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