Talairach Failed: Distorted T1

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Harkey, Thomas Jarrott

23 Mar 2021 23 Mar '21

10:54 p.m.

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Hello, My name is Thomas Harkey and I am conducting research using FreeSurfer. After running recon-all on this patient, the Talairach failed according to the .log file. No stats were calculated but loading the orig.mgz file into FreeView looks like this (see image attached). This DICOM file was successfully uploaded into other programs. How can I fix this error? Kind regards, -- Thomas Harkey University of Arkansas for Medical Sciences College of Medicine, Class of 2022 501-553-6318 TJHarkey@uams.edumailto:TJHarkey@uams.edu

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Douglas N. Greve

25 Mar 25 Mar

10:11 a.m.

It looks like something is wrong with your input. For starters, the voxel size looks huge. Run mri_info subject/mri/orig/001.mgz and send the result

On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:

...

External Email - Use Caution

Hello,

My name is Thomas Harkey and I am conducting research using FreeSurfer. After running recon-all on this patient, the Talairach failed according to the .log file. No stats were calculated but loading the orig.mgz file into FreeView looks like this (see image attached). This DICOM file was successfully uploaded into other programs.

How can I fix this error?

Kind regards,

--

*Thomas Harkey ** University of Arkansas for Medical Sciences***

*College of Medicine, Class of 2022 501-553-6318*

*TJHarkey@uams.edu mailto:TJHarkey@uams.edu*

Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Harkey, Thomas Jarrott

9:07 p.m.

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Douglas, Thank you for your help. I have pasted the result below.

Volume information for 2020-24axialScalarvolumeall/mri/orig/001.mgz type: MGH dimensions: 384 x 384 x 25 voxel sizes: 0.598958, 0.598958, 1.000000 type: SHORT (4) fov: 230.000 dof: 1 xstart: -115.0, xend: 115.0 ystart: -115.0, yend: 115.0 zstart: -12.5, zend: 12.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9841, y_r = -0.0087, z_r = -0.1777, c_r = 15.3722 : x_a = 0.0272, y_a = -0.9944, z_a = -0.1022, c_a = 14.0701 : x_s = -0.1758, y_s = -0.1054, z_s = 0.9788, c_s = -75.3479

talairach xfm : Orientation : LPS Primary Slice Direction: axial

voxel to ras transform: -0.5894 -0.0052 -0.1777 131.7540 0.0163 -0.5956 -0.1022 126.5760 -0.1053 -0.0631 0.9788 -55.2497 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant 0.358751

ras to voxel transform: -1.6429 0.0454 -0.2935 194.5030 -0.0144 -1.6602 -0.1759 202.3262 -0.1777 -0.1022 0.9788 90.4171 0.0000 0.0000 0.0000 1.0000

Kindly, Thomas Harkey UAMS College of Medicine class of 2022 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, March 25, 2021 9:11 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

It looks like something is wrong with your input. For starters, the voxel size looks huge. Run mri_info subject/mri/orig/001.mgz and send the result

On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution

Hello,

My name is Thomas Harkey and I am conducting research using FreeSurfer. After running recon-all on this patient, the Talairach failed according to the .log file. No stats were calculated but loading the orig.mgz file into FreeView looks like this (see image attached). This DICOM file was successfully uploaded into other programs.

How can I fix this error?

Kind regards,

Thomas Harkey University of Arkansas for Medical Sciences

College of Medicine, Class of 2022 501-553-6318

TJHarkey@uams.edumailto:TJHarkey@uams.edu

________________________________ Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Douglas N. Greve

10:48 p.m.

That is an axial scan that only covers 25mm of the brain inferior-superior. This is not whole brain coverage, which is causing the problem

On 3/25/2021 9:07 PM, Harkey, Thomas Jarrott wrote:

...

External Email - Use Caution

Douglas, Thank you for your help. I have pasted the result below.

Volume information for 2020-24axialScalarvolumeall/mri/orig/001.mgz type: MGH dimensions: 384 x 384 x 25 voxel sizes: 0.598958, 0.598958, 1.000000 type: SHORT (4) fov: 230.000 dof: 1 xstart: -115.0, xend: 115.0 ystart: -115.0, yend: 115.0 zstart: -12.5, zend: 12.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9841, y_r = -0.0087, z_r = -0.1777, c_r = 15.3722 : x_a = 0.0272, y_a = -0.9944, z_a = -0.1022, c_a = 14.0701 : x_s = -0.1758, y_s = -0.1054, z_s = 0.9788, c_s = -75.3479

talairach xfm : Orientation : LPS Primary Slice Direction: axial

voxel to ras transform: -0.5894 -0.0052 -0.1777 131.7540 0.0163 -0.5956 -0.1022 126.5760 -0.1053 -0.0631 0.9788 -55.2497 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant 0.358751

ras to voxel transform: -1.6429 0.0454 -0.2935 194.5030 -0.0144 -1.6602 -0.1759 202.3262 -0.1777 -0.1022 0.9788 90.4171 0.0000 0.0000 0.0000 1.0000

Kindly, Thomas Harkey UAMS College of Medicine class of 2022

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Thursday, March 25, 2021 9:11 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 It looks like something is wrong with your input. For starters, the voxel size looks huge. Run mri_info subject/mri/orig/001.mgz and send the result

On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:

...
External Email - Use Caution

Hello,

My name is Thomas Harkey and I am conducting research using FreeSurfer. After running recon-all on this patient, the Talairach failed according to the .log file. No stats were calculated but loading the orig.mgz file into FreeView looks like this (see image attached). This DICOM file was successfully uploaded into other programs.

How can I fix this error?

Kind regards,

--

*Thomas Harkey ** University of Arkansas for Medical Sciences***

*College of Medicine, Class of 2022 501-553-6318*

*TJHarkey@uams.edu mailto:TJHarkey@uams.edu*

Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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/18lwJ8ggT8lQsC3RV4AI233AXT66H_7W_CVE2Esl92gAM9_fUi6s4y-8l19x89Ytoad5cJUFr-y-IhslQUPpqneZDXpY0GdYyQ9LejZY5-YMVIzc_HuquDJ02-JAy7EkITlUa6v3zgtWwg5KV1H449G3OADuw4_E4041vep-Cs9NzRA1oW_exZD-1jvejL8k50Wpf_TOU7g3KTrXRNiOjHBerRKj8U-sg_FyjtUdch_Aa7XERO6W5hVgJvLnfrUdIfmaUT8ijMUVRbke5x7UgOg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwMDaQ%26c%3D27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk%26r%3Dlni-DQNMfZ-oN8R6xJFbHeLbIOeuCDm_BNtoxxmTiPk%26m%3Df_hRKBl8FfYqItx_YTHvwSb0eK7xmVStu8OohcmGpv4%26s%3DLmMgJVLtfQOHq2emGDgbFJVWNymeVRGFjJmt6z53LdY%26e%3D

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Harkey, Thomas Jarrott

30 Mar 30 Mar

7:03 p.m.

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Douglas, Thank you for your help. Another question. The FreeSurfer wiki states that for version 5.2 and later, the brainstem is not included in the global measures of volume because the amount of brainstem changes depending upon the field of view of the volume acquisition. We are interested in the obtaining the volume of the entire brain using the BrainVolNotVent value. Does this mean that BrainVolNotVent does not include the brainstem and therefore underestimates total brain volume? Is there a way to correct for this? Kind regards, Thomas Harkey UAMS College of Medicine M3

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, March 25, 2021 9:48 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

That is an axial scan that only covers 25mm of the brain inferior-superior. This is not whole brain coverage, which is causing the problem

On 3/25/2021 9:07 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution

Douglas, Thank you for your help. I have pasted the result below.

talairach xfm : Orientation : LPS Primary Slice Direction: axial

voxel to ras transform: -0.5894 -0.0052 -0.1777 131.7540 0.0163 -0.5956 -0.1022 126.5760 -0.1053 -0.0631 0.9788 -55.2497 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant 0.358751

ras to voxel transform: -1.6429 0.0454 -0.2935 194.5030 -0.0144 -1.6602 -0.1759 202.3262 -0.1777 -0.1022 0.9788 90.4171 0.0000 0.0000 0.0000 1.0000

Kindly, Thomas Harkey UAMS College of Medicine class of 2022 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu Sent: Thursday, March 25, 2021 9:11 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

It looks like something is wrong with your input. For starters, the voxel size looks huge. Run mri_info subject/mri/orig/001.mgz and send the result

On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution

Hello,

How can I fix this error?

Kind regards,

Thomas Harkey University of Arkansas for Medical Sciences

College of Medicine, Class of 2022 501-553-6318

TJHarkey@uams.edumailto:TJHarkey@uams.edu

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1c_OFfRMm8sXD9DhP-p9uVnyL-YUfyo0Gv7HO3vWcvGKA58...https://secure-web.cisco.com/1sxKYDyFUn1L-DRql-3YoGcdi9SZ0u-IIBFf8WTifb71AHd8A83Y7mi1D8Q_b3sJem_3CP6P6Bz5KZpSK6FygxYr9vGvpye1h0bwNMjDxvM3zuyNHuB56zih4z_ZSQ4jKk4EaUK0okKBh0EVGFxNCxhVUweRGN6NSXp_EKXikqwZSHR-c1MRwAy2ggZaSVybbUTkFDnrKbQIoL_cSB0vKpBto6jLQW75Q36gNrlzVSCOpnmxNmayQcY9itwgFVMFG/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwMD-g%26c%3D27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk%26r%3Dlni-DQNMfZ-oN8R6xJFbHeLbIOeuCDm_BNtoxxmTiPk%26m%3DawJnlMygdhBegQ_WVfcDMfdH55wc4KvX3PUeL4tsawc%26s%3D0KIJsfDq7yc4nhmTX7Uzb5-Ih5egtkYX2O_nB9sbd1o%26e%3D

Douglas N. Greve

5 Apr 5 Apr

9:56 a.m.

Correct. You can measure the volume of the brainstem and add it on. Eg, mri_segstats --ctab-default --seg aseg.mgz --id 16 --sum brainstem.dat

On 3/30/2021 7:03 PM, Harkey, Thomas Jarrott wrote:

...

External Email - Use Caution

Douglas, Thank you for your help. Another question. The FreeSurfer wiki states that for version 5.2 and later, the brainstem is not included in the global measures of volume because the amount of brainstem changes depending upon the field of view of the volume acquisition. We are interested in the obtaining the volume of the entire brain using the BrainVolNotVent value. Does this mean that BrainVolNotVent does not include the brainstem and therefore underestimates total brain volume? Is there a way to correct for this? Kind regards, Thomas Harkey UAMS College of Medicine M3

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Thursday, March 25, 2021 9:48 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 That is an axial scan that only covers 25mm of the brain inferior-superior. This is not whole brain coverage, which is causing the problem

On 3/25/2021 9:07 PM, Harkey, Thomas Jarrott wrote:

...
External Email - Use Caution

Douglas, Thank you for your help. I have pasted the result below.

Volume information for 2020-24axialScalarvolumeall/mri/orig/001.mgz type: MGH dimensions: 384 x 384 x 25 voxel sizes: 0.598958, 0.598958, 1.000000 type: SHORT (4) fov: 230.000 dof: 1 xstart: -115.0, xend: 115.0 ystart: -115.0, yend: 115.0 zstart: -12.5, zend: 12.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9841, y_r = -0.0087, z_r = -0.1777, c_r = 15.3722 : x_a = 0.0272, y_a = -0.9944, z_a = -0.1022, c_a = 14.0701 : x_s = -0.1758, y_s = -0.1054, z_s = 0.9788, c_s = -75.3479

talairach xfm : Orientation : LPS Primary Slice Direction: axial

voxel to ras transform: -0.5894 -0.0052 -0.1777 131.7540 0.0163 -0.5956 -0.1022 126.5760 -0.1053 -0.0631 0.9788 -55.2497 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant 0.358751

ras to voxel transform: -1.6429 0.0454 -0.2935 194.5030 -0.0144 -1.6602 -0.1759 202.3262 -0.1777 -0.1022 0.9788 90.4171 0.0000 0.0000 0.0000 1.0000

Kindly, Thomas Harkey UAMS College of Medicine class of 2022

*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Thursday, March 25, 2021 9:11 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 It looks like something is wrong with your input. For starters, the voxel size looks huge. Run mri_info subject/mri/orig/001.mgz and send the result

On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:

...
External Email - Use Caution

...

...
...
Hello,

My name is Thomas Harkey and I am conducting research using FreeSurfer. After running recon-all on this patient, the Talairach failed according to the .log file. No stats were calculated but loading the orig.mgz file into FreeView looks like this (see image attached). This DICOM file was successfully uploaded into other programs.

How can I fix this error?

Kind regards,

--

*Thomas Harkey ** University of Arkansas for Medical Sciences***

*College of Medicine, Class of 2022 501-553-6318*

*TJHarkey@uams.edu mailto:TJHarkey@uams.edu*

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Harkey, Thomas Jarrott

6 Apr 6 Apr

7:53 p.m.

External Email - Use Caution

Douglas, Thanks again. Is this value in the brainstem.dat file accurate or is it subject to the same limitation in that the value will depend on the field of view of volume acquisition? In other words, is it valid to add this number to the brain to obtain total brain volume? Kind regards, Thomas Harkey UAMS College of Medicine M3 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Harkey, Thomas Jarrott TJHarkey@uams.edu Sent: Tuesday, March 30, 2021 6:03 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

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That is an axial scan that only covers 25mm of the brain inferior-superior. This is not whole brain coverage, which is causing the problem

On 3/25/2021 9:07 PM, Harkey, Thomas Jarrott wrote:

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Douglas, Thank you for your help. I have pasted the result below.

talairach xfm : Orientation : LPS Primary Slice Direction: axial

voxel to ras transform: -0.5894 -0.0052 -0.1777 131.7540 0.0163 -0.5956 -0.1022 126.5760 -0.1053 -0.0631 0.9788 -55.2497 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant 0.358751

ras to voxel transform: -1.6429 0.0454 -0.2935 194.5030 -0.0144 -1.6602 -0.1759 202.3262 -0.1777 -0.1022 0.9788 90.4171 0.0000 0.0000 0.0000 1.0000

It looks like something is wrong with your input. For starters, the voxel size looks huge. Run mri_info subject/mri/orig/001.mgz and send the result

On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:

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Hello,

How can I fix this error?

Kind regards,

Thomas Harkey University of Arkansas for Medical Sciences

College of Medicine, Class of 2022 501-553-6318

TJHarkey@uams.edumailto:TJHarkey@uams.edu

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Douglas N. Greve

14 Apr 14 Apr

10:25 a.m.

Sorry, what is the brainstem.dat file? Is that something we create?

On 4/6/2021 7:53 PM, Harkey, Thomas Jarrott wrote:

...

External Email - Use Caution

Douglas, Thanks again. Is this value in the brainstem.dat file accurate or is it subject to the same limitation in that the value will depend on the field of view of volume acquisition? In other words, is it valid to add this number to the brain to obtain total brain volume? Kind regards, Thomas Harkey UAMS College of Medicine M3

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Harkey, Thomas Jarrott TJHarkey@uams.edu *Sent:* Tuesday, March 30, 2021 6:03 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1

External Email - Use Caution

Douglas, Thank you for your help. Another question. The FreeSurfer wiki states that for version 5.2 and later, the brainstem is not included in the global measures of volume because the amount of brainstem changes depending upon the field of view of the volume acquisition. We are interested in the obtaining the volume of the entire brain using the BrainVolNotVent value. Does this mean that BrainVolNotVent does not include the brainstem and therefore underestimates total brain volume? Is there a way to correct for this? Kind regards, Thomas Harkey UAMS College of Medicine M3

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Thursday, March 25, 2021 9:48 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 That is an axial scan that only covers 25mm of the brain inferior-superior. This is not whole brain coverage, which is causing the problem

On 3/25/2021 9:07 PM, Harkey, Thomas Jarrott wrote:

...
External Email - Use Caution

Douglas, Thank you for your help. I have pasted the result below.

Volume information for 2020-24axialScalarvolumeall/mri/orig/001.mgz type: MGH dimensions: 384 x 384 x 25 voxel sizes: 0.598958, 0.598958, 1.000000 type: SHORT (4) fov: 230.000 dof: 1 xstart: -115.0, xend: 115.0 ystart: -115.0, yend: 115.0 zstart: -12.5, zend: 12.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9841, y_r = -0.0087, z_r = -0.1777, c_r = 15.3722 : x_a = 0.0272, y_a = -0.9944, z_a = -0.1022, c_a = 14.0701 : x_s = -0.1758, y_s = -0.1054, z_s = 0.9788, c_s = -75.3479

talairach xfm : Orientation : LPS Primary Slice Direction: axial

voxel to ras transform: -0.5894 -0.0052 -0.1777 131.7540 0.0163 -0.5956 -0.1022 126.5760 -0.1053 -0.0631 0.9788 -55.2497 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant 0.358751

ras to voxel transform: -1.6429 0.0454 -0.2935 194.5030 -0.0144 -1.6602 -0.1759 202.3262 -0.1777 -0.1022 0.9788 90.4171 0.0000 0.0000 0.0000 1.0000

Kindly, Thomas Harkey UAMS College of Medicine class of 2022

*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Thursday, March 25, 2021 9:11 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 It looks like something is wrong with your input. For starters, the voxel size looks huge. Run mri_info subject/mri/orig/001.mgz and send the result

On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:

...
External Email - Use Caution

Hello,

My name is Thomas Harkey and I am conducting research using FreeSurfer. After running recon-all on this patient, the Talairach failed according to the .log file. No stats were calculated but loading the orig.mgz file into FreeView looks like this (see image attached). This DICOM file was successfully uploaded into other programs.

How can I fix this error?

Kind regards,

--

*Thomas Harkey ** University of Arkansas for Medical Sciences***

*College of Medicine, Class of 2022 501-553-6318*

*TJHarkey@uams.edu mailto:TJHarkey@uams.edu*

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Harkey, Thomas Jarrott

16 Apr 16 Apr

10:09 p.m.

External Email - Use Caution

Douglas,

Here is the advice you previously offered. You can measure the volume of the brainstem and add it on. Eg, mri_segstats --ctab-default --seg aseg.mgz --id 16 --sum brainstem.dat

My question is: Is this value in the brainstem.dat file accurate or is it subject to the same limitation in that the value will depend on the field of view of volume acquisition? In other words, is it valid to add this number to the brain to obtain total brain volume?

Thanks again for all your help. Kindly, Thomas Harkey UAMS College of Medicine M3

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Wednesday, April 14, 2021 9:25 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

Sorry, what is the brainstem.dat file? Is that something we create?

On 4/6/2021 7:53 PM, Harkey, Thomas Jarrott wrote:

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Douglas, Thanks again. Is this value in the brainstem.dat file accurate or is it subject to the same limitation in that the value will depend on the field of view of volume acquisition? In other words, is it valid to add this number to the brain to obtain total brain volume? Kind regards, Thomas Harkey UAMS College of Medicine M3 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Harkey, Thomas Jarrott TJHarkey@uams.edu mailto:TJHarkey@uams.edu Sent: Tuesday, March 30, 2021 6:03 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

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________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu Sent: Thursday, March 25, 2021 9:48 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

That is an axial scan that only covers 25mm of the brain inferior-superior. This is not whole brain coverage, which is causing the problem

On 3/25/2021 9:07 PM, Harkey, Thomas Jarrott wrote:

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Douglas, Thank you for your help. I have pasted the result below.

talairach xfm : Orientation : LPS Primary Slice Direction: axial

voxel to ras transform: -0.5894 -0.0052 -0.1777 131.7540 0.0163 -0.5956 -0.1022 126.5760 -0.1053 -0.0631 0.9788 -55.2497 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant 0.358751

ras to voxel transform: -1.6429 0.0454 -0.2935 194.5030 -0.0144 -1.6602 -0.1759 202.3262 -0.1777 -0.1022 0.9788 90.4171 0.0000 0.0000 0.0000 1.0000

It looks like something is wrong with your input. For starters, the voxel size looks huge. Run mri_info subject/mri/orig/001.mgz and send the result

On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:

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Hello,

How can I fix this error?

Kind regards,

Thomas Harkey University of Arkansas for Medical Sciences

College of Medicine, Class of 2022 501-553-6318

TJHarkey@uams.edumailto:TJHarkey@uams.edu

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Douglas N. Greve

18 Apr 18 Apr

10:44 p.m.

It is subject to the same limitations

On 4/16/2021 10:09 PM, Harkey, Thomas Jarrott wrote:

...

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Douglas,

Here is the advice you previously offered. /You can measure the volume of the brainstem and add it on. Eg, mri_segstats --ctab-default --seg aseg.mgz --id 16 --sum brainstem.dat/

My question is: /Is this value in the brainstem.dat file accurate or is it subject to the same limitation in that the value will depend on the field of view of volume acquisition?/ /In other words, is it valid to add this number to the brain to obtain total brain volume?///

Thanks again for all your help. Kindly, Thomas Harkey UAMS College of Medicine M3

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Wednesday, April 14, 2021 9:25 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 Sorry, what is the brainstem.dat file? Is that something we create?

On 4/6/2021 7:53 PM, Harkey, Thomas Jarrott wrote:

...
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Douglas, Thanks again. Is this value in the brainstem.dat file accurate or is it subject to the same limitation in that the value will depend on the field of view of volume acquisition? In other words, is it valid to add this number to the brain to obtain total brain volume? Kind regards, Thomas Harkey UAMS College of Medicine M3

*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Harkey, Thomas Jarrott TJHarkey@uams.edu mailto:TJHarkey@uams.edu *Sent:* Tuesday, March 30, 2021 6:03 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1

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Douglas, Thank you for your help. Another question. The FreeSurfer wiki states that for version 5.2 and later, the brainstem is not included in the global measures of volume because the amount of brainstem changes depending upon the field of view of the volume acquisition. We are interested in the obtaining the volume of the entire brain using the BrainVolNotVent value. Does this mean that BrainVolNotVent does not include the brainstem and therefore underestimates total brain volume? Is there a way to correct for this? Kind regards, Thomas Harkey UAMS College of Medicine M3

*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Thursday, March 25, 2021 9:48 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 That is an axial scan that only covers 25mm of the brain inferior-superior. This is not whole brain coverage, which is causing the problem

On 3/25/2021 9:07 PM, Harkey, Thomas Jarrott wrote:

...
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Douglas, Thank you for your help. I have pasted the result below.

Volume information for 2020-24axialScalarvolumeall/mri/orig/001.mgz type: MGH dimensions: 384 x 384 x 25 voxel sizes: 0.598958, 0.598958, 1.000000 type: SHORT (4) fov: 230.000 dof: 1 xstart: -115.0, xend: 115.0 ystart: -115.0, yend: 115.0 zstart: -12.5, zend: 12.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9841, y_r = -0.0087, z_r = -0.1777, c_r = 15.3722 : x_a = 0.0272, y_a = -0.9944,

z_a = -0.1022, c_a

...

...
...
= 14.0701 : x_s = -0.1758, y_s = -0.1054,

z_s = 0.9788, c_s

...

...
...
= -75.3479

talairach xfm : Orientation : LPS Primary Slice Direction: axial

voxel to ras transform: -0.5894 -0.0052 -0.1777 131.7540 0.0163 -0.5956 -0.1022 126.5760 -0.1053 -0.0631 0.9788 -55.2497 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant 0.358751

ras to voxel transform: -1.6429 0.0454 -0.2935 194.5030 -0.0144 -1.6602 -0.1759 202.3262 -0.1777 -0.1022 0.9788 90.4171 0.0000 0.0000 0.0000 1.0000

Kindly, Thomas Harkey UAMS College of Medicine class of 2022

*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Thursday, March 25, 2021 9:11 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 It looks like something is wrong with your input. For starters, the voxel size looks huge. Run mri_info subject/mri/orig/001.mgz and send the result

On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:

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Hello,

My name is Thomas Harkey and I am conducting research using FreeSurfer. After running recon-all on this patient, the Talairach failed according to the .log file. No stats were calculated but loading the orig.mgz file into FreeView looks like this (see image attached). This DICOM file was successfully uploaded into other programs.

How can I fix this error?

Kind regards,

--

*Thomas Harkey ** University of Arkansas for Medical Sciences***

*College of Medicine, Class of 2022 501-553-6318*

*TJHarkey@uams.edu mailto:TJHarkey@uams.edu*

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freesurfer@nmr.mgh.harvard.edu

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Douglas N. Greve
Harkey, Thomas Jarrott