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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Harkey, Thomas Jarrott
<tjhar...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu><mailto:dgr...@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
tjhar...@uams.edu<mailto:tjhar...@uams.edu>
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