Hi Gari - The command is: freeview dmri/dtifit_FA.nii.gz dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.5
a.y
On Tue, 15 Oct 2013, Garikoitz Lerma-Usabiaga wrote:
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, 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:
- 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
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