[HCP-Users] FW: GenericfMRIVolumeProcessingPipelineBatch motion correction

Tue, 16 Dec 2014 10:06:47 -0800 

WARNING: This e-mail has been altered by MIMEDefang.  Following this
paragraph are indications of the actual changes made.  For more
information about your site's MIMEDefang policy, contact
MIMEDefang Administrator's Full Name <postmaster@localhost>.  For more 
information about MIMEDefang, see:

            http://www.roaringpenguin.com/mimedefang/enduser.php3

An attachment named GenericfMRIVolumeProcessingPipeline_mcflirt.sh was removed 
from this document as it
constituted a security hazard.  If you require this document, please contact
the sender and arrange an alternate means of receiving it.


An attachment named MotionCorrection_MCFLIRTbased.sh was removed from this 
document as it
constituted a security hazard.  If you require this document, please contact
the sender and arrange an alternate means of receiving it.


_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Hi Julien,

Thanks for sending this in.  Why do you think the mid volume is better than the first volume?

I’d like Mark to look over the mcflirt call and Mike to have a look as well.  

Tim, we’ll want this to be set up as an optional argument to GenericfMRIVolumeProcessingPipeline.sh that defaults to mcflirt_acc (for now at least), but allows setting the pipeline to run mcflirt as well.  

Thanks,

Matt.

From: Julien Dubois <[email protected]>
Date: Tuesday, December 16, 2014 at 11:51 AM
To: Matt Glasser <[email protected]>
Cc: "[email protected]" <[email protected]>
Subject: Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion correction

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]> 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]> wrote:
>
> Hi Julien,
>
> You are not the first to report this for lower resolution fMRI data.
> We¹re 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]> 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]> 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
>>>
>>
>> _______________________________________________
>> HCP-Users mailing list
>> [email protected]
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> ________________________________
> The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Reply via email to