echo%d.mgz 4
Can the -dura flag with the four files be used with fMRIprep?
Finally, we also collect T2 FLAIR and T2 CUBE scans. I’m guessing the -FLAIRpial or -T2pial flags do a better job than the multi-echo dura improvement, but can they both be used? Did the Freesurfer team ever complete the pial refinement in FS v6.0? This thread indicated there was still work to be done: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-February/050019.html
On Tue, 7 Feb 2017
yes, V6 was not meant for T2/FLAIR and we didn’t test it extensively. We
have been optimizing things in the past week for T2/FLAIR and I expect 6.1
will be better for them. We can give you a beta soon if you like.