Hi Dan and Bruce,
Thanks for your getting back on the problem. My concern is more about the dura being incorrectly labeled - It appears to me that the grey-CSF boundary has been incorrectly labeled as the GM-WM boundary across the entire image. Any ideas what may have gone wrong?
Thanks, Mayuresh
On Sat, Apr 2, 2011 at 3:28 AM, freesurfer-request@nmr.mgh.harvard.eduwrote:
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Today's Topics:
- Re: incorrect GM/WM surfaces (Daniel G Wakeman)
- problems with loading a pial surface (Iris Steinmann)
- Re: incorrect GM/WM surfaces (Bruce Fischl)
- Re: problems with loading a pial surface (Bruce Fischl)
- preproc-sess OSX bug fix getrunlist (Juli Dolzhenko)
- MRI analyst position (Keith Schneider)
- Distance between two points along cortical (caoaize)
Message: 1 Date: Fri, 1 Apr 2011 05:53:20 +0100 From: Daniel G Wakeman Daniel.Wakeman@mrc-cbu.cam.ac.uk Subject: Re: [Freesurfer] incorrect GM/WM surfaces To: freesurfer@nmr.mgh.harvard.edu Message-ID: 471C0967-FE19-409E-8174-31FBB56CDE1E@mrc-cbu.cam.ac.uk Content-Type: text/plain; charset="us-ascii"
Hi Mayuresh,
I assume you are talking about the area in the posterior midline, where the pial surface seems to go 'squiggly'. You also seem to have a problem with the right hemisphere (left visually: I hate radiology ;)), where some dura seems incorrectly labeled as pial surface (although the grey matter is very difficult to see on this sequence/ at this setting).
To fix these I recommend this wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits
Good Luck! Dan
On 2011 Apr 1, at 05:08 , freesurfer-request@nmr.mgh.harvard.edu < freesurfer-request@nmr.mgh.harvard.edu> wrote:
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When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- incorrect GM/WM surfaces (Mayuresh K)
Message: 1 Date: Fri, 1 Apr 2011 15:21:18 +1100 From: Mayuresh K mayureshk.82@gmail.com Subject: [Freesurfer] incorrect GM/WM surfaces To: freesurfer@nmr.mgh.harvard.edu Message-ID: AANLkTi=BLTOKkZngtH5SxhsQvmFrUHakzG9u07Xzworn@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Hello freesurfer experts,
I have successfully finished running the recon-all analysis without any errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM surfaces however look incorrect and I am not sure what may have gone
wrong.
See attached screenshot from tkmedit. Any suggestions how to fix this would be helpful.
I have processed other datasets collected from the same scanner using the same sequence which seem to have correctly identified the pial and grey-white boundaries. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1.
Thanks, Mayuresh
oh, sorry, you are completely right! What version are you using? If you tar and gzip the subject's dir we'll take a look. Has this happened on other datasets with these acquisition parameters? What sequence/coil/scanner are you using?
Bruce
On Mon, 4 Apr 2011, Mayuresh K wrote:
Hi Dan and Bruce,
Thanks for your getting back on the problem. My concern is more about the dura being incorrectly labeled - It appears to me that the grey-CSF boundary has been incorrectly labeled as the GM-WM boundary across the entire image. Any ideas what may have gone wrong?
Thanks, Mayuresh
On Sat, Apr 2, 2011 at 3:28 AM, freesurfer-request@nmr.mgh.harvard.eduwrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- Re: incorrect GM/WM surfaces (Daniel G Wakeman)
- problems with loading a pial surface (Iris Steinmann)
- Re: incorrect GM/WM surfaces (Bruce Fischl)
- Re: problems with loading a pial surface (Bruce Fischl)
- preproc-sess OSX bug fix getrunlist (Juli Dolzhenko)
- MRI analyst position (Keith Schneider)
- Distance between two points along cortical (caoaize)
Message: 1 Date: Fri, 1 Apr 2011 05:53:20 +0100 From: Daniel G Wakeman Daniel.Wakeman@mrc-cbu.cam.ac.uk Subject: Re: [Freesurfer] incorrect GM/WM surfaces To: freesurfer@nmr.mgh.harvard.edu Message-ID: 471C0967-FE19-409E-8174-31FBB56CDE1E@mrc-cbu.cam.ac.uk Content-Type: text/plain; charset="us-ascii"
Hi Mayuresh,
I assume you are talking about the area in the posterior midline, where the pial surface seems to go 'squiggly'. You also seem to have a problem with the right hemisphere (left visually: I hate radiology ;)), where some dura seems incorrectly labeled as pial surface (although the grey matter is very difficult to see on this sequence/ at this setting).
To fix these I recommend this wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits
Good Luck! Dan
On 2011 Apr 1, at 05:08 , freesurfer-request@nmr.mgh.harvard.edu < freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- incorrect GM/WM surfaces (Mayuresh K)
Message: 1 Date: Fri, 1 Apr 2011 15:21:18 +1100 From: Mayuresh K mayureshk.82@gmail.com Subject: [Freesurfer] incorrect GM/WM surfaces To: freesurfer@nmr.mgh.harvard.edu Message-ID: AANLkTi=BLTOKkZngtH5SxhsQvmFrUHakzG9u07Xzworn@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Hello freesurfer experts,
I have successfully finished running the recon-all analysis without any errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM surfaces however look incorrect and I am not sure what may have gone
wrong.
See attached screenshot from tkmedit. Any suggestions how to fix this would be helpful.
I have processed other datasets collected from the same scanner using the same sequence which seem to have correctly identified the pial and grey-white boundaries. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1.
Thanks, Mayuresh
Hi Bruce,
Thanks for offering to take a look at the data. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1. Yes I have had this problem on a few other data-sets - more like 1 every 8 datasets. Teh data is collected using a 3D SPGR scan (TR=13, TE=6.2, flip=20, sagittal, 256*256, 1mm slice thickness, isotropic voxels), HNS head coil, on a 1.5 clinical GE scanner.
How should I send you the subject's processed dir? Its a bit big to email after tar and gzip.
Regards, Mayuresh
On Mon, Apr 4, 2011 at 11:11 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
oh, sorry, you are completely right! What version are you using? If you tar and gzip the subject's dir we'll take a look. Has this happened on other datasets with these acquisition parameters? What sequence/coil/scanner are you using?
Bruce
On Mon, 4 Apr 2011, Mayuresh K wrote:
Hi Dan and Bruce,
Thanks for your getting back on the problem. My concern is more about the dura being incorrectly labeled - It appears to me that the grey-CSF boundary has been incorrectly labeled as the GM-WM boundary across the entire image. Any ideas what may have gone wrong?
Thanks, Mayuresh
On Sat, Apr 2, 2011 at 3:28 AM, <freesurfer-request@nmr.mgh.harvard.edu
wrote:
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.eduTo subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- Re: incorrect GM/WM surfaces (Daniel G Wakeman)
- problems with loading a pial surface (Iris Steinmann)
- Re: incorrect GM/WM surfaces (Bruce Fischl)
- Re: problems with loading a pial surface (Bruce Fischl)
- preproc-sess OSX bug fix getrunlist (Juli Dolzhenko)
- MRI analyst position (Keith Schneider)
- Distance between two points along cortical (caoaize)
Message: 1 Date: Fri, 1 Apr 2011 05:53:20 +0100 From: Daniel G Wakeman Daniel.Wakeman@mrc-cbu.cam.ac.uk Subject: Re: [Freesurfer] incorrect GM/WM surfaces To: freesurfer@nmr.mgh.harvard.edu Message-ID: 471C0967-FE19-409E-8174-31FBB56CDE1E@mrc-cbu.cam.ac.uk Content-Type: text/plain; charset="us-ascii"
Hi Mayuresh,
I assume you are talking about the area in the posterior midline, where the pial surface seems to go 'squiggly'. You also seem to have a problem with the right hemisphere (left visually: I hate radiology ;)), where some dura seems incorrectly labeled as pial surface (although the grey matter is very difficult to see on this sequence/ at this setting).
To fix these I recommend this wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits
Good Luck! Dan
On 2011 Apr 1, at 05:08 , freesurfer-request@nmr.mgh.harvard.edu < freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.eduTo subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- incorrect GM/WM surfaces (Mayuresh K)
Message: 1 Date: Fri, 1 Apr 2011 15:21:18 +1100 From: Mayuresh K mayureshk.82@gmail.com Subject: [Freesurfer] incorrect GM/WM surfaces To: freesurfer@nmr.mgh.harvard.edu Message-ID: AANLkTi=BLTOKkZngtH5SxhsQvmFrUHakzG9u07Xzworn@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Hello freesurfer experts,
I have successfully finished running the recon-all analysis without any errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM surfaces however look incorrect and I am not sure what may have gone
wrong.
See attached screenshot from tkmedit. Any suggestions how to fix this would be helpful.
I have processed other datasets collected from the same scanner using the same sequence which seem to have correctly identified the pial and grey-white boundaries. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1.
Thanks, Mayuresh
Hi Mayuresh
actually, could you try version 5 and see if it fixes this problem? I think it might. The SPGRs aren't great contrast-to-noise. Can you shorten the TE? In any case, it might work with the newer version
Bruce
On Mon, 4 Apr 2011, Mayuresh K wrote:
Hi Bruce,
Thanks for offering to take a look at the data. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1. Yes I have had this problem on a few other data-sets - more like 1 every 8 datasets. Teh data is collected using a 3D SPGR scan (TR=13, TE=6.2, flip=20, sagittal, 256*256, 1mm slice thickness, isotropic voxels), HNS head coil, on a 1.5 clinical GE scanner.
How should I send you the subject's processed dir? Its a bit big to email after tar and gzip.
Regards, Mayuresh
On Mon, Apr 4, 2011 at 11:11 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
oh, sorry, you are completely right! What version are you using? If you tar and gzip the subject's dir we'll take a look. Has this happened on other datasets with these acquisition parameters? What sequence/coil/scanner are you using?
Bruce
On Mon, 4 Apr 2011, Mayuresh K wrote:
Hi Dan and Bruce,
Thanks for your getting back on the problem. My concern is more about the dura being incorrectly labeled - It appears to me that the grey-CSF boundary has been incorrectly labeled as the GM-WM boundary across the entire image. Any ideas what may have gone wrong?
Thanks, Mayuresh
On Sat, Apr 2, 2011 at 3:28 AM, <freesurfer-request@nmr.mgh.harvard.edu
wrote:
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.eduTo subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- Re: incorrect GM/WM surfaces (Daniel G Wakeman)
- problems with loading a pial surface (Iris Steinmann)
- Re: incorrect GM/WM surfaces (Bruce Fischl)
- Re: problems with loading a pial surface (Bruce Fischl)
- preproc-sess OSX bug fix getrunlist (Juli Dolzhenko)
- MRI analyst position (Keith Schneider)
- Distance between two points along cortical (caoaize)
Message: 1 Date: Fri, 1 Apr 2011 05:53:20 +0100 From: Daniel G Wakeman Daniel.Wakeman@mrc-cbu.cam.ac.uk Subject: Re: [Freesurfer] incorrect GM/WM surfaces To: freesurfer@nmr.mgh.harvard.edu Message-ID: 471C0967-FE19-409E-8174-31FBB56CDE1E@mrc-cbu.cam.ac.uk Content-Type: text/plain; charset="us-ascii"
Hi Mayuresh,
I assume you are talking about the area in the posterior midline, where the pial surface seems to go 'squiggly'. You also seem to have a problem with the right hemisphere (left visually: I hate radiology ;)), where some dura seems incorrectly labeled as pial surface (although the grey matter is very difficult to see on this sequence/ at this setting).
To fix these I recommend this wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits
Good Luck! Dan
On 2011 Apr 1, at 05:08 , freesurfer-request@nmr.mgh.harvard.edu < freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.eduTo subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- incorrect GM/WM surfaces (Mayuresh K)
Message: 1 Date: Fri, 1 Apr 2011 15:21:18 +1100 From: Mayuresh K mayureshk.82@gmail.com Subject: [Freesurfer] incorrect GM/WM surfaces To: freesurfer@nmr.mgh.harvard.edu Message-ID: AANLkTi=BLTOKkZngtH5SxhsQvmFrUHakzG9u07Xzworn@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Hello freesurfer experts,
I have successfully finished running the recon-all analysis without any errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM surfaces however look incorrect and I am not sure what may have gone
wrong.
See attached screenshot from tkmedit. Any suggestions how to fix this would be helpful.
I have processed other datasets collected from the same scanner using the same sequence which seem to have correctly identified the pial and grey-white boundaries. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1.
Thanks, Mayuresh
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Mayuresh K