So, what bvec/bvec file should be associated with the BASE scan? It isn’t clear to me how the bvec/bval in the BASE scan get used in trac-paths.
I see the point of your note of caution, but unless someone moved the same amount (and for the same frames) for their sessions in a longitudinal study, the same issue applies, even if you use all frames “as is”. In that case, the potential bias would be due to using data of differing quality across sessions. In a sense, we are just making the issue explicit by discarding bad frames as part of a QC step. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 7/4/16, 2:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ayend...@nmr.mgh.harvard.edu> wrote: Hi Michael - Indeed it should not be too difficult to add the feature of specifying the b-value table for each scan and I can add this in the next version. However, I would be a bit careful with removing different DWI volumes for different time points. The acquisition should be as consistent as possible across time points. If you find that there's a longitudinal change, would this be because there were different directions/b-values in each time point or because of an actual change in the brain? I suppose that, unless there's a systematic bias, you might expect that these changes will be in different directions for different subjects and would then average out. But it's a tricky issue. Best, a.y On Fri, 1 Jul 2016, Harms, Michael wrote: > > Hi Anastasia, > Looking through the trac-preproc and trac-paths scripts, it is now clear >to me that all the time points for a given subject have to be >contained/specified > within the same dmrirc configuration file in order to implement a >longitudinal TRACULA analysis. So, I've answered my previous question in >that regard. > > The challenge in our case is that we have separately pre-processed the >dMRI data for each subject and time point, removing bad frames/volumes >(using the > DTIPrep QA tool). Thus, the bvecs/bvals are not identical for all the >time points of a given subject. We can specify the bvec file for each >subject/time > point using the bveclist configuration parameter. But there is no >analog available for bvals, since only a single bvalfile can be >specified. > > I see that this issue has been raised in a couple other posts relatively >recently (2015): > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html > but no working solution was provided at that time. > > I’m wondering if there is perhaps now a development version of TRACULA >that supports a “bvallist” capability? If not, it doesn’t look like it >would be too > difficult to modify trac-all to include that capability (modeling after >what is already in trac-all for the bveclist/bvecfile stuff). But, in >that case, > it isn’t immediately clear to me if there are other downstream “gotchas” >in the preproc, paths, or stats stage specific scripts/binaries that >would need > modifications as well. [I don’t see anything in the sections related to >the BASE-specific processing in trac-preproc involving bvals/bvecs, so >think we are > fine there. But it is harder for me to tell what is going on in >trac-paths]. > > thanks, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Harms, >Michael" <mha...@wustl.edu> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Wednesday, June 29, 2016 at 5:00 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] longitudinal tracula > > > Hi, > When running TRACULA with longitudinal data, is it necessary for all >scan waves of a given subject to be included in a single dmrirc file? My >initial > thought was “no”, that it would be fine to run one scan wave per subject >per dmrirc file (as long as the “baselist” variable is set appropriately >for each > scan wave and subject). > > But looking at the ‘trac-all’ script, I see > > if ($#baselist == 0) then#--->>> A single time point for each subject > … > else#--->>> Multiple time points for each subject > … > > So, I’m wondering why different sections in the code would be necessary >if in fact it is ok to process a single scan wave per dmrirc file. > > thanks, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > > > > >__________________________________________________________________________ >__________________________________________________________________________ >________ > > > The materials in this message are private and may contain Protected >Healthcare Information or other information of a sensitive nature. 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