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FSL  January 2012

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Subject:

Re: Re : [FSL] TBSS some questions

From:

Michael Harms <[log in to unmask]>

Reply-To:

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

Date:

Tue, 24 Jan 2012 13:17:57 -0600

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (170 lines)

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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