External Email - Use Caution
Hi Freesurfer experts,
I was looking to run the three steps of group analysis-mris preproc, mri surf2surf using the measure volume and unsure of how to go about it since the wiki page talks about thickness only. I would appreciate any help.
Best, Sara
Hi Sara,
You may want to use asegstats2table. Follow these links to learn more about mris_preproc, mri_glmfit, and asegstats2table:
http://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit?highlight=%28asegstats%...
https://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table?highlight=%28asegs...
Best, Jocelyn ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sara Lyn saralyn543@gmail.com Sent: Wednesday, November 18, 2020 6:37 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Group Analysis
External Email - Use Caution
Hi Freesurfer experts,
I was looking to run the three steps of group analysis-mris preproc, mri surf2surf using the measure volume and unsure of how to go about it since the wiki page talks about thickness only. I would appreciate any help.
Best, Sara
External Email - Use Caution
Hi Jocelyn,
The links talk about measuring thickness and I’m trying to do a volumetric Group analysis using Glm. I was wondering if you could point me towards that.
Sara
On Thursday, November 19, 2020, Mora, Jocelyn S. JSMORA@mgh.harvard.edu wrote:
Hi Sara,
You may want to use asegstats2table. Follow these links to learn more about mris_preproc, mri_glmfit, and asegstats2table:
http://secure-web.cisco.com/1GcyAZ4TLbRGiuwf3mK0o8IKvcNsxwTULArjRsgQ5-qwwWHs...
https://secure-web.cisco.com/1OylzWdn9KNXiaXZXnAXy6Y4zKLT3o_SWqfBObqbSeLwwdc... highlight=%28asegstats%29
https://secure-web.cisco.com/1v3oCpx-Uv895Hjxj-klxnZ5JfvSWRtw-oWz6bxIOFQbCON... 28asegstats%29
Best, Jocelyn
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sara Lyn < saralyn543@gmail.com> *Sent:* Wednesday, November 18, 2020 6:37 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Group Analysis
External Email - Use CautionHi Freesurfer experts,
I was looking to run the three steps of group analysis-mris preproc, mri surf2surf using the measure volume and unsure of how to go about it since the wiki page talks about thickness only. I would appreciate any help.
Best, Sara
Just use --meas volume instead of --meas area ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sara Lyn saralyn543@gmail.com Sent: Thursday, November 19, 2020 12:41 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Analysis {Disarmed}
External Email - Use Caution
Hi Jocelyn,
The links talk about measuring thickness and I’m trying to do a volumetric Group analysis using Glm. I was wondering if you could point me towards that.
Sara
On Thursday, November 19, 2020, Mora, Jocelyn S. <JSMORA@mgh.harvard.edumailto:JSMORA@mgh.harvard.edu> wrote: Hi Sara,
You may want to use asegstats2table. Follow these links to learn more about mris_preproc, mri_glmfit, and asegstats2table:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/mris_preprochttp://secure-web.cisco.com/1GcyAZ4TLbRGiuwf3mK0o8IKvcNsxwTULArjRsgQ5-qwwWHseO7Av6RqT8xdhHsL8LHTuIoRLCNHWJBGJo8Agt99_QoT95gst9PbZMUpV2KB70uY9UQ9u_d_-hUpKT_FeCzOVvl_lfE4h9bW6yCb5jjb1LQ_MU8B1aU-8LZ-rOZ3Z_UxUqD99IHmZtQtuT3AfjYAQtdNUl3Y-k3Wh8Cxo4TeJbHILfSoBj3GfcLaPCha4Lkm7H-FDht547FiGBuaBs8Z7W9kOgEGho_vHNXh8yQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_preproc
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Best, Jocelyn ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sara Lyn <saralyn543@gmail.commailto:saralyn543@gmail.com> Sent: Wednesday, November 18, 2020 6:37 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Group Analysis
External Email - Use Caution
Hi Freesurfer experts,
I was looking to run the three steps of group analysis-mris preproc, mri surf2surf using the measure volume and unsure of how to go about it since the wiki page talks about thickness only. I would appreciate any help.
Best, Sara
Sorry, meant to say instead of --meas thickness ________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Thursday, November 19, 2020 1:01 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Analysis {Disarmed}
Just use --meas volume instead of --meas area ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sara Lyn saralyn543@gmail.com Sent: Thursday, November 19, 2020 12:41 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Analysis {Disarmed}
External Email - Use Caution
Hi Jocelyn,
The links talk about measuring thickness and I’m trying to do a volumetric Group analysis using Glm. I was wondering if you could point me towards that.
Sara
On Thursday, November 19, 2020, Mora, Jocelyn S. <JSMORA@mgh.harvard.edumailto:JSMORA@mgh.harvard.edu> wrote: Hi Sara,
You may want to use asegstats2table. Follow these links to learn more about mris_preproc, mri_glmfit, and asegstats2table:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/mris_preprochttp://secure-web.cisco.com/1GcyAZ4TLbRGiuwf3mK0o8IKvcNsxwTULArjRsgQ5-qwwWHseO7Av6RqT8xdhHsL8LHTuIoRLCNHWJBGJo8Agt99_QoT95gst9PbZMUpV2KB70uY9UQ9u_d_-hUpKT_FeCzOVvl_lfE4h9bW6yCb5jjb1LQ_MU8B1aU-8LZ-rOZ3Z_UxUqD99IHmZtQtuT3AfjYAQtdNUl3Y-k3Wh8Cxo4TeJbHILfSoBj3GfcLaPCha4Lkm7H-FDht547FiGBuaBs8Z7W9kOgEGho_vHNXh8yQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_preproc
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit?highlight=%28asegstats%...https://secure-web.cisco.com/13cmJBT-4LmJ_p41ob4SvqYUzE0Aax6xecNrB4OLlge5pPiXavpaEmeTqn9JDDK_rkzl96cA8Rumnanxwcda7wCuOfEwzk4dZAPPT-o_-ZvKceO3KqPPf61evKLe_XDLe4EZzINukOdv_nHmHTXrkf7nAKR0F6BjANEeu6Ntj405XpLSLWEWhu-zJ9FY-gSSXgQchjSt4GTk9DTJHZmU7NtwmE5dWg-zLKo8U3mknDxF2iirqE4tmpCxBX89tJukNPaOBCFtCHfGqSTF4V2NAkQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_glmfit%3Fhighlight%3D%2528asegstats%2529
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Best, Jocelyn ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sara Lyn <saralyn543@gmail.commailto:saralyn543@gmail.com> Sent: Wednesday, November 18, 2020 6:37 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Group Analysis
External Email - Use Caution
Hi Freesurfer experts,
I was looking to run the three steps of group analysis-mris preproc, mri surf2surf using the measure volume and unsure of how to go about it since the wiki page talks about thickness only. I would appreciate any help.
Best, Sara
By "volume" do you mean a surface-based, vertex-wise measure of volume or do you mean volume of an ROI?
On 11/19/2020 11:46 AM, Mora, Jocelyn S. wrote: Hi Sara,
You may want to use asegstats2table. Follow these links to learn more about mris_preproc, mri_glmfit, and asegstats2table:
http://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit?highlight=%28asegstats%...
https://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table?highlight=%28asegs...
Best, Jocelyn ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sara Lyn saralyn543@gmail.commailto:saralyn543@gmail.com Sent: Wednesday, November 18, 2020 6:37 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Group Analysis
External Email - Use Caution
Hi Freesurfer experts,
I was looking to run the three steps of group analysis-mris preproc, mri surf2surf using the measure volume and unsure of how to go about it since the wiki page talks about thickness only. I would appreciate any help.
Best, Sara
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Make sure that --meas volume was passed to mris_preproc was passed (this is the usual way you would do this) in which case it makes a jacobian correction. The only other thing to do would be to correct for intra-cranial volume. If you have 7.X, you can just add --etiv to mris_preproc
On 11/18/2020 6:37 PM, Sara Lyn wrote:
External Email - Use Caution
Hi Freesurfer experts,
I was looking to run the three steps of group analysis-mris preproc, mri surf2surf using the measure volume and unsure of how to go about it since the wiki page talks about thickness only. I would appreciate any help.
Best, Sara
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
Mora, Jocelyn S. -
Sara Lyn