Here is the code that I added to mcflirt_acc.sh:
echo Starting MCFLIRT
echo `pwd`
${FSLDIR}/bin/mcflirt -in $input -o ${output} -r ${3} -mats
-plots -report
mv ${output}.par ${output}/mc.par
mv ${output}.mat/* ${output}/
cd ${output}
find . -name 'MAT_*' -exec mv '{}' '{}'.mat \;
echo Finished MCFLIRT
It replaces the code starting at line 47 (fslsplit $input ${output}_tmp) and
goes all the way to end of the file. Mcflirt outputs all of the .mat files and
motion parameters
From: Glasser, Matthew [mailto:[email protected]]
Sent: Tuesday, December 16, 2014 1:34 PM
To: Book, Gregory; [email protected]
Subject: Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion
correction
I'd be interested in seeing your mcflirt call. I've not used it before so I'd
like to make sure we are using it optimally.
Matt.
From: <Book>, Gregory
<[email protected]<mailto:[email protected]>>
Date: Tuesday, December 16, 2014 at 12:07 PM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion
correction
We also experienced a problem with the FLIRT based motion correction. We fixed
it by using mcflirt instead. I can also post our version of the
MotionCorrection.sh script if that would be helpful.
-Greg
Dear all,
I have made changes to two files to make use of FSL's mcflirt instead of HCP's
flirt-based mcflirt_acc:
* in Pipelines/fMRIVolume : GenericfMRIVolumeProcessingPipeline.sh ->
GenericfMRIVolumeProcessingPipeline_mcflirt.sh
At line 121: I extract the midvolume as reference image when no SBref is
provided (the previous behavior was to use the first volume, which may be
problematic); At line 159: I call MotionCorrection_MCFLIRTbased.sh instead of
MotionCorrection_FLIRTbased.sh
* in Pipelines/fMRIVolume/scripts: MotionCorrection_FLIRTbased.sh
-> MotionCorrection_MCFLIRTbased.sh
Motion correction is now done with mcflirt (see line 18 if you want to change
parameters), and files are renamed and moved around to match the HCP pipeline
So, with these two new files, all you have to do is call
GenericfMRIVolumeProcessingPipeline_mcflirt.sh instead of
GenericfMRIVolumeProcessingPipeline.sh.
Hope this helps someone.
- Julien
Julien Dubois
Postdoctoral Scholar
California Institute of Technology, Pasadena, CA
http://www.emotion.caltech.edu/~jdubois
On Sun, Dec 14, 2014 at 11:31 AM, Julien Dubois
<[email protected]<mailto:[email protected]>> wrote:
>
> Thanks Matthew. My data is 2.5mm isotropic, slightly lower resolution
> than your 2mm isotropic but not exactly low res.
>
> I'm curious as to why you guys wrote your own mcflirt (seems like
> reinventing the wheel). Was FSL's mcflirt failing on HCP data?
>
> If no one else is working on a patch like you describe, I'll probably
> whip one up for my purposes so I'll keep you in the loop.
>
> - Julien
>
>
>
>
>
> > On Dec 14, 2014, at 12:45 PM, Glasser, Matthew
> > <[email protected]<mailto:[email protected]>>
> wrote:
> >
> > Hi Julien,
> >
> > You are not the first to report this for lower resolution fMRI data.
> > We?re not completely sure why the performance is different in these
> cases,
> > however we would definitely be interested in a patch for the
> > fMRIVolume pipeline that allowed choosing to use mcflirt instead of
> > mcflirt_acc for people who mcflirt_acc was not working correctly.
> >
> > Thanks,
> >
> > Matt.
> >
> >> On 12/14/14, 11:11 AM, "Julien Dubois"
> >> <[email protected]<mailto:[email protected]>> wrote:
> >>
> >> Sorry, ignore what I said for the aside: you take the average of 10
> >> volumes starting at volume 11. Better than taking the first 10.
> >> Sorry
> for
> >> my Sunday early morning confusion :-)
> >>
> >> But the main issue remains, that mc flirt_acc does not correct for
> motion
> >> as well as mcflirt. Let me know your thoughts on why this may be.
> >>
> >> Thanks,
> >> - Julien
> >>
> >>
> >>
> >>> On Dec 14, 2014, at 10:14 AM, Julien Dubois
> >>> <[email protected]<mailto:[email protected]>>
> wrote:
> >>>
> >>> Dear all,
> >>>
> >>> I want to weigh in here: the current default behavior of the
> >>> pipeline is not doing a good job at motion correction (in my own data).
> >>>
> >>> First a quick digression:
> >>> The code in global/mcflirt_acc.sh indicates that you are taking
> >>> the 10th volume as a reference, in the absence of a supplied reference:
> >>> line 29:
> >>> ${FSLDIR}/bin/fslroi $input ${output}_ref 10 10 I think that maybe
> >>> you meant to take the average of the first 10 volumes (as Greg B.
> >>> indicated, and given the following lines of code); so line 29
> >>> should likely be changed into:
> >>> ${FSLDIR}/bin/fslroi $input ${output}_ref 0 10
> >>>
> >>> But I don't think this is where the issue comes from. Indeed,
> >>> running mcflirt with the 10th volume gives a fine result. There is
> >>> thus something else in mcflirt_acc that is not functioning
> >>> properly (at
> least
> >>> for data other than HCP), compared to the standard FSL's mcflirt.
> >>>
> >>> Can you give the rationale for writing your own mcflirt function
> >>> (mcflirt_acc.sh), and explain how it differs from FSL's mcflirt?
> >>> (I could also go compare with the source code for mcflirt, but I
> >>> thought I would ask directly since you probably had a good reason)
> >>>
> >>> Thanks!
> >>> - Julien
> >>>
_________________________________________________
Gregory Book
Senior Technology Manager
Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital
200 Retreat Avenue
Hartford, CT 06106
Tel: 860-545-7267 Fax: 860-545-7797
[email protected]<mailto:[email protected]>
http://nidb.sourceforge.net
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