Re: [Freesurfer] Talairach Failed: Distorted T1

2021-04-16 Thread Harkey, Thomas Jarrott 
External 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 
 on behalf of Douglas N. Greve 

Sent: Wednesday, April 14, 2021 9:25 AM
To: 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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Harkey, Thomas Jarrott 
<mailto:tjhar...@uams.edu>
Sent: Tuesday, March 30, 2021 6:03 PM
To: Freesurfer support list 
<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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<mailto: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, 1.00
  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: 0.00
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.   0.   0. 1.

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   0.978890.4171
0.   0.   0. 1.

Kindly,
Thomas Harkey
UAMS College of Medicine class of 2022

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Fr

Re: [Freesurfer] Talairach Failed: Distorted T1

2021-04-06 Thread Harkey, Thomas Jarrott 
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 
 on behalf of Harkey, Thomas Jarrott 

Sent: Tuesday, March 30, 2021 6:03 PM
To: Freesurfer support list 
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 
 on behalf of Douglas N. Greve 

Sent: Thursday, March 25, 2021 9:48 PM
To: 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, 1.00
  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: 0.00
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.   0.   0. 1.

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   0.978890.4171
0.   0.   0. 1.

Kindly,
Thomas Harkey
UAMS College of Medicine class of 2022

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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>




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.



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Re: [Freesurfer] Talairach Failed: Distorted T1

2021-03-30 Thread Harkey, Thomas Jarrott 
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 
 on behalf of Douglas N. Greve 

Sent: Thursday, March 25, 2021 9:48 PM
To: 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, 1.00
  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: 0.00
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.   0.   0. 1.

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   0.978890.4171
0.   0.   0. 1.

Kindly,
Thomas Harkey
UAMS College of Medicine class of 2022

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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>




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.



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Re: [Freesurfer] Talairach Failed: Distorted T1

2021-03-25 Thread Harkey, Thomas Jarrott 
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, 1.00
  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: 0.00
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.   0.   0. 1.

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   0.978890.4171
0.   0.   0. 1.

Kindly,
Thomas Harkey
UAMS College of Medicine class of 2022

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, March 25, 2021 9:11 AM
To: 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>




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.



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Re: [Freesurfer] BrainSegNotVent {Disarmed}

2020-09-02 Thread Harkey, Thomas Jarrott 
External Email - Use Caution

Hello,
Two final questions: when I did autorecon1 and autorecon2-volonly, I then ran 
the following command:
mri_segstats –brain-vol-from-seg –seg aseg.presurf.mgz –sum stats

However, it is just printing the volumes of each segmentation and not adding 
them up. I want the BrainSegNotVent measurement without having to do the entire 
recon all. What am I doing wrong?

Is there a way to obtain the aseg.stats file or brainvol.stats file without 
using recon-all?
Just trying to save time.
Thanks for your help.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Monday, August 24, 2020 9:12 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] BrainSegNotVent {Disarmed}

Right, you will actually need to run both autorecon1 and -autorecon2-volonly
-autorecon2-volonly will take a few hours


On 8/23/2020 7:35 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution
Ok, I tried that command and it didn’t work because aseg.presurf.mgz doesn’t 
exist in that directory
I don’t think that file was generated with autorecon1.
So do you think I need to run reconall -all to get the BrainSegNotVent?
If there were a more efficient way to obtain this volume, I would be open to 
learning it.

--
Thomas Harkey
University of Arkansas for Medical Sciences
College of Medicine, Class of 2022
501-553-6318
tjhar...@uams.edu<mailto:tjhar...@uams.edu>


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, August 23, 2020 at 2:03 PM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] BrainSegNotVent

Actually, that file won't be there either because it does not get created until 
all processing is done (not just autorecon1). You can run mri_segststats like
mri_segstats --seg subject/mri/aseg.presurf.mgz --ctab-default --sum 
subject/stats/aseg.presurf.stats
Then add up all the segmentations you want to get BrainSegNotVent


On 8/23/2020 11:42 AM, Douglas N. Greve wrote:
Are you using v7? If so, look in subject/stats/brainvol.stats
On 8/22/2020 5:39 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution

Hello,
I am a student learning free surfer. I was able to obtain intracranial volume 
by running

recon-all   –i  file.dcm   –subject  bert –autorecon1

and then

mri_segstats --subject bert --etiv-only



How can I obtain the BrainSegNotVent volume? I have tried

mri_segstats --subject bert --brain-vol-from-seg



however, “ERROR: must specify a segmentation volume”



Can this be calculated using the data from autorecon1, or do I need to run 
-all? Which segmentation do I need to specify?

My contact information is below,
Thank you!
--
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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Re: [Freesurfer] BrainSegNotVent {Disarmed}

2020-08-24 Thread Harkey, Thomas Jarrott 
External Email - Use Caution

Ok thank you!
If we conducted a study measuring brain to intracranial volume ratio, do you 
think that BrainVolNotVent and Etiv-only ratio would provide accurate measures? 
Is there another more robust way to make this calculation using FreeSurfer?
We are studying brain atrophy in MCA stroke patients. I have seen studies 
indicating there is some bias regarding etiv but that the correlation with 
manual segmentations is roughly R =.8.
Is the BrainVolNotVent to Etiv-only ratio a valid estimation of atrophy or are 
there statistical normalizations or corrections that complicate that procedure?



Thank you so much for your time.
--
Thomas Harkey
University of Arkansas for Medical Sciences
College of Medicine, Class of 2022
501-553-6318
tjhar...@uams.edu<mailto:tjhar...@uams.edu>


From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Monday, August 24, 2020 at 9:14 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] BrainSegNotVent {Disarmed}

No, you need a segmentation
On 8/23/2020 8:18 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution
Will this work on the brainmask.auto.mgz if I use the --brain-vol-from-seg 
command?


--
Thomas Harkey
University of Arkansas for Medical Sciences
College of Medicine, Class of 2022
501-553-6318
tjhar...@uams.edu<mailto:tjhar...@uams.edu>


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, August 23, 2020 at 2:03 PM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] BrainSegNotVent

Actually, that file won't be there either because it does not get created until 
all processing is done (not just autorecon1). You can run mri_segststats like
mri_segstats --seg subject/mri/aseg.presurf.mgz --ctab-default --sum 
subject/stats/aseg.presurf.stats
Then add up all the segmentations you want to get BrainSegNotVent



On 8/23/2020 11:42 AM, Douglas N. Greve wrote:
Are you using v7? If so, look in subject/stats/brainvol.stats
On 8/22/2020 5:39 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution

Hello,
I am a student learning free surfer. I was able to obtain intracranial volume 
by running

recon-all   –i  file.dcm   –subject  bert –autorecon1

and then

mri_segstats --subject bert --etiv-only



How can I obtain the BrainSegNotVent volume? I have tried

mri_segstats --subject bert --brain-vol-from-seg



however, “ERROR: must specify a segmentation volume”



Can this be calculated using the data from autorecon1, or do I need to run 
-all? Which segmentation do I need to specify?

My contact information is below,
Thank you!
--
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. If you are not the intended recipient, please 
contact the sender by reply e-mail and destroy all copies of the original 
message.




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Re: [Freesurfer] BrainSegNotVent {Disarmed}

2020-08-23 Thread Harkey, Thomas Jarrott 
External Email - Use Caution

Will this work on the brainmask.auto.mgz if I use the --brain-vol-from-seg 
command?


--
Thomas Harkey
University of Arkansas for Medical Sciences
College of Medicine, Class of 2022
501-553-6318
tjhar...@uams.edu<mailto:tjhar...@uams.edu>


From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Sunday, August 23, 2020 at 2:03 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] BrainSegNotVent

Actually, that file won't be there either because it does not get created until 
all processing is done (not just autorecon1). You can run mri_segststats like
mri_segstats --seg subject/mri/aseg.presurf.mgz --ctab-default --sum 
subject/stats/aseg.presurf.stats
Then add up all the segmentations you want to get BrainSegNotVent


On 8/23/2020 11:42 AM, Douglas N. Greve wrote:
Are you using v7? If so, look in subject/stats/brainvol.stats
On 8/22/2020 5:39 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution

Hello,
I am a student learning free surfer. I was able to obtain intracranial volume 
by running

recon-all   –i  file.dcm   –subject  bert –autorecon1

and then

mri_segstats --subject bert --etiv-only



How can I obtain the BrainSegNotVent volume? I have tried

mri_segstats --subject bert --brain-vol-from-seg



however, “ERROR: must specify a segmentation volume”



Can this be calculated using the data from autorecon1, or do I need to run 
-all? Which segmentation do I need to specify?

My contact information is below,
Thank you!
--
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. If you are not the intended recipient, please 
contact the sender by reply e-mail and destroy all copies of the original 
message.



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Re: [Freesurfer] BrainSegNotVent {Disarmed}

2020-08-23 Thread Harkey, Thomas Jarrott 
External Email - Use Caution

Ok, I tried that command and it didn’t work because aseg.presurf.mgz doesn’t 
exist in that directory
I don’t think that file was generated with autorecon1.
So do you think I need to run reconall -all to get the BrainSegNotVent?
If there were a more efficient way to obtain this volume, I would be open to 
learning it.

--
Thomas Harkey
University of Arkansas for Medical Sciences
College of Medicine, Class of 2022
501-553-6318
tjhar...@uams.edu<mailto:tjhar...@uams.edu>


From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Sunday, August 23, 2020 at 2:03 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] BrainSegNotVent

Actually, that file won't be there either because it does not get created until 
all processing is done (not just autorecon1). You can run mri_segststats like
mri_segstats --seg subject/mri/aseg.presurf.mgz --ctab-default --sum 
subject/stats/aseg.presurf.stats
Then add up all the segmentations you want to get BrainSegNotVent


On 8/23/2020 11:42 AM, Douglas N. Greve wrote:
Are you using v7? If so, look in subject/stats/brainvol.stats
On 8/22/2020 5:39 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution

Hello,
I am a student learning free surfer. I was able to obtain intracranial volume 
by running

recon-all   –i  file.dcm   –subject  bert –autorecon1

and then

mri_segstats --subject bert --etiv-only



How can I obtain the BrainSegNotVent volume? I have tried

mri_segstats --subject bert --brain-vol-from-seg



however, “ERROR: must specify a segmentation volume”



Can this be calculated using the data from autorecon1, or do I need to run 
-all? Which segmentation do I need to specify?

My contact information is below,
Thank you!
--
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. If you are not the intended recipient, please 
contact the sender by reply e-mail and destroy all copies of the original 
message.



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[Freesurfer] BrainSegNotVent

2020-08-22 Thread Harkey, Thomas Jarrott 
External Email - Use Caution

Hello,
I am a student learning free surfer. I was able to obtain intracranial volume 
by running

recon-all   –i  file.dcm   –subject  bert –autorecon1

and then

mri_segstats --subject bert --etiv-only



How can I obtain the BrainSegNotVent volume? I have tried

mri_segstats --subject bert --brain-vol-from-seg



however, “ERROR: must specify a segmentation volume”



Can this be calculated using the data from autorecon1, or do I need to run 
-all? Which segmentation do I need to specify?

My contact information is below,
Thank you!
--
Thomas Harkey
University of Arkansas for Medical Sciences
College of Medicine, Class of 2022
501-553-6318
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. If you are not the intended recipient, please 
contact the sender by reply e-mail and destroy all copies of the original 
message.
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