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Subject:

Re: Data quality - was: FEAT - problems with design matrix

From:

Cornelius Werner <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 18 Nov 2004 09:14:54 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (301 lines)

Hi,

I finally figured out what was wrong: it was the processor between my ears
:-)
Our scanner spits out DICOMS named something like MRI.000.1.xxx.IMA,
MRI.000.10.xxx.IMA, MRI.000.11.xxx.IMA, and so on. So if you display those
files in a file manager (or try to read them into stdin by a *, for that
matter), all single-digit filenames get interspersed between all the
others. That's why I had jumpy images every 10 EPIs.

So, in the end, it was the following:
ANALYZE files created by SPM didn't work, because SPM hides information
about gray values in a ususally unused header field, so no other software
reading those images will get the "true" contrast and gray values.
Trying to convert from scratch with MRICro failed because of those
incredibly named DICOMS. Thus, there's no problem with MRICro so far.

The solution was using medcon with the -alias option - or even better,
with the provided mklinks script, which will create human-readable
symlinks to the original files, upon which you can perform any operation
you want to.

Thanks to you all for your invaluable help!
Cheers, Cornelius



On Thu, 18 Nov 2004 04:33:27 +0000, Stephen Smith <[log in to unmask]>
wrote:

> Hi - then neither approach sounds satisfactory. I'm sure Chris Rorden
> would want to see the MRIcro problem so he could fix that. Have you tried
> xmedcon?
>
> Cheers, Steve.
>
>
> On Fri, 12 Nov 2004, Cornelius Werner wrote:
>
>> Hi there,
>>
>> it seems as if the conversion process (we do it via a Matlab routine
>> provided with SPM2) inserted this random noise. But: if I do the
>> conversion with MRICro and view the data with FSLView in movie mode, the
>> absolute brightness (global signal) stays the same, but the brain starts
>> to, well, wiggle, at rate of around 3 TR (~9sec).
>> This introduces BIG motion artefacts, where I had global noise artefacts
>> before. Is this a known problem? The header files are a little
>> confusing.
>> When converting the DICOMs our way (via MATLAB), the header contain the
>> following info (as given by ImageJ):
>>
>> Title: f7508-005.img
>> Width:  200.00 mm   (64)
>> Height:  200.00 mm   (64)
>> Depth:  132.00 mm   (30)
>> Voxel size: 3.13x3.13x4.40
>> Resolution:  0.320 pixels per mm
>> Bits per pixel: 16 (unsigned short)
>> Display range: 0 - 32767
>> No Threshold
>>
>> Please note the Display range entry.
>>
>> Converting the same DICOM with MRICro gives something like this:
>>
>> Title: 7508_mricro_005.img
>> Width:  200.00      (64)
>> Height:  200.00      (64)
>> Depth:  158.40      (36)
>> Voxel size: 3.13x3.13x4.40
>> Resolution:  0.320 pixels per
>> Bits per pixel: 16 (unsigned short)
>> Display range: 0 - 1113
>> No Threshold
>>
>> So, for one, MRICro inserted 6 additional, but empty, slices, AND: it
>> reduced the display range. Interestingly, the display range changes over
>> volumes!! The next one (#006) has a display range of 1028, and so forth.
>> The *.hdrs of our MATLAB processed data stay at their (16bit)-value.
>> Now I am a little confused which images tell the "truth" about my data:
>> the shaky ones or the flickering ones?!
>>
>> Is there any experience with that sort of problem??
>> Thanks a lot in advance,
>> Cornelius
>>
>> On Sat, 06 Nov 2004 12:39:39 +0000, Stephen Smith <[log in to unmask]>
>> wrote:
>>
>> > Hi Cornelius - I'm pretty sure I have the answer to this. I can get
>> quite
>> > nice looking activation maps for all contrasts:
>> >
>> > The problem is that you have high frequency global noise in your data.
>> > The
>> > whole brain image is (ie globally) fluctuating at quite high
>> frequency,
>> > giving huge noise in the analysis. This might be due to a number of
>> > things, including even the data conversion process (for example,
>> Philips
>> > scanners can insert a random scaling factor for each image depending
>> on
>> > how you do the conversion).
>> >
>> > The reason that you didn't see this before was that SPM does intensity
>> > normalisation by default, which largely removes this problem. In FEAT
>> > this
>> > is an option which we have turned off by default (because it's
>> generally
>> > an oversimplistic solution to these general issues) but when I turn it
>> > back on for your data the results are then nice. (Also, it may well be
>> > that the temporal smoothing in SPM, if you've used that, also reduces
>> > this
>> > "noise". Temporal smoothing also is a non-default option in FEAT, as
>> > again
>> > it's generally a bad thing to do.)
>> >
>> > Note that this noise in the data is quite easy to see if you view the
>> > time
>> > series in FSLView in movie mode; it's also clear as strong global
>> > components (including one all-white-matter "activation" component) in
>> a
>> > MELODIC ICA analysis.
>> >
>> > So - hope that helps. Cheers, Steve.
>> >
>> >
>> >
>> > On Fri, 29 Oct 2004, Cornelius Werner wrote:
>> >
>> >> Hi there,
>> >> thanks for your offer. I'll try and get our IT staff to putting the
>> data
>> >> somewhere accessible. But this will take until the start of the next
>> >> week,
>> >> most probably...I'll keep you informed.
>> >> Thank you very much again, and have a nice weekend :-) !
>> >> Bye,
>> >> Cornelius
>> >>
>> >>
>> >> On Fri, 29 Oct 2004 10:16:07 +0100, Stephen Smith
>> <[log in to unmask]>
>> >> wrote:
>> >>
>> >> > Hi - it sounds from your description like you did things right, so
>> >> yes I
>> >> > suspect that the problem is somewhere in the details of the
>> 3-column
>> >> EV
>> >> > setups. The best thing to do is to make a tar file of the output
>> FEAT
>> >> > directory plus the input 3-column text files, and put it on a
>> web/ftp
>> >> > site and we'll take a look.
>> >> >
>> >> > Cheers.
>> >> >
>> >> >
>> >> > On Fri, 29 Oct 2004, Cornelius Werner wrote:
>> >> >
>> >> >> Dear all,
>> >> >>
>> >> >> I conducted an event related fMRI study, where people had to press
>> >> >> visually cued buttons and were to evaluate the (visual) result by
>> >> >> another
>> >> >> button press, which could be either the expected one (c for
>> >> congruent)
>> >> >> or
>> >> >> an unexpected one (ic for incongruent). Sometimes, there were null
>> >> >> events
>> >> >> interspersed (fixation cross only). (Actually, there was one more
>> >> >> factor,
>> >> >> which is of no interest right now).
>> >> >> During analysis, I was interested in the hemodynamic response to
>> the
>> >> >> visual presentation of both the expected result, the unexpected
>> >> result
>> >> >> and
>> >> >> the difference between both. Therefore, I created a
>> "three-columns"
>> >> >> design
>> >> >> matrix with the actual presentation times (in seconds) of the
>> >> respective
>> >> >> event, the actual duration (in s) and simply "1" for the weighting
>> >> >> factor.
>> >> >> My contrasts were specified as follows:
>> >> >>
>> >> >> c       ic      null
>> >> >> 1       0       -1      Main Effect Congruent
>> >> >> 0       1       -1      Main Effect Incongruent
>> >> >> -1      1       0       Differential Activation (ic > c)
>> >> >>
>> >> >> All preprocessing options were left on default (except for slice
>> >> timing,
>> >> >> which was turned on).
>> >> >>
>> >> >> The problem now is that there is NOTHING coming up in the results
>> on
>> >> the
>> >> >> single subjects level - no higher level visual cortices, simply
>> nil.
>> >> >> When
>> >> >> leaving the data unthresholded, some brainstem lights up, which
>> >> doesn't
>> >> >> help too much...
>> >> >> Now, this really makes me wonder, as the same analysis performed
>> with
>> >> >> SPM2
>> >> >> yields the expected results with not too weak t-values even in the
>> >> >> differential contrast. So I suppose I did something wrong with the
>> >> >> design
>> >> >> matrix!?! Or are there any other typical pitfalls a beginner might
>> >> >> stumble
>> >> >> into which I am not aware of??
>> >> >>
>> >> >> I'd greatly appreciate your help with this!
>> >> >> Best regards,
>> >> >> Cornelius Werner
>> >> >>
>> >> >> --
>> >> >> Cornelius Werner
>> >> >> Institut fuer Medizin (IME)
>> >> >> AG Kognitive Neurologie
>> >> >> Forschungszentrum Juelich
>> >> >> 52425  Juelich
>> >> >> Germany
>> >> >>
>> >> >> Tel. +49-(0)2461-61-8609
>> >> >>
>> >> >
>> >> > --
>> >> >  Stephen M. Smith  DPhil
>> >> >  Associate Director, FMRIB and Analysis Research Coordinator
>> >> >
>> >> >  Oxford University Centre for Functional MRI of the Brain
>> >> >  John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>> >> >  +44 (0) 1865 222726  (fax 222717)
>> >> >
>> >> >  [log in to unmask]  http://www.fmrib.ox.ac.uk/~steve
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Cornelius Werner
>> >> Institut fuer Medizin (IME)
>> >> AG Kognitive Neurologie
>> >> Forschungszentrum Juelich
>> >> 52425  Juelich
>> >> Germany
>> >>
>> >> Tel. +49-(0)2461-61-8609
>> >>
>> >
>> >  Stephen M. Smith  DPhil
>> >  Associate Director, FMRIB and Analysis Research Coordinator
>> >
>> >  Oxford University Centre for Functional MRI of the Brain
>> >  John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>> >  +44 (0) 1865 222726  (fax 222717)
>> >
>> >  [log in to unmask]  http://www.fmrib.ox.ac.uk/~steve
>> >
>>
>>
>>
>> --
>> Cornelius Werner
>> Institut fuer Medizin (IME)
>> AG Kognitive Neurologie
>> Forschungszentrum Juelich
>> 52425  Juelich
>> Germany
>>
>> Tel. +49-(0)2461-61-8609
>>
>
>  Stephen M. Smith  DPhil
>  Associate Director, FMRIB and Analysis Research Coordinator
>
>  Oxford University Centre for Functional MRI of the Brain
>  John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>  +44 (0) 1865 222726  (fax 222717)
>
>  [log in to unmask]  http://www.fmrib.ox.ac.uk/~steve
>



--
Cornelius Werner
Institut fuer Medizin (IME)
AG Kognitive Neurologie
Forschungszentrum Juelich
52425  Juelich
Germany

Tel. +49-(0)2461-61-8609

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