Dear Allison,
Your script looks fine, but I agree with Michael here.
All the best,
Mark
On 23 Aug 2013, at 17:21, "Harms, Michael" <[log in to unmask]> wrote:
> FWIW, my experience has been that absolute movement isn't particularly
> informative regarding fMRI data quality. Relative (frame-to-frame) is a
> better predictor of "bad" subjects.
>
> 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 8/23/13 10:34 AM, "Allison Jack" <[log in to unmask]> wrote:
>
>> Thank you for your reply, Mark. My apologies for failing to clarify the
>> content of the $INPUT variable in my fsl_motion_outliers call; it was to
>> non-motion-corrected functional data, not the matrix that was specified
>> as input in the previous set of code.
>>
>> Your explanation was very helpful. So, based on my understanding, if I
>> want to determine absolute amount of movement relative to the reference
>> volume, I should run something like the following (where $SUBJDIR links
>> to the subject-specific level 1 feat directory, and there are 237 volumes
>> in my functional data):
>>
>> MATDIR=$SUBJDIR/mc/prefiltered_func_data_mcf.mat
>> REGDIR=$SUBJDIR/reg
>>
>> REFVOL=$REGDIR/example_func.nii.gz
>> IDENT=/Applications/fsl/etc/flirtsch/ident.mat
>> RMSOUT=$SUBJDIR/rmsdiff.txt
>>
>> for ((i = 0; i < 237; ++i)); do
>> printf -v num '%04d' $i
>> rmsdiff $MATDIR/MAT_${num} $IDENT $REFVOL >> $RMSOUT
>> done
>>
>> Does that look approximately correct? (The numbers I generate with this
>> look much more reasonable, by the way.)
>> Thanks again for your help!
>> Best,
>> Allison
>
>
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