Hi FreeSurfer experts,
After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter.
Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region.
Thanks for your help!
BR
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look
cheers Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter.
Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region.
Thanks for your help!
BR
Hi Bruce, Thanks for your reply. It is actually brighter on the brainmask.mgz than the orig.mgz when I checked. I'm uploading the freesurfer subject here.
Thanks! BR
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 2:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look
cheers Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter.
Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region.
Thanks for your help!
BR
I mean to tar and gzip the entire subject dir, which will be too big to email. You can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks for your reply. It is actually brighter on the brainmask.mgz than the orig.mgz when I checked. I'm uploading the freesurfer subject here.
Thanks! BR
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 2:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look
cheers Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter.
Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region.
Thanks for your help!
BR
the problme is that you have several control points in voxels that aren't entirely wm. For example, 129, 134, 173 is a control point and it has no wm in it. This causes the intensity in that region to go up way too high, as we will normalize the control points to the desired wm intensity (110). I ran it without any control points and it worked pretty well. You should probably get rid of your control.dat. If you think that those thin frontal strands should go out a bit further, since some voxels that are entirely white matter (e.g. 134, 135, 162) but have an intensity that is less than 110 (this one is 103 after normalizating) and it will bring the intensity up a bit in that entire region (by the ratio of 110/103).
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks for your reply. It is actually brighter on the brainmask.mgz than the orig.mgz when I checked. I'm uploading the freesurfer subject here.
Thanks! BR
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 2:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look
cheers Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter.
Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region.
Thanks for your help!
BR
Hi Bruce, Thanks so much for the feedback, that is very helpful. We'll try deleting the control points then. Is there a quick way to rerun recon-all without having it take up to 5-8 hours?
Also, a separate question, when running autorecon, after edits to the white matter and pial surfaces, should we run the command -autorecon2 -autorecon3, or would that include too many steps? I read that it's recommended to run from -autorecon2-cp instead?
Thanks so much for your help, B
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
the problme is that you have several control points in voxels that aren't entirely wm. For example, 129, 134, 173 is a control point and it has no wm in it. This causes the intensity in that region to go up way too high, as we will normalize the control points to the desired wm intensity (110). I ran it without any control points and it worked pretty well. You should probably get rid of your control.dat. If you think that those thin frontal strands should go out a bit further, since some voxels that are entirely white matter (e.g. 134, 135, 162) but have an intensity that is less than 110 (this one is 103 after normalizating) and it will bring the intensity up a bit in that entire region (by the ratio of 110/103).
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks for your reply. It is actually brighter on the brainmask.mgz than the orig.mgz when I checked. I'm uploading the freesurfer subject here.
Thanks! BR
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 2:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look
cheers Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter.
Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region.
Thanks for your help!
BR
_______________________________________________ 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.
yes, you can remove the control.dat file and run autorecon2-cp and autorecon3. Should only take a couple of hours depending on your processor On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks so much for the feedback, that is very helpful. We'll try deleting the control points then. Is there a quick way to rerun recon-all without having it take up to 5-8 hours?
Also, a separate question, when running autorecon, after edits to the white matter and pial surfaces, should we run the command -autorecon2 -autorecon3, or would that include too many steps? I read that it's recommended to run from -autorecon2-cp instead?
Thanks so much for your help, B
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
the problme is that you have several control points in voxels that aren't entirely wm. For example, 129, 134, 173 is a control point and it has no wm in it. This causes the intensity in that region to go up way too high, as we will normalize the control points to the desired wm intensity (110). I ran it without any control points and it worked pretty well. You should probably get rid of your control.dat. If you think that those thin frontal strands should go out a bit further, since some voxels that are entirely white matter (e.g. 134, 135, 162) but have an intensity that is less than 110 (this one is 103 after normalizating) and it will bring the intensity up a bit in that entire region (by the ratio of 110/103).
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks for your reply. It is actually brighter on the brainmask.mgz than the orig.mgz when I checked. I'm uploading the freesurfer subject here.
Thanks! BR
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 2:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look
cheers Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter.
Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region.
Thanks for your help!
BR
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
Sounds great, thanks again for your help and will try out your recommendations. Have a great day!
B
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
yes, you can remove the control.dat file and run autorecon2-cp and autorecon3. Should only take a couple of hours depending on your processor On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks so much for the feedback, that is very helpful. We'll try deleting the control points then. Is there a quick way to rerun recon-all without having it take up to 5-8 hours?
Also, a separate question, when running autorecon, after edits to the white matter and pial surfaces, should we run the command -autorecon2 -autorecon3, or would that include too many steps? I read that it's recommended to run from -autorecon2-cp instead?
Thanks so much for your help, B
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
the problme is that you have several control points in voxels that aren't entirely wm. For example, 129, 134, 173 is a control point and it has no wm in it. This causes the intensity in that region to go up way too high, as we will normalize the control points to the desired wm intensity (110). I ran it without any control points and it worked pretty well. You should probably get rid of your control.dat. If you think that those thin frontal strands should go out a bit further, since some voxels that are entirely white matter (e.g. 134, 135, 162) but have an intensity that is less than 110 (this one is 103 after normalizating) and it will bring the intensity up a bit in that entire region (by the ratio of 110/103).
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks for your reply. It is actually brighter on the brainmask.mgz than the orig.mgz when I checked. I'm uploading the freesurfer subject here.
Thanks! BR
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 2:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look
cheers Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter.
Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region.
Thanks for your help!
BR
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sure, good luck Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Sounds great, thanks again for your help and will try out your recommendations. Have a great day!
B
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
yes, you can remove the control.dat file and run autorecon2-cp and autorecon3. Should only take a couple of hours depending on your processor On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks so much for the feedback, that is very helpful. We'll try deleting the control points then. Is there a quick way to rerun recon-all without having it take up to 5-8 hours?
Also, a separate question, when running autorecon, after edits to the white matter and pial surfaces, should we run the command -autorecon2 -autorecon3, or would that include too many steps? I read that it's recommended to run from -autorecon2-cp instead?
Thanks so much for your help, B
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
the problme is that you have several control points in voxels that aren't entirely wm. For example, 129, 134, 173 is a control point and it has no wm in it. This causes the intensity in that region to go up way too high, as we will normalize the control points to the desired wm intensity (110). I ran it without any control points and it worked pretty well. You should probably get rid of your control.dat. If you think that those thin frontal strands should go out a bit further, since some voxels that are entirely white matter (e.g. 134, 135, 162) but have an intensity that is less than 110 (this one is 103 after normalizating) and it will bring the intensity up a bit in that entire region (by the ratio of 110/103).
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks for your reply. It is actually brighter on the brainmask.mgz than the orig.mgz when I checked. I'm uploading the freesurfer subject here.
Thanks! BR
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 2:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look
cheers Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter.
Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region.
Thanks for your help!
BR
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
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
Hi Bruce, We re-ran these subjects using recon-all -all -autorecon2-cp -aurorecon3 -subjid freesurferfolder. We got no output files from that, but I'm wondering if freesurfer didn't run only because we incorrectly ran this command with the '-all', or do you think there was some other reason? We ran this on the cluster, and it generated no error logs.
Thanks again for your help!
Batool___________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 5:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
sure, good luck Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Sounds great, thanks again for your help and will try out your recommendations. Have a great day!
B
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
yes, you can remove the control.dat file and run autorecon2-cp and autorecon3. Should only take a couple of hours depending on your processor On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks so much for the feedback, that is very helpful. We'll try deleting the control points then. Is there a quick way to rerun recon-all without having it take up to 5-8 hours?
Also, a separate question, when running autorecon, after edits to the white matter and pial surfaces, should we run the command -autorecon2 -autorecon3, or would that include too many steps? I read that it's recommended to run from -autorecon2-cp instead?
Thanks so much for your help, B
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
the problme is that you have several control points in voxels that aren't entirely wm. For example, 129, 134, 173 is a control point and it has no wm in it. This causes the intensity in that region to go up way too high, as we will normalize the control points to the desired wm intensity (110). I ran it without any control points and it worked pretty well. You should probably get rid of your control.dat. If you think that those thin frontal strands should go out a bit further, since some voxels that are entirely white matter (e.g. 134, 135, 162) but have an intensity that is less than 110 (this one is 103 after normalizating) and it will bring the intensity up a bit in that entire region (by the ratio of 110/103).
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks for your reply. It is actually brighter on the brainmask.mgz than the orig.mgz when I checked. I'm uploading the freesurfer subject here.
Thanks! BR
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 2:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look
cheers Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter.
Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region.
Thanks for your help!
BR
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
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
Hi Batool
you don't need -all and -autorecon2-cp -aurorecon3 (-all is both of those and more). It must have generated some output. Is there a recon-all.log in the freesurferfolder/scripts dir?
cheers Bruce
On Mon, 12 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, We re-ran these subjects using recon-all -all -autorecon2-cp -aurorecon3 -subjid freesurferfolder. We got no output files from that, but I'm wondering if freesurfer didn't run only because we incorrectly ran this command with the '-all', or do you think there was some other reason? We ran this on the cluster, and it generated no error logs.
Thanks again for your help!
Batool___________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 5:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
sure, good luck Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Sounds great, thanks again for your help and will try out your recommendations. Have a great day!
B
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
yes, you can remove the control.dat file and run autorecon2-cp and autorecon3. Should only take a couple of hours depending on your processor On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks so much for the feedback, that is very helpful. We'll try deleting the control points then. Is there a quick way to rerun recon-all without having it take up to 5-8 hours?
Also, a separate question, when running autorecon, after edits to the white matter and pial surfaces, should we run the command -autorecon2 -autorecon3, or would that include too many steps? I read that it's recommended to run from -autorecon2-cp instead?
Thanks so much for your help, B
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
the problme is that you have several control points in voxels that aren't entirely wm. For example, 129, 134, 173 is a control point and it has no wm in it. This causes the intensity in that region to go up way too high, as we will normalize the control points to the desired wm intensity (110). I ran it without any control points and it worked pretty well. You should probably get rid of your control.dat. If you think that those thin frontal strands should go out a bit further, since some voxels that are entirely white matter (e.g. 134, 135, 162) but have an intensity that is less than 110 (this one is 103 after normalizating) and it will bring the intensity up a bit in that entire region (by the ratio of 110/103).
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks for your reply. It is actually brighter on the brainmask.mgz than the orig.mgz when I checked. I'm uploading the freesurfer subject here.
Thanks! BR
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 2:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look
cheers Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter.
Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region.
Thanks for your help!
BR
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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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Bruce, I noticed I did it incorrectly, so I started running an hour ago just recon-all -autorecon2-cp -autorecon2 without the -all, about an hour ago. It's starting to generate output now, not sure why it didn't at all last time (may have to do with our new cluster). Will let you know if anything goes wrong with the output this time..
Thanks! Batool
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, December 12, 2016 11:34 AM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
Hi Batool
you don't need -all and -autorecon2-cp -aurorecon3 (-all is both of those and more). It must have generated some output. Is there a recon-all.log in the freesurferfolder/scripts dir?
cheers Bruce
On Mon, 12 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, We re-ran these subjects using recon-all -all -autorecon2-cp -aurorecon3 -subjid freesurferfolder. We got no output files from that, but I'm wondering if freesurfer didn't run only because we incorrectly ran this command with the '-all', or do you think there was some other reason? We ran this on the cluster, and it generated no error logs.
Thanks again for your help!
Batool___________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 5:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
sure, good luck Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Sounds great, thanks again for your help and will try out your recommendations. Have a great day!
B
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
yes, you can remove the control.dat file and run autorecon2-cp and autorecon3. Should only take a couple of hours depending on your processor On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks so much for the feedback, that is very helpful. We'll try deleting the control points then. Is there a quick way to rerun recon-all without having it take up to 5-8 hours?
Also, a separate question, when running autorecon, after edits to the white matter and pial surfaces, should we run the command -autorecon2 -autorecon3, or would that include too many steps? I read that it's recommended to run from -autorecon2-cp instead?
Thanks so much for your help, B
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
the problme is that you have several control points in voxels that aren't entirely wm. For example, 129, 134, 173 is a control point and it has no wm in it. This causes the intensity in that region to go up way too high, as we will normalize the control points to the desired wm intensity (110). I ran it without any control points and it worked pretty well. You should probably get rid of your control.dat. If you think that those thin frontal strands should go out a bit further, since some voxels that are entirely white matter (e.g. 134, 135, 162) but have an intensity that is less than 110 (this one is 103 after normalizating) and it will bring the intensity up a bit in that entire region (by the ratio of 110/103).
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi Bruce, Thanks for your reply. It is actually brighter on the brainmask.mgz than the orig.mgz when I checked. I'm uploading the freesurfer subject here.
Thanks! BR
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 2:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look
cheers Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter.
Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region.
Thanks for your help!
BR
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
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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Rizvi, Batool