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 list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<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 list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<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 list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<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>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<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
_______________________________________________
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.
