 |
 |
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 >> >> >> >> > >> >> >> >> >> >> >> > >> >> > >> > >> > >> >> >> > >