[Freesurfer] Hippocampal subfields - molecular layer labelling Freesurfer 6.0
Hi, I know this has been addressed a bit before, but I remain confused! Apologies. 1…. The dentate anatomically has 3 layers [molecular layer/granular layer/polymorphic layer]. What layers exactly do Freesurfer output “GC_ML_DG” or “CG_ML" correspond to? Granular layer only? Or Granular layer with polymorphic layer? Or Granular layer, polymorphic layer and molecular layer? It’s mentioned in the Eugenio Iglesias’ article that the molecular layer of the dentate is included in the CA4 region. Is this where is it, or is it in the GC_ML_DG? 2…. By “molecular_layer_HP” does Freesurfer mean the ‘molecular layer’ i.e. ‘outermost’ band of Subiculum, CA1, CA2/3? Or Subiculum, CA1, CA2/3 and molecular layer of dentate? I would appreciate some clarification.. Wonderful application by the way. A great step forward for hippocampal research Many thanks.. Dr Darren Roddy Trinity College Institute of Neuroscience Room 3.36, The Lloyd Institute Trinity College Dublin Dublin 2 +353 86 6087927 ___ 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] Brain editing for TRACULA?
Dear DTI Expert: I wonder I may get help with this quick question - Is the brain editing necessary (or critical) for TRACULA processing? Thank you! Yuwen ___ 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] longitudinal TRACULA
Hi, I've run cross-sectional TRACULA on one subject, three different timepoints. Now I'm trying to run a longitudinal analysis on the same subject's 3 timepoints. My understanding was that for TRACULA, unlike for morphometry, I don't need to first run cross sectional before longitudinal, the only requirement is that I have a longitudinal dmrirc file that specifies the timepoints with their corresponding files. It crashed with these error messages: #@# Inter-subject registration (base template) lø. 29. juli 14:25:45 +0200 2017 cp /work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/mni2anatorig.mat /work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/anatorig2mni.mat /work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_base/dmri/xfms cp: cannot stat `/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/mni2anatorig.mat': No such file or directory cp: cannot stat `/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/anatorig2mni.mat': No such file or directory Linux compute-16-32.local 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Any idea what went wrong here? Thank you! Sincerely yours, Lars M. Rimol, PhD Senior Researcher Norwegian Advisory Unit for Functional MRI Department of Radiology St. Olav's University Hospital 7006 Trondheim Norway ___ 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.
