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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