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
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, miracooloz@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%C2%A0I 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: miracooloz@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 miracooloz@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
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, miracooloz@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%C2%A0I 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: miracooloz@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 miracooloz@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
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, miracooloz@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, miracooloz@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%C2%A0I 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: miracooloz@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 miracooloz@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
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, miracooloz@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, miracooloz@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%C2%A0I 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: miracooloz@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 miracooloz@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
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, miracooloz@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, miracooloz@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, miracooloz@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%C2%A0I 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: miracooloz@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 miracooloz@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
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, miracooloz@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, miracooloz@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, miracooloz@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%C2%A0I 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: miracooloz@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 miracooloz@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
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, miracooloz@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, miracooloz@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, miracooloz@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, miracooloz@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%C2%A0I 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: miracooloz@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 miracooloz@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
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, miracooloz@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, miracooloz@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, miracooloz@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, miracooloz@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%C2%A0I 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: miracooloz@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 miracooloz@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
Yes, I think so Bruce
On Nov 6, 2016, at 6:34 PM, miracooloz@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, miracooloz@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, miracooloz@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, miracooloz@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, miracooloz@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: miracooloz@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 miracooloz@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
Thank you very much Bruce. Last questions. 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. Also, 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, miracooloz@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, miracooloz@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, miracooloz@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, miracooloz@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, miracooloz@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: miracooloz@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 miracooloz@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
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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, miracooloz@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, miracooloz@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, miracooloz@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, miracooloz@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, miracooloz@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: miracooloz@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 miracooloz@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
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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.
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, miracooloz@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, miracooloz@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, miracooloz@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, miracooloz@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, miracooloz@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: miracooloz@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 miracooloz@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
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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.
The brainmask.auto.mgz will be our stripping, but the brain,ask.mgz will be yours
Cheers Bruce
On Nov 8, 2016, at 10:21 AM, miracooloz@gmail.com wrote:
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, miracooloz@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, miracooloz@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, miracooloz@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, miracooloz@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, miracooloz@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: miracooloz@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 miracooloz@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
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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.
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miracle ozzoude -
miracooloz＠gmail.com