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 <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

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
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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