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/1gRnpzcC-wyIJZvEJgw-_KtxFSVcGDUAjDIii5hXhZydgdmbsIZ13fBK1cF53oOVbi_xlaNUxv3v6fD5ZK6o_Q9tBX2IphATpwX7-CyY6WtZf41ytPjCorPIjrp-5twBXh6S6w5YXjoejKW4IMD53SnZ2YcKx4jhsZrrpPicbV1zHn2SGwFIFcTm0nU8k-noU-WGSgrI6sarabvG3slm6YBi0EqF0Z1d0rVJRzkrU-93RRODsmr8exkG6EOkf5H0-3Gwabq-25S8LLybrqZwQz8H6qngECf6O_O8Trk4tLrWlUOvw6nKVQY4zJAfSoRkFB00k0X05TFU5a4rKy7mg5w/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/1gRnpzcC-wyIJZvEJgw-_KtxFSVcGDUAjDIii5hXhZydgdmbsIZ13fBK1cF53oOVbi_xlaNUxv3v6fD5ZK6o_Q9tBX2IphATpwX7-CyY6WtZf41ytPjCorPIjrp-5twBXh6S6w5YXjoejKW4IMD53SnZ2YcKx4jhsZrrpPicbV1zHn2SGwFIFcTm0nU8k-noU-WGSgrI6sarabvG3slm6YBi0EqF0Z1d0rVJRzkrU-93RRODsmr8exkG6EOkf5H0-3Gwabq-25S8LLybrqZwQz8H6qngECf6O_O8Trk4tLrWlUOvw6nKVQY4zJAfSoRkFB00k0X05TFU5a4rKy7mg5w/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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