Hi,
No idea why this would happen originally, unless you created
the 4D input wrongly or you tried to run some simultaneously
in the same directory with the same output name, or you had
a problem with permissions and some temporary files were
not removed correctly. If it is none of these and you see the
problem again, please contact us and give us full details.
All the best,
Mark
On 29 Aug 2011, at 17:11, Woodman, Sandra wrote:
> Mark,
>
> I've checked the data.ecclog files (these are from two different sessions) and
> you are right, one file seems to process vol0000 through vol0069, and the other
> processes vol0000 through vol0069 twice. I guess I will just have to open each
> ec_rot file individualy and delete the access and rerun the script?
>
> Do you know why my file would proccess these acquisitions twice?
>
>
> Thank you,
>
> Sandra
>
> Sandra Woodman
> Mood and Motor Control Laboratory
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
> Sent: Mon 8/29/2011 11:45 AM
> To: [log in to unmask]
> Subject: Re: [FSL] motion correction help
>
> 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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