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>
>
0.000000 0.000000 0.000000
0.002542 0.001158 -0.005171
0.004908 0.002468 -0.005893
0.005267 0.003061 -0.006112
0.004459 0.003573 -0.007874
0.005220 0.004611 -0.010341
0.003628 0.001783 -0.003712
0.003466 0.002322 -0.005564
0.005309 0.002693 -0.007991
0.005608 0.003034 -0.011320
0.002664 0.002333 -0.005173
0.002829 0.002618 -0.009597
0.002771 0.003454 -0.008721
0.005189 0.003307 -0.007287
0.002491 0.005084 -0.010840
0.002976 0.018112 -0.015105
0.006197 0.006945 -0.014364
0.002728 0.003459 -0.007703
0.002633 0.004220 -0.003600
0.007517 0.014481 -0.006396
0.002003 0.016767 -0.000381
0.007028 0.016470 -0.006022
0.003607 0.005260 -0.006183
0.006018 0.008663 -0.008263
0.001741 0.004669 -0.015301
0.000950 0.005092 -0.002230
0.000192 0.004622 -0.007984
-0.002763 0.006733 -0.009676
0.002799 0.016343 -0.013482
0.003459 0.017073 -0.016563
-0.003470 0.016190 -0.008667
0.003370 0.012962 -0.008154
-0.002551 0.018118 -0.003302
0.003478 0.014630 -0.012485
0.006272 0.014076 -0.011345
0.006798 0.014814 -0.010689
0.008670 0.014025 -0.013606
0.000210 0.016944 -0.006248
0.003284 0.013727 -0.001331
0.010403 0.016142 -0.010654
0.013047 0.016055 -0.011212
0.014218 0.015438 -0.010889
0.013775 0.014019 -0.012413
0.013011 0.014442 -0.011196
0.011641 0.016745 -0.010599
0.008390 0.015922 -0.012386
0.002267 0.015639 -0.005885
0.008078 0.016603 -0.009416
0.014598 0.014462 -0.011311
0.018815 0.014702 -0.011905
0.018947 0.012166 -0.011166
0.020229 0.011159 -0.008835
0.021942 0.011494 -0.011976
0.017804 0.016808 -0.013348
0.019888 0.017231 -0.014706
0.020416 0.015393 -0.012939
0.019365 0.015324 -0.013811
0.019776 0.015068 -0.013317
0.019500 0.015953 -0.013447
0.020670 0.014106 -0.013777
0.019848 0.013920 -0.012696
0.021323 0.013342 -0.013521
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0.020038 0.014126 -0.010632
0.020057 0.014812 -0.009061
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0.021154 0.013707 -0.011930
0.020205 0.012294 -0.013915
0.020822 0.012667 -0.012654
0.000000 0.000000 0.000000
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0.005267 0.003061 -0.006112
0.004459 0.003573 -0.007874
0.005220 0.004611 -0.010341
0.003628 0.001783 -0.003712
0.003466 0.002322 -0.005564
0.005309 0.002693 -0.007991
0.005608 0.003034 -0.011320
0.002664 0.002333 -0.005173
0.002829 0.002618 -0.009597
0.002771 0.003454 -0.008721
0.005189 0.003307 -0.007287
0.002491 0.005084 -0.010840
0.002976 0.018112 -0.015105
0.006197 0.006945 -0.014364
0.002728 0.003459 -0.007703
0.002633 0.004220 -0.003600
0.007517 0.014481 -0.006396
0.002003 0.016767 -0.000381
0.007028 0.016470 -0.006022
0.003607 0.005260 -0.006183
0.006018 0.008663 -0.008263
0.001741 0.004669 -0.015301
0.000950 0.005092 -0.002230
0.000192 0.004622 -0.007984
-0.002763 0.006733 -0.009676
0.002799 0.016343 -0.013482
0.003459 0.017073 -0.016563
-0.003470 0.016190 -0.008667
0.003370 0.012962 -0.008154
-0.002551 0.018118 -0.003302
0.003478 0.014630 -0.012485
0.006272 0.014076 -0.011345
0.006798 0.014814 -0.010689
0.008670 0.014025 -0.013606
0.000210 0.016944 -0.006248
0.003284 0.013727 -0.001331
0.010403 0.016142 -0.010654
0.013047 0.016055 -0.011212
0.014218 0.015438 -0.010889
0.013775 0.014019 -0.012413
0.013011 0.014442 -0.011196
0.011641 0.016745 -0.010599
0.008390 0.015922 -0.012386
0.002267 0.015639 -0.005885
0.008078 0.016603 -0.009416
0.014598 0.014462 -0.011311
0.018815 0.014702 -0.011905
0.018947 0.012166 -0.011166
0.020229 0.011159 -0.008835
0.021942 0.011494 -0.011976
0.017804 0.016808 -0.013348
0.019888 0.017231 -0.014706
0.020416 0.015393 -0.012939
0.019365 0.015324 -0.013811
0.019776 0.015068 -0.013317
0.019500 0.015953 -0.013447
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0.019848 0.013920 -0.012696
0.021323 0.013342 -0.013521
0.020846 0.014226 -0.012629
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0.020038 0.014126 -0.010632
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0.021154 0.013707 -0.011930
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0.020822 0.012667 -0.012654
0.000000 0.000000 0.000000
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