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Hey guys. I'm using FMRIprep on the OASIS3 database and I've noticed that the processing time for each subject averages two days. 80% of that processing is due to the freesurfer. I will need to analyze many resonance images, more precisely the functional part. I tested SMRIprep and didn't get a significant improvement in processing time. How are you getting around this type of problem? How are they using freesurfer in a big dataset?
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For 1mm data, FS will generally run in 5-10 hours. Are you talking about high resolution data?
On 6/20/2023 10:11 AM, Michelle Diniz wrote:
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Hey guys. I'm using FMRIprep on the OASIS3 database and I've noticed that the processing time for each subject averages two days. 80% of that processing is due to the freesurfer. I will need to analyze many resonance images, more precisely the functional part. I tested SMRIprep and didn't get a significant improvement in processing time. How are you getting around this type of problem? How are they using freesurfer in a big dataset?
-- Michelle Diniz Lopes
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1qOlyBY-EW1phq7cja_yV9SaYanmwB__T9e4D6aXseSLG-R...
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Does 1mm mean 1 millimeter? I was in doubt! I am processing t1w anatomical sequences of subjects from the OASIS3 database. Each subject has many MRI images. My point is, freesurfer is excellent and I would like to apply in 2 thousand subjects. I would like to know if there is any way to improve the performance.
Em ter., 20 de jun. de 2023 às 11:15, Douglas N. Greve < dgreve@mgh.harvard.edu> escreveu:
External Email - Use CautionFor 1mm data, FS will generally run in 5-10 hours. Are you talking about high resolution data?
On 6/20/2023 10:11 AM, Michelle Diniz wrote:
External Email - Use CautionHey guys. I'm using FMRIprep on the OASIS3 database and I've noticed that the processing time for each subject averages two days. 80% of that processing is due to the freesurfer. I will need to analyze many resonance images, more precisely the functional part. I tested SMRIprep and didn't get a significant improvement in processing time. How are you getting around this type of problem? How are they using freesurfer in a big dataset?
-- Michelle Diniz Lopes
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With current versions, you can only specify multithreaded (more than one cpu), but this is often counter productive when you have a lot of cases to run through. It is more efficient to run two cases simultaneously than one case with two CPUs.
On 6/20/2023 10:31 AM, Michelle Diniz wrote:
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Does 1mm mean 1 millimeter? I was in doubt! I am processing t1w anatomical sequences of subjects from the OASIS3 database. Each subject has many MRI images. My point is, freesurfer is excellent and I would like to apply in 2 thousand subjects. I would like to know if there is any way to improve the performance.
Em ter., 20 de jun. de 2023 às 11:15, Douglas N. Greve dgreve@mgh.harvard.edu escreveu:
External Email - Use Caution For 1mm data, FS will generally run in 5-10 hours. Are you talking about high resolution data? On 6/20/2023 10:11 AM, Michelle Diniz wrote:External Email - Use Caution Hey guys. I'm using FMRIprep on the OASIS3 database and I've noticed that the processing time for each subject averages two days. 80% of that processing is due to the freesurfer. I will need to analyze many resonance images, more precisely the functional part. I tested SMRIprep and didn't get a significant improvement in processing time. How are you getting around this type of problem? How are they using freesurfer in a big dataset? -- Michelle Diniz Lopes _______________________________________________ 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/1gTC-sL4N4DZOYQn_thAAZt0Rq5e6BELC-u1ESDXDES-OsTGjzUAGIBcQI8-rbLVEmXJ6m0iAMxxTI_3v0pQx2a3UcVDuemMb-PATTkvAv1078K-U1-Mz-A0uxH4nHZuPasDDvLYfFgko3cQYCjFP8ddED2IGJQ3QQHV2mZu95CDF6NOtiYnxvUhjEP8DQgOg_3i2l-MonBUXn3XksTreHj9yanl5WUWE7SlXumBiaguQVDCQr5dHnCVMfiMi9TlJidcpO4C-m9bvK6upBl-rbQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1qOlyBY-EW1phq7cja_yV9SaYanmwB__T9e4D6aXseSLG-Rm69dW3KTaulGGlHMCCLwIyu8dG8Jn48IbnUJo-rS0uHKFfgfK-xzTrQoNS_37wcDG9EiJ4Bfcfzi32yAnVvY9VJ32RXCwLmD4JMbxcUnAMTzOPcfdYd2BxMPk-YHqvqP1U8S0qBPPyyYVb5qtNEXwTxwOL8SYHy7WVDQcRZouMCL6P2w95CuOb4Is10XrFcYJd3965h3lbfvruLmARO6mscAzikpYfXTsQ0mM51Q/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/1gTC-sL4N4DZOYQn_thAAZt0Rq5e6BELC-u1ESDXDES-OsTGjzUAGIBcQI8-rbLVEmXJ6m0iAMxxTI_3v0pQx2a3UcVDuemMb-PATTkvAv1078K-U1-Mz-A0uxH4nHZuPasDDvLYfFgko3cQYCjFP8ddED2IGJQ3QQHV2mZu95CDF6NOtiYnxvUhjEP8DQgOg_3i2l-MonBUXn3XksTreHj9yanl5WUWE7SlXumBiaguQVDCQr5dHnCVMfiMi9TlJidcpO4C-m9bvK6upBl-rbQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1mvuK9FnyDxa-_zGCDCCDglPK7r6HT0974mgoHEODtIHixMIy4SHp4K1Nl6bxlmsf-_EX9lBHLtKv5Vvuy1IQgFzAYqc-vutZ7l-Tv6NDat3zWvdFEUjgg4Lfvc-AMKOOTEGsFrL59cwZI0GXR-f3OBG8iPrB6uSfeqdVgcQVYz1U4R2mo0G2ptvqVZLnhQ6pkHnQt8E8LQky1K3r4LBZlG2ewkPnPTDmBu6TP7K1xBPdSYx3aHIWynbAS1sYahAmA7GfQ6qu9NHrZZcNgs_sn3uiCuGFJWRGoa61E_FVwAn1Ke0Appjn8KhmcKFxcfhg_6GpMnlbxYbE8J9T7Ef2kw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/13OfgMbqjDacl9ITJuf17vh89fJ2ZpPCeY07B3g9GlZ1TDdHVTpufi9_L6N6O1qQDx-CP6ry23MvPMtMM-6XOt9MU0Lvf6SPHrS3NFJ74HNyiHrmHC5bUxtd5j5Ik4Cun7eNATUhQNjM9e5rS-H1vfef44NGxgXnkRPPeDBaZTY8KaWVoEkNmpfbaSERqbY4fuN2H3YQ5Yr0rdZmkryoCHvnAhAXa16WQDbyqw_6rn2kh-LuqWS94tI0tCAeDCtHhOHQv3D9MBjVdFstYlyf6_Q/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <https://secure-web.cisco.com/1uXCJun8Ki0tHxEGCKuTd_CepkS41LlDatXAqKFMaGA_NZCRMmGa_NjnARWX3A-SjM7JPjrx7mI93qIRJuluHpMlFWQ8OIj7wzICM4asw9i7sFH0D-_cPyLXO0EGAgcoTaGWA_LKCfBMYQ2DSV2_0TvAZnXX0bvuCV6FWsSKrZG583g_NA2my2734IT1zS2S3htVgv3N-WrtYQaOmTGp-6quqBFBLSYuRPVCL5hTeqmOAefQ3WgZPRHoSptKrV4V1hkcs29P0B8bkvp9CN6VOMi2ISIk1LyXXQPl4v5wr1bEu5YK10hkuYCKcesQ-rQ-wSJDtuAiT53HxdxK6bBLZCQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/13OfgMbqjDacl9ITJuf17vh89fJ2ZpPCeY07B3g9GlZ1TDdHVTpufi9_L6N6O1qQDx-CP6ry23MvPMtMM-6XOt9MU0Lvf6SPHrS3NFJ74HNyiHrmHC5bUxtd5j5Ik4Cun7eNATUhQNjM9e5rS-H1vfef44NGxgXnkRPPeDBaZTY8KaWVoEkNmpfbaSERqbY4fuN2H3YQ5Yr0rdZmkryoCHvnAhAXa16WQDbyqw_6rn2kh-LuqWS94tI0tCAeDCtHhOHQv3D9MBjVdFstYlyf6_Q/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <https://secure-web.cisco.com/1uXCJun8Ki0tHxEGCKuTd_CepkS41LlDatXAqKFMaGA_NZCRMmGa_NjnARWX3A-SjM7JPjrx7mI93qIRJuluHpMlFWQ8OIj7wzICM4asw9i7sFH0D-_cPyLXO0EGAgcoTaGWA_LKCfBMYQ2DSV2_0TvAZnXX0bvuCV6FWsSKrZG583g_NA2my2734IT1zS2S3htVgv3N-WrtYQaOmTGp-6quqBFBLSYuRPVCL5hTeqmOAefQ3WgZPRHoSptKrV4V1hkcs29P0B8bkvp9CN6VOMi2ISIk1LyXXQPl4v5wr1bEu5YK10hkuYCKcesQ-rQ-wSJDtuAiT53HxdxK6bBLZCQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .-- Michelle Diniz Lopes
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Michelle Diniz