Hi Anastasia, could explain a little bit more what do you check exactly here?
"What I usually look at is dlabel/diff/aparc+aseg.bbr.nii.gz, overlaid on dmri/dtifit_FA.nii.gz." Which would be the freeview command to visualize it? Thanks! Gari On Mon, Oct 14, 2013 at 11:12 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Vincent, > > 3. It's a pain, isn't it? I sympathize but looking at the data is always a > good idea. Since you'll see all 3 views in fslview, the dark slices will > look like dark lines in two of these views, so you don't have to scroll > through slices. There's a couple of things you can do about motion, for > example you can remove the DWI volumes that have the artifacts. But you'll > have to make sure you're not doing this more for one group than the other. > > 2. What I usually look at is dlabel/diff/aparc+aseg.bbr.nii.gz, overlaid > on dmri/dtifit_FA.nii.gz. And yes, I do this for all subjects and yes, it > takes a while. Listening to music helps. > > Let me know if you have more questions! > a.y > > On Mon, 14 Oct 2013, Vincent Brunsch wrote: > > > Hi Anastasia! > > > > I will go backwards with increasing difficulty to understand everything: > > > > 4. I see, yes this would not make sense. Thank you for the explanation! > > > > 3. With fslview I will have to run through 393,120 slices, then. (72 > slices > > in z-direction for our 70 DWI scans for tp1 and tp2 for each of our 39 > > subjects) I will go dwi image by dwi image running through the 72 slices > > rather fast. Just to make sure I am not wasting a lot of time: is this > what I > > should do? If I detect slices that are much darker than their neighbors, > will > > I need to exclude this subject for the analysis or can I do something > about > > it? > > > > 2. Yes, I use bbregister and I also use the anatomical T1 weighted scan > to > > extract the brain mask (usemaskanat=1). To make sure that everything is > > alright, I would go slice by slice in tkmedit with > > tkmedit [subject] brainmask.mgz -surfs -aparc+aseg where [subject] would > be > > the base AND both longitudinal runs. I understand that I need to check if > > white matter is where it should be, if the cortical and pial surfaces are > > where they should be and if the labelling is correct. Again, as this will > > take probably even longer than 3. I would like to make sure this is the > right > > thing to do before starting the quality check. > > > > Thanks again! > > Vincent > > > > > > > > Am 10/11/2013 2:13 PM, schrieb Anastasia Yendiki: > >> > >> Hi Vincent - I'll take on the tracula-related parts: > >> > >> 2. For tracula, the part of the recon-all output that matters is the > >> aparc+aseg. The surfaces will play a role only the DWI-to-T1 > registration > >> (assuming you opt to use bbregister). > >> > >> 3. It's important to check your DWI data for obvious motion artifacts, > >> (slices that are much darker than their neighbors). Right now this has > to > >> be done visually, but it's on my list to produce some motion metrics as > >> part of the preprocessing. > >> > >> 4. The ball-and-stick model (that bedpostx fits to your data) is used by > >> the tractography algorithm in tracula, but there are no stats produced > on > >> the parameters of that model currently. That's something that can be > added > >> in the future as well. Note though that it wouldn't make sense to just > >> average f1 or f2 over the pathway, because compartment 1 in one voxel > may > >> correspond to compartment 2 in some other voxel. > >> > >> Hope this helps, > >> a.y > >> > >> On Fri, 11 Oct 2013, vbrun...@nmr.mgh.harvard.edu wrote: > >> > >>> Dear Freesurfer experts, > >>> > >>> I want to do a quality check on our imaging data. I used the > longitudinal > >>> stream for SBA and as the first step for the longitudinal white matter > >>> analysis with TRACULA. > >>> We had two time points in our study and thus, in the freesurfer output > >>> directory there are 5 folders per subject (2 cross-sectional runs, 2 > long > >>> runs and the base). > >>> > >>> 1. Would you recommend to use (all of) the QA_TOOLS on all of these 5 > >>> folders per subject for the SBA? > >>> 2. Independent of the previous question, for the longitudinal version > of > >>> TRACULA would you recommend to use (all of) the QA_TOOLS on the > freesurfer > >>> base folder only / additional folders? > >>> 3. In addition to the late visual check for well reconstructed pathways > >>> with freeview, is there another automated possibility to check the > quality > >>> of the diffusion weighted images beforehand/do you think this is > >>> necessary? > >>> > >>> 4. On another note: If I understand correctly, in TRACULA bedpostX is > used > >>> to reconstruct the pathways but then the mean over the voxels that were > >>> hit (by the MCMC sampling of the paths) of measures from the tensor > model > >>> are taken as outputs. I wonder, is there also the possibility of using > the > >>> partial volumes f1, f2,.. as output measures? > >>> > >>> Best, > >>> Vincent > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >> > >> > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
