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Dear Freesurfer experts,
We hope you are well.
We are having problems with using vol2subfield when attempting to extract hippocampal subfield info from DTI images.
Our T1 images have been co-registered to their matching DTI images in SPM prior to being run through the recon-all pipeline output files - this looks good.
We have run segmentHA_T1.sh and the results look good.
We created a register.lta between the DTI image and the orig.mgz:
bbregister --s sub1/ --mov DTI.nii --reg register.lta --t2
The bbregister register.lta output looks good when checked with tkregister.
We then run vol2subfield as recommended:
vol2subfield --i DTI.nii --reg register.lta --sf sub1/mri/lh.hippoAmygLabels-T1-T2.v22.FS60.mgz --o dti.rh.FS60.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol avgwfvol.mgz
When we look at the output image overlayed on the DTI.nii/orig.mgz, it looks like everything has been shifted down (on the output image - dti.rh.FS60.mgz) and it doesn’t line up with the anatomy (e.g. subfields are overlayed over the ventricles). However, when we overlay the hippocampal subfield segmentation on our original DTI image, this still looks fine.
We can provide images of the various scans/registrations on request
Are the stats files produced by vol2subfield related to the vol2subfield output image (and therefore look like they're sampling the wrong area), and could you help us figure out where we're going wrong if so, please?
We are using Freesurfer version 7.3.2 with Linux (freesurfer-linux-centos8_x86_64-7.3.2-20220804-6354275, Linux login1.nan.kcl.ac.uk 4.18.0-425.19.2.el8_7.x86_64 #1 SMP Tue Apr 4 05:30:47 EDT 2023 x86_64 x86_64 x86_64 GNU/Linux)
Kind regards, Thank you Anya & Pete
Anya Borissova (she/her) Academic Clinical Fellow, CT3 Psychiatry South London and Maudsley NHS Trust / King's College London Co-host The Thinking Mind podcast - https://secure-web.cisco.com/1_bQVYLS5BbWl03V1Zr9cgJ7t9uyj-JYZOohziGCJ-gD6IA...https://secure-web.cisco.com/1IRLk-P7rXb1Y1y9yU1Xvow2yPs6XwcJtMdZA62FbEy_9qhD4JMUpGyk2rv1qlhbp5TZArLif94W0OEjn-4IFthONwEXPIguRwCqKm6cqYpVmNie9IALf7mmz82NfAs05wYlVUZuWwwV1_nBZfv3i-T9NOlmNwiT1qBRxCU-m1Oc6HfkJlSqwvxBzjnWTYKbUmCc_UwF_GlpQ5Ume9RciKmvUUVyLJFX_QVHYA3a9l8YWoLfm2OuIPCjqOlKOQsdq3E4HhPZuSNpf8Fd3EKiu2drc-fY2FMo6MF5KidlyyMZIzgDRNgnNlP9cl3B8dDUEANG6PsbiOn_Y8OqK7DQ7hw/https%3A%2F%2Flnk.bio%2FtOJq%3Ffbclid%3DIwAR011uxB6SSS0BK4ymyJGezayM9jtuQZimLn0QzTVB0TmfAsNkbMTWPIKRQ