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
Hi Vincent,
for the surface based analysis (SBA) base and long runs need to be correct. You mainly need to do potential edits in the base. For a full description of potential manual edits (and where to make them) see: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits If you edit base, you need to re-run all longitudinals.
QAtools http://freesurfer.net/fswiki/QATools may be helpful for checking things and you can run them on the base and the longitudinals to make sure everything is right. I usually check skull strip and surfaces etc. manually and never used the QATools.
For Tracula, also base and long runs need to be correct.
Best, Martin
On 10/11/2013 11:17 AM, 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
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, 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
Hi Anastasia!
I will go backwards with increasing difficulty for me 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 labeling 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
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
Dear Anastasia,
To 4.: I am comparing TBSS with Tracula results and it seems TBSS now additionaly allows to analyze the partial volumes f1, f2.. of the bedpostX step in a sensible way. My question is: Can I use the bedpostX output from Tracula? I guess so but I am not 100 % sure as with Tracula I have used the T1 weighted image as the volume with no diffusion weighting in order to construct the nodif_brain_mask that is necessary for bedpostX whereas the TBSS processing steps were all run with a mask extracted with BET. Is this different mask a problem for following voxelwise TBSS analysis of the data in all_F*_skeletonised?
Best, 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
--- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com
Hi Vincent - TBSS shouldn't care what mask was applied to the FA maps that you feed into it. Of course it's best if the same mask has been applied to both the FA maps and bedpostx outputs. However, the diffusion and structural masks should only differ in voxels around the brain, not deep in the WM. So I think you'll be fine.
a.y
On Sat, 14 Dec 2013, Vincent Brunsch wrote:
Dear Anastasia,
To 4.: I am comparing TBSS with Tracula results and it seems TBSS now additionaly allows to analyze the partial volumes f1, f2.. of the bedpostX step in a sensible way. My question is: Can I use the bedpostX output from Tracula? I guess so but I am not 100 % sure as with Tracula I have used the T1 weighted image as the volume with no diffusion weighting in order to construct the nodif_brain_mask that is necessary for bedpostX whereas the TBSS processing steps were all run with a mask extracted with BET. Is this different mask a problem for following voxelwise TBSS analysis of the data in all_F*_skeletonised?
Best, 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
This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Martin Reuter -
vbrunsch＠nmr.mgh.harvard.edu -
Vincent Brunsch