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/1v6TlAXVkTURRbMgaTbvOwCu5DC2s1X-aForrBtXff5-2rgcsq2hXslcqOQhmf7q7NHUTETS0neQ0liC3nNuDjfyaKLnbiV-NTdVsXdLZzPHhD07vQd_Aq8KlWoHjaEti6To0JUT7C8RBfN1ephtC35haijaNJWPZ0fb651iI6n-EYSpJfYLFmKR2OLD1JFEvRfUhG7AQKamRTjSBlyZsXJNRHx-5T7RQ-IFngaPLo4n7pOFRyBY8J68GLZpchyPHPITZP8lK6ep9JfvH3AAvjZ5NKynzBYgLkzvoakF6WFiWHtHV5nHRdrJjLMAGFXwkmM4N85yZ1n7B-KwbttDukQ/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/1v6TlAXVkTURRbMgaTbvOwCu5DC2s1X-aForrBtXff5-2rgcsq2hXslcqOQhmf7q7NHUTETS0neQ0liC3nNuDjfyaKLnbiV-NTdVsXdLZzPHhD07vQd_Aq8KlWoHjaEti6To0JUT7C8RBfN1ephtC35haijaNJWPZ0fb651iI6n-EYSpJfYLFmKR2OLD1JFEvRfUhG7AQKamRTjSBlyZsXJNRHx-5T7RQ-IFngaPLo4n7pOFRyBY8J68GLZpchyPHPITZP8lK6ep9JfvH3AAvjZ5NKynzBYgLkzvoakF6WFiWHtHV5nHRdrJjLMAGFXwkmM4N85yZ1n7B-KwbttDukQ/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). If you do not >>> wish to continue communication over unencrypted e-mail, please notify the >>> sender of this message immediately. Continuing to send or respond to >>> e-mail after receiving this message means you understand and accept this >>> risk and wish to continue to communicate over unencrypted e-mail. >>> >> >> _______________________________________________ >> 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/1v6TlAXVkTURRbMgaTbvOwCu5DC2s1X-aForrBtXff5-2rgcsq2hXslcqOQhmf7q7NHUTETS0neQ0liC3nNuDjfyaKLnbiV-NTdVsXdLZzPHhD07vQd_Aq8KlWoHjaEti6To0JUT7C8RBfN1ephtC35haijaNJWPZ0fb651iI6n-EYSpJfYLFmKR2OLD1JFEvRfUhG7AQKamRTjSBlyZsXJNRHx-5T7RQ-IFngaPLo4n7pOFRyBY8J68GLZpchyPHPITZP8lK6ep9JfvH3AAvjZ5NKynzBYgLkzvoakF6WFiWHtHV5nHRdrJjLMAGFXwkmM4N85yZ1n7B-KwbttDukQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <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> >> >> >> _______________________________________________ >> 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/1v6TlAXVkTURRbMgaTbvOwCu5DC2s1X-aForrBtXff5-2rgcsq2hXslcqOQhmf7q7NHUTETS0neQ0liC3nNuDjfyaKLnbiV-NTdVsXdLZzPHhD07vQd_Aq8KlWoHjaEti6To0JUT7C8RBfN1ephtC35haijaNJWPZ0fb651iI6n-EYSpJfYLFmKR2OLD1JFEvRfUhG7AQKamRTjSBlyZsXJNRHx-5T7RQ-IFngaPLo4n7pOFRyBY8J68GLZpchyPHPITZP8lK6ep9JfvH3AAvjZ5NKynzBYgLkzvoakF6WFiWHtHV5nHRdrJjLMAGFXwkmM4N85yZ1n7B-KwbttDukQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <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> >> Please note that this e-mail is not secure (encrypted). If you do not >> wish to continue communication over unencrypted e-mail, please notify the >> sender of this message immediately. Continuing to send or respond to >> e-mail after receiving this message means you understand and accept this >> risk and wish to continue to communicate over unencrypted e-mail. >> > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1v6TlAXVkTURRbMgaTbvOwCu5DC2s1X-aForrBtXff5-2rgcsq2hXslcqOQhmf7q7NHUTETS0neQ0liC3nNuDjfyaKLnbiV-NTdVsXdLZzPHhD07vQd_Aq8KlWoHjaEti6To0JUT7C8RBfN1ephtC35haijaNJWPZ0fb651iI6n-EYSpJfYLFmKR2OLD1JFEvRfUhG7AQKamRTjSBlyZsXJNRHx-5T7RQ-IFngaPLo4n7pOFRyBY8J68GLZpchyPHPITZP8lK6ep9JfvH3AAvjZ5NKynzBYgLkzvoakF6WFiWHtHV5nHRdrJjLMAGFXwkmM4N85yZ1n7B-KwbttDukQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
