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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Harkey, Thomas Jarrott TJHarkey@uams.edumailto:TJHarkey@uams.edu Sent: Tuesday, March 30, 2021 6:03 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto: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.edumailto: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.edumailto:TJHarkey@uams.edu
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