BrainSegNotVent

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Harkey, Thomas Jarrott

22 Aug 2020 22 Aug '20

5:39 p.m.

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 TJHarkey@uams.edumailto:TJHarkey@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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Douglas N. Greve

23 Aug 23 Aug

11:42 a.m.

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*

*TJHarkey@uams.edu mailto:TJHarkey@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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Douglas N. Greve

3:02 p.m.

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*

*TJHarkey@uams.edu mailto:TJHarkey@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.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Harkey, Thomas Jarrott

7:35 p.m.

New subject: BrainSegNotVent {Disarmed}

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 TJHarkey@uams.edumailto:TJHarkey@uams.edu

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Sunday, August 23, 2020 at 2:03 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 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 TJHarkey@uams.edumailto:TJHarkey@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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Douglas N. Greve

24 Aug 24 Aug

10:12 a.m.

New subject: 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*

*TJHarkey@uams.edu mailto:TJHarkey@uams.edu*

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Sunday, August 23, 2020 at 2:03 PM *To: *"freesurfer@nmr.mgh.harvard.edu" 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*

    *TJHarkey@uams.edu <mailto:TJHarkey@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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Harkey, Thomas Jarrott

2 Sep 2 Sep

2:04 p.m.

New subject: BrainSegNotVent {Disarmed}

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu 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 TJHarkey@uams.edumailto:TJHarkey@uams.edu

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 TJHarkey@uams.edumailto:TJHarkey@uams.edu

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Douglas N. Greve

3 Sep 3 Sep

9:16 a.m.

New subject: BrainSegNotVent {Disarmed}

Not really, since it requires having the surfaces. You can add them up yourself, or you can binarize aseg.presurf.mgz to just the regions you want (mri_binarize --match id1 id2 ...), then run mri_segstats on that

On 9/2/2020 2:04 PM, Harkey, Thomas Jarrott wrote:

...

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *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*

*TJHarkey@uams.edu mailto:TJHarkey@uams.edu*

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Sunday, August 23, 2020 at 2:03 PM *To: *"freesurfer@nmr.mgh.harvard.edu" 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*

    *TJHarkey@uams.edu <mailto:TJHarkey@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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Harkey, Thomas Jarrott

8 Sep 8 Sep

1:44 p.m.

New subject: BrainSegNotVent {Disarmed}

External Email - Use Caution

Douglas, We are conducting a study with stroke patients using DWI MRI. Image attached. Is Freesurfer capable of taking an MRI with an infarct (as you can see in the picture) and providing a volume for that hyperintense area? Is there a command we can run do specify for that? Would recon all do it? Thanks

-- Thomas Harkey University of Arkansas for Medical Sciences College of Medicine, Class of 2022 501-553-6318 TJHarkey@uams.edumailto:TJHarkey@uams.edu

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, September 3, 2020 at 8:17 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] BrainSegNotVent {Disarmed}

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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu Sent: Monday, August 24, 2020 9:12 AM To: freesurfer@nmr.mgh.harvard.edumailto: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:

-- Thomas Harkey University of Arkansas for Medical Sciences College of Medicine, Class of 2022 501-553-6318 TJHarkey@uams.edumailto:TJHarkey@uams.edu

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 TJHarkey@uams.edumailto:TJHarkey@uams.edu

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Douglas N. Greve

6:46 p.m.

New subject: BrainSegNotVent {Disarmed}

That scan looks low res and T2 weighted, so you would not run recon-all on it. But even if it were the right contrast/resolution, I think it is too extensive. I don't know if there is going to be something that we have that is going to do that for you.

On 9/8/2020 1:44 PM, Harkey, Thomas Jarrott wrote:

...

External Email - Use Caution

Douglas,

We are conducting a study with stroke patients using DWI MRI. Image attached. Is Freesurfer capable of taking an MRI with an infarct (as you can see in the picture) and providing a volume for that hyperintense area?

Is there a command we can run do specify for that?

Would recon all do it?

Thanks

*Thomas Harkey ** University of Arkansas for Medical Sciences***

*College of Medicine, Class of 2022 501-553-6318*

*TJHarkey@uams.edu mailto:TJHarkey@uams.edu*

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, September 3, 2020 at 8:17 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] BrainSegNotVent {Disarmed}

On 9/2/2020 2:04 PM, Harkey, Thomas Jarrott wrote:

*        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-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
<freesurfer-bounces@nmr.mgh.harvard.edu>
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve <dgreve@mgh.harvard.edu>
<mailto:dgreve@mgh.harvard.edu>
*Sent:* Monday, August 24, 2020 9:12 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto: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*

    *TJHarkey@uams.edu <mailto:TJHarkey@uams.edu>*

    *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
    <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
    "Douglas N. Greve" <dgreve@mgh.harvard.edu>
    <mailto:dgreve@mgh.harvard.edu>
    *Reply-To: *Freesurfer support list
    <freesurfer@nmr.mgh.harvard.edu>
    <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>
    <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*

            *TJHarkey@uams.edu <mailto:TJHarkey@uams.edu>*

            ------------------------------------------------------------------------

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Harkey, Thomas Jarrott

23 Aug 23 Aug

8:18 p.m.

New subject: BrainSegNotVent {Disarmed}

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 TJHarkey@uams.edumailto:TJHarkey@uams.edu

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 TJHarkey@uams.edumailto:TJHarkey@uams.edu

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Douglas N. Greve

24 Aug 24 Aug

10:13 a.m.

New subject: 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*

*TJHarkey@uams.edu mailto:TJHarkey@uams.edu*

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

    *TJHarkey@uams.edu <mailto:TJHarkey@uams.edu>*

    ------------------------------------------------------------------------

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    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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Harkey, Thomas Jarrott

1 p.m.

New subject: BrainSegNotVent {Disarmed}

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 TJHarkey@uams.edumailto:TJHarkey@uams.edu

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, August 24, 2020 at 9:14 AM To: "freesurfer@nmr.mgh.harvard.edu" 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 TJHarkey@uams.edumailto:TJHarkey@uams.edu

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 TJHarkey@uams.edumailto:TJHarkey@uams.edu

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Douglas N. Greve

25 Aug 25 Aug

11:26 a.m.

New subject: BrainSegNotVent {Disarmed}

I have not studied the issue, but I think that BrainVolNotVent is probably a good way to go.

On 8/24/2020 1:00 PM, Harkey, Thomas Jarrott wrote:

...

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*

*TJHarkey@uams.edu mailto:TJHarkey@uams.edu*

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, August 24, 2020 at 9:14 AM *To: *"freesurfer@nmr.mgh.harvard.edu" 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*

*TJHarkey@uams.edu <mailto:TJHarkey@uams.edu>*

*From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" <dgreve@mgh.harvard.edu>
<mailto:dgreve@mgh.harvard.edu>
*Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<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>
<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*

        *TJHarkey@uams.edu <mailto:TJHarkey@uams.edu>*

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Douglas N. Greve
Harkey, Thomas Jarrott