Hi Freesurfer experts,
I am running FS on a patient with a chronic right occipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help!
Best, Mariana
Hi Mariana
yes, control points would mess everything up. It looks like the rest of the surface was generated pretty accurately though - do you need to correct anything?
cheers Bruce
On Wed, 21 Jun 2017, Budge, Mariana wrote:
Hi Freesurfer experts,
I am running FS on a patient with a chronic right occipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help!
Best,
Mariana
Hello Bruce,
I am interested in this thread because I have encountered similar problems with my stroke patients. How do I solve it? Should I only edit the aseg and assign a label called "Lesion" in the FS LookUpTable? or Should I edit both the wm.mgz and aseg.mgz files? If the former, How do I achieve it? My goal is to make sure that WH and GM surfaces are traced properly. Any help will be appreciated. Thank you.
Best, Paul
On Wed, Jun 21, 2017 at 12:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mariana
yes, control points would mess everything up. It looks like the rest of the surface was generated pretty accurately though - do you need to correct anything?
cheers Bruce
On Wed, 21 Jun 2017, Budge, Mariana wrote:
Hi Freesurfer experts,
I am running FS on a patient with a chronic right occipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help!
Best,
Mariana
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.
Hi Paul
if they are WM lesions I think you should edit the aseg and label them as such, then run from there forward. It should propagate the lesions from aseg to wm.mgz, so you shouldn't have to do both Bruce
On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce, I am interested in this thread because I have encountered similar problems with my stroke patients. How do I solve it? Should I only edit the aseg and assign a label called "Lesion" in the FS LookUpTable? or Should I edit both the wm.mgz and aseg.mgz files? If the former, How do I achieve it? My goal is to make sure that WH and GM surfaces are traced properly. Any help will be appreciated. Thank you.
Best, Paul
On Wed, Jun 21, 2017 at 12:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Mariana
yes, control points would mess everything up. It looks like the rest of the surface was generated pretty accurately though - do you need to correct anything? cheers Bruce On Wed, 21 Jun 2017, Budge, Mariana wrote: Hi Freesurfer experts, I am running FS on a patient with a chronic right occipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help! Best, Mariana
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.
Hello Bruce,
Thank you very much. I'm guessing I should follow the tutorial for editing aseg; or is there a different tutorial on how to edit and label WM lesions on aseg? One last question, what if it's a combination of WM and GM lesions like cortical stroke that extended into the WM? Should I use the same procedure?
Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Sunday, September 3, 2017 11:47 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer with infarct patients
Hi Paul
if they are WM lesions I think you should edit the aseg and label them as such, then run from there forward. It should propagate the lesions from aseg to wm.mgz, so you shouldn't have to do both Bruce
On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce, I am interested in this thread because I have encountered similar problems with my stroke patients. How do I solve it? Should I only edit the aseg and assign a label called "Lesion" in the FS LookUpTable? or Should I edit both the wm.mgz and aseg.mgz files? If the former, How do I achieve it? My goal is to make sure that WH and GM surfaces are traced properly. Any help will be appreciated. Thank you.
Best, Paul
On Wed, Jun 21, 2017 at 12:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Mariana
yes, control points would mess everything up. It looks like the rest of the surface was generated pretty accurately though - do you need to correct anything?
cheers Bruce
On Wed, 21 Jun 2017, Budge, Mariana wrote:
Hi Freesurfer experts,
I am running FS on a patient with a chronic right occipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help!
Best,
Mariana
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.
Hi Paul
GM ones are harder and I'm not sure we have a working procedure for them yet. I think we have separate labels for wm and gm lesions - try using them when you edit the aseg.
cheers Bruce On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you very much. I'm guessing I should follow the tutorial for editing aseg; or is there a different tutorial on how to edit and label WM lesions on aseg? One last question, what if it's a combination of WM and GM lesions like cortical stroke that extended into the WM? Should I use the same procedure?
Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Sunday, September 3, 2017 11:47 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer with infarct patients
Hi Paul
if they are WM lesions I think you should edit the aseg and label them as such, then run from there forward. It should propagate the lesions from aseg to wm.mgz, so you shouldn't have to do both Bruce
On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce, I am interested in this thread because I have encountered similar problems with my stroke patients. How do I solve it? Should I only edit the aseg and assign a label called "Lesion" in the FS LookUpTable? or Should I edit both the wm.mgz and aseg.mgz files? If the former, How do I achieve it? My goal is to make sure that WH and GM surfaces are traced properly. Any help will be appreciated. Thank you.
Best, Paul
On Wed, Jun 21, 2017 at 12:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Mariana
yes, control points would mess everything up. It looks like the rest of the surface was generated pretty accurately though - do you need to correct anything?
cheers Bruce
On Wed, 21 Jun 2017, Budge, Mariana wrote:
Hi Freesurfer experts,
I am running FS on a patient with a chronic right occipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help!
Best,
Mariana
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
Hello Bruce,
Thank you. I looked at the LookUpTable.txt for GM and I couldn't find any. I only found labels for Right Lesion, Left lesion, WM lesions (wmsa and other_wmsa). What does wmsa mean and which of these should I use as GM lesion?
Best, Paul
On Sun, Sep 3, 2017 at 12:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Paul
GM ones are harder and I'm not sure we have a working procedure for them yet. I think we have separate labels for wm and gm lesions - try using them when you edit the aseg.
cheers Bruce On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you very much. I'm guessing I should follow the tutorial for editing aseg; or is there a different tutorial on how to edit and label WM lesions on aseg? One last question, what if it's a combination of WM and GM lesions like cortical stroke that extended into the WM? Should I use the same procedure?
Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Sunday, September 3, 2017 11:47 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer with infarct patients
Hi Paul
if they are WM lesions I think you should edit the aseg and label them as such, then run from there forward. It should propagate the lesions from aseg to wm.mgz, so you shouldn't have to do both Bruce
On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce,
I am interested in this thread because I have encountered similar problems with my stroke patients. How do I solve it? Should I only edit the aseg and assign a label called "Lesion" in the FS LookUpTable? or Should I edit both the wm.mgz and aseg.mgz files? If the former, How do I achieve it? My goal is to make sure that WH and GM surfaces are traced properly. Any help will be appreciated. Thank you.
Best, Paul
On Wed, Jun 21, 2017 at 12:45 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Mariana
yes, control points would mess everything up. It looks like the rest of the surface was generated pretty accurately though - do you need to correct anything?
cheers Bruce
On Wed, 21 Jun 2017, Budge, Mariana wrote:
Hi Freesurfer experts,
I am running FS on a patient with a chronic right occipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help!
Best,
Mariana
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
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.
nope, I would use Left-non-WM-hypointensities and Right-non-WM-hypointensities
On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce, Thank you. I looked at the LookUpTable.txt for GM and I couldn't find any. I only found labels for Right Lesion, Left lesion, WM lesions (wmsa and other_wmsa). What does wmsa mean and which of these should I use as GM lesion?
Best, Paul
On Sun, Sep 3, 2017 at 12:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Paul
GM ones are harder and I'm not sure we have a working procedure for them yet. I think we have separate labels for wm and gm lesions - try using them when you edit the aseg. cheers Bruce On Sun, 3 Sep 2017, miracle ozzoude wrote: Hello Bruce, Thank you very much. I'm guessing I should follow the tutorial for editing aseg; or is there a different tutorial on how to edit and label WM lesions on aseg? One last question, what if it's a combination of WM and GM lesions like cortical stroke that extended into the WM? Should I use the same procedure? Best, Paul Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Sunday, September 3, 2017 11:47 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer with infarct patients Hi Paul if they are WM lesions I think you should edit the aseg and label them as such, then run from there forward. It should propagate the lesions from aseg to wm.mgz, so you shouldn't have to do both Bruce On Sun, 3 Sep 2017, miracle ozzoude wrote: Hello Bruce, I am interested in this thread because I have encountered similar problems with my stroke patients. How do I solve it? Should I only edit the aseg and assign a label called "Lesion" in the FS LookUpTable? or Should I edit both the wm.mgz and aseg.mgz files? If the former, How do I achieve it? My goal is to make sure that WH and GM surfaces are traced properly. Any help will be appreciated. Thank you. Best, Paul On Wed, Jun 21, 2017 at 12:45 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Mariana yes, control points would mess everything up. It looks like the rest of the surface was generated pretty accurately though - do you need to correct anything? cheers Bruce On Wed, 21 Jun 2017, Budge, Mariana wrote: Hi Freesurfer experts, I am running FS on a patient with a chronic right occipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help! Best, Mariana _______________________________________________ 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
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.
Hello Bruce,
Thank you very much. To reiterate our discussion, I should use Left/Right non-WM-hypointensities for GM lesions and Left/Right-WM-hypointensities for WM lesions when editing the aseg.presurf.mgz. Correct?
Best, Paul
On Sun, Sep 3, 2017 at 1:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
nope, I would use Left-non-WM-hypointensities and Right-non-WM-hypointensities
On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you. I looked at the LookUpTable.txt for GM and I couldn't find any. I only found labels for Right Lesion, Left lesion, WM lesions (wmsa and other_wmsa). What does wmsa mean and which of these should I use as GM lesion?
Best, Paul
On Sun, Sep 3, 2017 at 12:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Paul
GM ones are harder and I'm not sure we have a working procedure forthem yet. I think we have separate labels for wm and gm lesions - try using them when you edit the aseg.
cheers Bruce On Sun, 3 Sep 2017, miracle ozzoude wrote: Hello Bruce, Thank you very much. I'm guessing I should follow thetutorial for editing aseg; or is there a different tutorial on how to edit and label WM lesions on aseg? One last question, what if it's a combination of WM and GM lesions like cortical stroke that extended into the WM? Should I use the same procedure?
Best, Paul Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Sunday, September 3, 2017 11:47 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer with infarct patients Hi Paul if they are WM lesions I think you should edit the aseg andlabel them as such, then run from there forward. It should propagate the lesions from aseg to wm.mgz, so you shouldn't have to do both Bruce
On Sun, 3 Sep 2017, miracle ozzoude wrote: Hello Bruce, I am interested in this thread because I haveencountered similar problems with my stroke patients. How do I solve it? Should I only edit the aseg and assign a label called "Lesion" in the FS LookUpTable? or Should I edit both the wm.mgz and aseg.mgz files? If the former, How do I achieve it? My goal is to make sure that WH and GM surfaces are traced properly. Any help will be appreciated. Thank you.
Best, Paul On Wed, Jun 21, 2017 at 12:45 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Mariana yes, control points would mess everything up. It lookslike the rest of the surface was generated pretty accurately though - do you need to correct anything?
cheers Bruce On Wed, 21 Jun 2017, Budge, Mariana wrote: Hi Freesurfer experts, I am running FS on a patient with a chronic rightoccipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help!
Best, Mariana _______________________________________________ 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 theperson 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
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.
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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.
yes, I think so. It may not work for the GM ones at the moment, but should at least be fixable On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce, Thank you very much. To reiterate our discussion, I should use Left/Right non-WM-hypointensities for GM lesions and Left/Right-WM-hypointensities for WM lesions when editing the aseg.presurf.mgz. Correct?
Best, Paul
On Sun, Sep 3, 2017 at 1:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: nope, I would use Left-non-WM-hypointensities and Right-non-WM-hypointensities
On Sun, 3 Sep 2017, miracle ozzoude wrote: Hello Bruce, Thank you. I looked at the LookUpTable.txt for GM and I couldn't find any. I only found labels for Right Lesion, Left lesion, WM lesions (wmsa and other_wmsa). What does wmsa mean and which of these should I use as GM lesion? Best, Paul On Sun, Sep 3, 2017 at 12:45 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Paul GM ones are harder and I'm not sure we have a working procedure for them yet. I think we have separate labels for wm and gm lesions - try using them when you edit the aseg. cheers Bruce On Sun, 3 Sep 2017, miracle ozzoude wrote: Hello Bruce, Thank you very much. I'm guessing I should follow the tutorial for editing aseg; or is there a different tutorial on how to edit and label WM lesions on aseg? One last question, what if it's a combination of WM and GM lesions like cortical stroke that extended into the WM? Should I use the same procedure? Best, Paul Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Sunday, September 3, 2017 11:47 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer with infarct patients Hi Paul if they are WM lesions I think you should edit the aseg and label them as such, then run from there forward. It should propagate the lesions from aseg to wm.mgz, so you shouldn't have to do both Bruce On Sun, 3 Sep 2017, miracle ozzoude wrote: Hello Bruce, I am interested in this thread because I have encountered similar problems with my stroke patients. How do I solve it? Should I only edit the aseg and assign a label called "Lesion" in the FS LookUpTable? or Should I edit both the wm.mgz and aseg.mgz files? If the former, How do I achieve it? My goal is to make sure that WH and GM surfaces are traced properly. Any help will be appreciated. Thank you. Best, Paul On Wed, Jun 21, 2017 at 12:45 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Mariana yes, control points would mess everything up. It looks like the rest of the surface was generated pretty accurately though - do you need to correct anything? cheers Bruce On Wed, 21 Jun 2017, Budge, Mariana wrote: Hi Freesurfer experts, I am running FS on a patient with a chronic right occipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help! Best, Mariana _______________________________________________ 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 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
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.
Thank you very much Bruce. I do appreciate.
Best, Paul
On Sun, Sep 3, 2017 at 2:30 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
yes, I think so. It may not work for the GM ones at the moment, but should at least be fixable
On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you very much. To reiterate our discussion, I should use Left/Right non-WM-hypointensities for GM lesions and Left/Right-WM-hypointensities for WM lesions when editing the aseg.presurf.mgz. Correct?
Best, Paul
On Sun, Sep 3, 2017 at 1:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: nope, I would use Left-non-WM-hypointensities and Right-non-WM-hypointensities
On Sun, 3 Sep 2017, miracle ozzoude wrote: Hello Bruce, Thank you. I looked at the LookUpTable.txt for GM and Icouldn't find any. I only found labels for Right Lesion, Left lesion, WM lesions (wmsa and other_wmsa). What does wmsa mean and which of these should I use as GM lesion?
Best, Paul On Sun, Sep 3, 2017 at 12:45 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Paul
GM ones are harder and I'm not sure we have a workingprocedure for them yet. I think we have separate labels for wm and gm lesions - try using them when you edit the aseg.
cheers Bruce On Sun, 3 Sep 2017, miracle ozzoude wrote: Hello Bruce, Thank you very much. I'm guessing I should followthe tutorial for editing aseg; or is there a different tutorial on how to edit and label WM lesions on aseg? One last question, what if it's a combination of WM and GM lesions like cortical stroke that extended into the WM? Should I use the same procedure?
Best, Paul Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Sunday, September 3, 2017 11:47 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer with infarctpatients
Hi Paul if they are WM lesions I think you should editthe aseg and label them as such, then run from there forward. It should propagate the lesions from aseg to wm.mgz, so you shouldn't have to do both Bruce
On Sun, 3 Sep 2017, miracle ozzoude wrote: Hello Bruce, I am interested in this thread because Ihave encountered similar problems with my stroke patients. How do I solve it? Should I only edit the aseg and assign a label called "Lesion" in the FS LookUpTable? or Should I edit both the wm.mgz and aseg.mgz files? If the former, How do I achieve it? My goal is to make sure that WH and GM surfaces are traced properly. Any help will be appreciated. Thank you.
Best, Paul On Wed, Jun 21, 2017 at 12:45 PM, BruceFischl fischl@nmr.mgh.harvard.edu wrote: Hi Mariana
yes, control points would mess everythingup. It looks like the rest of the surface was generated pretty accurately though - do you need to correct anything?
cheers Bruce On Wed, 21 Jun 2017, Budge, Mariana wrote: Hi Freesurfer experts, I am running FS on a patient with a chronicright occipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help!
Best, Mariana ______________________________
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_______________________________________________ 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 theperson 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
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
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@nmr.mgh.harvard.edu
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Bruce Fischl -
Budge, Mariana -
miracle ozzoude