Hi FS expert,
When I run recon-all -autorecon1 -subjid <subjid>, the Talaitach transform failed. Please see the attached log file. Is there a way to correct the error? Thanks!
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 13, 2017 5:48 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [strip skull for unregistered images]
Hi Yi
yes, brainmask.mgz is the skull stripped image.
And no, n3 is pretty gentle so I would think letting our normal intensity normalization run would be fine (and better than not doing it)
cheers Bruce
On Mon, 13 Nov 2017, Yi Li wrote:
Hi Bruce,
Thanks for the help! Is the skull-stripped image in Brainmask.mgz?
Another question: since my raw image has gone through B1 correction and N3 normalization, will you suggest I omit the nu and normalize step in -autorecon1?
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 13, 2017 10:50 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [strip skull for unregistered images]
Hi Yi
autorecon1 should do the skull stripping, so there is no need for the separate mri_mask call. The threshold of '5' is so to preserve edits in which voxels are turned 'off' (they are set to 1 I believe, but we reserve 2-4 as additional 'off' values).
The masking will not transform the voxel coordinates of the image
cheers Bruce
On Mon, 13 Nov 2017, Yi Li wrote:
Dear FS experts,
I would like to strip skulls from unregistered images which have gone through GradWarp, B1-correction, N3 normalization and phantom-based scaling. I run the following two commands in freeSurfer:
recon-all -autorecon1 -subjid <subjid>
mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz
My questions are
1) Currently I use 5 as threshold (-T 5). Is there a guidance for the setting of this parameter?
2) In the output file T1.final.mgz, is the skull-stripped image represented in ijk space (image index space) or in XYZ space (via transformation matrix)?
3) If the skull-stripped image is represented in XYZ space, how do I get it in ijk space?
Thanks in advance for the help!
Best Regards,
Yi Li (PhD)
Senior Computational Scientist
Computational Sciences
The Jackson Laboratory
Farmington, CT 06032
Tel: 860-837-2156
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---
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does this fail on all your subjects or just this one? Have you looked at the input image to make sure that there is nothing wrong with it?
On 11/16/2017 11:32 AM, Yi Li wrote:
Hi FS expert,
When I run recon-all -autorecon1 -subjid <subjid>, the Talaitach transform failed. Please see the attached log file. Is there a way to correct the error? Thanks!
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 13, 2017 5:48 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [strip skull for unregistered images]
Hi Yi
yes, brainmask.mgz is the skull stripped image.
And no, n3 is pretty gentle so I would think letting our normal intensity normalization run would be fine (and better than not doing it)
cheers Bruce
On Mon, 13 Nov 2017, Yi Li wrote:
Hi Bruce,
Thanks for the help! Is the skull-stripped image in Brainmask.mgz?
Another question: since my raw image has gone through B1 correction and N3 normalization, will you suggest I omit the nu and normalize step in -autorecon1?
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 13, 2017 10:50 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [strip skull for unregistered images]
Hi Yi
autorecon1 should do the skull stripping, so there is no need for the separate mri_mask call. The threshold of '5' is so to preserve edits in which voxels are turned 'off' (they are set to 1 I believe, but we reserve 2-4 as additional 'off' values).
The masking will not transform the voxel coordinates of the image
cheers Bruce
On Mon, 13 Nov 2017, Yi Li wrote:
Dear FS experts,
I would like to strip skulls from unregistered images which have gone through GradWarp, B1-correction, N3 normalization and phantom-based scaling. I run the following two commands in freeSurfer:
recon-all -autorecon1 -subjid <subjid>
mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz
My questions are
1) Currently I use 5 as threshold (-T 5). Is there a guidance for the setting of this parameter?
2) In the output file T1.final.mgz, is the skull-stripped image represented in ijk space (image index space) or in XYZ space (via transformation matrix)?
3) If the skull-stripped image is represented in XYZ space, how do I get it in ijk space?
Thanks in advance for the help!
Best Regards,
Yi Li (PhD)
Senior Computational Scientist
Computational Sciences
The Jackson Laboratory
Farmington, CT 06032
Tel: 860-837-2156
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Douglas,
This fails just on this one. Seems image is good. I attached it here. Thanks!
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, November 16, 2017 11:37 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Talairach failed when striping skull]
does this fail on all your subjects or just this one? Have you looked at the input image to make sure that there is nothing wrong with it?
On 11/16/2017 11:32 AM, Yi Li wrote:
Hi FS expert,
When I run recon-all -autorecon1 -subjid <subjid>, the Talaitach transform failed. Please see the attached log file. Is there a way to correct the error? Thanks!
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 13, 2017 5:48 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [strip skull for unregistered images]
Hi Yi
yes, brainmask.mgz is the skull stripped image.
And no, n3 is pretty gentle so I would think letting our normal intensity normalization run would be fine (and better than not doing it)
cheers Bruce
On Mon, 13 Nov 2017, Yi Li wrote:
Hi Bruce,
Thanks for the help! Is the skull-stripped image in Brainmask.mgz?
Another question: since my raw image has gone through B1 correction and N3 normalization, will you suggest I omit the nu and normalize step in -autorecon1?
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 13, 2017 10:50 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [strip skull for unregistered images]
Hi Yi
autorecon1 should do the skull stripping, so there is no need for the separate mri_mask call. The threshold of '5' is so to preserve edits in which voxels are turned 'off' (they are set to 1 I believe, but we reserve 2-4 as additional 'off' values).
The masking will not transform the voxel coordinates of the image
cheers Bruce
On Mon, 13 Nov 2017, Yi Li wrote:
Dear FS experts,
I would like to strip skulls from unregistered images which have gone through GradWarp, B1-correction, N3 normalization and phantom-based scaling. I run the following two commands in freeSurfer:
recon-all -autorecon1 -subjid <subjid>
mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz
My questions are
1) Currently I use 5 as threshold (-T 5). Is there a guidance for the setting of this parameter?
2) In the output file T1.final.mgz, is the skull-stripped image represented in ijk space (image index space) or in XYZ space (via transformation matrix)?
3) If the skull-stripped image is represented in XYZ space, how do I get it in ijk space?
Thanks in advance for the help!
Best Regards,
Yi Li (PhD)
Senior Computational Scientist
Computational Sciences
The Jackson Laboratory
Farmington, CT 06032
Tel: 860-837-2156
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Douglas,
This fails just on this one. Image seems good. I attached it in the previous mail but being held. Thanks!
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, November 16, 2017 11:37 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Talairach failed when striping skull]
does this fail on all your subjects or just this one? Have you looked at the input image to make sure that there is nothing wrong with it?
On 11/16/2017 11:32 AM, Yi Li wrote:
Hi FS expert,
When I run recon-all -autorecon1 -subjid <subjid>, the Talaitach transform failed. Please see the attached log file. Is there a way to correct the error? Thanks!
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 13, 2017 5:48 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [strip skull for unregistered images]
Hi Yi
yes, brainmask.mgz is the skull stripped image.
And no, n3 is pretty gentle so I would think letting our normal intensity normalization run would be fine (and better than not doing it)
cheers Bruce
On Mon, 13 Nov 2017, Yi Li wrote:
Hi Bruce,
Thanks for the help! Is the skull-stripped image in Brainmask.mgz?
Another question: since my raw image has gone through B1 correction and N3 normalization, will you suggest I omit the nu and normalize step in -autorecon1?
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 13, 2017 10:50 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [strip skull for unregistered images]
Hi Yi
autorecon1 should do the skull stripping, so there is no need for the separate mri_mask call. The threshold of '5' is so to preserve edits in which voxels are turned 'off' (they are set to 1 I believe, but we reserve 2-4 as additional 'off' values).
The masking will not transform the voxel coordinates of the image
cheers Bruce
On Mon, 13 Nov 2017, Yi Li wrote:
Dear FS experts,
I would like to strip skulls from unregistered images which have gone through GradWarp, B1-correction, N3 normalization and phantom-based scaling. I run the following two commands in freeSurfer:
recon-all -autorecon1 -subjid <subjid>
mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz
My questions are
1) Currently I use 5 as threshold (-T 5). Is there a guidance for the setting of this parameter?
2) In the output file T1.final.mgz, is the skull-stripped image represented in ijk space (image index space) or in XYZ space (via transformation matrix)?
3) If the skull-stripped image is represented in XYZ space, how do I get it in ijk space?
Thanks in advance for the help!
Best Regards,
Yi Li (PhD)
Senior Computational Scientist
Computational Sciences
The Jackson Laboratory
Farmington, CT 06032
Tel: 860-837-2156
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Douglas,
I wonder whether you have received the image I attached. Have you got time to have a look at why Talairach transform failed. Appreciate much on your opinions.
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yi Li Sent: Thursday, November 16, 2017 12:01 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Talairach failed when striping skull]
Dear Douglas,
This fails just on this one. Image seems good. I attached it in the previous mail but being held. Thanks!
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, November 16, 2017 11:37 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Talairach failed when striping skull]
does this fail on all your subjects or just this one? Have you looked at the input image to make sure that there is nothing wrong with it?
On 11/16/2017 11:32 AM, Yi Li wrote:
Hi FS expert,
When I run recon-all -autorecon1 -subjid <subjid>, the Talaitach transform failed. Please see the attached log file. Is there a way to correct the error? Thanks!
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 13, 2017 5:48 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [strip skull for unregistered images]
Hi Yi
yes, brainmask.mgz is the skull stripped image.
And no, n3 is pretty gentle so I would think letting our normal intensity normalization run would be fine (and better than not doing it)
cheers Bruce
On Mon, 13 Nov 2017, Yi Li wrote:
Hi Bruce,
Thanks for the help! Is the skull-stripped image in Brainmask.mgz?
Another question: since my raw image has gone through B1 correction and N3 normalization, will you suggest I omit the nu and normalize step in -autorecon1?
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 13, 2017 10:50 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [strip skull for unregistered images]
Hi Yi
autorecon1 should do the skull stripping, so there is no need for the separate mri_mask call. The threshold of '5' is so to preserve edits in which voxels are turned 'off' (they are set to 1 I believe, but we reserve 2-4 as additional 'off' values).
The masking will not transform the voxel coordinates of the image
cheers Bruce
On Mon, 13 Nov 2017, Yi Li wrote:
Dear FS experts,
I would like to strip skulls from unregistered images which have gone through GradWarp, B1-correction, N3 normalization and phantom-based scaling. I run the following two commands in freeSurfer:
recon-all -autorecon1 -subjid <subjid>
mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz
My questions are
1) Currently I use 5 as threshold (-T 5). Is there a guidance for the setting of this parameter?
2) In the output file T1.final.mgz, is the skull-stripped image represented in ijk space (image index space) or in XYZ space (via transformation matrix)?
3) If the skull-stripped image is represented in XYZ space, how do I get it in ijk space?
Thanks in advance for the help!
Best Regards,
Yi Li (PhD)
Senior Computational Scientist
Computational Sciences
The Jackson Laboratory
Farmington, CT 06032
Tel: 860-837-2156
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Yi Li