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.
Dears freesurfers,
I have just finished a GLM analysis in freesurfer and found a cluster whose thickness significantlyassociated with some behavior index. I would like to extract data from this cluster for further analysis, i.e., mean thickness in this cluster for each subject.
How could I extract the thickness value of this cluster for all subjects?
Thanks a lot if you guys can kindly provide some clues!
best regards,
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.
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chenchunhuichina -
Mark Fletcher -
Martin Reuter