Hi,
I used recon-all with all and its taking a lot of time. My main concern is only to get the stripped brain. I tried with autorecon1 as well but its also taking not less than 15min and I need to deal with a huge data. Last stage of autorecon1 is skull stripping which takes the NU corrected input (as it FS works as a pipeline). Is there any way to directly get the "stripped brain" and its binary mask.
I also need to ask, which file of the output (name with extension) is the "binary brain mask" ?
Best regards, Gunjan
Hi Gunjan
15 min is about what it is going to take. You could do it faster but then the failure rate would go up. We've tuned it to improve automaticity and reduce failures quite a bit.
cheers Bruce
On Sat, 22 Nov 2014, Gunjan Gautam wrote:
Hi,
I used recon-all with all and its taking a lot of time. My main concern is only to get the stripped brain. I tried with autorecon1 as well but its also taking not less than 15min and I need to deal with a huge data. Last stage of autorecon1 is skull stripping which takes the NU corrected input (as it FS works as a pipeline). Is there any way to directly get the "stripped brain" and its binary mask.
I also need to ask, which file of the output (name with extension) is the "binary brain mask" ?
Best regards, Gunjan
Thanks,
And what about the binary brain mask? I am able to see only the stripped volume but need the binary brain mask as well.
Gunjan On Nov 23, 2014 8:49 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Gunjan
15 min is about what it is going to take. You could do it faster but then the failure rate would go up. We've tuned it to improve automaticity and reduce failures quite a bit.
cheers Bruce
On Sat, 22 Nov 2014, Gunjan Gautam wrote:
Hi,
I used recon-all with all and its taking a lot of time. My main concern is only to get the stripped brain. I tried with autorecon1 as well but its also taking not less than 15min and I need to deal with a huge data. Last stage of autorecon1 is skull stripping which takes the NU corrected input (as it FS works as a pipeline). Is there any way to directly get the "stripped brain" and its binary mask.
I also need to ask, which file of the output (name with extension) is the "binary brain mask" ?
Best regards, Gunjan
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we don't have a binary one, but all voxels in brainmask.mgz that are >5 are in brain and everything <5 is not in brain
cheers Bruce
On Sun, 23 Nov 2014, Gunjan Gautam wrote:
Thanks,
And what about the binary brain mask? I am able to see only the stripped volume but need the binary brain mask as well.
Gunjan
On Nov 23, 2014 8:49 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote: Hi Gunjan
15 min is about what it is going to take. You could do it faster but then the failure rate would go up. We've tuned it to improve automaticity and reduce failures quite a bit. cheers Bruce On Sat, 22 Nov 2014, Gunjan Gautam wrote: Hi, I used recon-all with all and its taking a lot of time. My main concern is only to get the stripped brain. I tried with autorecon1 as well but its also taking not less than 15min and I need to deal with a huge data. Last stage of autorecon1 is skull stripping which takes the NU corrected input (as it FS works as a pipeline). Is there any way to directly get the "stripped brain" and its binary mask. I also need to ask, which file of the output (name with extension) is the "binary brain mask" ? Best regards, Gunjan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Ok thank you Bruce On Nov 23, 2014 10:37 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
we don't have a binary one, but all voxels in brainmask.mgz that are >5 are in brain and everything <5 is not in brain
cheers Bruce
On Sun, 23 Nov 2014, Gunjan Gautam wrote:
Thanks,
And what about the binary brain mask? I am able to see only the stripped volume but need the binary brain mask as well.
Gunjan
On Nov 23, 2014 8:49 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote: Hi Gunjan
15 min is about what it is going to take. You could do it faster but then the failure rate would go up. We've tuned it to improve automaticity and reduce failures quite a bit. cheers Bruce On Sat, 22 Nov 2014, Gunjan Gautam wrote: Hi, I used recon-all with all and its taking a lot of time. My main concern is only to get the stripped brain. I tried with autorecon1 as well but its also taking not less than 15min and I need to deal with a huge data. Last stage of autorecon1 is skull stripping which takes the NU corrected input (as it FS works as a pipeline). Is there any way to directly get the "stripped brain" and its binary mask. I also need to ask, which file of the output (name with extension) is the "binary brain mask" ? Best regards, Gunjan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Bruce,
What about the voxels having value equal to 5 (if exists) ?
Gunjan
On Sun, Nov 23, 2014 at 10:39 PM, Gunjan Gautam gunjan.gemini29@gmail.com wrote:
Ok thank you Bruce On Nov 23, 2014 10:37 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
we don't have a binary one, but all voxels in brainmask.mgz that are >5 are in brain and everything <5 is not in brain
cheers Bruce
On Sun, 23 Nov 2014, Gunjan Gautam wrote:
Thanks,
And what about the binary brain mask? I am able to see only the stripped volume but need the binary brain mask as well.
Gunjan
On Nov 23, 2014 8:49 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote: Hi Gunjan
15 min is about what it is going to take. You could do it faster but then the failure rate would go up. We've tuned it to improve automaticity and reduce failures quite a bit. cheers Bruce On Sat, 22 Nov 2014, Gunjan Gautam wrote: Hi, I used recon-all with all and its taking a lot of time. My main concern is only to get the stripped brain. I tried with autorecon1 as well but its also taking not less than 15min and I need to deal with a huge data. Last stage of autorecon1 is skull stripping which takes the NU corrected input (as it FS works as a pipeline). Is there any way to directly get the "stripped brain" and its binary mask. I also need to ask, which file of the output (name with extension) is the "binary brain mask" ? Best regards, Gunjan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
sorry, I think >=5 is in brain
On Mon, 24 Nov 2014, Gunjan Gautam wrote:
Hi Bruce, What about the voxels having value equal to 5 (if exists) ?
Gunjan
On Sun, Nov 23, 2014 at 10:39 PM, Gunjan Gautam gunjan.gemini29@gmail.com wrote:
Ok thank you Bruce On Nov 23, 2014 10:37 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: we don't have a binary one, but all voxels in brainmask.mgz that are >5 are in brain and everything <5 is not in brain cheers Bruce On Sun, 23 Nov 2014, Gunjan Gautam wrote: Thanks, And what about the binary brain mask? I am able to see only the stripped volume but need the binary brain mask as well. Gunjan On Nov 23, 2014 8:49 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: Hi Gunjan 15 min is about what it is going to take. You could do it faster but then the failure rate would go up. We've tuned it to improve automaticity and reduce failures quite a bit. cheers Bruce On Sat, 22 Nov 2014, Gunjan Gautam wrote: Hi, I used recon-all with all and its taking a lot of time. My main concern is only to get the stripped brain. I tried with autorecon1 as well but its also taking not less than 15min and I need to deal with a huge data. Last stage of autorecon1 is skull stripping which takes the NU corrected input (as it FS works as a pipeline). Is there any way to directly get the "stripped brain" and its binary mask. I also need to ask, which file of the output (name with extension) is the "binary brain mask" ? Best regards, Gunjan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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