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Hi Zeyu,
It looks like your files are in 'interfile' format.
If you have access to pmod, you might be able to use that to convert your files to nifti. https://secure-web.cisco.com/1zqVVdVIc7totHjAN-r1V2oHpo0YeUbAKoFLyEzf5hGF_2Q....
Or you could try using this: https://secure-web.cisco.com/1V87W-pEHHar2tKNTfSutV2rBhxv4QVhkEBhm-a5RZ9q6Gz...
Good luck!
-Paul
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zhou, Zeyu zeyu.zhou@emory.edu Sent: Friday, July 28, 2023 10:14 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] PetSurfer, PET data format, mri_convert
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Hi Freesurfer developers,
I am new to PET and FreeSurfer. I am trying to go through the PetSurfer tutorial (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1WIdRjlXspzVNAAubGnxONoOi-JQqlKFaZgFpmpGW_4cj_N...https://secure-web.cisco.com/1SgXjbJz8ibehnENjVYIj14hM83pSJC3l0yNLV0Ubo9CVpoRewK5OxES53m1g56UEZ-L0ETzo4Rc8IsDydiXIeeWmtig-JVTf38MrXJgEig7jBCmIH1m-rCOdppmfFR5wfgg1_moJvMlaGmh_k1ETKxXWg2Wacf0cZvhVYuR5DFR1BJXYCAXEtP7FsfLzyU1CzhIPaI_b5kMDFt1eR8x60qTqr2FUBBzv_u8-A5VIvRrR-59G_W4Aac7OxqLCUzVxEYoa18Z0bBEgjXS-hCBj12Hv8QQmoyM5U0sU9HZrh0U40Wqke505AyMtqaJUm9EXuWiDjKfFEkEzXAenqlKtQA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer). In Part 4 "Register your PET image with the anatomical", the PET data format in example is .nii.gz. However, here are the PET data I have (collected from SIEMENS HRRT PET):
309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i.hdr 309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i 309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i.hdr 309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i 309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i.hdr 309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i 309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i.hdr 309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i 309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i.hdr 309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i 309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i.hdr
I tried converting the .i file to (for example) an .nii file by mri_convert but got the following error message:
mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i 309Fally0.nii ERROR: cannot determine file type for 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i
Then I changed the .i file's extension to .img and the .i.hdr file's extension to .hdr and run mri_convert, but still got an error message:
mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img 309Fally0.nii reading from 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img... error: ReadAnalyzeHeader: unsupported data type 17741
I couldn't find anywhere about how to process PET data in .i and .i.hdr files. Any suggestions? I attached one .i.hdr file for your reference.
1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 2) Platform: macOS Ventura 13.4.1 (c) 3) uname -a: Darwin rad-rsch-pc85 22.5.0 Darwin Kernel Version 22.5.0: Thu Jun 8 22:22:23 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T6020 arm64
Thanks.
Best, Zeyu Zhou