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-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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