External Email - Use Caution 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_2QpNKUkYjapa61k7l3PSjeARv8qdfQNsmsWgyLM_x7yRo7uvps9iIp9uwO7a2TINpqT1lUcfZcSARBl8Fns-rGgqjVdinmxYTRRJW7qEhjB7TFy_Akeg1X6PozmQwtUClLKAap1CgLy0N6P-i1td6Epv8GJIS-_NewalfMvYf-uyOe7TemfME6k238__pKMda6B1y1hwLdR5PEBewmHUOTI5Z0xkuVuplriFkvuAaw/https%3A%2F%2Fwww.pmod.com%2Ffiles%2Fdownload%2Fv31%2Fdoc%2Fpbas%2F684.htm%23%3A%7E%3Atext%3DInterfile%2520is%2520a%2520file%2520format,version%203.3%2C%20Nucl%20Med%20Commun. Or you could try using this: https://secure-web.cisco.com/1V87W-pEHHar2tKNTfSutV2rBhxv4QVhkEBhm-a5RZ9q6Gz-7E2XdigrjJkwDqcX7klh7tFuRWLL-91eC6kvPzjRRqZhQnS5wwjEH2gT566KrsPTsUSgBpXi1HnBlucbgC5JunCkl-6FVnKsvzu3cCbBMp82g0-NeCBdJM_xFIERvYEYDp6ArkE6kKJ18zQhGHc3KX4095fGBoZgt7_PI5_RP7B5AEA-HCHemz72hJe_7FTpJkw6Giy3l28FBafW09nazM9MZx3-XJ1nWYzDVRA/https%3A%2F%2Fgithub.com%2Frordenlab%2Fi2nii Good luck! -Paul ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zhou, Zeyu <zeyu.z...@emory.edu> Sent: Friday, July 28, 2023 10:14 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] PetSurfer, PET data format, mri_convert External Email - Use Caution 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_NGoWMbZCmxAW1Lx2XUGPrto07cKnoNmWSMabwUBhdizuJ3mimj9Xd_MWpUSafdFT4ojOiEHnwrT0iBPizzRaKXMlYsvKENtDO5ccRa8UEo9gWeMyQ0bNS2k2tUOQgdDchNUPKBRvJq54IaFi4y0eKS3ZSLgf78xNoL7Ng6qOqEMXMWX71tcHgARz3rerCE6795uAmZuqzjgij7h-thEDV9w3pPcJD-2qnuXbJpekQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer<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 "Reg ister 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). 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