Dear FS experts, Is it possible to merge the label obtained from tksurfer to T1 weighted image?
If yes, which method I should follow?
Dear Bruce,
Sorry and to be more precise... After creating a label, say DLPFC, I want to merge it on the subject's T1 sagittal section. I'd like to know whether that's possible with FS?
________________________________ From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Anupa AV av.anupa@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Saturday, April 20, 2013 7:25 PM Subject: Re: [Freesurfer] Merging the labels to T1 image
Hi Anupa
I'm not sure what you mean, but mri_label2vol might do what you want
cheers Bruce On Fri, 19 Apr 2013, Anupa AV wrote:
Dear FS experts, Is it possible to merge the label obtained from tksurfer to T1 weighted image?
If yes, which method I should follow?
_______________________________________________ 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.
Sorry, I still don't understand. What do you mean by "merge"?
On Apr 20, 2013, at 10:37 PM, Anupa AV av.anupa@yahoo.com wrote:
Dear Bruce,
Sorry and to be more precise... After creating a label, say DLPFC, I want to merge it on the subject's T1 sagittal section. I'd like to know whether that's possible with FS?
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Anupa AV av.anupa@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Saturday, April 20, 2013 7:25 PM Subject: Re: [Freesurfer] Merging the labels to T1 image
Hi Anupa
I'm not sure what you mean, but mri_label2vol might do what you want
cheers Bruce On Fri, 19 Apr 2013, Anupa AV wrote:
Dear FS experts, Is it possible to merge the label obtained from tksurfer to T1 weighted image?
If yes, which method I should follow?
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.
Ok... I mean overlaying the label to T1W image
________________________________ Fm: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Anupa AV av.anupa@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, April 21, 2013 8:09 AM Subject: Re: [Freesurfer] Merging the labels to T1 image
Sorry, I still don't understand. What do you mean by "merge"?
On Apr 20, 2013, at 10:37 PM, Anupa AV av.anupa@yahoo.com wrote:
Dear Bruce,
Sorry and to be more precise... After creating a label, say DLPFC, I want to merge it on the subject's T1 sagittal section. I'd like to know whether that's possible with FS?
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Anupa AV av.anupa@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Saturday, April 20, 2013 7:25 PM Subject: Re: [Freesurfer] Merging the labels to T1 image
Hi Anupa
I'm not sure what you mean, but mri_label2vol might do what you want
cheers Bruce On Fri, 19 Apr 2013, Anupa AV wrote:
Dear FS experts, Is it possible to merge the label obtained from tksurfer to T1 weighted image?
If yes, which method I should follow?
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 Anupa- you can use tkmedit with -overlay flag shantanu
On Sat, April 20, 2013 10:56 pm, Anupa AV wrote:
Ok... I mean overlaying the label to T1W image
Fm: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Anupa AV av.anupa@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, April 21, 2013 8:09 AM Subject: Re: [Freesurfer] Merging the labels to T1 image
Sorry, I still don't understand. What do you mean by "merge"?
On Apr 20, 2013, at 10:37 PM, Anupa AV av.anupa@yahoo.com wrote:
Dear Bruce,
Sorry and to be more precise... After creating a label, say DLPFC, I want to merge it on the subject's T1 sagittal section. I'd like to know whether that's possible with FS?
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Anupa AV av.anupa@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Saturday, April 20, 2013 7:25 PM Subject: Re: [Freesurfer] Merging the labels to T1 image
Hi Anupa
I'm not sure what you mean, but mri_label2vol might do what you want
cheers Bruce On Fri, 19 Apr 2013, Anupa AV wrote:
Dear FS experts, Is it possible to merge the label obtained from tksurfer to T1 weighted image?
If yes, which method I should follow?
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
Dear Ghosh,
I tried to use the overlay command.
tkmedit -f /home/mbial/JPJ/freesurfer/SZ01/mri/brain.mgz -overlay DLPFC.label
Kindly check whether the command line is correct or not.
But it's throwing some error.
Error: Loading functional overlay ./DLPFC.label
Couldn't load MRI volume.
Tkmedit couldn't read the functional volume you specified. This could be because the volume wasn't found or was unreadable, or because a valid header type couldn't be find, or a registration file couldn't be found or opened.
________________________________ From: Shantanu Ghosh shantanu@nmr.mgh.harvard.edu To: Anupa AV av.anupa@yahoo.com Cc: Bruce Fischl fischl@nmr.mgh.harvard.edu; Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, April 21, 2013 9:44 AM Subject: Re: [Freesurfer] Merging the labels to T1 image
Hi Anupa- you can use tkmedit with -overlay flag shantanu
On Sat, April 20, 2013 10:56 pm, Anupa AV wrote:
Ok... I mean overlaying the label to T1W image
Fm: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Anupa AV av.anupa@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, April 21, 2013 8:09 AM Subject: Re: [Freesurfer] Merging the labels to T1 image
Sorry, I still don't understand. What do you mean by "merge"?
On Apr 20, 2013, at 10:37 PM, Anupa AV av.anupa@yahoo.com wrote:
Dear Bruce,
Sorry and to be more precise... After creating a label, say DLPFC, I want to merge it on the subject's T1 sagittal section. I'd like to know whether that's possible with FS?
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Anupa AV av.anupa@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Saturday, April 20, 2013 7:25 PM Subject: Re: [Freesurfer] Merging the labels to T1 image
Hi Anupa
I'm not sure what you mean, but mri_label2vol might do what you want
cheers Bruce On Fri, 19 Apr 2013, Anupa AV wrote:
Dear FS experts, Is it possible to merge the label obtained from tksurfer to T1 weighted image?
If yes, which method I should follow?
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
Hi Anupa
try loading it as a label, not an overlay (e.g. go into the tkmedit file menu and load it there). Or you could use freeview:
freeview -v -f /home/mbial/JPJ/freesurfer/SZ01/mri/brain.mgz -l DLPFC.label
cheers Bruce On Sun, 21 Apr 2013, Anupa AV wrote:
Dear Ghosh,
I tried to use the overlay command.
tkmedit -f /home/mbial/JPJ/freesurfer/SZ01/mri/brain.mgz -overlay DLPFC.label
Kindly check whether the command line is correct or not.
But it's throwing some error.
Error: Loading functional overlay ./DLPFC.label
Couldn't load MRI volume.
Tkmedit couldn't read the functional volume you specified. This could be because the volume wasn't found or was unreadable, or because a valid header type couldn't be find, or a registration file couldn't be found or opened.
From: Shantanu Ghosh shantanu@nmr.mgh.harvard.edu To: Anupa AV av.anupa@yahoo.com Cc: Bruce Fischl fischl@nmr.mgh.harvard.edu; Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, April 21, 2013 9:44 AM Subject: Re: [Freesurfer] Merging the labels to T1 image
Hi Anupa- you can use tkmedit with -overlay flag shantanu
On Sat, April 20, 2013 10:56 pm, Anupa AV wrote:
Ok... I mean overlaying the label to T1W image
Fm: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Anupa AV av.anupa@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, April 21, 2013 8:09 AM Subject: Re: [Freesurfer] Merging the labels to T1 image
Sorry, I still don't understand. What do you mean by "merge"?
On Apr 20, 2013, at 10:37 PM, Anupa AV av.anupa@yahoo.com wrote:
Dear Bruce,
Sorry and to be more precise... After creating a label, say DLPFC, I want to merge it on the subject's T1 sagittal section. I'd like to know whether that's possible with FS?
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Anupa AV av.anupa@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Saturday, April 20, 2013 7:25 PM Subject: Re: [Freesurfer] Merging the labels to T1 image
Hi Anupa
I'm not sure what you mean, but mri_label2vol might do what you want
cheers Bruce On Fri, 19 Apr 2013, Anupa AV wrote:
Dear FS experts, Is it possible to merge the label obtained from tksurfer to T1 weighted image?
If yes, which method I should follow?
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
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging
freesurfer@nmr.mgh.harvard.edu
-
Anupa AV -
Bruce Fischl -
Shantanu Ghosh