Re: [Freesurfer] Query about transformations in the recon-all
we use a procedure from Avi Snyder to compute (but not apply) a 12 degree of freedom transform to MNI space. This is available for coordinate reporting and we use it a bit for things like finding the approximate center of the brain cheers Bruce On Wed, 19 Aug 2015, chenhf_uestc wrote: Hi, Bruce Thanks for your reply. Another question is What is talairach transformationprocedure (This computes the affine transform from the orig volume to the M NI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer scrip t called talairach). Why I need to transform from native space to MNI305 (We perform recon-all in the native space)? Best, Feng 发件人：Bruce Fischl 发送时间：2015-08-18 22:09 主题：Re: [Freesurfer] Query about transformations in the recon-all 收件人："Freesurfer support list" 抄送： Hi Feng we compute many transforms for many reasons. The em reg is computed once in the image with skull to help with skull stripping, then again to the GCA atlas to initialize the nonlinear transform for computing the aseg segmentation. cheers Bruce On Tue, 18 Aug 2015, chenhf_uestc wrote: > Dear Freesurfer experts, > > I have some questions in the recon-all. After reading online manual and d iscussing with the experts in > the maillist, I have known all the recon-all procedures performed in the ?? ?individual native space. > However, I very confuse that there are many transformations in the recon- all, e.g., 1. talairach > transformation (This computes the affine transform from the orig volume t o the MNI305 atlas using the > MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer scr ipt called talairach), why I > need transform from native space to MNI305; 2. EM (GCA) Registration (Com putes transform to align the > mri/nu.mgz volume to the default GCA atlas found in FREESURFER_HOME/avera ge). What is the GCA atlas? > what is the usage of this atlas? 3. CA Register (Computes a nonlinear tra nsform to align with GCA > atlas. Creates the file mri/transform/talairach.m3z). Why we should align with GCA atlas? This > transform is nonlinear, and what is the transform in the EM (GCA) Registr ation (Affine? 12 dof?); 4. > EM Registration, with Skull (Computes transform to align volume mri/nu_no neck.mgz with GCA volume > possessing the skull); > > Is there any detailed documentation in the online manual to introduce the se transformation? Could > anyone give me a website? > > Any help would be greatly appreciate. > > Best, > Feng > > > ___ 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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly 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.
Re: [Freesurfer] Query about transformations in the recon-all
Hi, Bruce Thanks for your reply. Another question is What is talairach transformation procedure (This computes the affine transform from the orig volume to the MNI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer script called talairach). Why I need to transform from native space to MNI305 (We perform recon-all in the native space)? Best, Feng 发件人：Bruce Fischl 发送时间：2015-08-18 22:09 主题：Re: [Freesurfer] Query about transformations in the recon-all 收件人："Freesurfer support list" 抄送： Hi Feng we compute many transforms for many reasons. The em reg is computed once in the image with skull to help with skull stripping, then again to the GCA atlas to initialize the nonlinear transform for computing the aseg segmentation. cheers Bruce On Tue, 18 Aug 2015, chenhf_uestc wrote: > Dear Freesurfer experts, > > I have some questions in the recon-all. After reading online manual and > discussing with the experts in > the maillist, I have known all the recon-all procedures performed in the > individual native space. > However, I very confuse that there are many transformations in the recon-all, > e.g., 1. talairach > transformation (This computes the affine transform from the orig volume to > the MNI305 atlas using the > MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer script > called talairach), why I > need transform from native space to MNI305; 2. EM (GCA) Registration > (Computes transform to align the > mri/nu.mgz volume to the default GCA atlas found in FREESURFER_HOME/average). > What is the GCA atlas? > what is the usage of this atlas? 3. CA Register (Computes a nonlinear > transform to align with GCA > atlas. Creates the file mri/transform/talairach.m3z). Why we should align > with GCA atlas? This > transform is nonlinear, and what is the transform in the EM (GCA) > Registration (Affine? 12 dof?); 4. > EM Registration, with Skull (Computes transform to align volume > mri/nu_noneck.mgz with GCA volume > possessing the skull); > > Is there any detailed documentation in the online manual to introduce these > transformation? Could > anyone give me a website? > > Any help would be greatly appreciate. > > Best, > Feng > > > ___ 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.
Re: [Freesurfer] Query about transformations in the recon-all
Hi Feng we compute many transforms for many reasons. The em reg is computed once in the image with skull to help with skull stripping, then again to the GCA atlas to initialize the nonlinear transform for computing the aseg segmentation. cheers Bruce On Tue, 18 Aug 2015, chenhf_uestc wrote: Dear Freesurfer experts, I have some questions in the recon-all. After reading online manual and discussing with the experts in the maillist, I have known all the recon-all procedures performed in the individual native space. However, I very confuse that there are many transformations in the recon-all, e.g., 1. talairach transformation (This computes the affine transform from the orig volume to the MNI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer script called talairach), why I need transform from native space to MNI305; 2. EM (GCA) Registration (Computes transform to align the mri/nu.mgz volume to the default GCA atlas found in FREESURFER_HOME/average). What is the GCA atlas? what is the usage of this atlas? 3. CA Register (Computes a nonlinear transform to align with GCA atlas. Creates the file mri/transform/talairach.m3z). Why we should align with GCA atlas? This transform is nonlinear, and what is the transform in the EM (GCA) Registration (Affine? 12 dof?); 4. EM Registration, with Skull (Computes transform to align volume mri/nu_noneck.mgz with GCA volume possessing the skull); Is there any detailed documentation in the online manual to introduce these transformation? Could anyone give me a website? Any help would be greatly appreciate. Best, Feng ___ 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] Query about transformations in the recon-all
Dear Freesurfer experts, I have some questions in the recon-all. After reading online manual and discussing with the experts in the maillist, I have known all the recon-all procedures performed in the individual native space. However, I very confuse that there are many transformations in the recon-all, e.g., 1. talairach transformation (This computes the affine transform from the orig volume to the MNI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer script called talairach), why I need transform from native space to MNI305; 2. EM (GCA) Registration (Computes transform to align the mri/nu.mgz volume to the default GCA atlas found in FREESURFER_HOME/average). What is the GCA atlas? what is the usage of this atlas? 3. CA Register (Computes a nonlinear transform to align with GCA atlas. Creates the file mri/transform/talairach.m3z). Why we should align with GCA atlas? This transform is nonlinear, and what is the transform in the EM (GCA) Registration (Affine? 12 dof?); 4. EM Registration, with Skull (Computes transform to align volume mri/nu_noneck.mgz with GCA volume possessing the skull); Is there any detailed documentation in the online manual to introduce these transformation? Could anyone give me a website? Any help would be greatly appreciate. Best, Feng___ 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.
