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Hi Douglas,
First of all, thank you for your help. I forgot to mention that I am already using skull-stripped data for the recon-all processing stream. Therefore, I stopped after -autorecon1 and copied the T1.mgz to brainmask.mgz and brainmask.auto.mgz and continued processing with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas -s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine without errors. I also compared the T1.mgz from both approaches and they looked identical. My question, can I use this approach with the "-no-wsgcaatlas" for all subjects or is there something to consider here?
Best, René
Are all your subjects skull stripped or just this one?
On 5/24/2020 9:08 AM, Schranzer René wrote:
External Email - Use Caution
Hi Douglas,
First of all, thank you for your help.
I forgot to mention that I am already using skull-stripped data for the recon-all processing stream. Therefore, I stopped after -autorecon1 and copied the T1.mgz to brainmask.mgz and brainmask.auto.mgz and continued processing with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas -s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine without errors. I also compared the T1.mgz from both approaches and they looked identical.
My question, can I use this approach with the "-no-wsgcaatlas" for all subjects or is there something to consider here?
Best, René
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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All subjects.
Best, René
Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Douglas N. Greve Gesendet: Mittwoch, 27. Mai 2020 18:37 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)
Are all your subjects skull stripped or just this one? On 5/24/2020 9:08 AM, Schranzer René wrote:
External Email - Use Caution Hi Douglas,
First of all, thank you for your help. I forgot to mention that I am already using skull-stripped data for the recon-all processing stream. Therefore, I stopped after -autorecon1 and copied the T1.mgz to brainmask.mgz and brainmask.auto.mgz and continued processing with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas -s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine without errors. I also compared the T1.mgz from both approaches and they looked identical. My question, can I use this approach with the "-no-wsgcaatlas" for all subjects or is there something to consider here?
Best, René
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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You can use it with all subjects then
On 5/28/2020 3:28 AM, Schranzer René wrote:
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All subjects.
Best,
René
*Von:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *Im Auftrag von *Douglas N. Greve *Gesendet:* Mittwoch, 27. Mai 2020 18:37 *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)
Are all your subjects skull stripped or just this one?
On 5/24/2020 9:08 AM, Schranzer René wrote:
* External Email - Use Caution * Hi Douglas, First of all, thank you for your help. I forgot to mention that I am already using skull-stripped data for the recon-all processing stream. Therefore, I stopped after -autorecon1 and copied the T1.mgz to brainmask.mgz and brainmask.auto.mgz and continued processing with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas -s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine without errors. I also compared the T1.mgz from both approaches and they looked identical. My question, can I use this approach with the "-no-wsgcaatlas" for all subjects or is there something to consider here? Best, René _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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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Hi Douglas,
Thanks for your help! Two more questions: Is it possible to use the individual brain mask of my skull stripped data as a "mask image" for the step of the NU Intensity correction in recon-all with an additional flag to carry out a better bias correction? And is it possible to use ANTsN3 instead of ANTsN4, if someone wants it?
Best, René Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Douglas N. Greve Gesendet: Donnerstag, 28. Mai 2020 17:47 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)
You can use it with all subjects then On 5/28/2020 3:28 AM, Schranzer René wrote:
External Email - Use Caution All subjects.
Best, René
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Douglas N. Greve Gesendet: Mittwoch, 27. Mai 2020 18:37 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)
Are all your subjects skull stripped or just this one? On 5/24/2020 9:08 AM, Schranzer René wrote:
External Email - Use Caution Hi Douglas,
First of all, thank you for your help. I forgot to mention that I am already using skull-stripped data for the recon-all processing stream. Therefore, I stopped after -autorecon1 and copied the T1.mgz to brainmask.mgz and brainmask.auto.mgz and continued processing with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas -s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine without errors. I also compared the T1.mgz from both approaches and they looked identical. My question, can I use this approach with the "-no-wsgcaatlas" for all subjects or is there something to consider here?
Best, René
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can use ANTS N3 by adding -ants-n3 to the command line. In theory, you can use a mask, but I vaguely remember that there was a bug when someone tried it in our code
On 5/28/2020 12:37 PM, Schranzer René wrote:
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Hi Douglas,
Thanks for your help!
Two more questions:
Is it possible to use the individual brain mask of my skull stripped data as a "mask image" for the step of the NU Intensity correction in recon-all with an additional flag to carry out a better bias correction?
And is it possible to use ANTsN3 instead of ANTsN4, if someone wants it?
Best,
René
*Von:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *Im Auftrag von *Douglas N. Greve *Gesendet:* Donnerstag, 28. Mai 2020 17:47 *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)
You can use it with all subjects then
On 5/28/2020 3:28 AM, Schranzer René wrote:
* External Email - Use Caution * All subjects. Best, René *Von:*freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *Im Auftrag von *Douglas N. Greve *Gesendet:* Mittwoch, 27. Mai 2020 18:37 *An:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Betreff:* Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1) Are all your subjects skull stripped or just this one? On 5/24/2020 9:08 AM, Schranzer René wrote: * External Email - Use Caution * Hi Douglas, First of all, thank you for your help. I forgot to mention that I am already using skull-stripped data for the recon-all processing stream. Therefore, I stopped after -autorecon1 and copied the T1.mgz to brainmask.mgz and brainmask.auto.mgz and continued processing with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas -s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine without errors. I also compared the T1.mgz from both approaches and they looked identical. My question, can I use this approach with the "-no-wsgcaatlas" for all subjects or is there something to consider here? Best, René _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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@nmr.mgh.harvard.edu
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Schranzer René