[Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all
Hi, As of version 5.1 the Talairach stage precedes the nu-correction stage. Is there an option or possibility to switch this order? Cheers, Ed ___ 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.
[Freesurfer] WM modification
Dear freesurfers,May be a silly question:I'd modified the wm.mgz using the lastest current version of FS as suggested in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits?highlight=%28matter%29%7C%28White%29Is there any output on FS that quantifies the lesions as volume or something like?When I'd checked the aseg.stats the cortical wm for both hemispheres has changed, as a matter of fact it has been increased when I filled the lesions, which I'm guessing would be a normal behavior, but I'm wondering how to know how much of this wm is lesioned ?Could you guide me on this?Many thanks in advanced,Gabriel.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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.
[Freesurfer] Segmentation
Hi, We're trying to edit the aseg segmentation and reconstruct it. If we run 'recon-all -s subject -make all' does that depend on any information from the surfaces or brainmask volume, or are the stats independent of that? Thank you, Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia___ 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.
Re: [Freesurfer] Longitudinal Edits, skull strip and wmcp, how to do this longitudinally
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
Re: [Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all
Ed, Hi, no there is not an option to switch them. The nu correct stage in 5.1 needs the talairach to run. However, if your intent is to get a better talairach result by using the nu corrected input (as it did prior to v5.1), then you can do the following: recon-all -s subjid -motioncor -talairach -nuintensitycor then run: recon-all -s subjid -all -talairach-nu -clean-tal on the second run, it will use the nu.mgz in the talairach stage. Note that in the next version, v5.2, one iteration of nu_correct will be run prior to the talairach stage to use as input to the talairach stage, in order to get the better talairach results that people were seeing prior to v5.1. it will still run the current nu_correct stage to create nu.mgz (the nu used in talairach gets discarded). Nick On Mon, 2012-04-16 at 09:10 +0200, Ed Gronenschild wrote: Hi, As of version 5.1 the Talairach stage precedes the nu-correction stage. Is there an option or possibility to switch this order? Cheers, Ed ___ 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.
Re: [Freesurfer] Segmentation
Hi Jordan, I'm not sure I understand your question. If you run -make all, it will run recon-all again starting at the earliest step in which there are files that were changed that affect that step. It will run all the way through to the end as each step affects the next one. This will change your stats which are produced in autorecon3. Allison On Apr 16, 2012, at 10:28 AM, Jordan Pierce jepierc...@yahoo.com wrote: Hi, We're trying to edit the aseg segmentation and reconstruct it. If we run 'recon-all -s subject -make all' does that depend on any information from the surfaces or brainmask volume, or are the stats independent of that? Thank you, Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia ___ 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.
