Re: [Freesurfer] Caret to Freesurfer
Matt, Yes, I think the plan is to discuss this and other potential options. I had a feeling you may know the most, but I thought I would send out the question in case anyone else has tried. As it stands, it sounds like no method currently exists for a Caret surface-to-Freesurfer transition? I am still trying to understand Freesurfer basics, but it sounds like the longitudinal pipeline generally requires the same input data as across-subject. My hope is that, since the surfaces are already constructed, I can avoid the need for an (infant) atlas, but I am still figuring out what that means in terms of files I need/conversion/etc. Thanks for your help, and I look forward to further discussion this afternoon. Kara From: Matt Glasser [m...@ma-tea.com] Sent: Thursday, March 14, 2013 7:14 PM To: Bruce Fischl; Ellspermann, Kara Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Caret to Freesurfer She wants to go from Caret to FreeSurfer, rather than from FreeSurfer to Caret, which is what I do. Kara, I believe we are meeting tomorrow to discuss the options for this? I don't know anything about the FreeSurfer longitudinal pipeline, but it would take going through the pipeline and finding all of the inputs needed and converting them or generating them. I think the main goal here is to use the longitudinal surface registration. Matt. On 3/14/13 8:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kara I think the answer is yes as there are people at Wash U that do this routinely. Maybe Matt Glasser or someone else can chime in? cheers Bruce On Thu, 14 Mar 2013, Ellspermann, Kara wrote: I am new to Freesurfer, and I am trying to input/process preterm infant brain data (ultimately attempting longitudinal registration). I already have surfaces generated from Caret, as well as the original T1/T2 images. My question is: Does anything exist to take processed data from Caret into Freesurfer? If not, is there a good way to process the T1/T2 images in Freesurfer despite the differences in contrast and intensity (and anatomy)? Thank you in advance for your advice, Kara ___ 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] Caret to Freesurfer
Kara, the gifti format is used to convert between caret and freesurfer surfaces. use mris_convert (see --help). Nick Matt, Yes, I think the plan is to discuss this and other potential options. I had a feeling you may know the most, but I thought I would send out the question in case anyone else has tried. As it stands, it sounds like no method currently exists for a Caret surface-to-Freesurfer transition? I am still trying to understand Freesurfer basics, but it sounds like the longitudinal pipeline generally requires the same input data as across-subject. My hope is that, since the surfaces are already constructed, I can avoid the need for an (infant) atlas, but I am still figuring out what that means in terms of files I need/conversion/etc. Thanks for your help, and I look forward to further discussion this afternoon. Kara From: Matt Glasser [m...@ma-tea.com] Sent: Thursday, March 14, 2013 7:14 PM To: Bruce Fischl; Ellspermann, Kara Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Caret to Freesurfer She wants to go from Caret to FreeSurfer, rather than from FreeSurfer to Caret, which is what I do. Kara, I believe we are meeting tomorrow to discuss the options for this? I don't know anything about the FreeSurfer longitudinal pipeline, but it would take going through the pipeline and finding all of the inputs needed and converting them or generating them. I think the main goal here is to use the longitudinal surface registration. Matt. On 3/14/13 8:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kara I think the answer is yes as there are people at Wash U that do this routinely. Maybe Matt Glasser or someone else can chime in? cheers Bruce On Thu, 14 Mar 2013, Ellspermann, Kara wrote: I am new to Freesurfer, and I am trying to input/process preterm infant brain data (ultimately attempting longitudinal registration). I already have surfaces generated from Caret, as well as the original T1/T2 images. My question is: Does anything exist to take processed data from Caret into Freesurfer? If not, is there a good way to process the T1/T2 images in Freesurfer despite the differences in contrast and intensity (and anatomy)? Thank you in advance for your advice, Kara ___ 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] Caret to Freesurfer
I am new to Freesurfer, and I am trying to input/process preterm infant brain data (ultimately attempting longitudinal registration). I already have surfaces generated from Caret, as well as the original T1/T2 images. My question is: Does anything exist to take processed data from Caret into Freesurfer? If not, is there a good way to process the T1/T2 images in Freesurfer despite the differences in contrast and intensity (and anatomy)? Thank you in advance for your advice, Kara ___ 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] Caret to Freesurfer
Hi Kara I think the answer is yes as there are people at Wash U that do this routinely. Maybe Matt Glasser or someone else can chime in? cheers Bruce On Thu, 14 Mar 2013, Ellspermann, Kara wrote: I am new to Freesurfer, and I am trying to input/process preterm infant brain data (ultimately attempting longitudinal registration). I already have surfaces generated from Caret, as well as the original T1/T2 images. My question is: Does anything exist to take processed data from Caret into Freesurfer? If not, is there a good way to process the T1/T2 images in Freesurfer despite the differences in contrast and intensity (and anatomy)? Thank you in advance for your advice, Kara ___ 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] Caret to Freesurfer
She wants to go from Caret to FreeSurfer, rather than from FreeSurfer to Caret, which is what I do. Kara, I believe we are meeting tomorrow to discuss the options for this? I don't know anything about the FreeSurfer longitudinal pipeline, but it would take going through the pipeline and finding all of the inputs needed and converting them or generating them. I think the main goal here is to use the longitudinal surface registration. Matt. On 3/14/13 8:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kara I think the answer is yes as there are people at Wash U that do this routinely. Maybe Matt Glasser or someone else can chime in? cheers Bruce On Thu, 14 Mar 2013, Ellspermann, Kara wrote: I am new to Freesurfer, and I am trying to input/process preterm infant brain data (ultimately attempting longitudinal registration). I already have surfaces generated from Caret, as well as the original T1/T2 images. My question is: Does anything exist to take processed data from Caret into Freesurfer? If not, is there a good way to process the T1/T2 images in Freesurfer despite the differences in contrast and intensity (and anatomy)? Thank you in advance for your advice, Kara ___ 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
