Re: [Freesurfer] white matter segmentation incorrect after intensity change
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@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-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@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! >>>
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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@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-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@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-boun...@nmr.mgh.harvard.edu >>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>>> [fis...@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
Re: [Freesurfer] white matter segmentation incorrect after intensity change
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@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-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@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 no
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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@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-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@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 >
Re: [Freesurfer] white matter segmentation incorrect after intensity change
Sounds great, thanks again for your help and will try out your recommendations. Have a great day! B From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@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 wa
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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@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
Re: [Freesurfer] white matter segmentation incorrect after intensity change
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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
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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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.
Re: [Freesurfer] white matter segmentation incorrect after intensity change
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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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.
Re: [Freesurfer] white matter segmentation incorrect after intensity change
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@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 > > > FTLDES008_FS.tar Description: FTLDES008_FS.tar ___ 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.
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.
