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Hi,
I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year ago. Do I have to pre-process all my data again? I randomly segmented few subjects with versions 6.0 and 7.2 and I implemented a visual quality check but it seems to me that the images segmented with version 7.0 are good. I runned also t-tests between the extracted cortical volumes of the three versions and there are overall few differences across the versions. Where could I see if my data are not good? Which are the effects of the bug in version 7.0?
Thanks a lot for any help you could give to me!
Best regards,
Annalisa Lella
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Hi,
I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year ago. Do I have to pre-process all my data again? I randomly segmented few subjects with versions 6.0 and 7.2 and I implemented a visual quality check but it seems to me that the images segmented with version 7.0 are good. I runned also t-tests between the extracted cortical volumes of the three versions and there are overall few differences across the versions. Where could I see if my data are not good? Which are the effects of the bug in version 7.0?
Thanks!
Annalisa
The 7.0.0 release was recalled because the intensity normalization *sometimes* did the wrong thing. It would not surprise me if you were not seeing any of these effects, but I can't guarantee that it won't happen in your data. If it was happening, you would see some big differences in the thickness, and maybe the subcortical volume. If you have edited your data, you can run version 7.2 on edited 7.0 data and 7.2 will respect and incorporate your edits.
On 9/27/2021 6:37 AM, Annalisa Lella wrote:
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Hi, I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year ago. Do I have to pre-process all my data again? I randomly segmented few subjects with versions 6.0 and 7.2 and I implemented a visual quality check but it seems to me that the images segmented with version 7.0 are good. I runned also t-tests between the extracted cortical volumes of the three versions and there are overall few differences across the versions. Where could I see if my data are not good? Which are the effects of the bug in version 7.0?
Thanks!
Annalisa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1akPrdQzffjqy3vX0uUabfKfKkuLHH5OwDbaVZLwBv0TV7D...
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Dear Mr. Greve,
thanks so much for your reply! I have been running t-tests on cortical and subcortical volumes FDR corrected on 50 subjects to compare versions 6, 7 and 7.2 but I didn't see so much differences. What should I do? Should I run again recon all with version 7.2 on all the subjects? Or can I use version 7.2 for my analysis on data pre-processed with version 7?
Thanks a lot in advance!
Annalisa
________________________________ Da: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu per conto di Douglas N. Greve dgreve@MGH.HARVARD.EDU Inviato: venerdì 1 ottobre 2021 17:18 A: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] Freesurfer version
The 7.0.0 release was recalled because the intensity normalization *sometimes* did the wrong thing. It would not surprise me if you were not seeing any of these effects, but I can't guarantee that it won't happen in your data. If it was happening, you would see some big differences in the thickness, and maybe the subcortical volume. If you have edited your data, you can run version 7.2 on edited 7.0 data and 7.2 will respect and incorporate your edits.
On 9/27/2021 6:37 AM, Annalisa Lella wrote:
External Email - Use Caution
External Email - Use Caution
Hi,
I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year ago. Do I have to pre-process all my data again? I randomly segmented few subjects with versions 6.0 and 7.2 and I implemented a visual quality check but it seems to me that the images segmented with version 7.0 are good. I runned also t-tests between the extracted cortical volumes of the three versions and there are overall few differences across the versions. Where could I see if my data are not good? Which are the effects of the bug in version 7.0?
Thanks!
Annalisa
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Sorry, I'm not sure what you are asking when you ask what you should do. Do about what?
On 10/4/2021 5:30 AM, Annalisa Lella wrote:
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Dear Mr. Greve,
thanks so much for your reply! I have been running t-tests on cortical and subcortical volumes FDR corrected on 50 subjects to compare versions 6, 7 and 7.2 but I didn't see so much differences. What should I do? Should I run again recon all with version 7.2 on all the subjects? Or can I use version 7.2 for my analysis on data pre-processed with version 7?
Thanks a lot in advance!
Annalisa
*Da:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu per conto di Douglas N. Greve dgreve@MGH.HARVARD.EDU *Inviato:* venerdì 1 ottobre 2021 17:18 *A:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Oggetto:* Re: [Freesurfer] Freesurfer version The 7.0.0 release was recalled because the intensity normalization *sometimes* did the wrong thing. It would not surprise me if you were not seeing any of these effects, but I can't guarantee that it won't happen in your data. If it was happening, you would see some big differences in the thickness, and maybe the subcortical volume. If you have edited your data, you can run version 7.2 on edited 7.0 data and 7.2 will respect and incorporate your edits.
On 9/27/2021 6:37 AM, Annalisa Lella wrote:
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Hi, I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year ago. Do I have to pre-process all my data again? I randomly segmented few subjects with versions 6.0 and 7.2 and I implemented a visual quality check but it seems to me that the images segmented with version 7.0 are good. I runned also t-tests between the extracted cortical volumes of the three versions and there are overall few differences across the versions. Where could I see if my data are not good? Which are the effects of the bug in version 7.0?
Thanks!
Annalisa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1akPrdQzffjqy3vX0uUabfKfKkuLHH5OwDbaVZLwBv0TV7D... https://secure-web.cisco.com/1akPrdQzffjqy3vX0uUabfKfKkuLHH5OwDbaVZLwBv0TV7DNLFWYYJ9bfR4-vecoSB4czek6-JkCN3LcE7wIqTEO5S6czbbLcKoxgQOR0pcEv2lMDGRZ4zrO-91wji7eppLoW7_va9iWdEmSp3vG8nkzGUTo-_eaYHE8yxxUdLPeir6zl6j6DfG7pF5raD_DmC8VmsONzjrGwnpcPuS4ts9RvwtLSHMbcKhCuYDLjwH9vRuzUjZSZ7aBPb3aIr2fx0SlE866YrwsTDb-ZIbabHQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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What do you mean by "elaborated"?
On 10/8/2021 1:29 PM, Annalisa Lella wrote:
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I have elaborated all my data with recon all version 7.0. I am doubting whether I should elaborate them again with 7.2 or I can simply run the normalisation with 7.2 on the data preprocessed with 7.0, since you told me that the problem with version 7.0 is with the normalisation process. I ran few t-test on the volumes and the thickness between version 6, 7 and 7.2 and there are few differences across all the versions. So actually it doesn't seem that the results of recon all with version 7 are bugged.
Il 8 ott 2021 18:53, "Douglas N. Greve" dgreve@MGH.HARVARD.EDU ha scritto:
Sorry, I'm not sure what you are asking when you ask what you should do. Do about what? On 10/4/2021 5:30 AM, Annalisa Lella wrote: External Email - Use Caution External Email - Use Caution Dear Mr. Greve, thanks so much for your reply! I have been running t-tests on cortical and subcortical volumes FDR corrected on 50 subjects to compare versions 6, 7 and 7.2 but I didn't see so much differences. What should I do? Should I run again recon all with version 7.2 on all the subjects? Or can I use version 7.2 for my analysis on data pre-processed with version 7? Thanks a lot in advance! Annalisa ------------------------------------------------------------------------ *Da:* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> per conto di Douglas N. Greve <dgreve@MGH.HARVARD.EDU> <mailto:dgreve@MGH.HARVARD.EDU> *Inviato:* venerdì 1 ottobre 2021 17:18 *A:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Oggetto:* Re: [Freesurfer] Freesurfer version The 7.0.0 release was recalled because the intensity normalization *sometimes* did the wrong thing. It would not surprise me if you were not seeing any of these effects, but I can't guarantee that it won't happen in your data. If it was happening, you would see some big differences in the thickness, and maybe the subcortical volume. If you have edited your data, you can run version 7.2 on edited 7.0 data and 7.2 will respect and incorporate your edits. On 9/27/2021 6:37 AM, Annalisa Lella wrote: External Email - Use Caution External Email - Use Caution Hi, I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year ago. Do I have to pre-process all my data again? I randomly segmented few subjects with versions 6.0 and 7.2 and I implemented a visual quality check but it seems to me that the images segmented with version 7.0 are good. I runned also t-tests between the extracted cortical volumes of the three versions and there are overall few differences across the versions. Where could I see if my data are not good? Which are the effects of the bug in version 7.0? Thanks! Annalisa _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1akPrdQzffjqy3vX0uUabfKfKkuLHH5OwDbaVZLwBv0TV7DNLFWYYJ9bfR4-vecoSB4czek6-JkCN3LcE7wIqTEO5S6czbbLcKoxgQOR0pcEv2lMDGRZ4zrO-91wji7eppLoW7_va9iWdEmSp3vG8nkzGUTo-_eaYHE8yxxUdLPeir6zl6j6DfG7pF5raD_DmC8VmsONzjrGwnpcPuS4ts9RvwtLSHMbcKhCuYDLjwH9vRuzUjZSZ7aBPb3aIr2fx0SlE866YrwsTDb-ZIbabHQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1hh9f1waCfRgOtSLliou6EyCJxnslY1S63XtNnNYjx0etpWM3rl1NncKnTxlFwFlnb4D5t1Ig8PSTtEoBgharwFpkzB2Pan_6tVsiRTYTUhgZekQstSZYU1dL9X9nyZa51NoJ_1If1z2C_O0Nh9BX4s33vMAipAmP6wkElWBivPmrrdXLMoJURpkY-GxO8_NindNP0LUFvO5DKf4V_ncKxq66mL8UT9n5XgXlS0Eeb17EEbOPaMWkg5G05TZPrGzJKKQrr4fYVlT67t97Qvg2Fw/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail> Virus-free. *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* www.avast.com <https://secure-web.cisco.com/1hh9f1waCfRgOtSLliou6EyCJxnslY1S63XtNnNYjx0etpWM3rl1NncKnTxlFwFlnb4D5t1Ig8PSTtEoBgharwFpkzB2Pan_6tVsiRTYTUhgZekQstSZYU1dL9X9nyZa51NoJ_1If1z2C_O0Nh9BX4s33vMAipAmP6wkElWBivPmrrdXLMoJURpkY-GxO8_NindNP0LUFvO5DKf4V_ncKxq66mL8UT9n5XgXlS0Eeb17EEbOPaMWkg5G05TZPrGzJKKQrr4fYVlT67t97Qvg2Fw/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/15sAgHUzMEb_AyuIOA2x3LcGAxK_Eh0gwnf8ktaxYxlUrdwgKQFHDEXMmjhs01RFLPsHm0Cs_cQyHqvIvA-M5WJ6cGpsGIMkdkvOATkF0gG7rxgYl562vIcnyv2_kCNBf58XQgzJadqEEmFjMdN7XoIq9PHMgdbpYSUr-D0FLNDAFJmh1s4ViJ6ESNVfUsGeSShIWPMZCol6n5oWhEcvr1m5GUnTKJ1dOH8VSsW_8fTKx6bOU-CYxkE8KGAgvlieBrDoG0OarSBxDLKM138imEQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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If you have not done manual editing, then just rerun in 7.2 from scratch
On 10/8/2021 1:52 PM, Annalisa Lella wrote:
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Pre-processed with recon all
Il 8 ott 2021 19:50, "Douglas N. Greve" dgreve@MGH.HARVARD.EDU ha scritto:
What do you mean by "elaborated"? On 10/8/2021 1:29 PM, Annalisa Lella wrote: External Email - Use Caution External Email - Use Caution I have elaborated all my data with recon all version 7.0. I am doubting whether I should elaborate them again with 7.2 or I can simply run the normalisation with 7.2 on the data preprocessed with 7.0, since you told me that the problem with version 7.0 is with the normalisation process. I ran few t-test on the volumes and the thickness between version 6, 7 and 7.2 and there are few differences across all the versions. So actually it doesn't seem that the results of recon all with version 7 are bugged. Il 8 ott 2021 18:53, "Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> <mailto:dgreve@MGH.HARVARD.EDU> ha scritto: Sorry, I'm not sure what you are asking when you ask what you should do. Do about what? On 10/4/2021 5:30 AM, Annalisa Lella wrote: External Email - Use Caution External Email - Use Caution Dear Mr. Greve, thanks so much for your reply! I have been running t-tests on cortical and subcortical volumes FDR corrected on 50 subjects to compare versions 6, 7 and 7.2 but I didn't see so much differences. What should I do? Should I run again recon all with version 7.2 on all the subjects? Or can I use version 7.2 for my analysis on data pre-processed with version 7? Thanks a lot in advance! Annalisa ------------------------------------------------------------------------ *Da:* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> per conto di Douglas N. Greve <dgreve@MGH.HARVARD.EDU> <mailto:dgreve@MGH.HARVARD.EDU> *Inviato:* venerdì 1 ottobre 2021 17:18 *A:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Oggetto:* Re: [Freesurfer] Freesurfer version The 7.0.0 release was recalled because the intensity normalization *sometimes* did the wrong thing. It would not surprise me if you were not seeing any of these effects, but I can't guarantee that it won't happen in your data. If it was happening, you would see some big differences in the thickness, and maybe the subcortical volume. If you have edited your data, you can run version 7.2 on edited 7.0 data and 7.2 will respect and incorporate your edits. On 9/27/2021 6:37 AM, Annalisa Lella wrote: External Email - Use Caution External Email - Use Caution Hi, I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year ago. Do I have to pre-process all my data again? I randomly segmented few subjects with versions 6.0 and 7.2 and I implemented a visual quality check but it seems to me that the images segmented with version 7.0 are good. I runned also t-tests between the extracted cortical volumes of the three versions and there are overall few differences across the versions. Where could I see if my data are not good? Which are the effects of the bug in version 7.0? Thanks! Annalisa _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1akPrdQzffjqy3vX0uUabfKfKkuLHH5OwDbaVZLwBv0TV7DNLFWYYJ9bfR4-vecoSB4czek6-JkCN3LcE7wIqTEO5S6czbbLcKoxgQOR0pcEv2lMDGRZ4zrO-91wji7eppLoW7_va9iWdEmSp3vG8nkzGUTo-_eaYHE8yxxUdLPeir6zl6j6DfG7pF5raD_DmC8VmsONzjrGwnpcPuS4ts9RvwtLSHMbcKhCuYDLjwH9vRuzUjZSZ7aBPb3aIr2fx0SlE866YrwsTDb-ZIbabHQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1hh9f1waCfRgOtSLliou6EyCJxnslY1S63XtNnNYjx0etpWM3rl1NncKnTxlFwFlnb4D5t1Ig8PSTtEoBgharwFpkzB2Pan_6tVsiRTYTUhgZekQstSZYU1dL9X9nyZa51NoJ_1If1z2C_O0Nh9BX4s33vMAipAmP6wkElWBivPmrrdXLMoJURpkY-GxO8_NindNP0LUFvO5DKf4V_ncKxq66mL8UT9n5XgXlS0Eeb17EEbOPaMWkg5G05TZPrGzJKKQrr4fYVlT67t97Qvg2Fw/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail> Virus-free. *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* www.avast.com <https://secure-web.cisco.com/1hh9f1waCfRgOtSLliou6EyCJxnslY1S63XtNnNYjx0etpWM3rl1NncKnTxlFwFlnb4D5t1Ig8PSTtEoBgharwFpkzB2Pan_6tVsiRTYTUhgZekQstSZYU1dL9X9nyZa51NoJ_1If1z2C_O0Nh9BX4s33vMAipAmP6wkElWBivPmrrdXLMoJURpkY-GxO8_NindNP0LUFvO5DKf4V_ncKxq66mL8UT9n5XgXlS0Eeb17EEbOPaMWkg5G05TZPrGzJKKQrr4fYVlT67t97Qvg2Fw/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/15sAgHUzMEb_AyuIOA2x3LcGAxK_Eh0gwnf8ktaxYxlUrdwgKQFHDEXMmjhs01RFLPsHm0Cs_cQyHqvIvA-M5WJ6cGpsGIMkdkvOATkF0gG7rxgYl562vIcnyv2_kCNBf58XQgzJadqEEmFjMdN7XoIq9PHMgdbpYSUr-D0FLNDAFJmh1s4ViJ6ESNVfUsGeSShIWPMZCol6n5oWhEcvr1m5GUnTKJ1dOH8VSsW_8fTKx6bOU-CYxkE8KGAgvlieBrDoG0OarSBxDLKM138imEQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1KGe7t4jIxJV2SyO2vk4bemMOyuvzNx2GvTpMJFOz1UovRj5lGGascg730l2IYDZmxBdZBSMIUj5kqPgJvsWQGNhVbwKXAeqnCTVq6I5r5KiiZz63o8eyrNbhZj5DGcsI4usr8ou8tI6n8jhBMuMsdO0kGUUhhuHocC5IG459KOJgCZO1FYbitrr6EOJX5nh3meGcTS-UkaDSCVUWJPBRSOfaTjv_zrfXBrJtWwbB9GQkh9ft9c-s0dao0my83wezJDIAYhrBWwU-cXw6AMTkfQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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It will be the easiest. If you have not edited them, then it is just computer time, right?
On 10/8/2021 2:38 PM, Annalisa Lella wrote:
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That's what I wanted to avoid: reprocess all the data. Am I forced to?
Il 8 ott 2021 19:52, Annalisa Lella annalisalella@hotmail.it ha scritto:
External Email - Use Caution Pre-processed with recon all Il 8 ott 2021 19:50, "Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> ha scritto: What do you mean by "elaborated"? On 10/8/2021 1:29 PM, Annalisa Lella wrote: External Email - Use Caution External Email - Use Caution I have elaborated all my data with recon all version 7.0. I am doubting whether I should elaborate them again with 7.2 or I can simply run the normalisation with 7.2 on the data preprocessed with 7.0, since you told me that the problem with version 7.0 is with the normalisation process. I ran few t-test on the volumes and the thickness between version 6, 7 and 7.2 and there are few differences across all the versions. So actually it doesn't seem that the results of recon all with version 7 are bugged. Il 8 ott 2021 18:53, "Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> <mailto:dgreve@MGH.HARVARD.EDU> ha scritto: Sorry, I'm not sure what you are asking when you ask what you should do. Do about what? On 10/4/2021 5:30 AM, Annalisa Lella wrote: External Email - Use Caution External Email - Use Caution Dear Mr. Greve, thanks so much for your reply! I have been running t-tests on cortical and subcortical volumes FDR corrected on 50 subjects to compare versions 6, 7 and 7.2 but I didn't see so much differences. What should I do? Should I run again recon all with version 7.2 on all the subjects? Or can I use version 7.2 for my analysis on data pre-processed with version 7? Thanks a lot in advance! Annalisa ------------------------------------------------------------------------ *Da:* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> per conto di Douglas N. Greve <dgreve@MGH.HARVARD.EDU> <mailto:dgreve@MGH.HARVARD.EDU> *Inviato:* venerdì 1 ottobre 2021 17:18 *A:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Oggetto:* Re: [Freesurfer] Freesurfer version The 7.0.0 release was recalled because the intensity normalization *sometimes* did the wrong thing. It would not surprise me if you were not seeing any of these effects, but I can't guarantee that it won't happen in your data. If it was happening, you would see some big differences in the thickness, and maybe the subcortical volume. If you have edited your data, you can run version 7.2 on edited 7.0 data and 7.2 will respect and incorporate your edits. On 9/27/2021 6:37 AM, Annalisa Lella wrote: External Email - Use Caution External Email - Use Caution Hi, I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year ago. Do I have to pre-process all my data again? I randomly segmented few subjects with versions 6.0 and 7.2 and I implemented a visual quality check but it seems to me that the images segmented with version 7.0 are good. I runned also t-tests between the extracted cortical volumes of the three versions and there are overall few differences across the versions. Where could I see if my data are not good? Which are the effects of the bug in version 7.0? Thanks! Annalisa _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1akPrdQzffjqy3vX0uUabfKfKkuLHH5OwDbaVZLwBv0TV7DNLFWYYJ9bfR4-vecoSB4czek6-JkCN3LcE7wIqTEO5S6czbbLcKoxgQOR0pcEv2lMDGRZ4zrO-91wji7eppLoW7_va9iWdEmSp3vG8nkzGUTo-_eaYHE8yxxUdLPeir6zl6j6DfG7pF5raD_DmC8VmsONzjrGwnpcPuS4ts9RvwtLSHMbcKhCuYDLjwH9vRuzUjZSZ7aBPb3aIr2fx0SlE866YrwsTDb-ZIbabHQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1hh9f1waCfRgOtSLliou6EyCJxnslY1S63XtNnNYjx0etpWM3rl1NncKnTxlFwFlnb4D5t1Ig8PSTtEoBgharwFpkzB2Pan_6tVsiRTYTUhgZekQstSZYU1dL9X9nyZa51NoJ_1If1z2C_O0Nh9BX4s33vMAipAmP6wkElWBivPmrrdXLMoJURpkY-GxO8_NindNP0LUFvO5DKf4V_ncKxq66mL8UT9n5XgXlS0Eeb17EEbOPaMWkg5G05TZPrGzJKKQrr4fYVlT67t97Qvg2Fw/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail> Virus-free. *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* www.avast.com <https://secure-web.cisco.com/1hh9f1waCfRgOtSLliou6EyCJxnslY1S63XtNnNYjx0etpWM3rl1NncKnTxlFwFlnb4D5t1Ig8PSTtEoBgharwFpkzB2Pan_6tVsiRTYTUhgZekQstSZYU1dL9X9nyZa51NoJ_1If1z2C_O0Nh9BX4s33vMAipAmP6wkElWBivPmrrdXLMoJURpkY-GxO8_NindNP0LUFvO5DKf4V_ncKxq66mL8UT9n5XgXlS0Eeb17EEbOPaMWkg5G05TZPrGzJKKQrr4fYVlT67t97Qvg2Fw/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/15sAgHUzMEb_AyuIOA2x3LcGAxK_Eh0gwnf8ktaxYxlUrdwgKQFHDEXMmjhs01RFLPsHm0Cs_cQyHqvIvA-M5WJ6cGpsGIMkdkvOATkF0gG7rxgYl562vIcnyv2_kCNBf58XQgzJadqEEmFjMdN7XoIq9PHMgdbpYSUr-D0FLNDAFJmh1s4ViJ6ESNVfUsGeSShIWPMZCol6n5oWhEcvr1m5GUnTKJ1dOH8VSsW_8fTKx6bOU-CYxkE8KGAgvlieBrDoG0OarSBxDLKM138imEQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1KGe7t4jIxJV2SyO2vk4bemMOyuvzNx2GvTpMJFOz1UovRj5lGGascg730l2IYDZmxBdZBSMIUj5kqPgJvsWQGNhVbwKXAeqnCTVq6I5r5KiiZz63o8eyrNbhZj5DGcsI4usr8ou8tI6n8jhBMuMsdO0kGUUhhuHocC5IG459KOJgCZO1FYbitrr6EOJX5nh3meGcTS-UkaDSCVUWJPBRSOfaTjv_zrfXBrJtWwbB9GQkh9ft9c-s0dao0my83wezJDIAYhrBWwU-cXw6AMTkfQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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What do you mean with "edited"? I have just segmented the thalamus after recon all but I guess I should do everything again. I mean, it is fine, I was just wondering if I needed to do it since the data didn't seem bugged to me from the t-test results.
________________________________ Da: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu per conto di Douglas N. Greve dgreve@mgh.harvard.edu Inviato: venerdì 8 ottobre 2021 21:34 A: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] R: Freesurfer version
It will be the easiest. If you have not edited them, then it is just computer time, right?
On 10/8/2021 2:38 PM, Annalisa Lella wrote:
External Email - Use Caution
External Email - Use Caution
That's what I wanted to avoid: reprocess all the data. Am I forced to?
Il 8 ott 2021 19:52, Annalisa Lella annalisalella@hotmail.itmailto:annalisalella@hotmail.it ha scritto:
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Pre-processed with recon all
Il 8 ott 2021 19:50, "Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU ha scritto: What do you mean by "elaborated"?
On 10/8/2021 1:29 PM, Annalisa Lella wrote:
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External Email - Use Caution
I have elaborated all my data with recon all version 7.0. I am doubting whether I should elaborate them again with 7.2 or I can simply run the normalisation with 7.2 on the data preprocessed with 7.0, since you told me that the problem with version 7.0 is with the normalisation process. I ran few t-test on the volumes and the thickness between version 6, 7 and 7.2 and there are few differences across all the versions. So actually it doesn't seem that the results of recon all with version 7 are bugged.
Il 8 ott 2021 18:53, "Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU ha scritto: Sorry, I'm not sure what you are asking when you ask what you should do. Do about what?
On 10/4/2021 5:30 AM, Annalisa Lella wrote:
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External Email - Use Caution
Dear Mr. Greve,
thanks so much for your reply! I have been running t-tests on cortical and subcortical volumes FDR corrected on 50 subjects to compare versions 6, 7 and 7.2 but I didn't see so much differences. What should I do? Should I run again recon all with version 7.2 on all the subjects? Or can I use version 7.2 for my analysis on data pre-processed with version 7?
Thanks a lot in advance!
Annalisa
________________________________ Da: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu per conto di Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Inviato: venerdì 1 ottobre 2021 17:18 A: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] Freesurfer version
The 7.0.0 release was recalled because the intensity normalization *sometimes* did the wrong thing. It would not surprise me if you were not seeing any of these effects, but I can't guarantee that it won't happen in your data. If it was happening, you would see some big differences in the thickness, and maybe the subcortical volume. If you have edited your data, you can run version 7.2 on edited 7.0 data and 7.2 will respect and incorporate your edits.
On 9/27/2021 6:37 AM, Annalisa Lella wrote:
External Email - Use Caution
External Email - Use Caution
Hi,
I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year ago. Do I have to pre-process all my data again? I randomly segmented few subjects with versions 6.0 and 7.2 and I implemented a visual quality check but it seems to me that the images segmented with version 7.0 are good. I runned also t-tests between the extracted cortical volumes of the three versions and there are overall few differences across the versions. Where could I see if my data are not good? Which are the effects of the bug in version 7.0?
Thanks!
Annalisa
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