It is subject to the same limitations On 4/16/2021 10:09 PM, Harkey, Thomas Jarrott wrote:
z_a = -0.1022, c_aExternal 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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@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: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 <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Harkey, Thomas Jarrott <tjhar...@uams.edu> <mailto:tjhar...@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 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 <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 9:48 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 T1That is an axial scan that only covers 25mm of the brain inferior-superior. This is not whole brain coverage, which is causing the problemOn 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: 12.5TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degreesnframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform presentxform 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_s = 0.9788, c_s= 14.0701: x_s = -0.1758, y_s = -0.1054,
= -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 T1It looks like something is wrong with your input. For starters, the voxel size looks huge. Runmri_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>* ------------------------------------------------------------------------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. 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