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FSL  January 2012

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Subject:

Re: Re : [FSL] TBSS some questions

From:

Angela Favaro <[log in to unmask]>

Reply-To:

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

Date:

Tue, 24 Jan 2012 20:48:58 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (202 lines)

Thank you for your answers!
May I ask you one more question?
How can I check for the quality of DTI acquisition in terms of motion? It
is easy to do for functional MRI, but I am not aware of how to do it with
DTI acquisition.
Thank you!

Angela


> Also, one other thing to at least consider is that, even if you have the
> exact same set of 16 gradient directions available as part of your 32
> direction acquisition, the 32 direction scan itself was presumably twice
> as long, so there is the possibility that movement related problems may
> be more severe in your 32 direction data sets.  Or, artifacts arising
> from table vibration (a known problem for Siemen's Trio scanners) may
> well be different between the two sets of acquisitions.  So, in my
> opinion, even if TR, TE, voxel size, head coil, etc were identical, it
> still wouldn't be completely sufficient to simply use 16 of the 32
> directions without first demonstrating that the data from those 16
> directions was of comparable average quality across the two sets of
> acquisitions.
>
> cheers,
> -MH
>
> On Tue, 2012-01-24 at 13:50 -0500, David Gutman wrote:
>> Just to check... is EVERYTHING else in your scans the same?    I.e.
>> TR, TE, voxel size, and head coil?
>>
>> Again I think we discussed this recently in the group listserve... but
>> basically if there are any systematic differences between group 1 and
>> group 2 in terms of acquisition parameters,  it's really impossible to
>> draw any firm conclusions between differences in the group, unless you
>> also model the effect of scanner.     Adding 5-10 subjects that are
>> scanned with both a 16 and 32 gradient protocol is one possibility.
>> Or you should add some more controls with the 32 gradient protocol  so
>> you can account for the effects of scan parameters  in your model.
>>
>>
>> I've really wanted to do the same thing in the past where we take old
>> "control" subjects  or old patient populations scanned with sequence X
>> at time X and compare them to time Y with sequence Y to do some
>> exploratory analysis.... but since there are so many known (and
>> unknown things) that seem to effect the exact FA value I have never
>> felt comfortable doing it for the reasons discussed above.
>>
>>
>> On Tue, Jan 24, 2012 at 12:57 PM, Gwenaëlle DOUAUD
>> <[log in to unmask]> wrote:
>> > Dear Angela,
>> >
>> > considering only the 16 directions that are shared by the two groups
>> sounds
>> > like a reasonable option. You will need to change your bvecs and bvals
>> files
>> > accordingly, and use fslroi to get rid of the 16 non-corresponding
>> > directions in your 32 gradients dataset before using dtifit etc. to
>> create
>> > the FA (and other) maps.
>> >
>> > Cheers,
>> > Gwenaelle
>> >
>> >
>> > ________________________________
>> > De : Christine Zakrzewski <[log in to unmask]>
>> > À : [log in to unmask]
>> > Envoyé le : Mardi 24 janvier 2012 17h51
>> > Objet : Re: [FSL] TBSS some questions
>> >
>> > I doubt it.  The images with 32 diffusion gradients will provide a
>> more
>> > accurate measure of the dependent measure (Fractional Anisotropy,
>> > Radial/Mean Diffusivity, etc).  There is probably no way to limit the
>> number
>> > of gradients used to make these calculations. Wait for a more certain
>> answer
>> > from one of the experts.
>> > Christine
>> >
>> >> Date: Tue, 24 Jan 2012 18:43:20 +0100
>> >> From: [log in to unmask]
>> >> Subject: Re: [FSL] TBSS some questions
>> >> To: [log in to unmask]
>> >>
>> >> I intend after scanning. Can I consider only the 16 directions that
>> are
>> >> shared by the two groups?
>> >> Thank you
>> >>
>> >> >
>> >> > The technician, or physicist at your scanner can probably best
>> answer
>> >> > this
>> >> > question.Christine
>> >> > > Date: Tue, 24 Jan 2012 17:16:32 +0100
>> >> >> From: [log in to unmask]
>> >> >> Subject: Re: [FSL] TBSS some questions
>> >> >> To: [log in to unmask]
>> >> >>
>> >> >> Is there a way to 'reduce' the number of directions from 32 to 16
>> (same
>> >> >> scanner) to be able to compare groups?
>> >> >>
>> >> >> thank you!
>> >> >> Angela
>> >> >>
>> >> >>
>> >> >> > the answer is no..... especiallu if group one was scanned with
>> low
>> >> >> > directions and group two was scanned with more directoons
>> >> >> > On Jan 24, 2012 10:32 AM, "Angela Favaro"
>> <[log in to unmask]>
>> >> >> wrote:
>> >> >> >
>> >> >> >> Thank you
>> >> >> >> But my question is: can I (after performing TBSS scripts)
>> compare
>> >> >> >> subjects
>> >> >> >> with a different number of directions in their DTI? If the
>> quality
>> >> >> >> is
>> >> >> >> different - as you are saying - I think the answer is no.
>> >> >> >>
>> >> >> >> Angela
>> >> >> >>
>> >> >> >>
>> >> >> >> >
>> >> >> >> > I can provide the following insight:1. The more diffusion
>> >> >> directions,
>> >> >> >> the
>> >> >> >> > better the dependent measure will be.2. You will have perform
>> >> >> >> across-group
>> >> >> >> > analyses with FEAT.3. You should probably resample your
>> original
>> >> >> image
>> >> >> >> to
>> >> >> >> > 1x1x1mm resolution before spatially normailizing to the MNI
>> >> >> >> templae.Hope
>> >> >> >> > this helps.Christine
>> >> >> >> > > Date: Tue, 24 Jan 2012 12:40:50 +0100
>> >> >> >> >> From: [log in to unmask]
>> >> >> >> >> Subject: [FSL] TBSS some questions
>> >> >> >> >> To: [log in to unmask]
>> >> >> >> >>
>> >> >> >> >> Dear FSL experts,
>> >> >> >> >> I have some questions about TBSS for which I have not found
>> >> >> answers
>> >> >> >> in
>> >> >> >> >> the
>> >> >> >> >> mailing list.
>> >> >> >> >>
>> >> >> >> >> 1. Which is the influence of the number of directions on the
>> >> >> quality
>> >> >> >> of
>> >> >> >> >> TBSS?
>> >> >> >> >>
>> >> >> >> >> I have a set of DTI images with B0=800 and number of
>> >> >> >> >> directions=16
>> >> >> >> and
>> >> >> >> >> another set with the same B0 and 32 directions.
>> >> >> >> >> I guess that probabilistic tracking is not reliable with
>> only 16
>> >> >> >> >> directions, but what about TBSS? Can images of the two
>> groups be
>> >> >> >> >> compared
>> >> >> >> >> with TBSS in some way?
>> >> >> >> >>
>> >> >> >> >> 2. During the TBSS procedure there is a registration to the
>> >> >> standard
>> >> >> >> >> image
>> >> >> >> >> with resultion 1mm*1mm*1mm. This result in a very long time
>> when
>> >> >> >> >> performing statistics with randomise. My original scanning
>> >> >> resolution
>> >> >> >> is
>> >> >> >> >> 2mm. Do you think that registration of the skeletonised
>> images
>> >> >> >> >> and
>> >> >> >> mask
>> >> >> >> >> to
>> >> >> >> >> a 2mm resolution would impair the statistical analyses? Or
>> is it
>> >> >> >> >> a
>> >> >> >> >> feasable approach?
>> >> >> >> >>
>> >> >> >> >> Thank you for your help!
>> >> >> >> >>
>> >> >> >> >> Angela
>> >> >> >> >
>> >> >> >>
>> >> >> >
>> >> >
>> >
>> >
>>
>>
>>
>
>

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