Hi Mark, did you see our wiki page about longitudinal editing? It discusses these things in detail (e.g. where to edit what): http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
also the tutorial has several examples on how to edit: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial Let me know if this does not answer your questions. Generally it is a good idea to first fix the cross sectionals, then you also need to fix the base if still necessary. The longitudinals should be fine and should need no fixes. In several cases you might be able to get away with only fixing the base, that will save a lot of time, but is not the best option as problems from the cross can creep into the longs (through the aseg mainly, not the surfaces as they come from the base). Best, Martin On Sat, 2012-04-14 at 21:27 -0500, Mark Fletcher wrote: > For some of my subjects, I need to make many different types of edits > on my longitudinal data, but have a few questions regarding the > order/how to do this. I have read the details of this website > (http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) but > wanted to confirm a few things. In regards to the following > questions, I have not yet run the "create base" yet for anything. > Also, I am asking these questions because I already made all of the > following edits (and others) on the cross-sectionals as described at > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData), > and need to know if this was the right time to do this, and what to do after? > > > For subjects that just need white matter control points: For > subjects that just need white matter control points, I have added them > on each cross-sectional time point, and reprocessed them via the > command (recon-all -autorecon2-cp -autorecon3 -subjid cp_before). Is > the next step to simply run (recon-all -base <templateid> -tp <tp1id> > -tp <tp2id> ... -all) pointing to the subjects that have been > corrected with control points? Do I need to add any flags or > additional commands for the base creation to take the white matter > control points into account? Should I need to make any further edits > to the "base" or longitudinals after this? > > For subjects needing skull stripping and white matter control points: > A few of my subjects need both WMCP's and skull stripping adjustments? > I'm assuming that you should do the skull stripping first and then the > WMCP, is this correct? Does it matter? I am doing this to the cross > sectionals only. After reprocessing these, is the next step to simply > run (recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all) > pointing to the subjects that have been corrected with control points > and skull strip? Do I need to add any flags or additional commands for > the base creation to take the white matter control points into > account? Should I need to make any further edits to the "base" or > longitudinals after this? Does all this hold true if making manual > edits of the skull > > Subjects that need Pial Edits amidst other things: A few subjects > need pial edits? I've done this to the crossectionals, is this > appropriate (I couldn't tell from the longitudinal edits page? Any > order that this should fit in? After reprocessing them for the edits, > is the next step to simply run (recon-all -base <templateid> -tp > <tp1id> -tp <tp2id> ... -all) pointing to the subjects that have been > corrected with the pial edits? Do I need to add any flags or > additional commands for the base creation to take the white matter > control points into account? Should I need to make any further edits > to the "base" or longitudinals after this? > > Making Edits to White Matter: One of my subjects seem to have > lesions similar to those described here > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits). > When/where do I edit this in the longitudinal processing stream? These > subject also needs WMCP, is their an important order for doing these. After > reprocessing them for the edits, is the next step to simply run (recon-all > -base <templateid> -tp <tp1id> -tp <tp2id> ... -all) pointing to the subjects > that have been corrected to the white matter? Do I need to add any flags or > additional commands for the base creation to take the white matter control > points into account? Should I need to make any further edits to the "base" > or longitudinals after this? > > Correcting Topological Defects: When should I correct topological > defects as described here > ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect ). > Same end questions as ones above about what to do after fixing these. > > Filling Lateral Ventricle: Another question about White matter edits. > One of my subjects needs to have its lateral ventricle filled (aka, > adding it to the white matter). When/where should I do this. After > processing it, what commands to run to create base? > > > Thanks for answering my many questions. I am very impressed at the > functionality of FreeSurfer, but want to be sure I am using them > correctly. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
