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 < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Vincent,
- 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.
- 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:
I see, yes this would not make sense. Thank you for the explanation!
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?
- 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:
- 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).
- 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.
- 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, vbrunsch@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).
- 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?
- 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.