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On Sat, Jan 13, 2024 at 11:00 AM Mirsol Choi <mir...@ualberta.ca> wrote: > 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/1rk41X_Wgl55cngAOVnp8CUZOyrhGpb9l5sm3U2UFASq2_B2a_ZiPPa062jQBuwIawFqa_fbz4G7YUbP6yCfBRflyvYLrh-jX_ArTlH1TWmPhUytebNdDAHwLzR32Cggvv2suWogNXN6DBdOhxAkXpl4JoVFhIR-bFko4O9wS1NOpjXMAeV6Rdu7juykmoX7n1NV2Q0MOHK0vqgtOZApP2jnMUT6zDEuuc9iWhZxCHkn1TY1YwV3eQPyl3faoEHTZSA4pKwpsb0DMIm-Hp5eDNHYeKXctTxS1jT95woNnxc6Xx53-fRs_ehmx3jKDVvIo0_LqF4aoVKlwJCN0Nb4JOA/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/1rk41X_Wgl55cngAOVnp8CUZOyrhGpb9l5sm3U2UFASq2_B2a_ZiPPa062jQBuwIawFqa_fbz4G7YUbP6yCfBRflyvYLrh-jX_ArTlH1TWmPhUytebNdDAHwLzR32Cggvv2suWogNXN6DBdOhxAkXpl4JoVFhIR-bFko4O9wS1NOpjXMAeV6Rdu7juykmoX7n1NV2Q0MOHK0vqgtOZApP2jnMUT6zDEuuc9iWhZxCHkn1TY1YwV3eQPyl3faoEHTZSA4pKwpsb0DMIm-Hp5eDNHYeKXctTxS1jT95woNnxc6Xx53-fRs_ehmx3jKDVvIo0_LqF4aoVKlwJCN0Nb4JOA/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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