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FSL  August 2011

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Subject:

Re: motion correction help

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 29 Aug 2011 16:45:07 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (145 lines)

Dear Sandra,

Is seems that the double length version is just a repetition.
Is this also the case in the ecclog file?

All the best,
	Mark


On 29 Aug 2011, at 16:33, Woodman, Sandra wrote:

> Hi again Mark (or anyone else familiar with this script),
> 
> Thank you for all your help thus far, this is very helpful to us.  We are
> getting ready to analyze the output data from the script (ec_plot.sh, found at
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;e2a42b99.1101) and we are
> wondering why some files don't have the same number of rows?  It seems as if
> there should be an equal number for each scan, with one per acquisition.  If
> this is not the case, do you know what each number reported means,i.e do they
> only report ones for which there was a correction and leave out those where
> there was no movement at all? This may not be likely, but we just can not figure
> out why the rows would be different (some about double in length) for the same
> file type when we are using the same sequence to scan.
> 
> As an example, I've attached two such files.
> 
> Thanks so much!
> 
> Sandra 
> 
> 
> 
> 
> Sandra Woodman
> Mood and Motor Control Laboratory
> 
> 
> 
> 
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
> Sent: Mon 8/8/2011 12:03 PM
> To: [log in to unmask]
> Subject: Re: [FSL] motion correction help
> 
> Hi,
> 
> It should say on the png images what the units are.
> It is also in the script.
> They are: radians for rotations and mm for translations.
> 
> All the best,
> 	Mark
> 
> On 8 Aug 2011, at 16:39, Woodman, Sandra wrote:
> 
>> Hi Mark (and anyone else who may know),
>> 
>> Thank you so much for that script on eddy current correction, we believe this
>> will be very helpful!  We just want to be sure of what each column contains in
>> the following files: ec_disp.txt, ec_rot.txt, ec_trans.txt.  What are the
> units
>> for the numbers?  We assume that ec_rot.txt (for example) is rotation in the
> xyz
>> plane, we would just like to confirm. 
>> 
>> Thank you,
>> 
>> Sandra
>> 
>> 
>> 
>> Sandra Woodman
>> Mood and Motor Control Laboratory
>> Athinoula Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital 
>> 
>> 
>> 
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
>> Sent: Thu 8/4/2011 11:36 AM
>> To: [log in to unmask]
>> Subject: Re: [FSL] motion correction help
>> 
>> Dear Sandra,
>> 
>> The email below (from the list) contains a script that lets you extract
>> the parameters of the eddy-current correction in the same way that
>> they are done for the functional pipeline in FEAT.  I think that should
>> give you what you want.
>> 
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;e2a42b99.1101
>> 
>> All the best,
>> 	Mark
>> 
>> 
>> On 4 Aug 2011, at 15:46, Woodman, Sandra wrote:
>> 
>>> Hello FSL users,
>>> 
>>> We were wondering if there is any way to obtain the parameters used for
>>> motion correction in the preprocessing of DTI images during the Eddy
>>> Current correction (eddy_correct)? We know that motion correction and eddy
>>> current correction are done with the same tool, but are not sure how the
>>> two are separated and where we can find a report of what was done. We
>>> have found one file (data.ecclog) but are not sure what the
>>> values in the file correspond to.
>>> 
>>> We are trying to pull out these parameters in a way similar to what one
>>> would do with fMRI if one wanted to use motion as a covariate in the
>>> analyses. In our particular case we would like to calculate actual
>>> motion correction values (in each plane) for each subject and show that
>>> our patient cohort did not move more than our control cohort.
>>> 
>>> We have searched around the forums and we found some info regarding
>>> rotating the bvec files, but we did not think that was what we wanted.
>>> 
>>> Thank you for any help!
>>> 
>>> Sandra
>>> 
>>> 
>>> Sandra Woodman
>>> Mood and Motor Control Laboratory
>>> Athinoula Martinos Center for Biomedical Imaging
>>> 
>>> 
>>> 
>>> 
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>>> contains patient information, please contact the Partners Compliance HelpLine
>> at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>>> but does not contain patient information, please contact the sender and
>> properly
>>> dispose of the e-mail.
>>> <data.ecclog>
>> 
> 
> 
> <ec_rot.txt><ec_rot.txt>

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