External Email - Use Caution Hello,
My goal is to compare the FA and MD values of hippocampal subfields (only inside the hippocampus) between cognitively normal, MCI, and AD subjects. I am unsure if this would require a voxel wise analysis or an ROI analysis… to my understanding this is more of a ROI analysis between subjects - is this assumption incorrect? Thank you, Peter On Sat, Jan 13, 2024 at 10:44 AM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > So this is where I get confused on your intentions because you say that > you want to do a voxel-wise analysis of an ROI. Do you mean you want to do > a voxelwise analysis but only inside, eg, whole hippocampus? > > On 1/12/2024 6:07 PM, Mirsol Choi wrote: > > External Email - Use Caution > Hello, > > Sorry I should have clarified. Yes, I would like to perform voxelwise > analysis of FA and MD values of hippocampal subfield between subjects. Is > this possible with free surfer? > > Thank you again for your time. > > M > > On Fri, Jan 12, 2024 at 4:05 PM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> oh, I thought you wanted to do an ROI analysis. You mean for a voxelwise >> analysis? >> >> On 1/12/2024 5:46 PM, Mirsol Choi wrote: >> >> External Email - Use Caution >> Hi there, >> >> >> Following the first registration step, should I also run another >> registration command to put all fa-in-subfields.mgz for each subject onto >> the same space for inter subject analysis of FA values? >> >> Thanks again, >> M >> >> On Fri, Jan 12, 2024 at 3:00 PM Douglas N. Greve <dgr...@mgh.harvard.edu> >> wrote: >> >>> Map the diffusion data to the subfield space, eg, >>> mri_vol2vol --mov fa.nii.gz --reg register.lta --targ subfields.mgz --o >>> fa-in-subfields.mgz >>> Then run mri_segstats >>> mri_segstats --ctab-default --i fa-in-subfields.mgz --seg subfields.mgz >>> --sum fa-in-subfields.dat >>> >>> >>> >>> On 1/12/2024 4:53 PM, Mirsol Choi wrote: >>> >>> External Email - Use Caution >>> Hi there, >>> >>> Is there a way to successfully obtain FA/MD values from the hippocampus >>> subfields? >>> >>> Thank you, >>> M >>> >>> >>> On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve <dgr...@mgh.harvard.edu> >>> wrote: >>> >>> I'm not sure what you mean. The subfields are an ROI-based analysis. Are >>>> you saying you want to do a voxel-based analysis (without reference to >>>> ROIs)? >>>> >>>> On 1/9/2024 12:05 PM, Mirsol Choi wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Hi there Freesurfer, >>>> >>>> I am currently using freesurfer to take DTI metrics (FA, MD) from >>>> hippocampal subfields. >>>> At this point of my exploration with freesurfer, I am able to correctly >>>> register the hippocampal subfields and diffusion data, and obtain my FA >>>> values from the subfields. However, this is at the individual subject >>>> level. >>>> >>>> I will eventually need to register all of my samples in the same space >>>> for me to do a group analysis. However I am unsure what the order of >>>> registration should be for this process to be feasible. >>>> >>>> Does this order seem feasible for accurate analysis? >>>> >>>> 1) recon-all all of my subjects >>>> 2) dt_recon all of my subjects (one of the outputs is a registration >>>> file, which has registered the DTI data to outputs of recon-all) >>>> 3) run the hippocampus segmentation command on all subjects >>>> (segmentHA_T1.sh) to obtain hippocampal subfield segmentation >>>> 4) register the segmentation file to the FA maps (output of dt_recon) >>>> using vol2subfield command >>>> 5) After creating a subfield-FA map for each subject, spatial normalize >>>> the samples onto the same space using *mri_vol2vol* >>>> >>>> Thank you so much for taking the time reading my question. If there is >>>> a different method to spatially normalizing my datasets, or if there is a >>>> more optimal order of registration, I'd be happy to hear from you. >>>> >>>> Thank you, >>>> M >>>> >>>> _______________________________________________ >>>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu >>>> >>>> *MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/1fvcHnbj5YznlhOVAEHRHe3xmjVhE32aLnGhWNwLaaisvOpzJpaM2UQgaKanvk7Dbg7Fn95gy0QSIbhTmbvtg6mqE9LPNG2h2Zqwh2JCO6c4elHNiKReQp4jRz-4x4Bapzvmgy10nPESXJJv_83tXfkFBP7BP95nWqUm2DUG_moM_fC8oX-RZTESv_hAT8XHt7X0W9vuR-h5IyTYg75mmZkWkx3eR13wKr_SHMJxq8Orewm7hS2JGGvK1XA6aD9fy4MyzjeeiZ4a9LM13em3RMo28BwCrAUWVdsaG-BWf-xSJSP_U6FwjBnrpmtrE0EYPNhoJUPt9gfQ-pcVRu96uEw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> >>>> <https://secure-web.cisco.com/1KU4jXJB1CrsIlaMiid17Ht9H8dz8aaMrgEllh75BASm41YPJpFvV9YGaQw-aq9ywLjQPjU-JEFjbZiQWZfEndP8uhI_K8iXBEN-wwTFN6ZjK7syWmvB8P5YpyqjFXSJToS93Qqgg1MSw6C82X7rFFhq057nFheAfGqu-gv0nkPsP_vD2_WtDhJFdeGBAQf7P03R9ZJw5Z70vUKbgy1lxUxP5RW6aBx9zSLvaWhcZleoNAU0n_Tp1Cx4jzMOFGjTSwDdjr6FdJnAehsOeF6nsAFwgWILwSDahrWq6e0Yo6kjc--71AFBb0tbcs27_rlaFkEkcvbXrcxUQn2g31PjLRQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> *MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/1fvcHnbj5YznlhOVAEHRHe3xmjVhE32aLnGhWNwLaaisvOpzJpaM2UQgaKanvk7Dbg7Fn95gy0QSIbhTmbvtg6mqE9LPNG2h2Zqwh2JCO6c4elHNiKReQp4jRz-4x4Bapzvmgy10nPESXJJv_83tXfkFBP7BP95nWqUm2DUG_moM_fC8oX-RZTESv_hAT8XHt7X0W9vuR-h5IyTYg75mmZkWkx3eR13wKr_SHMJxq8Orewm7hS2JGGvK1XA6aD9fy4MyzjeeiZ4a9LM13em3RMo28BwCrAUWVdsaG-BWf-xSJSP_U6FwjBnrpmtrE0EYPNhoJUPt9gfQ-pcVRu96uEw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> <https://secure-web.cisco.com/1KU4jXJB1CrsIlaMiid17Ht9H8dz8aaMrgEllh75BASm41YPJpFvV9YGaQw-aq9ywLjQPjU-JEFjbZiQWZfEndP8uhI_K8iXBEN-wwTFN6ZjK7syWmvB8P5YpyqjFXSJToS93Qqgg1MSw6C82X7rFFhq057nFheAfGqu-gv0nkPsP_vD2_WtDhJFdeGBAQf7P03R9ZJw5Z70vUKbgy1lxUxP5RW6aBx9zSLvaWhcZleoNAU0n_Tp1Cx4jzMOFGjTSwDdjr6FdJnAehsOeF6nsAFwgWILwSDahrWq6e0Yo6kjc--71AFBb0tbcs27_rlaFkEkcvbXrcxUQn2g31PjLRQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>> >>> >>>> Please note that this e-mail is not secure (encrypted). 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