External Email - Use Caution
Hello,
We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference?
Thanks,
Samuel
[image: image.png]
This does not make sense to me. What resolution is your 3T and 7T data? Can you run the 7T data at 1mm (ie, without the -hires option) and see if it changes?
On 3/20/2022 9:42 AM, Samuel Paré wrote:
External Email - Use Caution
Hello,
We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference?
Thanks,
Samuel
image.png
*Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Dough,
Thanks for your response. We followed your suggestion and ran the 7T data without the -highres option. This gave us values which are in the normal range of what we get when using 3T mean curvature data. We looked whether there was a fixed scaling factor between the data with and without the -highres option. This did not seem to be the case as the scaling factor for the different subregions varied between 1,18 (for the left G_subcallosal) and 2,95 (for the left S_collat_transv_ant). I attached a pdf with the results.
Thank you again
On Sun, Mar 27, 2022 at 5:31 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
This does not make sense to me. What resolution is your 3T and 7T data? Can you run the 7T data at 1mm (ie, without the -hires option) and see if it changes?
On 3/20/2022 9:42 AM, Samuel Paré wrote:
External Email - Use CautionHello,
We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference?
Thanks,
Samuel
[image: image.png]
*Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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That's so weird. Can you make the data available to us?
On 3/29/2022 8:00 AM, Samuel Paré wrote:
External Email - Use Caution
Hi Dough,
Thanks for your response. We followed your suggestion and ran the 7T data without the -highres option. This gave us values which are in the normal range of what we get when using 3T mean curvature data. We looked whether there was a fixed scaling factor between the data with and without the -highres option. This did not seem to be the case as the scaling factor for the different subregions varied between 1,18 (for the left G_subcallosal) and 2,95 (for the left S_collat_transv_ant). I attached a pdf with the results.
Thank you again
On Sun, Mar 27, 2022 at 5:31 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
This does not make sense to me. What resolution is your 3T and 7T data? Can you run the 7T data at 1mm (ie, without the -hires option) and see if it changes? On 3/20/2022 9:42 AM, Samuel Paré wrote:External Email - Use Caution Hello, We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference? Thanks, Samuel image.png -- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1Js5RYkF9g9o-TCQiLwHtezjqoE_SjgaOLPtPqH7T07AInOANzncfH2EL1ydhUgEvP1AjUlQOkCMgWi34epgPlAog5D0bBAQmWAOL1sMFeE5NFk7H9YQgAdNDKn8Wuqd2j3Jyz0dqI0roZWyKucvttXkj4ozp2NbcB3z98C0_Mm-tIdvdIjH3t1fxnlEbw-p6OpXpORjBLy6YgUOFpKjDbwZ4erLTrwFozrOJ3_RIb8K8bG4gPa0JYQ2raxD4ErlJjFu8alnp6D8DCkf_gK6sunf1rEngI2BbxOhTaOrzcfzUxORhFXwZskVlWxrzA6ec5XA0ZKJlJy2TDBYv4rDaTg/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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1Js5RYkF9g9o-TCQiLwHtezjqoE_SjgaOLPtPqH7T07AInOANzncfH2EL1ydhUgEvP1AjUlQOkCMgWi34epgPlAog5D0bBAQmWAOL1sMFeE5NFk7H9YQgAdNDKn8Wuqd2j3Jyz0dqI0roZWyKucvttXkj4ozp2NbcB3z98C0_Mm-tIdvdIjH3t1fxnlEbw-p6OpXpORjBLy6YgUOFpKjDbwZ4erLTrwFozrOJ3_RIb8K8bG4gPa0JYQ2raxD4ErlJjFu8alnp6D8DCkf_gK6sunf1rEngI2BbxOhTaOrzcfzUxORhFXwZskVlWxrzA6ec5XA0ZKJlJy2TDBYv4rDaTg/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://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1JXdd6MYX-VQtezfpq-dNMmmZAXsMbDaE4p6OdadfpU9gWv52sHDXpQvdYQc6WerTWhCM6AjFO1SvI4wynGCMC85riKw5-mNG3IqFw11ja7tg3g074vG8yvLWQzI-4t7z_EBOIgBnmc9eMTtASnV1lX4lVTcNIaD3-OKl8gzmHCmwI9dltuSmgHAeFjGTZis5rhLuycTz7PBzgHpU6bkTEKv4k5DbvUSB8taytPhBPBqNrbUMJG_kVBznd9rf9pzgY1rVD4pbgJ4ycoAW0Oj0uMHXPbli1BO5wvL10O6SZLsp_0NCg_zAxCYvdNy9uhv-NCIptgoMHVv77tuX0aG6Rg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1JXdd6MYX-VQtezfpq-dNMmmZAXsMbDaE4p6OdadfpU9gWv52sHDXpQvdYQc6WerTWhCM6AjFO1SvI4wynGCMC85riKw5-mNG3IqFw11ja7tg3g074vG8yvLWQzI-4t7z_EBOIgBnmc9eMTtASnV1lX4lVTcNIaD3-OKl8gzmHCmwI9dltuSmgHAeFjGTZis5rhLuycTz7PBzgHpU6bkTEKv4k5DbvUSB8taytPhBPBqNrbUMJG_kVBznd9rf9pzgY1rVD4pbgJ4ycoAW0Oj0uMHXPbli1BO5wvL10O6SZLsp_0NCg_zAxCYvdNy9uhv-NCIptgoMHVv77tuX0aG6Rg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.-- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you again for your help. Here is one subject, let me know if you need more.
Kind regards, Samuel
On Mon, Apr 4, 2022 at 10:40 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
That's so weird. Can you make the data available to us?
On 3/29/2022 8:00 AM, Samuel Paré wrote:
External Email - Use CautionHi Dough,
Thanks for your response. We followed your suggestion and ran the 7T data without the -highres option. This gave us values which are in the normal range of what we get when using 3T mean curvature data. We looked whether there was a fixed scaling factor between the data with and without the -highres option. This did not seem to be the case as the scaling factor for the different subregions varied between 1,18 (for the left G_subcallosal) and 2,95 (for the left S_collat_transv_ant). I attached a pdf with the results.
Thank you again
On Sun, Mar 27, 2022 at 5:31 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
This does not make sense to me. What resolution is your 3T and 7T data? Can you run the 7T data at 1mm (ie, without the -hires option) and see if it changes?
On 3/20/2022 9:42 AM, Samuel Paré wrote:
External Email - Use CautionHello,
We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference?
Thanks,
Samuel
[image: image.png]
*Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
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-- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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External Email - Use Caution
Hi,
I was wondering if you had new information on this matter.
Thank you very much, Samuel
On Tue, Apr 5, 2022 at 9:04 AM Samuel Paré pare.samuel19@gmail.com wrote:
Thank you again for your help. Here is one subject, let me know if you need more.
Kind regards, Samuel
On Mon, Apr 4, 2022 at 10:40 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
That's so weird. Can you make the data available to us?
On 3/29/2022 8:00 AM, Samuel Paré wrote:
External Email - Use CautionHi Dough,
Thanks for your response. We followed your suggestion and ran the 7T data without the -highres option. This gave us values which are in the normal range of what we get when using 3T mean curvature data. We looked whether there was a fixed scaling factor between the data with and without the -highres option. This did not seem to be the case as the scaling factor for the different subregions varied between 1,18 (for the left G_subcallosal) and 2,95 (for the left S_collat_transv_ant). I attached a pdf with the results.
Thank you again
On Sun, Mar 27, 2022 at 5:31 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
This does not make sense to me. What resolution is your 3T and 7T data? Can you run the 7T data at 1mm (ie, without the -hires option) and see if it changes?
On 3/20/2022 9:42 AM, Samuel Paré wrote:
External Email - Use CautionHello,
We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference?
Thanks,
Samuel
[image: image.png]
*Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
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-- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
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-- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
sorry, just looking at it now. Can you send the 1mm results as well?
On 4/25/2022 7:42 PM, Samuel Paré wrote:
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Hi,
I was wondering if you had new information on this matter.
Thank you very much, Samuel
On Tue, Apr 5, 2022 at 9:04 AM Samuel Paré pare.samuel19@gmail.com wrote:
B15.zip <https://secure-web.cisco.com/1d2-h6246ghO1ZWMP33mOl8JR3DNWRGoJVMDMShomFlz3LhGlhOAjOxmLYC9J9wJJbmRKCn70sZPPUxkFnhrqnHTucHKGpQRg24MWiM5SVfBBAQyyYdF1kpdaSDQ5H4T7Ouqez8zZ1EHGeGBvfRc-3J3B1-w0HLm2oEkM1Yi2i0KgY0c2ctSRFjTktX9efnlsVWnl4SwlnJds_B_bjgcg-eEgJ-yb0n7wVU4fIM4ZRDuzZ72FjVEEr8Yq6jsvN0d5uIl0i9CJX7G0m6UsgEVd_S1oRQWhZfusM1T8ciErowlYibCRhJHRpBHi6sdXtT4rfPu8SZg5sp0ckDlmEsQx9rqXHEFJd6duhfoswRVZD7U/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1CatLZC5ca1Q4CvfSzXB3MMC62f6vNnXX%2Fview%3Fusp%3Ddrive_web> Hi Douglas, Thank you again for your help. Here is one subject, let me know if you need more. Kind regards, Samuel On Mon, Apr 4, 2022 at 10:40 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: That's so weird. Can you make the data available to us? On 3/29/2022 8:00 AM, Samuel Paré wrote:External Email - Use Caution Hi Dough, Thanks for your response. We followed your suggestion and ran the 7T data without the -highres option. This gave us values which are in the normal range of what we get when using 3T mean curvature data. We looked whether there was a fixed scaling factor between the data with and without the -highres option. This did not seem to be the case as the scaling factor for the different subregions varied between 1,18 (for the left G_subcallosal) and 2,95 (for the left S_collat_transv_ant). I attached a pdf with the results. Thank you again On Sun, Mar 27, 2022 at 5:31 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: This does not make sense to me. What resolution is your 3T and 7T data? Can you run the 7T data at 1mm (ie, without the -hires option) and see if it changes? On 3/20/2022 9:42 AM, Samuel Paré wrote:External Email - Use Caution Hello, We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference? Thanks, Samuel image.png -- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1Js5RYkF9g9o-TCQiLwHtezjqoE_SjgaOLPtPqH7T07AInOANzncfH2EL1ydhUgEvP1AjUlQOkCMgWi34epgPlAog5D0bBAQmWAOL1sMFeE5NFk7H9YQgAdNDKn8Wuqd2j3Jyz0dqI0roZWyKucvttXkj4ozp2NbcB3z98C0_Mm-tIdvdIjH3t1fxnlEbw-p6OpXpORjBLy6YgUOFpKjDbwZ4erLTrwFozrOJ3_RIb8K8bG4gPa0JYQ2raxD4ErlJjFu8alnp6D8DCkf_gK6sunf1rEngI2BbxOhTaOrzcfzUxORhFXwZskVlWxrzA6ec5XA0ZKJlJy2TDBYv4rDaTg/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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1Js5RYkF9g9o-TCQiLwHtezjqoE_SjgaOLPtPqH7T07AInOANzncfH2EL1ydhUgEvP1AjUlQOkCMgWi34epgPlAog5D0bBAQmWAOL1sMFeE5NFk7H9YQgAdNDKn8Wuqd2j3Jyz0dqI0roZWyKucvttXkj4ozp2NbcB3z98C0_Mm-tIdvdIjH3t1fxnlEbw-p6OpXpORjBLy6YgUOFpKjDbwZ4erLTrwFozrOJ3_RIb8K8bG4gPa0JYQ2raxD4ErlJjFu8alnp6D8DCkf_gK6sunf1rEngI2BbxOhTaOrzcfzUxORhFXwZskVlWxrzA6ec5XA0ZKJlJy2TDBYv4rDaTg/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. 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Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. -- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1xcU95EcaGhdAvG-WaSrfzRyHvUVu5RzABLySYs_ryLbRTVI-G5ztefK8d21R6XbTvzDBOVTi4eLLnqvCgZzgHRgMngKprTYs8JUkcgt-lBA7k_M6Lej7k1qqDMH631dIidJ9aT3EuiA4QThvQyx224MK24XImjGV9lHsBcGF0LJ7fn3RVc6fnoTi0N8ZO4lc-5Sxu-l2rTaTVEVfIwDtYuYAcTJuPaBp_A1thmPBaLbQEixW_F40bg8lcWbaBb7ZAD3cKRJlPtsBiTVjLgpgWDYs6AzCxqqCgucQmpGt9mgOehBBOcRmiWeuRvSB5X1aaL_H7UU-f3WP45u7WLC-n9SfU7BNHjXuhbTMKkyQjCA/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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1xcU95EcaGhdAvG-WaSrfzRyHvUVu5RzABLySYs_ryLbRTVI-G5ztefK8d21R6XbTvzDBOVTi4eLLnqvCgZzgHRgMngKprTYs8JUkcgt-lBA7k_M6Lej7k1qqDMH631dIidJ9aT3EuiA4QThvQyx224MK24XImjGV9lHsBcGF0LJ7fn3RVc6fnoTi0N8ZO4lc-5Sxu-l2rTaTVEVfIwDtYuYAcTJuPaBp_A1thmPBaLbQEixW_F40bg8lcWbaBb7ZAD3cKRJlPtsBiTVjLgpgWDYs6AzCxqqCgucQmpGt9mgOehBBOcRmiWeuRvSB5X1aaL_H7UU-f3WP45u7WLC-n9SfU7BNHjXuhbTMKkyQjCA/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. 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No worries! Here are the 1mm results.
Thank you so so much for your help. Have a great day, Sam B15mm1.zip https://secure-web.cisco.com/1gk4MzgSFXbma4zGOMu7To3AnlfwAnVtoL3R2UMrrXhvQ24Q7JrOdfMcTh0HvIeqJfUx1ym9-2-eG1LfEmoVmcD9V-nGI3aF_RdaA-xMJaZ6st3MR9Y2z3G9FqDGk14-mXxosQyTZLGDBVPvWQLUpkr8fqVsjbzl3hLrpYecptwKCdW5yfK9MJyXcZhatQ6ZHojExEbpXMupWgWHuV1FkCwhs6wQEzenxYeKzYog_0ceW3yR0BFDwdSsY9824fIRSujPxu-zEnS8I3uk9VygytdF_QaP6ofIUC8ZtiUubqJZ8Qw6JWqvJJvzBBSLljeLtBZqyprJgRP68IcOBJhM0gw/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1fMbXPspqlq-yVRqSuWcM9qireeQDFjj4%2Fview%3Fusp%3Ddrive_web
On Tue, Apr 26, 2022 at 2:07 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
sorry, just looking at it now. Can you send the 1mm results as well?
On 4/25/2022 7:42 PM, Samuel Paré wrote:
External Email - Use CautionHi,
I was wondering if you had new information on this matter.
Thank you very much, Samuel
On Tue, Apr 5, 2022 at 9:04 AM Samuel Paré pare.samuel19@gmail.com wrote:
Thank you again for your help. Here is one subject, let me know if you need more.
Kind regards, Samuel
On Mon, Apr 4, 2022 at 10:40 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
That's so weird. Can you make the data available to us?
On 3/29/2022 8:00 AM, Samuel Paré wrote:
External Email - Use CautionHi Dough,
Thanks for your response. We followed your suggestion and ran the 7T data without the -highres option. This gave us values which are in the normal range of what we get when using 3T mean curvature data. We looked whether there was a fixed scaling factor between the data with and without the -highres option. This did not seem to be the case as the scaling factor for the different subregions varied between 1,18 (for the left G_subcallosal) and 2,95 (for the left S_collat_transv_ant). I attached a pdf with the results.
Thank you again
On Sun, Mar 27, 2022 at 5:31 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
This does not make sense to me. What resolution is your 3T and 7T data? Can you run the 7T data at 1mm (ie, without the -hires option) and see if it changes?
On 3/20/2022 9:42 AM, Samuel Paré wrote:
External Email - Use CautionHello,
We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference?
Thanks,
Samuel
[image: image.png]
*Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
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-- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
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-- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
-- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
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External Email - Use Caution
Hi,
I apologize for the repeated emails, but I was wondering if you had the time to look at the 1mm data.
Sorry again and thank you so much, Samuel
On Wed., Apr. 27, 2022, 11:03 a.m. Samuel Paré, pare.samuel19@gmail.com wrote:
No worries! Here are the 1mm results.
Thank you so so much for your help. Have a great day, Sam B15mm1.zip https://secure-web.cisco.com/1Mue4-mv2gc8lPVbiGq7vbxafsOugGxUqXTC71h8yj0zOpciBKNm-8E-OMrTb7OqryONcoZpMDn5Bo1g4MRW3QOFkwYG3k61OluNL0PnHH3cjKOwKjcmbrMU0zvOltDCq2LQQVre45AihhpqWRGr8AW-B2HHtrbHIl4vWahqD4oNzxGDCOnwyooZ7iQMIcLAG9Z12LqK-uWTPFedTVKkDiuY63eYFo9YCrptO7tMaxvJSI2xuh2UEqA1TKbS70Y3uOcoRYO1Pzwv0beewA8v6FF_PlcOstzIEV7-SkcXUZv6ChVtq9rnwiFqE5yxt-SZiZ5owaDpCNhdDqAHcxHWJI_cqcfaWjsO7mWSbuPjpSvw/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1fMbXPspqlq-yVRqSuWcM9qireeQDFjj4%2Fview%3Fusp%3Ddrive_web
On Tue, Apr 26, 2022 at 2:07 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
sorry, just looking at it now. Can you send the 1mm results as well?
On 4/25/2022 7:42 PM, Samuel Paré wrote:
External Email - Use CautionHi,
I was wondering if you had new information on this matter.
Thank you very much, Samuel
On Tue, Apr 5, 2022 at 9:04 AM Samuel Paré pare.samuel19@gmail.com wrote:
Thank you again for your help. Here is one subject, let me know if you need more.
Kind regards, Samuel
On Mon, Apr 4, 2022 at 10:40 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
That's so weird. Can you make the data available to us?
On 3/29/2022 8:00 AM, Samuel Paré wrote:
External Email - Use CautionHi Dough,
Thanks for your response. We followed your suggestion and ran the 7T data without the -highres option. This gave us values which are in the normal range of what we get when using 3T mean curvature data. We looked whether there was a fixed scaling factor between the data with and without the -highres option. This did not seem to be the case as the scaling factor for the different subregions varied between 1,18 (for the left G_subcallosal) and 2,95 (for the left S_collat_transv_ant). I attached a pdf with the results.
Thank you again
On Sun, Mar 27, 2022 at 5:31 PM Douglas N. Greve < dgreve@mgh.harvard.edu> wrote:
This does not make sense to me. What resolution is your 3T and 7T data? Can you run the 7T data at 1mm (ie, without the -hires option) and see if it changes?
On 3/20/2022 9:42 AM, Samuel Paré wrote:
External Email - Use CautionHello,
We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference?
Thanks,
Samuel
[image: image.png]
*Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
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-- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
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-- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
-- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
not yet
On 5/4/2022 7:43 AM, Samuel Paré wrote:
External Email - Use Caution
Hi,
I apologize for the repeated emails, but I was wondering if you had the time to look at the 1mm data.
Sorry again and thank you so much, Samuel
On Wed., Apr. 27, 2022, 11:03 a.m. Samuel Paré, pare.samuel19@gmail.com wrote:
No worries! Here are the 1mm results. Thank you so so much for your help. Have a great day, Sam B15mm1.zip <https://secure-web.cisco.com/1Mue4-mv2gc8lPVbiGq7vbxafsOugGxUqXTC71h8yj0zOpciBKNm-8E-OMrTb7OqryONcoZpMDn5Bo1g4MRW3QOFkwYG3k61OluNL0PnHH3cjKOwKjcmbrMU0zvOltDCq2LQQVre45AihhpqWRGr8AW-B2HHtrbHIl4vWahqD4oNzxGDCOnwyooZ7iQMIcLAG9Z12LqK-uWTPFedTVKkDiuY63eYFo9YCrptO7tMaxvJSI2xuh2UEqA1TKbS70Y3uOcoRYO1Pzwv0beewA8v6FF_PlcOstzIEV7-SkcXUZv6ChVtq9rnwiFqE5yxt-SZiZ5owaDpCNhdDqAHcxHWJI_cqcfaWjsO7mWSbuPjpSvw/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1fMbXPspqlq-yVRqSuWcM9qireeQDFjj4%2Fview%3Fusp%3Ddrive_web> On Tue, Apr 26, 2022 at 2:07 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: sorry, just looking at it now. Can you send the 1mm results as well? On 4/25/2022 7:42 PM, Samuel Paré wrote:External Email - Use Caution Hi, I was wondering if you had new information on this matter. Thank you very much, Samuel On Tue, Apr 5, 2022 at 9:04 AM Samuel Paré <pare.samuel19@gmail.com> wrote: B15.zip <https://secure-web.cisco.com/1d2-h6246ghO1ZWMP33mOl8JR3DNWRGoJVMDMShomFlz3LhGlhOAjOxmLYC9J9wJJbmRKCn70sZPPUxkFnhrqnHTucHKGpQRg24MWiM5SVfBBAQyyYdF1kpdaSDQ5H4T7Ouqez8zZ1EHGeGBvfRc-3J3B1-w0HLm2oEkM1Yi2i0KgY0c2ctSRFjTktX9efnlsVWnl4SwlnJds_B_bjgcg-eEgJ-yb0n7wVU4fIM4ZRDuzZ72FjVEEr8Yq6jsvN0d5uIl0i9CJX7G0m6UsgEVd_S1oRQWhZfusM1T8ciErowlYibCRhJHRpBHi6sdXtT4rfPu8SZg5sp0ckDlmEsQx9rqXHEFJd6duhfoswRVZD7U/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1CatLZC5ca1Q4CvfSzXB3MMC62f6vNnXX%2Fview%3Fusp%3Ddrive_web> Hi Douglas, Thank you again for your help. Here is one subject, let me know if you need more. Kind regards, Samuel On Mon, Apr 4, 2022 at 10:40 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: That's so weird. Can you make the data available to us? On 3/29/2022 8:00 AM, Samuel Paré wrote:External Email - Use Caution Hi Dough, Thanks for your response. We followed your suggestion and ran the 7T data without the -highres option. This gave us values which are in the normal range of what we get when using 3T mean curvature data. We looked whether there was a fixed scaling factor between the data with and without the -highres option. This did not seem to be the case as the scaling factor for the different subregions varied between 1,18 (for the left G_subcallosal) and 2,95 (for the left S_collat_transv_ant). I attached a pdf with the results. Thank you again On Sun, Mar 27, 2022 at 5:31 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: This does not make sense to me. What resolution is your 3T and 7T data? Can you run the 7T data at 1mm (ie, without the -hires option) and see if it changes? On 3/20/2022 9:42 AM, Samuel Paré wrote:External Email - Use Caution Hello, We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference? Thanks, Samuel image.png -- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1Js5RYkF9g9o-TCQiLwHtezjqoE_SjgaOLPtPqH7T07AInOANzncfH2EL1ydhUgEvP1AjUlQOkCMgWi34epgPlAog5D0bBAQmWAOL1sMFeE5NFk7H9YQgAdNDKn8Wuqd2j3Jyz0dqI0roZWyKucvttXkj4ozp2NbcB3z98C0_Mm-tIdvdIjH3t1fxnlEbw-p6OpXpORjBLy6YgUOFpKjDbwZ4erLTrwFozrOJ3_RIb8K8bG4gPa0JYQ2raxD4ErlJjFu8alnp6D8DCkf_gK6sunf1rEngI2BbxOhTaOrzcfzUxORhFXwZskVlWxrzA6ec5XA0ZKJlJy2TDBYv4rDaTg/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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1Js5RYkF9g9o-TCQiLwHtezjqoE_SjgaOLPtPqH7T07AInOANzncfH2EL1ydhUgEvP1AjUlQOkCMgWi34epgPlAog5D0bBAQmWAOL1sMFeE5NFk7H9YQgAdNDKn8Wuqd2j3Jyz0dqI0roZWyKucvttXkj4ozp2NbcB3z98C0_Mm-tIdvdIjH3t1fxnlEbw-p6OpXpORjBLy6YgUOFpKjDbwZ4erLTrwFozrOJ3_RIb8K8bG4gPa0JYQ2raxD4ErlJjFu8alnp6D8DCkf_gK6sunf1rEngI2BbxOhTaOrzcfzUxORhFXwZskVlWxrzA6ec5XA0ZKJlJy2TDBYv4rDaTg/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. 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I re-ran your data and could not replicate. The only thing I can think is that you first ran the hires data at 1mm, then you reran with -hires. When I run from scratch with -hires, the data agree with the 1mm. btw, I noticed that your 1mm was run with a development version of FS -- generally you should not do this.
On 5/4/2022 7:43 AM, Samuel Paré wrote:
External Email - Use Caution
Hi,
I apologize for the repeated emails, but I was wondering if you had the time to look at the 1mm data.
Sorry again and thank you so much, Samuel
On Wed., Apr. 27, 2022, 11:03 a.m. Samuel Paré, pare.samuel19@gmail.com wrote:
No worries! Here are the 1mm results. Thank you so so much for your help. Have a great day, Sam B15mm1.zip <https://secure-web.cisco.com/1Mue4-mv2gc8lPVbiGq7vbxafsOugGxUqXTC71h8yj0zOpciBKNm-8E-OMrTb7OqryONcoZpMDn5Bo1g4MRW3QOFkwYG3k61OluNL0PnHH3cjKOwKjcmbrMU0zvOltDCq2LQQVre45AihhpqWRGr8AW-B2HHtrbHIl4vWahqD4oNzxGDCOnwyooZ7iQMIcLAG9Z12LqK-uWTPFedTVKkDiuY63eYFo9YCrptO7tMaxvJSI2xuh2UEqA1TKbS70Y3uOcoRYO1Pzwv0beewA8v6FF_PlcOstzIEV7-SkcXUZv6ChVtq9rnwiFqE5yxt-SZiZ5owaDpCNhdDqAHcxHWJI_cqcfaWjsO7mWSbuPjpSvw/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1fMbXPspqlq-yVRqSuWcM9qireeQDFjj4%2Fview%3Fusp%3Ddrive_web> On Tue, Apr 26, 2022 at 2:07 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: sorry, just looking at it now. Can you send the 1mm results as well? On 4/25/2022 7:42 PM, Samuel Paré wrote:External Email - Use Caution Hi, I was wondering if you had new information on this matter. Thank you very much, Samuel On Tue, Apr 5, 2022 at 9:04 AM Samuel Paré <pare.samuel19@gmail.com> wrote: B15.zip <https://secure-web.cisco.com/1d2-h6246ghO1ZWMP33mOl8JR3DNWRGoJVMDMShomFlz3LhGlhOAjOxmLYC9J9wJJbmRKCn70sZPPUxkFnhrqnHTucHKGpQRg24MWiM5SVfBBAQyyYdF1kpdaSDQ5H4T7Ouqez8zZ1EHGeGBvfRc-3J3B1-w0HLm2oEkM1Yi2i0KgY0c2ctSRFjTktX9efnlsVWnl4SwlnJds_B_bjgcg-eEgJ-yb0n7wVU4fIM4ZRDuzZ72FjVEEr8Yq6jsvN0d5uIl0i9CJX7G0m6UsgEVd_S1oRQWhZfusM1T8ciErowlYibCRhJHRpBHi6sdXtT4rfPu8SZg5sp0ckDlmEsQx9rqXHEFJd6duhfoswRVZD7U/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1CatLZC5ca1Q4CvfSzXB3MMC62f6vNnXX%2Fview%3Fusp%3Ddrive_web> Hi Douglas, Thank you again for your help. Here is one subject, let me know if you need more. Kind regards, Samuel On Mon, Apr 4, 2022 at 10:40 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: That's so weird. Can you make the data available to us? On 3/29/2022 8:00 AM, Samuel Paré wrote:External Email - Use Caution Hi Dough, Thanks for your response. We followed your suggestion and ran the 7T data without the -highres option. This gave us values which are in the normal range of what we get when using 3T mean curvature data. We looked whether there was a fixed scaling factor between the data with and without the -highres option. This did not seem to be the case as the scaling factor for the different subregions varied between 1,18 (for the left G_subcallosal) and 2,95 (for the left S_collat_transv_ant). I attached a pdf with the results. Thank you again On Sun, Mar 27, 2022 at 5:31 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: This does not make sense to me. What resolution is your 3T and 7T data? Can you run the 7T data at 1mm (ie, without the -hires option) and see if it changes? On 3/20/2022 9:42 AM, Samuel Paré wrote:External Email - Use Caution Hello, We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference? 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