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, 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 > > -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu _______________________________________________ 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.
