Hi Mark,
To get absolute motion wrt the reference volume, wouldn't you want to use
the matrix corresponding to the reference volume as the second matrix (not
the identity matrix)?
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: [log in to unmask]
On 8/21/13 2:42 AM, "Mark Jenkinson" <[log in to unmask]> wrote:
>Hi,
>
>Your use of rmsdiff is completely different to how you should use it to
>assess the within-timeseries fmri motion. What you are doing instead is
>measuring the change between the structural scan (highres) and the
>functional scan, which will also take into account the change in FOV, and
>is pretty much useless.
>
>Instead, you need to take the matrices output by mcflirt with the -mats
>option on and use these with rmsdiff, using the example_func as the
>refvol and either (a) the matrix for timepoint N and the identity matrix,
>or (b) the matrices for timepoint N and timepoint N-1. In (a) you get
>the absolute motion wrt the reference volume, whereas in (b) you get the
>relative motion from one timepoint to the next.
>
>I don't quite understand how you are running fsl_motion_outliers, as
>INPUT=$REGDIR/example_func2highres.mat is not sensible in this context.
>You need to use the original 4D image data (prior to motion correction)
>or the motion corrected data and the --nomoco option. Also, the values
>from dvars are not a measure of mm motion, they are related to
>differences in the image intensities, so it is perfectly reasonable to
>get larger values. Normalising dvars does not turn it into a measurement
>of movement.
>
>All the best,
> Mark
>
>
>
>
>On 20 Aug 2013, at 16:42, Allison Jack <[log in to unmask]> wrote:
>
>> Hello FSL experts,
>>
>> I would like to report an RMS movement value for each of my
>>participants, so I was attempting to use rmsdiff. However, the results I
>>get from my calculation seem FAR larger than anything I have ever seen
>>reported. For example, for participant 1, the MCFLIRT results in
>>prestats indicate a relative mean displacement of .06mm & an absolute
>>mean displacement of .05mm; by my calculations from the par file, their
>>maximum deviation from one volume to the next is .31 mm. However, the
>>same participant's result from rmsdiff is 54.3698. (!) I assume I have
>>missed some very important step, but although I have read through the
>>rmsdiff wiki and the technical report I cannot seem to figure out my
>>error.
>>
>> I ran rmsdiff using the following, based on a thread I had seen in the
>>listserv:
>>
>> REGDIR=$STUDYDIR/ANALYSIS/FSL/LEVELONE/$SUBJ/runA.feat/reg
>> REFVOL=$REGDIR/highres.nii.gz
>> INPUT=$REGDIR/example_func2highres.mat
>> IDENT=/Applications/fsl/etc/flirtsch/ident.mat
>>
>> rmsdiff $INPUT $IDENT $REFVOL
>>
>> As a side note, my DVARS values (the text file produced by
>>fsl_motion_outliers, e.g.:
>>
>> fsl_motion_outliers -i $INPUT -o $OUTPUT --dvars -s $DVARS)
>>
>> are also similarly large. I saw a technical note by Thom Nichols on
>>standardizing DVARs and I was wondering if that is what I might need to
>>implement here; if so, could someone provide some examples of use of his
>>DVARS.sh script
>>(http://www2.warwick.ac.uk/fac/sci/statistics/staff/academic-research/nic
>>hols/scripts/fsl/dvars.sh)?
>>
>> Any correct usage examples would be helpful here.
>>
>> Thanks so much!,
>> Allison
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