Thank you very much Bruce. Last questions. When I replace FS generated brainmask.mgz with mine, does the original also remain in the mri folder( that's having 2 brainmask.mgz) or is the original permanently replaced with my own brainmask.mgz ( that's only 1 brainmask.mgz which is mine)? Second, any reasons why you suggested I avoid " - no" flags? This is because I searched through the forum and it seem the " -no flag" was encouraged whenever someone wanted to replace FS generated volume with their own, especially in the case of skull stripping. Third, should my last recon step be "recon-all -autorecon2-wm -autorecon3 " once I have replaced the FS generated wm.seg.mgz with mine in order to complete the recon-all processing? Lastly, how do I check if my replaced volumes are correctly aligned with FS volumes from recon-all -all ? Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Sunday, November 6, 2016 7:08 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] Fw: recon-all steps question Yes, I think so Bruce > On Nov 6, 2016, at 6:34 PM, miracoo...@gmail.com wrote: > > Hence, you are saying I should run recon-all -autorecon1 -i -s subjid then > replace the FS generated brainmask.mgz with my own stripped volume. Also, > should I run recon-all -autorecon2 with wm segmentation ( after replacing the > stripped volume ) and replace FS generated wm.seg.mgz with my wm segmentation > volume? Thank you. > Best, > Paul > Sent from my BlackBerry 10 smartphone. > Original Message > From: Bruce Fischl > Sent: Sunday, November 6, 2016 6:15 PM > To: Freesurfer support list > Reply To: Freesurfer support list > Subject: Re: [Freesurfer] Fw: recon-all steps question > > I would run autorecon1 witth skull stripping, then replace it with your > own stripped volume (the brainmask.mgz). It will treat that as a "manual > edit" since brainmask.mgz will be different than brainmask.auto.mgz, and > hence it won't override it > > cheers > Bruce > > > On Sun, 6 Nov 2016, > miracoo...@gmail.com wrote: > >> Thank very much Bruce. Does it mean I have to run recon-all -autorecon1 >> -noskullstrip, then recon-all -autorecon2 -nosegmentation ( with the skull >> stripped volume) . Finally, recon-all -autorecon2-wm -autorecon3 -s subjid( >> with the wm and lesion stuff)? >> Thanks > >> Sent from my BlackBerry 10 smartphone. >> Original Message >> From: Bruce Fischl >> Sent: Sunday, November 6, 2016 12:14 PM >> To: Freesurfer support list >> Reply To: Freesurfer support list >> Subject: Re: [Freesurfer] Fw: recon-all steps question >> >> Hi Paul >> >> hmm, you have to be a bit careful with the -no* flags as you want to avoid >> running those steps, but you want make sure FS knows that the typical >> output of the steps you skipped exists and should be used. Others can help >> you with the logic of recon-all better than I can, but I think you are >> probably best off replacing the relevant volumes and running from there >> forward. You might need to run autorecon1, then insert your skull-stripped >> volume, then autorecon2, insert your wm and lesion stuff, then run >> autorecon2-wm, but I'm not totally sure since what you are doing is so >> non-standard. >> >> cheers >> Bruce >> >> >> On Fri, 4 Nov 2016, >> miracoo...@gmail.com wrote: >> >>> We have already skull stripped and white matter segmented volume ( used >>> lesion explorer) . Hence, I want to replace freesurfer 's generated outputs >>> for this steps ( brainmask.mgz for skull strip and wm.seg.mgz (not wm.mgz ) >>> for white matter) with ours. I know recon-all -all performs all 31 steps >>> and inserting " -nostep " flag tells freesurfer to skip that step. Covering >>> and Creating a symbolic link to our files and then, running the remaining >>> steps of recon-all might help achieve this ( I believe) . Replacing this >>> freesurfer outputs with ours will reduce time spent on pial and white >>> matter edits. >>> Best, >>> Paul >>> >>> Sent from my BlackBerry 10 smartphone. >>> Original Message >>> From: Bruce Fischl >>> Sent: Friday, November 4, 2016 3:37 PM >>> To: Freesurfer support list >>> Reply To: Freesurfer support list >>> Subject: Re: [Freesurfer] Fw: recon-all steps question >>> >>> >>> Hi Paul >>> >>> can we take a step back. What are you trying to achieve by avoiding these >>> steps? >>> >>> cheers >>> Bruce >>> >>> >>>> On Fri, 4 Nov 2016, miracoo...@gmail.com wrote: >>>> >>>> Thanks Bruce. Another question, since " -no segmentation " flag skips the >>>> white matter segmentation step of recon-all. Can I also use the same >>>> logic as the "-noskullstrip" flag to replace the wm.seg.mgz file? That's, >>>> run " recon-all -autorecon1 -autorecon2 -nosegmentation -s subjid ". Then >>>> copy/convert my already segmented brain and name it wm.seg.mgz. After >>>> that, treat it as if I had freesurfer's wm.seg.mgz and finally, run " >>>> recon-all -autorecon3 -s " to complete the process. What do you think? >>>> Best, Paul >>>> >>>> Sent from my BlackBerry 10 smartphone. >>>> Original Message >>>> From: Bruce Fischl >>>> Sent: Friday, November 4, 2016 10:50 AM >>>> To: Freesurfer support list >>>> Reply To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Fw: recon-all steps question >>>> >>>> Hi Paul >>>> >>>> >>>> we required the T1.mgz, brainmask.auto.mgz and brainmask.mgz volumes so >>>> must create them somehow. I think if you copy/convert your already-stripped >>>> and name it brainmask.mgz we should treat that as if you had edited our >>>> skull stripping and you should be able to run from their forward >>>> (autorecon2 and autorecon3 I believe) >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>>> On Fri, 4 Nov 2016, miracoo...@gmail.com wrote: >>>>> >>>>> Please can someone answer this. Thanks >>>>> " >>>>> Hello Freesurfer, I have couple of questions. While going through the >>>>> frequently asked questions on your >>>>> pagehttp://freesurfer.net/fswiki/UserContributions/FAQ I came across a >>>>> question regarding how to integrate a skull stripped from another problem >>>>> into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid ----> >>>>> create a symbolic link from T1.mgz to brainmask.auto.mgz and another like >>>>> from brainmask.auto.mgz to brainmask.mgz ------> after run the finall >>>>> stages >>>>> of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). >>>>> >>>>> First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created >>>>> during skull stripping? why are they present if I included the "-no >>>>> skullstrip" flag? >>>>> >>>>> Second question, where do I insert my already skull stripped data in the >>>>> symbolic link? >>>>> >>>>> Last question, the final stages of recon-all ( recon-all -autorecon2 >>>>> -autorecon3) doesn't include skull stripping, how can I be sure my skull >>>>> stripped data was incorporated into the freesurfer recon-all process? >>>>> >>>>> Best, >>>>> Paul >>>>> >>>>> Sent from my BlackBerry 10 smartphone. >>>>> From: miracoo...@gmail.com >>>>> Sent: Wednesday, November 2, 2016 9:39 AM >>>>> To: Freesurfer support list >>>>> Subject: Fw: recon-all steps question >>>>> >>>>> >>>>> >>>>> Sent from my BlackBerry 10 smartphone. >>>>> From: miracle ozzoude <miracoo...@gmail.com> >>>>> Sent: Monday, October 31, 2016 8:39 AM >>>>> To: Douglas N Greve >>>>> Subject: recon-all steps question >>>>> >>>>> Hello Freesurfer, I have couple of questions. While going through the >>>>> frequently asked questions on your >>>>> page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a >>>>> question regarding how to integrate a skull stripped from another problem >>>>> into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid ----> >>>>> create a symbolic link from T1.mgz to brainmask.auto.mgz and another like >>>>> from brainmask.auto.mgz to brainmask.mgz ------> after run the finall >>>>> stages >>>>> of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). >>>>> >>>>> First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created >>>>> during skull stripping? why are they present if I included the "-no >>>>> skullstrip" flag? >>>>> >>>>> Second question, where do I insert my already skull stripped data in the >>>>> symbolic link? >>>>> >>>>> Last question, the final stages of recon-all doesn't include skull >>>>> stripping, how can I be sure my skull stripped data was incorporated into >>>>> the freesurfer recon-all process? >>>>> >>>>> Best, >>>>> Paul >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> >> >> _______________________________________________ >> 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 > > _______________________________________________ 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. 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