Re: [Freesurfer] too much white matter
Hi Bruce, it worked! The surfaces now look so much better. Thanks for your help! Cheers, Clara - Ursprüngliche Mail - Von: ckuehn cku...@cbs.mpg.de An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 17:18:26 Betreff: Re: [Freesurfer] too much white matter Hi Bruce, yes, it is an mp2rage image. I'm gonna work in your suggestions and see if it changes anything after rerunning the the recon-all process. Thank you! Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 16:18:06 Betreff: Re: [Freesurfer] too much white matter Hi Clara the second control point (135, 152, 163) is outside the brainmask. You will need to correct the skull stripping first. In general I wouldn't put control points in that type of location as it is certainly partial volumed. I would try something like 139, 145, 163 instead (and maybe a couple around there). Also, I assume the skull stripping failed as this is not the typical type of image we expect (since the background is so bright and noisy). Is it an mp2rage or something? There appears to be very little space between skull and brain so the stripping may be challenging, particularly in the orbitofrontal region where you had this control point (it looks like fat is shifting upwards either into or adjacent to brain) cheers Bruce On Tue, 30 Jun 2015, Clara Kühn wrote: oh, and here are the Freesurfer coordinates for the control points: 86, 143, 147 135, 152, 163 Cheers, Clara - Ursprüngliche Mail - Von: ckuehn cku...@cbs.mpg.de An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 11:39:40 Betreff: Re: [Freesurfer] too much white matter Hi Bruce, thanks for your reply. As far as I can tell the cps are in the WM. I'd be grateful if you could take a closer look, though. You can download the dataset here: https://bigmail.cbs.mpg.de/i/2581030103b072173ff426e67d298cf4.zip Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 29. Juni 2015 18:07:28 Betreff: Re: [Freesurfer] too much white matter Hi Clara are you sure you put the control points in the interior of the WM? If you want to upload the subject we will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2) control points and rerunning the recon-all process with the -cp flag I get huge areas of white matter including the subcortical areas and lots of the cortical ribbon. See attached picture. Could you explain how this happens because the logfile says it ran without error. In these cases I've deleted the whole thing and preprocessed the scan from scratch. I was wondering if there's a better way to deal with this like going a step back if that's possible. Cheers, Clara Kühn ___ 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 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] too much white matter
glad to hear it Bruce On Mon, 6 Jul 2015, Clara Kühn wrote: Hi Bruce, it worked! The surfaces now look so much better. Thanks for your help! Cheers, Clara - Ursprüngliche Mail - Von: ckuehn cku...@cbs.mpg.de An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 17:18:26 Betreff: Re: [Freesurfer] too much white matter Hi Bruce, yes, it is an mp2rage image. I'm gonna work in your suggestions and see if it changes anything after rerunning the the recon-all process. Thank you! Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 16:18:06 Betreff: Re: [Freesurfer] too much white matter Hi Clara the second control point (135, 152, 163) is outside the brainmask. You will need to correct the skull stripping first. In general I wouldn't put control points in that type of location as it is certainly partial volumed. I would try something like 139, 145, 163 instead (and maybe a couple around there). Also, I assume the skull stripping failed as this is not the typical type of image we expect (since the background is so bright and noisy). Is it an mp2rage or something? There appears to be very little space between skull and brain so the stripping may be challenging, particularly in the orbitofrontal region where you had this control point (it looks like fat is shifting upwards either into or adjacent to brain) cheers Bruce On Tue, 30 Jun 2015, Clara Kühn wrote: oh, and here are the Freesurfer coordinates for the control points: 86, 143, 147 135, 152, 163 Cheers, Clara - Ursprüngliche Mail - Von: ckuehn cku...@cbs.mpg.de An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 11:39:40 Betreff: Re: [Freesurfer] too much white matter Hi Bruce, thanks for your reply. As far as I can tell the cps are in the WM. I'd be grateful if you could take a closer look, though. You can download the dataset here: https://bigmail.cbs.mpg.de/i/2581030103b072173ff426e67d298cf4.zip Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 29. Juni 2015 18:07:28 Betreff: Re: [Freesurfer] too much white matter Hi Clara are you sure you put the control points in the interior of the WM? If you want to upload the subject we will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2) control points and rerunning the recon-all process with the -cp flag I get huge areas of white matter including the subcortical areas and lots of the cortical ribbon. See attached picture. Could you explain how this happens because the logfile says it ran without error. In these cases I've deleted the whole thing and preprocessed the scan from scratch. I was wondering if there's a better way to deal with this like going a step back if that's possible. Cheers, Clara Kühn ___ 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 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] too much white matter
oh, and here are the Freesurfer coordinates for the control points: 86, 143, 147 135, 152, 163 Cheers, Clara - Ursprüngliche Mail - Von: ckuehn cku...@cbs.mpg.de An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 11:39:40 Betreff: Re: [Freesurfer] too much white matter Hi Bruce, thanks for your reply. As far as I can tell the cps are in the WM. I'd be grateful if you could take a closer look, though. You can download the dataset here: https://bigmail.cbs.mpg.de/i/2581030103b072173ff426e67d298cf4.zip Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 29. Juni 2015 18:07:28 Betreff: Re: [Freesurfer] too much white matter Hi Clara are you sure you put the control points in the interior of the WM? If you want to upload the subject we will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2) control points and rerunning the recon-all process with the -cp flag I get huge areas of white matter including the subcortical areas and lots of the cortical ribbon. See attached picture. Could you explain how this happens because the logfile says it ran without error. In these cases I've deleted the whole thing and preprocessed the scan from scratch. I was wondering if there's a better way to deal with this like going a step back if that's possible. Cheers, Clara Kühn ___ 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] too much white matter
Hi Bruce, yes, it is an mp2rage image. I'm gonna work in your suggestions and see if it changes anything after rerunning the the recon-all process. Thank you! Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 16:18:06 Betreff: Re: [Freesurfer] too much white matter Hi Clara the second control point (135, 152, 163) is outside the brainmask. You will need to correct the skull stripping first. In general I wouldn't put control points in that type of location as it is certainly partial volumed. I would try something like 139, 145, 163 instead (and maybe a couple around there). Also, I assume the skull stripping failed as this is not the typical type of image we expect (since the background is so bright and noisy). Is it an mp2rage or something? There appears to be very little space between skull and brain so the stripping may be challenging, particularly in the orbitofrontal region where you had this control point (it looks like fat is shifting upwards either into or adjacent to brain) cheers Bruce On Tue, 30 Jun 2015, Clara Kühn wrote: oh, and here are the Freesurfer coordinates for the control points: 86, 143, 147 135, 152, 163 Cheers, Clara - Ursprüngliche Mail - Von: ckuehn cku...@cbs.mpg.de An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 11:39:40 Betreff: Re: [Freesurfer] too much white matter Hi Bruce, thanks for your reply. As far as I can tell the cps are in the WM. I'd be grateful if you could take a closer look, though. You can download the dataset here: https://bigmail.cbs.mpg.de/i/2581030103b072173ff426e67d298cf4.zip Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 29. Juni 2015 18:07:28 Betreff: Re: [Freesurfer] too much white matter Hi Clara are you sure you put the control points in the interior of the WM? If you want to upload the subject we will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2) control points and rerunning the recon-all process with the -cp flag I get huge areas of white matter including the subcortical areas and lots of the cortical ribbon. See attached picture. Could you explain how this happens because the logfile says it ran without error. In these cases I've deleted the whole thing and preprocessed the scan from scratch. I was wondering if there's a better way to deal with this like going a step back if that's possible. Cheers, Clara Kühn ___ 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 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] too much white matter
Hi Clara the second control point (135, 152, 163) is outside the brainmask. You will need to correct the skull stripping first. In general I wouldn't put control points in that type of location as it is certainly partial volumed. I would try something like 139, 145, 163 instead (and maybe a couple around there). Also, I assume the skull stripping failed as this is not the typical type of image we expect (since the background is so bright and noisy). Is it an mp2rage or something? There appears to be very little space between skull and brain so the stripping may be challenging, particularly in the orbitofrontal region where you had this control point (it looks like fat is shifting upwards either into or adjacent to brain) cheers Bruce On Tue, 30 Jun 2015, Clara Kühn wrote: oh, and here are the Freesurfer coordinates for the control points: 86, 143, 147 135, 152, 163 Cheers, Clara - Ursprüngliche Mail - Von: ckuehn cku...@cbs.mpg.de An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 11:39:40 Betreff: Re: [Freesurfer] too much white matter Hi Bruce, thanks for your reply. As far as I can tell the cps are in the WM. I'd be grateful if you could take a closer look, though. You can download the dataset here: https://bigmail.cbs.mpg.de/i/2581030103b072173ff426e67d298cf4.zip Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 29. Juni 2015 18:07:28 Betreff: Re: [Freesurfer] too much white matter Hi Clara are you sure you put the control points in the interior of the WM? If you want to upload the subject we will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2) control points and rerunning the recon-all process with the -cp flag I get huge areas of white matter including the subcortical areas and lots of the cortical ribbon. See attached picture. Could you explain how this happens because the logfile says it ran without error. In these cases I've deleted the whole thing and preprocessed the scan from scratch. I was wondering if there's a better way to deal with this like going a step back if that's possible. Cheers, Clara Kühn ___ 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 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] too much white matter
Hi Bruce, thanks for your reply. As far as I can tell the cps are in the WM. I'd be grateful if you could take a closer look, though. You can download the dataset here: https://bigmail.cbs.mpg.de/i/2581030103b072173ff426e67d298cf4.zip Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 29. Juni 2015 18:07:28 Betreff: Re: [Freesurfer] too much white matter Hi Clara are you sure you put the control points in the interior of the WM? If you want to upload the subject we will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2) control points and rerunning the recon-all process with the -cp flag I get huge areas of white matter including the subcortical areas and lots of the cortical ribbon. See attached picture. Could you explain how this happens because the logfile says it ran without error. In these cases I've deleted the whole thing and preprocessed the scan from scratch. I was wondering if there's a better way to deal with this like going a step back if that's possible. Cheers, Clara Kühn ___ 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] too much white matter
Hi Clara are you sure you put the control points in the interior of the WM? If you want to upload the subject we will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2) control points and rerunning the recon-all process with the -cp flag I get huge areas of white matter including the subcortical areas and lots of the cortical ribbon. See attached picture. Could you explain how this happens because the logfile says it ran without error. In these cases I've deleted the whole thing and preprocessed the scan from scratch. I was wondering if there's a better way to deal with this like going a step back if that's possible. Cheers, Clara Kühn ___ 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.
