thanks much, Wolf. I'll give flirt_average a try, after normalizing
with fslmaths. I'll use sinc interpolation anyway (because
computation time will not be a bottleneck -- the script will run
overnight as subjects are accrued)
any advice on automated detection of degraded MPRAGEs (to avoid those
rare instances when averaging would degrade SNR)?
--Jeremy
On Mar 8, 2008, at 8:49 AM, wolf zinke wrote:
> Hi Jeremy,
>
> You just might want to use the command line tool flirt_average.
> This takes care of most of the things you mentioned and gives
> pretty good results. It also allows all options for flirt.
>
> By combining two images you increase the SNR of the image, thus it
> is good to combine images.
>
> If you use the same modality and the same subject it is not really
> necessary to extract the brain. However, to simplify things you can
> run bet and create a binary brain mask, that you could use as
> weight (flirt options refweight and inweight).
>
> As cost function I would recomend normalized correlation, because
> you have the same modality. However, I haven't notice much
> difference than using correlation ratio.
>
> Using sinc interpolation in my opinion does not improve the quality
> much, but increases computational time quiet a bit, thus I would
> recommend trilinear.
>
> A thin the flirt_average script is not doing is the normalization
> of the single scans before averaging. This step might be usefull
> when there is a difference in image intensities. Just change the
> last line of the script for example to:
> fslmaths $output -inm 1000 -Tmean $output
>
> Good luck,
> wolf
>
>
> Jeremy R. Gray wrote:
>> Hi FSL'ers,
>>
>> I'm new to FSL (really liking it so far). I'm hoping for advice on
>> the best
>> approach to combining two MPRAGE images from the same subject.
>> This is for
>> 100+ subjects, and so I will script it. the idea is to end up with
>> one
>> higher-quality image to use in structural analyses. one image is
>> from the
>> start of the scan session, and the other from the end (~1.25 hours
>> later).
>>
>> flirt seems like the way to go, so I searched the archives and the
>> flirt
>> lecture notes from the web (pdf), but did not see something on
>> combining
>> MPRAGES. my apologies if I missed it.
>>
>> one question is:
>> - is it always better to combine two images? presumably there
>> could be
>> pathological cases (e.g., lots of movement resulting in a blurry
>> image)
>> where a single good MPRAGE is better than combining one good and
>> one bad --
>> so is there a way to tell that you are in such a situation
>> (especially for a
>> script to tell this)? just inspect afterwards?
>>
>> using flirt seems straightforward:
>> - prior to flirt, run bet -B on each image (= my interpretation of
>> flirt
>> lecture slide #45). but maybe for having the same sequence, the
>> non-brain
>> stuff will actually help the alignment? and maybe doing bet on the
>> combined
>> image will give a better extraction (for having a higher-quality
>> input)?
>>
>> - just pick one image to use as the reference, "better quality"
>> should be
>> moot with 2 MPRAGEs (except in pathological cases)
>>
>> - a rigid body 6-parameter model seems fine because the images are
>> from the
>> same subject, same scanner, same day. is there any possible
>> advantage to
>> more df for my situation?
>>
>> - search option = "already virtually aligned" is probably fine
>>
>> - cost function: correlation ratio is the default in the GUI.
>> however, I've
>> heard that normalized mutual information is very good, in
>> particular is
>> robust to small non-brain bits left over from brain extraction.
>> any reason
>> not to use NMI (especially if I do bet prior to flirt)?
>>
>> - trilinear interpolation (= default) -- any advantage to sinc?
>>
>> thanks much,
>>
>> --Jeremy
>>
>>
>> /*-------------------------------------------------------------
>> Jeremy R. Gray, PhD
>> Assistant Professor, Yale University
>> Dept. of Psychology & Interdepartmental Neuroscience
>> Program mail Box 208205, New Haven, CT 06520-8205 USA
>> office SSS 212 http://maps.google.com/maps?q=1
>> +Prospect+St,New+Haven
>> phone 203-432-9615 (office) fax 203-432-7172
>> (include Attn J. Gray)
>> web http://www.yale.edu/scan/
>> -------------------------------------------------------------*/
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