Re: [Freesurfer] fsaverage across versions
Hi Satra, certainly fsaverage will change if we change things in spherical registration, or potentially elsewhere. I don't anticipate any large changes, but I wouldn't count on them being identical Bruce On Mon, 4 Feb 2013, Satrajit Ghosh wrote: hi bruce and others, are there any specific implications we should be worried about (e.g., with qdec or surf2surf) when using an fsaverage that's from a different version that ran the recon. cheers, satra ___ 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] fsaverage across versions
thanks bruce. indeed, we are not expecting identical output and in these cases that we are looking at it's all 5.x for most part. cheers, satra On Mon, Feb 4, 2013 at 9:34 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Satra, certainly fsaverage will change if we change things in spherical registration, or potentially elsewhere. I don't anticipate any large changes, but I wouldn't count on them being identical Bruce On Mon, 4 Feb 2013, Satrajit Ghosh wrote: hi bruce and others, are there any specific implications we should be worried about (e.g., with qdec or surf2surf) when using an fsaverage that's from a different version that ran the recon. cheers, satra 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/**compliancelinehttp://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] fsaverage across versions
Can anybody confirm my assumption about fsaverage from last week? Is it ok to rerun mri_surfcluster with the new aparc.annot? Thanks a lot, Georg -- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Georg Homola Gesendet: Mittwoch, 1. Juli 2009 17:05 An: 'Freesurfer Mailing List' Betreff: Re: [Freesurfer] fsaverage across versions Hi, my follow up question would be, how much has changed regarding fsaverage between freesurfer version 4.1.0 and 4.3.1? Is the added insula label the only change that has been made? Besides, when I load both annotations, the old and the new one, it seems to me almost every border of the parcellation has been shifted slightly. Is it how it's meant to be? I ask because I forgot to update the fsaverage in my separately stored Subjects_dir since version 4.1.0 and made a lot of analysis in the last months. To my mind it's good enough to rerun mri_surfcluster with the new fsaverage to get the updated annotations into my summary tables. Should that do the trick? Thanks again, Georg --- Iris, the registration targets were derived differently. With version 4, we automatically fill in all the ventricles. In verion 3, they were partially filled in manually. Version 3 creates a surface around the ventrical making it look like a sulcus, and this affects both the target and the registration to the target. So, on most of the surface, the registration will be very close, but it will deviate signifiacntly around the ventricles/medial wall. I think the fsfast in version 4 should work fine with the anatomicals (including fsaverage) of version 3. doug Steinmann, Iris wrote: Hi, we have several reconstructed brains, which were processed by freesurfer 3.0.5. We also kept using the fsaverage data from 3.0.5 in order to be consistent. We wish to do fMRI analysis with freesurfer/fs-fast 4.0.5 and found that talairach coordinates differ slightly when using the fsaverage from version 3.0.5 and the current fsaverage from 4.0.5. Yet, the both volumes appear pretty similar, the newer one maybe a little bit smoother. We would like to know what constitutes the exact difference between these two fsaverage datasets and whether it is possible to use the new version for analysis with the old fsaverage data without getting inconsistent results. Thanks a lot, Iris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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
Re: [Freesurfer] fsaverage across versions
Hi, my follow up question would be, how much has changed regarding fsaverage between freesurfer version 4.1.0 and 4.3.1? Is the added insula label the only change that has been made? Besides, when I load both annotations, the old and the new one, it seems to me almost every border of the parcellation has been shifted slightly. Is it how it's meant to be? I ask because I forgot to update the fsaverage in my separately stored Subjects_dir since version 4.1.0 and made a lot of analysis in the last months. To my mind it's good enough to rerun mri_surfcluster with the new fsaverage to get the updated annotations into my summary tables. Should that do the trick? Thanks again, Georg --- Iris, the registration targets were derived differently. With version 4, we automatically fill in all the ventricles. In verion 3, they were partially filled in manually. Version 3 creates a surface around the ventrical making it look like a sulcus, and this affects both the target and the registration to the target. So, on most of the surface, the registration will be very close, but it will deviate signifiacntly around the ventricles/medial wall. I think the fsfast in version 4 should work fine with the anatomicals (including fsaverage) of version 3. doug Steinmann, Iris wrote: Hi, we have several reconstructed brains, which were processed by freesurfer 3.0.5. We also kept using the fsaverage data from 3.0.5 in order to be consistent. We wish to do fMRI analysis with freesurfer/fs-fast 4.0.5 and found that talairach coordinates differ slightly when using the fsaverage from version 3.0.5 and the current fsaverage from 4.0.5. Yet, the both volumes appear pretty similar, the newer one maybe a little bit smoother. We would like to know what constitutes the exact difference between these two fsaverage datasets and whether it is possible to use the new version for analysis with the old fsaverage data without getting inconsistent results. Thanks a lot, Iris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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
