Re: [Freesurfer] Mean thickness estimation

[Greve, Douglas N.,Ph.D.]

Are you talking about outliers across subject? Or across region? I would just 
take the FS-supplied value instead of averaging the regions.

On 11/19/2020 2:14 AM, Stephanie K wrote:

External Email - Use Caution

Hi Bruce,

Thanks for the prompt reply. It is my understanding that l_thickness, 
r_thickness and estimated intracranial volume are accurately measured. Would I 
still need to identify and remove outliers if visual inspection of the images 
has not been done?

Many thanks,
Stephanie

On Wed, Nov 18, 2020 at 5:24 PM Stephanie K 
mailto:rklin...@gmail.com>> wrote:
Hi,
I want to estimate the mean cortical thickness. For this I have summed the 
thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, 
I also have the average mean thickness of left and right hemispheres (direct 
output variables of Freesurfer). As there is no visual inspection of the 
imaging in the particular cohort, I remove measures that are 3 standard 
deviations above or below the mean. Hence, I may expect more outliers to be 
removed when I take the average across the regions. I am using these brain 
measures as outcomes in association analyses with the genetic score as the 
exposure. For the mean thickness (averaged across the left and right hemisphere 
thickness variables of freesurfer after removing outliers), the regression 
coefficients have a smaller standard deviation than with thickness averaged 
across the 34 regions. I’m not sure which one to use - which one is more 
accurate? When I look at the mean thickness (which I derived using 34 regions) 
and it’s standard deviation, it is similar to that of the average mean 
thickness across the two hemispheres as well as the standard deviation of that. 
Can you suggest what is most accurate please and what the difference is between 
the mean thickness across the two hemispheres obtained from freesurfer and 
those calculated across the regions? Why does one result in more precision than 
in the other?

Thank you!



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Re: [Freesurfer] Mean thickness estimation {Disarmed}

[Fischl, Bruce]

Hi Stephanie

I see. Yes, I guess this is ok, you just want to be careful when tossing 
datasets that you aren’t biasing your results. Always better to look at them if 
you can. Big errors are pretty obvious and can be found quite rapidly (e.g. by 
zipping through a bunch of snapshots with nmovie_qt)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stephanie K
Sent: Friday, November 20, 2020 6:25 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Mean thickness estimation {Disarmed}


External Email - Use Caution
Hi Bruce,

No, I don’t think that you’ve misunderstood. I was asking about cohorts that 
had not been visually inspected in my first message and then in my last message 
I wanted to check that I didn’t need to also remove people from visually 
inspected data based on statistical outliers (as a further step). In 
conclusion, from what I’ve understood: if there is no visual inspection of 
data, it is best to remove statistical outliers (based on standard deviations) 
even for global measures such estimated intracranial volume, mean thickness 
from left and right hemispheres. When data is visually inspected, there is no 
need to remove any data based on statistical outliers even if those exist as 
these should be good quality.  For the visual inspected data, I have kept all 
participants (which have an acceptable cortical surface reconstruction rating)  
for the regional variables and I also retained all participants for global 
measures (thickness of mean hemisphere, estimated intracranial volume) as the 
data had been processed and removed from further Freesurfer processing if they 
had severe artifacts or irregularities.

Many thanks for your advice.

On Thursday, November 19, 2020, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Stephanie

Sorry, I think I misunderstood. If you have visually inspected the analysis 
results and think that they are accurate then you definitely should leave those 
subjects in

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Stephanie K
Sent: Thursday, November 19, 2020 4:19 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Mean thickness estimation {Disarmed}


External Email - Use Caution
Hi Bruce,

Is it also necessary to remove outliers (eg. 3 SD from the mean) for  
Freesurfer structural measures of MRI images that have been visually inspected 
as a further data cleaning step?

I really appreciate your help.

Thanks

On Thu, Nov 19, 2020 at 3:55 PM Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Stephanie

I think that is always a  good idea, unless for some reason it isn’t possible

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Stephanie K
Sent: Thursday, November 19, 2020 2:14 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Mean thickness estimation


External Email - Use Caution
Hi Bruce,

Thanks for the prompt reply. It is my understanding that l_thickness, 
r_thickness and estimated intracranial volume are accurately measured. Would I 
still need to identify and remove outliers if visual inspection of the images 
has not been done?

Many thanks,
Stephanie

On Wed, Nov 18, 2020 at 5:24 PM Stephanie K 
mailto:rklin...@gmail.com>> wrote:
Hi,
I want to estimate the mean cortical thickness. For this I have summed the 
thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, 
I also have the average mean thickness of left and right hemispheres (direct 
output variables of Freesurfer). As there is no visual inspection of the 
imaging in the particular cohort, I remove measures that are 3 standard 
deviations above or below the mean. Hence, I may expect more outliers to be 
removed when I take the average across the regions. I am using these brain 
measures as outcomes in association analyses with the genetic score as the 
exposure. For the mean thickness (averaged across the left and right hemisphere 
thickness variables of freesurfer after removing outliers), the regression 
coefficients have a smaller standard deviation than with thickness averaged 
across the 34 regions. I’m not sure which one to use - which one is more 
accurate? When I look at the mean thickness (which I derived using 34 regions) 
and it’s standard deviation, it is similar to that of the average mean 
thickness across the two hemispheres as well as the standard deviation of that. 
Can you suggest what is most accurate please and what the difference is between 
the mean thickness across the two hemispheres obtained from freesurfer and 
those calculated across the regions? Why does one r

Re: [Freesurfer] Mean thickness estimation {Disarmed}

[Stephanie K]

External Email - Use Caution

Hi Bruce,

No, I don’t think that you’ve misunderstood. I was asking about cohorts
that had not been visually inspected in my first message and then in my
last message I wanted to check that I didn’t need to also remove people
from visually inspected data based on statistical outliers (as a further
step). In conclusion, from what I’ve understood: if there is no visual
inspection of data, it is best to remove statistical outliers (based on
standard deviations) even for global measures such estimated intracranial
volume, mean thickness from left and right hemispheres. When data is
visually inspected, there is no need to remove any data based on
statistical outliers even if those exist as these should be good quality.
For the visual inspected data, I have kept all participants (which have an
acceptable cortical surface reconstruction rating)  for the regional
variables and I also retained all participants for global measures
(thickness of mean hemisphere, estimated intracranial volume) as the data
had been processed and removed from further Freesurfer processing if they
had severe artifacts or irregularities.

Many thanks for your advice.

On Thursday, November 19, 2020, Fischl, Bruce 
wrote:

> Hi Stephanie
>
>
>
> Sorry, I think I misunderstood. If you have visually inspected the
> analysis results and think that they are accurate then you definitely
> should leave those subjects in
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Stephanie K
> *Sent:* Thursday, November 19, 2020 4:19 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Mean thickness estimation {Disarmed}
>
>
>
> *External Email - Use Caution*
>
> Hi Bruce,
>
>
>
> Is it also necessary to remove outliers (eg. 3 SD from the mean)
> for  Freesurfer structural measures of MRI images that have been visually
> inspected as a further data cleaning step?
>
>
>
> I really appreciate your help.
>
>
>
> Thanks
>
>
>
> On Thu, Nov 19, 2020 at 3:55 PM Fischl, Bruce 
> wrote:
>
> Hi Stephanie
>
>
>
> I think that is always a  good idea, unless for some reason it isn’t
> possible
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Stephanie K
> *Sent:* Thursday, November 19, 2020 2:14 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Mean thickness estimation
>
>
>
> *External Email - Use Caution*
>
> Hi Bruce,
>
>
>
> Thanks for the prompt reply. It is my understanding that l_thickness,
> r_thickness and estimated intracranial volume are accurately measured.
> Would I still need to identify and remove outliers if visual inspection of
> the images has not been done?
>
>
>
> Many thanks,
>
> Stephanie
>
>
>
> On Wed, Nov 18, 2020 at 5:24 PM Stephanie K  wrote:
>
> Hi,
>
> I want to estimate the mean cortical thickness. For this I have summed the
> thickness across all 34 regions mapped to the Desikan-Killiany atlas.
> However, I also have the average mean thickness of left and right
> hemispheres (direct output variables of Freesurfer). As there is no visual
> inspection of the imaging in the particular cohort, I remove measures that
> are 3 standard deviations above or below the mean. Hence, I may expect more
> outliers to be removed when I take the average across the regions. I am
> using these brain measures as outcomes in association analyses with the
> genetic score as the exposure. For the mean thickness (averaged across the
> left and right hemisphere thickness variables of freesurfer after removing
> outliers), the regression coefficients have a smaller standard deviation
> than with thickness averaged across the 34 regions. I’m not sure which one
> to use - which one is more accurate? When I look at the mean thickness
> (which I derived using 34 regions) and it’s standard deviation, it is
> similar to that of the average mean thickness across the two hemispheres as
> well as the standard deviation of that. Can you suggest what is most
> accurate please and what the difference is between the mean thickness
> across the two hemispheres obtained from freesurfer and those calculated
> across the regions? Why does one result in more precision than in the other?
>
>
>
> Thank you!
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to

Re: [Freesurfer] Mean thickness estimation {Disarmed}

[Fischl, Bruce]

Hi Stephanie

Sorry, I think I misunderstood. If you have visually inspected the analysis 
results and think that they are accurate then you definitely should leave those 
subjects in

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stephanie K
Sent: Thursday, November 19, 2020 4:19 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Mean thickness estimation {Disarmed}


External Email - Use Caution
Hi Bruce,

Is it also necessary to remove outliers (eg. 3 SD from the mean) for  
Freesurfer structural measures of MRI images that have been visually inspected 
as a further data cleaning step?

I really appreciate your help.

Thanks

On Thu, Nov 19, 2020 at 3:55 PM Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Stephanie

I think that is always a  good idea, unless for some reason it isn’t possible

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Stephanie K
Sent: Thursday, November 19, 2020 2:14 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Mean thickness estimation


External Email - Use Caution
Hi Bruce,

Thanks for the prompt reply. It is my understanding that l_thickness, 
r_thickness and estimated intracranial volume are accurately measured. Would I 
still need to identify and remove outliers if visual inspection of the images 
has not been done?

Many thanks,
Stephanie

On Wed, Nov 18, 2020 at 5:24 PM Stephanie K 
mailto:rklin...@gmail.com>> wrote:
Hi,
I want to estimate the mean cortical thickness. For this I have summed the 
thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, 
I also have the average mean thickness of left and right hemispheres (direct 
output variables of Freesurfer). As there is no visual inspection of the 
imaging in the particular cohort, I remove measures that are 3 standard 
deviations above or below the mean. Hence, I may expect more outliers to be 
removed when I take the average across the regions. I am using these brain 
measures as outcomes in association analyses with the genetic score as the 
exposure. For the mean thickness (averaged across the left and right hemisphere 
thickness variables of freesurfer after removing outliers), the regression 
coefficients have a smaller standard deviation than with thickness averaged 
across the 34 regions. I’m not sure which one to use - which one is more 
accurate? When I look at the mean thickness (which I derived using 34 regions) 
and it’s standard deviation, it is similar to that of the average mean 
thickness across the two hemispheres as well as the standard deviation of that. 
Can you suggest what is most accurate please and what the difference is between 
the mean thickness across the two hemispheres obtained from freesurfer and 
those calculated across the regions? Why does one result in more precision than 
in the other?

Thank you!
___
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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
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Re: [Freesurfer] Mean thickness estimation {Disarmed}

[Stephanie K]

External Email - Use Caution

Hi Bruce,

Is it also necessary to remove outliers (eg. 3 SD from the mean)
for  Freesurfer structural measures of MRI images that have been visually
inspected as a further data cleaning step?

I really appreciate your help.

Thanks

On Thu, Nov 19, 2020 at 3:55 PM Fischl, Bruce 
wrote:

> Hi Stephanie
>
>
>
> I think that is always a  good idea, unless for some reason it isn’t
> possible
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Stephanie K
> *Sent:* Thursday, November 19, 2020 2:14 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Mean thickness estimation
>
>
>
> *External Email - Use Caution*
>
> Hi Bruce,
>
>
>
> Thanks for the prompt reply. It is my understanding that l_thickness,
> r_thickness and estimated intracranial volume are accurately measured.
> Would I still need to identify and remove outliers if visual inspection of
> the images has not been done?
>
>
>
> Many thanks,
>
> Stephanie
>
>
>
> On Wed, Nov 18, 2020 at 5:24 PM Stephanie K  wrote:
>
> Hi,
>
> I want to estimate the mean cortical thickness. For this I have summed the
> thickness across all 34 regions mapped to the Desikan-Killiany atlas.
> However, I also have the average mean thickness of left and right
> hemispheres (direct output variables of Freesurfer). As there is no visual
> inspection of the imaging in the particular cohort, I remove measures that
> are 3 standard deviations above or below the mean. Hence, I may expect more
> outliers to be removed when I take the average across the regions. I am
> using these brain measures as outcomes in association analyses with the
> genetic score as the exposure. For the mean thickness (averaged across the
> left and right hemisphere thickness variables of freesurfer after removing
> outliers), the regression coefficients have a smaller standard deviation
> than with thickness averaged across the 34 regions. I’m not sure which one
> to use - which one is more accurate? When I look at the mean thickness
> (which I derived using 34 regions) and it’s standard deviation, it is
> similar to that of the average mean thickness across the two hemispheres as
> well as the standard deviation of that. Can you suggest what is most
> accurate please and what the difference is between the mean thickness
> across the two hemispheres obtained from freesurfer and those calculated
> across the regions? Why does one result in more precision than in the other?
>
>
>
> Thank you!
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1KPUR-tLJEURgzYmremNK46BwlQzhr2HuE-Vgj0d_IfX_gecAUGN6QjCWYLIn3brTZNmVndmFck4JXbECP-4ChBCCB9on11GCIcDXo_CeNsBG78TW3Un3dAkQZk9obRuWPnrYHXzp4kS7t-Y4GsaRBH04naRD0rppbxKez7XlIyHvl1NMwlQaEMRHOk6FqYoTIVHV6UrlC5oR6DZFRClnWLATwzWDCvj5zCYsdJ7pt7xmr1fz3Jml3iS6BjOivmfV4vWBZ-x-rpFZ_zoHRv07WA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Re: [Freesurfer] Mean thickness estimation

[Fischl, Bruce]

Hi Stephanie

I think that is always a  good idea, unless for some reason it isn’t possible

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stephanie K
Sent: Thursday, November 19, 2020 2:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Mean thickness estimation


External Email - Use Caution
Hi Bruce,

Thanks for the prompt reply. It is my understanding that l_thickness, 
r_thickness and estimated intracranial volume are accurately measured. Would I 
still need to identify and remove outliers if visual inspection of the images 
has not been done?

Many thanks,
Stephanie

On Wed, Nov 18, 2020 at 5:24 PM Stephanie K 
mailto:rklin...@gmail.com>> wrote:
Hi,
I want to estimate the mean cortical thickness. For this I have summed the 
thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, 
I also have the average mean thickness of left and right hemispheres (direct 
output variables of Freesurfer). As there is no visual inspection of the 
imaging in the particular cohort, I remove measures that are 3 standard 
deviations above or below the mean. Hence, I may expect more outliers to be 
removed when I take the average across the regions. I am using these brain 
measures as outcomes in association analyses with the genetic score as the 
exposure. For the mean thickness (averaged across the left and right hemisphere 
thickness variables of freesurfer after removing outliers), the regression 
coefficients have a smaller standard deviation than with thickness averaged 
across the 34 regions. I’m not sure which one to use - which one is more 
accurate? When I look at the mean thickness (which I derived using 34 regions) 
and it’s standard deviation, it is similar to that of the average mean 
thickness across the two hemispheres as well as the standard deviation of that. 
Can you suggest what is most accurate please and what the difference is between 
the mean thickness across the two hemispheres obtained from freesurfer and 
those calculated across the regions? Why does one result in more precision than 
in the other?

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

Re: [Freesurfer] Mean thickness estimation

[Stephanie K]

External Email - Use Caution

Hi Bruce,

Thanks for the prompt reply. It is my understanding that l_thickness,
r_thickness and estimated intracranial volume are accurately measured.
Would I still need to identify and remove outliers if visual inspection of
the images has not been done?

Many thanks,
Stephanie

On Wed, Nov 18, 2020 at 5:24 PM Stephanie K  wrote:

> Hi,
> I want to estimate the mean cortical thickness. For this I have summed the
> thickness across all 34 regions mapped to the Desikan-Killiany atlas.
> However, I also have the average mean thickness of left and right
> hemispheres (direct output variables of Freesurfer). As there is no visual
> inspection of the imaging in the particular cohort, I remove measures that
> are 3 standard deviations above or below the mean. Hence, I may expect more
> outliers to be removed when I take the average across the regions. I am
> using these brain measures as outcomes in association analyses with the
> genetic score as the exposure. For the mean thickness (averaged across the
> left and right hemisphere thickness variables of freesurfer after removing
> outliers), the regression coefficients have a smaller standard deviation
> than with thickness averaged across the 34 regions. I’m not sure which one
> to use - which one is more accurate? When I look at the mean thickness
> (which I derived using 34 regions) and it’s standard deviation, it is
> similar to that of the average mean thickness across the two hemispheres as
> well as the standard deviation of that. Can you suggest what is most
> accurate please and what the difference is between the mean thickness
> across the two hemispheres obtained from freesurfer and those calculated
> across the regions? Why does one result in more precision than in the other?
>
> Thank you!
>
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Mean thickness estimation

[Fischl, Bruce]

Hi Stephanie

By using the average/std within region, then averaging those, you are weighting 
small regions more. I would just use the average/std across cortex.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stephanie K
Sent: Wednesday, November 18, 2020 12:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Mean thickness estimation


External Email - Use Caution
Hi,
I want to estimate the mean cortical thickness. For this I have summed the 
thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, 
I also have the average mean thickness of left and right hemispheres (direct 
output variables of Freesurfer). As there is no visual inspection of the 
imaging in the particular cohort, I remove measures that are 3 standard 
deviations above or below the mean. Hence, I may expect more outliers to be 
removed when I take the average across the regions. I am using these brain 
measures as outcomes in association analyses with the genetic score as the 
exposure. For the mean thickness (averaged across the left and right hemisphere 
thickness variables of freesurfer after removing outliers), the regression 
coefficients have a smaller standard deviation than with thickness averaged 
across the 34 regions. I’m not sure which one to use - which one is more 
accurate? When I look at the mean thickness (which I derived using 34 regions) 
and it’s standard deviation, it is similar to that of the average mean 
thickness across the two hemispheres as well as the standard deviation of that. 
Can you suggest what is most accurate please and what the difference is between 
the mean thickness across the two hemispheres obtained from freesurfer and 
those calculated across the regions? Why does one result in more precision than 
in the other?

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

[Freesurfer] Mean thickness estimation

[Stephanie K]

External Email - Use Caution

Hi,
I want to estimate the mean cortical thickness. For this I have summed the
thickness across all 34 regions mapped to the Desikan-Killiany atlas.
However, I also have the average mean thickness of left and right
hemispheres (direct output variables of Freesurfer). As there is no visual
inspection of the imaging in the particular cohort, I remove measures that
are 3 standard deviations above or below the mean. Hence, I may expect more
outliers to be removed when I take the average across the regions. I am
using these brain measures as outcomes in association analyses with the
genetic score as the exposure. For the mean thickness (averaged across the
left and right hemisphere thickness variables of freesurfer after removing
outliers), the regression coefficients have a smaller standard deviation
than with thickness averaged across the 34 regions. I’m not sure which one
to use - which one is more accurate? When I look at the mean thickness
(which I derived using 34 regions) and it’s standard deviation, it is
similar to that of the average mean thickness across the two hemispheres as
well as the standard deviation of that. Can you suggest what is most
accurate please and what the difference is between the mean thickness
across the two hemispheres obtained from freesurfer and those calculated
across the regions? Why does one result in more precision than in the other?

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

Re: [Freesurfer] Mean thickness values from sig.mgh

[Greve, Douglas N.,Ph.D.]

you will have to create a binary mask from the sig map by thresholding at a 
given level, eg,
mri_binarize --i sig.mgh --min 2 --o sig.bin2.mgh
Then run
mri_segstats --i y.mgh --seg sig.bin2.mgh --id 1 --avgwf y.bin2.dat
where y.mgh is the --y input to mri_glmfit
--id 1 means to take the forground of sig.bin2.mgh
y.bin2.dat will be a text file with the mean of y for each subject in the 
binarized map



On 1/22/2020 9:32 AM, Amrita Bedi wrote:

External Email - Use Caution

Hello Freesurfer developers,

I wanted to extract mean thickness values of all participants from the 
uncorrected significance maps obtained from mri glmfit for structural data 
instead of extracting it from the corrected maps from glmfit sim. Is there a 
way to do this?

Thank you.

Amrita



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[Freesurfer] Mean thickness values from sig.mgh

[Amrita Bedi]

External Email - Use Caution

Hello Freesurfer developers,

I wanted to extract mean thickness values of all participants from the
uncorrected significance maps obtained from mri glmfit for structural data
instead of extracting it from the corrected maps from glmfit sim. Is there
a way to do this?

Thank you.

Amrita
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Re: [Freesurfer] mean thickness

[Douglas N Greve]

the table file lh.aparc.thickness.table should be an ascii file. when you look 
at it with cat/more/less, what do you see? Can you send that table file?



On 03/07/2016 04:33 AM, Caroline Beelen wrote:
> Hi Bruce,
>
> I'm a beginner in FS, so I just followed tutorial instructions for generating 
> the files carefully...
> I generated it by typing in for instance (after recon-all process was done): 
> aparcstats2table --hemi lh --meas thickness --subjects A01_T1 A02_T1 etc... 
> A10_T1 --tablefile lh.aparc.thickness.table followed by the command: gnumeric 
> lh.aparc.thickness.table
>
> It's a linux pc with Ubuntu 12.04 LTS (processor intel core i7-3770 CPU @ 
> 3.4GHz x 8)
>
> Attached the log file (A09).
>
> Thank you very much!
>
> Greetings, Caroline
>
> -Oorspronkelijk bericht-
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
> Verzonden: zondag 6 maart 2016 16:14
> Aan: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Onderwerp: Re: [Freesurfer] mean thickness
>
> Hi Caroline
>
> how  did you generate the Gnumeric file? And what operating system/hardware 
> are you using? Also, please send us the recon-all.log for one of the subjects 
> that you see this happening
>
> cheers
> Bruce
>
> On Fri, 4 Mar 2016,
> Caroline Beelen wrote:
>
>> Dear Freesurfer team,
>>
>>   
>>
>> Forgive me if this is a foolish question…
>>
>>   
>>
>> I wanted to overlook cortical thickness, area and volume measures in
>> Gnumeric file after recon-all (checking edits made). However, for
>> several subjects I noticed that the values of mean thickness (final
>> column) were calculated wrong, whereas this is not the case for their
>> independent cortical thickness values. For instance, this happened to
>> subject A09. I’m including the excel file to show the example. In the
>> gnumeric file the number for this subject was depicted as 2/4964
>> instead of 2.4 etc.. What could have went wrong?
>>
>>   
>>
>> Thank you for your answer in advance.
>>
>>   
>>
>> Kind regards, Caroline
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mean thickness

[Bruce Fischl]

Hi Caroline

how  did you generate the Gnumeric file? And what operating 
system/hardware are you using? Also, please send us the recon-all.log for 
one of the subjects that you see this happening


cheers
Bruce

On Fri, 4 Mar 2016, 
Caroline Beelen wrote:




Dear Freesurfer team,

 

Forgive me if this is a foolish question…

 

I wanted to overlook cortical thickness, area and volume measures in
Gnumeric file after recon-all (checking edits made). However, for several
subjects I noticed that the values of mean thickness (final column) were
calculated wrong, whereas this is not the case for their independent
cortical thickness values. For instance, this happened to subject A09. I’m
including the excel file to show the example. In the gnumeric file the
number for this subject was depicted as 2/4964 instead of 2.4 etc.. What
could have went wrong?

 

Thank you for your answer in advance.

 

Kind regards, Caroline


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mean thickness

[Caroline Beelen]

Dear Freesurfer team,

Forgive me if this is a foolish question...

I wanted to overlook cortical thickness, area and volume measures in Gnumeric 
file after recon-all (checking edits made). However, for several subjects I 
noticed that the values of mean thickness (final column) were calculated wrong, 
whereas this is not the case for their independent cortical thickness values. 
For instance, this happened to subject A09. I'm including the excel file to 
show the example. In the gnumeric file the number for this subject was depicted 
as 2/4964 instead of 2.4 etc.. What could have went wrong?

Thank you for your answer in advance.

Kind regards, Caroline


Map1.xlsx
Description: Map1.xlsx
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

[amirhossein manzouri]

Thanks Doug,
I used the first link and works perfectly now!

Best regards,
Amirhossein Manzouri





On Tue, May 20, 2014 at 5:03 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:


 I just ran it, and it works fine. It may be that I need to give you more
 libraries.

 Start with this one
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsutils.py

 Copy it into $FREESURFER_HOME/bin (after making a backup of the original
 one)

 If that still does not work, then copy this one

 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsutils.pyc

 doug



 On 05/20/2014 04:36 AM, amirhossein manzouri wrote:

 Dear Doug,
 Kindly find attached a sample of my lh.aparc.stats file!

 Best regards,
 Amirhossein Manzouri




 On Mon, May 19, 2014 at 7:59 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:

 Can you send me your lh.aparc.stats file?
 doug


 On 05/14/2014 01:41 PM, amirhossein manzouri wrote:


 Yes!


 On May 14, 2014 7:16 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:


 Is the mean thickness in the ?h.aparc.stats file?
 Something like

 # Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm


 On 05/13/2014 05:18 PM, amirhossein manzouri wrote:

 Hi,
 The same result! the last is insula !


 Best regards,
 Amirhossein Manzouri




 On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu

 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:

 Try this version
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/
 greve/aparcstats2table



 On 05/12/2014 03:41 AM, amirhossein manzouri wrote:

 Hi again,
 I think I missed my question, How can I get
 the Mean
 Thickness
 of each hemisphere for several subjects using the
 aparcstats2table command?

 On Fri, May 9, 2014 at 4:28 PM, amirhossein
 manzouri
 a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com wrote:

 Dear Doug,
 I have read this
  post(
 https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html
 )
 regarding
 extracting Mean Cth of each hemisphere and
 I just get
 insula as
 the last and totally 34 numbers, I use
 aparcstats2table --hemi lh --subjects bert -m
 thickness
 --tablefile lh.Cth.bert.txt



 Best regards,
 Amirhossein Manzouri




 -- Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu

 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 tel:617-724-2358
 tel:617-724-2358 tel:617-724-2358
 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358
 tel:617-724-2358
 Fax: 617-726-7422 tel:617-726-7422
 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422
 tel:617-726-7422

 tel:617-726-7422 tel:617-726-7422


 Bugs:
 surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

[amirhossein manzouri]

Dear Doug,
Kindly find attached a sample of my lh.aparc.stats file!

Best regards,
Amirhossein Manzouri





On Mon, May 19, 2014 at 7:59 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 Can you send me your lh.aparc.stats file?
 doug


 On 05/14/2014 01:41 PM, amirhossein manzouri wrote:


 Yes!


 On May 14, 2014 7:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:
 gr...@nmr.mgh.harvard.edu wrote:


 Is the mean thickness in the ?h.aparc.stats file? Something like

 # Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm


 On 05/13/2014 05:18 PM, amirhossein manzouri wrote:

 Hi,
 The same result! the last is insula !


 Best regards,
 Amirhossein Manzouri




 On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu

 mailto:gr...@nmr.mgh.harvard.edu wrote:

 Try this version
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/
 greve/aparcstats2table



 On 05/12/2014 03:41 AM, amirhossein manzouri wrote:

 Hi again,
 I think I missed my question, How can I get the Mean
 Thickness
 of each hemisphere for several subjects using the
 aparcstats2table command?

 On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri
 a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com wrote:

 Dear Doug,
 I have read this
   post(https://www.mail-archive.
 com/freesurfer@nmr.mgh.harvard.edu/msg25218.html)
 regarding
 extracting Mean Cth of each hemisphere and I just get
 insula as
 the last and totally 34 numbers, I use
 aparcstats2table --hemi lh --subjects bert -m
 thickness
 --tablefile lh.Cth.bert.txt



 Best regards,
 Amirhossein Manzouri




 -- Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu

 mailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 tel:617-724-2358
 tel:617-724-2358 tel:617-724-2358
 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422

 tel:617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



 The information in this e-mail is intended only for the
 person to
 whom it is
 addressed. If you believe this e-mail was sent to you in
 error and
 the e-mail
 contains patient information, please contact the Partners
 Compliance HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent
 to
 you in error
 but does not contain patient information, please contact the
 sender and properly
 dispose of the e-mail.



 -- Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 tel:617-724-2358
 Fax: 617-726-7422 tel:617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/




lh.aparc.stats
Description: Binary data
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Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

[Douglas N Greve]

Can you send me your lh.aparc.stats file?
doug

On 05/14/2014 01:41 PM, amirhossein manzouri wrote:

 Yes!

 On May 14, 2014 7:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:


 Is the mean thickness in the ?h.aparc.stats file? Something like

 # Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm


 On 05/13/2014 05:18 PM, amirhossein manzouri wrote:

 Hi,
 The same result! the last is insula !


 Best regards,
 Amirhossein Manzouri




 On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:

 Try this version
 
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/aparcstats2table



 On 05/12/2014 03:41 AM, amirhossein manzouri wrote:

 Hi again,
 I think I missed my question, How can I get the Mean
 Thickness
 of each hemisphere for several subjects using the
 aparcstats2table command?

 On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri
 a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com wrote:

 Dear Doug,
 I have read this
  
  
 post(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html)
 regarding
 extracting Mean Cth of each hemisphere and I just get
 insula as
 the last and totally 34 numbers, I use
 aparcstats2table --hemi lh --subjects bert -m
 thickness
 --tablefile lh.Cth.bert.txt



 Best regards,
 Amirhossein Manzouri




 -- Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 tel:617-724-2358
 tel:617-724-2358 tel:617-724-2358
 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422
 tel:617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



 The information in this e-mail is intended only for the
 person to
 whom it is
 addressed. If you believe this e-mail was sent to you in
 error and
 the e-mail
 contains patient information, please contact the Partners
 Compliance HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to
 you in error
 but does not contain patient information, please contact the
 sender and properly
 dispose of the e-mail.



 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 tel:617-724-2358
 Fax: 617-726-7422 tel:617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

[Douglas N Greve]

Is the mean thickness in the ?h.aparc.stats file? Something like

# Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm


On 05/13/2014 05:18 PM, amirhossein manzouri wrote:
 Hi,
 The same result! the last is insula !


 Best regards,
 Amirhossein Manzouri




 On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:

 Try this version
 
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/aparcstats2table



 On 05/12/2014 03:41 AM, amirhossein manzouri wrote:

 Hi again,
 I think I missed my question, How can I get the Mean Thickness
 of each hemisphere for several subjects using the
 aparcstats2table command?

 On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri
 a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com wrote:

 Dear Doug,
 I have read this

 
 post(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html)
 regarding
 extracting Mean Cth of each hemisphere and I just get
 insula as
 the last and totally 34 numbers, I use
 aparcstats2table --hemi lh --subjects bert -m thickness
 --tablefile lh.Cth.bert.txt



 Best regards,
 Amirhossein Manzouri




 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 tel:617-724-2358
 Fax: 617-726-7422 tel:617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



 The information in this e-mail is intended only for the person to
 whom it is
 addressed. If you believe this e-mail was sent to you in error and
 the e-mail
 contains patient information, please contact the Partners
 Compliance HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to
 you in error
 but does not contain patient information, please contact the
 sender and properly
 dispose of the e-mail.



-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

[amirhossein manzouri]

Yes!
On May 14, 2014 7:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:


 Is the mean thickness in the ?h.aparc.stats file? Something like

 # Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm


 On 05/13/2014 05:18 PM, amirhossein manzouri wrote:

 Hi,
 The same result! the last is insula !


 Best regards,
 Amirhossein Manzouri




 On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:

 Try this version
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/
 greve/aparcstats2table



 On 05/12/2014 03:41 AM, amirhossein manzouri wrote:

 Hi again,
 I think I missed my question, How can I get the Mean Thickness
 of each hemisphere for several subjects using the
 aparcstats2table command?

 On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri
 a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com
 mailto:a.h.manzo...@gmail.com wrote:

 Dear Doug,
 I have read this
post(https://www.mail-archive.com/freesurfer@nmr.mgh.
 harvard.edu/msg25218.html)
 regarding
 extracting Mean Cth of each hemisphere and I just get
 insula as
 the last and totally 34 numbers, I use
 aparcstats2table --hemi lh --subjects bert -m thickness
 --tablefile lh.Cth.bert.txt



 Best regards,
 Amirhossein Manzouri




 -- Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 tel:617-724-2358
 Fax: 617-726-7422 tel:617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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 the e-mail
 contains patient information, please contact the Partners
 Compliance HelpLine at
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

[amirhossein manzouri]

Hi,
The same result! the last is insula !


Best regards,
Amirhossein Manzouri





On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 Try this version
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/
 greve/aparcstats2table


 On 05/12/2014 03:41 AM, amirhossein manzouri wrote:

 Hi again,
 I think I missed my question, How can I get the Mean Thickness of each
 hemisphere for several subjects using the aparcstats2table command?

 On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri 
 a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com wrote:

 Dear Doug,
 I have read this
 post(https://www.mail-archive.com/freesurfer@nmr.mgh.
 harvard.edu/msg25218.html) regarding
 extracting Mean Cth of each hemisphere and I just get insula as
 the last and totally 34 numbers, I use
 aparcstats2table --hemi lh --subjects bert -m thickness
 --tablefile lh.Cth.bert.txt



 Best regards,
 Amirhossein Manzouri




 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



 The information in this e-mail is intended only for the person to whom it
 is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
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Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

[amirhossein manzouri]

Hi again,
I think I missed my question, How can I get the Mean Thickness of each
hemisphere for several subjects using the aparcstats2table command?

On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri a.h.manzo...@gmail.com
 wrote:

 Dear Doug,
 I have read this post(
 https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html) 
 regarding
 extracting Mean Cth of each hemisphere and I just get insula as the last
 and totally 34 numbers, I use
 aparcstats2table --hemi lh --subjects bert -m thickness --tablefile
 lh.Cth.bert.txt



 Best regards,
 Amirhossein Manzouri




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Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

[Douglas N Greve]

Try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/aparcstats2table

On 05/12/2014 03:41 AM, amirhossein manzouri wrote:
 Hi again,
 I think I missed my question, How can I get the Mean Thickness of each 
 hemisphere for several subjects using the aparcstats2table command?

 On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri 
 a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com wrote:

 Dear Doug,
 I have read this
 
 post(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html)
  regarding
 extracting Mean Cth of each hemisphere and I just get insula as
 the last and totally 34 numbers, I use
 aparcstats2table --hemi lh --subjects bert -m thickness
 --tablefile lh.Cth.bert.txt



 Best regards,
 Amirhossein Manzouri




-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

[amirhossein manzouri]

Dear Doug,
I have read this post(
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html)
regarding
extracting Mean Cth of each hemisphere and I just get insula as the last
and totally 34 numbers, I use
aparcstats2table --hemi lh --subjects bert -m thickness --tablefile
lh.Cth.bert.txt



Best regards,
Amirhossein Manzouri
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mean thickness over hemisphere in stats file

[Bruce Fischl]

Hi Ines

sorry, this was my mistake. The command is mris_anatomical_stats NOT 
mris_anatomical_thickness. If your SUBJECTS_DIR is set properly, you can 
run:


mris_anatomical_stats -l $SUBJECTS_DIR/$subject/label/$hemi.cortex \
   $subject $hemi

where $hemi is lh or rh and $subject is the subject id you want to quantify

cheers
Bruce


On Mon, 12 Aug 2013, Mürner-Lavanchy, Ines wrote:




From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, 9 August 2013 3:36 PM
To: Mürner-Lavanchy, Ines
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mean thickness over hemisphere in stats file

Hi Ines

I think mris_anatomical_thickness is your best bet. You probably want to
specify the ?h.cortex.label file with the -l flag so that it ignores
non-cortical regions

cheers
Bruce


On Fri, 9 Aug 2013, Mürner-Lavanchy, Ines wrote:


Dear experts,

please excuse my question, I'm a beginner. I really searched for an answer
in the archive, but I couldn't find out what I was doing wrong.

I would like to write the mean cortical thickness of a hemisphere in the
stats file. I read one can do that by using -m thickness.
Where in the command line do I have to put it? I tried various versions, but
it doesn't work.

This would be the command:

aparcstats2table --hemi rh --parc aparc --meas thickness --tablefile
directory//filename --m thickness --subjects 1 2 3 4
SUBJECTS_DIR : directory

Where do I include the -m thickness option? Or do I have to add something
else?

Thank you very much for your help,
Ines





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[Freesurfer] mean thickness over hemisphere in stats file

[Mürner-Lavanchy , Ines]

Dear experts,

please excuse my question, I'm a beginner. I really searched for an answer in 
the archive, but I couldn't find out what I was doing wrong.

I would like to write the mean cortical thickness of a hemisphere in the stats 
file. I read one can do that by using -m thickness.
Where in the command line do I have to put it? I tried various versions, but it 
doesn't work.

This would be the command:

aparcstats2table --hemi rh --parc aparc --meas thickness --tablefile 
directory//filename --m thickness --subjects 1 2 3 4
SUBJECTS_DIR : directory

Where do I include the -m thickness option? Or do I have to add something else?

Thank you very much for your help,
Ines
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Re: [Freesurfer] mean thickness over hemisphere in stats file

[Bruce Fischl]

Hi Ines

I think mris_anatomical_thickness is your best bet. You probably want to 
specify the ?h.cortex.label file with the -l flag so that it ignores 
non-cortical regions


cheers
Bruce


On Fri, 9 Aug 2013, Mürner-Lavanchy, Ines wrote:


Dear experts,

please excuse my question, I'm a beginner. I really searched for an answer
in the archive, but I couldn't find out what I was doing wrong.

I would like to write the mean cortical thickness of a hemisphere in the
stats file. I read one can do that by using -m thickness.
Where in the command line do I have to put it? I tried various versions, but
it doesn't work.

This would be the command:

aparcstats2table --hemi rh --parc aparc --meas thickness --tablefile
directory//filename --m thickness --subjects 1 2 3 4
SUBJECTS_DIR : directory

Where do I include the -m thickness option? Or do I have to add something
else?

Thank you very much for your help,
Ines

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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mean thickness over hemisphere in stats file

[Douglas N Greve]

you can also use mri_segstats with the --slabel option (spec 
?h.cortex.label) and the thickness as the input


On 08/09/2013 09:36 AM, Bruce Fischl wrote:
 Hi Ines

 I think mris_anatomical_thickness is your best bet. You probably want 
 to specify the ?h.cortex.label file with the -l flag so that it 
 ignores non-cortical regions

 cheers
 Bruce


 On Fri, 9 Aug 2013, Mürner-Lavanchy, Ines wrote:

 Dear experts,

 please excuse my question, I'm a beginner. I really searched for an 
 answer
 in the archive, but I couldn't find out what I was doing wrong.

 I would like to write the mean cortical thickness of a hemisphere in the
 stats file. I read one can do that by using -m thickness.
 Where in the command line do I have to put it? I tried various 
 versions, but
 it doesn't work.

 This would be the command:

 aparcstats2table --hemi rh --parc aparc --meas thickness --tablefile
 directory//filename --m thickness --subjects 1 2 3 4
 SUBJECTS_DIR : directory

 Where do I include the -m thickness option? Or do I have to add 
 something
 else?

 Thank you very much for your help,
 Ines




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

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mean thickness covariate, mean area covariate, mri_anatomical_stats for multiple subjects

[Laura M. Tully]

Thank you Michael!

LT


On Mon, Mar 11, 2013 at 8:54 AM, Michael Harms mha...@conte.wustl.eduwrote:


 Hi Laura,
 If you're looking for another reference that has used this approach, you
 could see our 2010 paper:
 http://www.ncbi.nlm.nih.gov/pubmed/20118463

 cheers,
 -MH

 --
 Michael Harms, Ph.D.
 ---
 Conte Center for the Neuroscience of Mental Disorders
 Washington University School of Medicine
 Department of Psychiatry, Box 8134
 660 South Euclid Ave. Tel: 314-747-6173
 St. Louis, MO  63110 Email: mha...@wustl.edu

 From: Laura M. Tully tully.la...@googlemail.com
 Date: Saturday, March 9, 2013 5:58 PM
 To: Anderson M. Winkler wink...@fmrib.ox.ac.uk
 Cc: free freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] mean thickness covariate, mean area covariate,
  mri_anatomical_stats for multiple subjects

 Hi Anderson,

 Thanks, that reference is particularly helpful.

 Re: the usage of the white versus pial area question - I believe that the
 default area calculation in freesurfer is the white surface area, so unless
 one specifies the pial in calculations, the standard surface area output
 for surface area by parcellation will be white. This suggests the use of
 the global measurement of white surface area as a covariate would be an
 appropriate, whereas if one was specifically using pial surface area in the
 aparc calculations, it may make more sense to use the global measure of
 pial surface area as a covariate, correct? As for which one to use in
 analysis, I'm not sure - conceptually it might be that the pial surface
 area is more sensitive to atrophy but I don't know if that is born out in
 the data...

 Laura.


 On Sat, Mar 9, 2013 at 11:49 AM, Anderson M. Winkler 
 wink...@fmrib.ox.ac.uk wrote:

 Hi Laura,



1. Is there a paper that I could cite that recommends using mean
cortical thickness rather than ICV?


 If it helps, we used cortical thickness and area as covariate for the
 respective analysis of regional thickness and area. Brain volume, which is
 more closely related to ICV, correlates well with area, but not with
 thickness. We computed a global thickness average by weighting the
 thickness of each region by their respective areas. The paper is this:
 http://surfer.nmr.mgh.harvard.edu/ftp/articles/Winkler2010_Neuroimage.pdf



1. Would the same logic be applied to surface area analyses? i.e.
would it make more sense to use mean surface area as a covariate in 
 surface
area analyses? If so, which mean surface area calculation should be used?
mri_anatomical_stats can produce both pial and white matter mean surface
area stats.


 Yes, I think so. It seems more logical to have a global measurement of
 area in the model than a measurement of brain volume. On the other hand,
 area and thickness are not correlated one to another (as shown in the paper
 above and also in Panizzon et al, 2009, in Cereb Cortex). I don't think
 there is a clear answer on which, pial or white, should be used. I'd
 probably go with the white, as I think it may be more robust to image
 quality, but I admit this is a rather weak justification and if the images
 are good, perhaps the pial could be just as good, despite the fact that it
 somewhat depends on the white for its construction.




1. Is there a way to run mri_anatomical_stats on multiple subjects
at once and write to a tablefile (similar to asegstats2table output)?


 I think you can use aparcstats2table, then add up all regions in a
 spreadsheet (or even with awk/gawk). Alternatively, you can use grep to
 pick the WhiteSurfArea for each hemisphere from the ?h.aparc.stats file for
 each subject.

 Hope this helps!

 All the best,

 Anderson




 --
 --
 Laura M. Tully, MA
 Social Neuroscience  Psychopathology, Harvard University
 Center for the Assessment and Prevention of Prodromal States, UCLA Semel
 Institute of Neuroscience
 ltu...@mednet.ucla.edu
 ltu...@fas.harvard.edu
 310-267-0170
 --
 My musings as a young clinical scientist:
 http://theclinicalbrain.blogspot.com/
 Follow me on Twitter: @tully_laura
 ___ Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The
 information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail contains patient information, please contact the Partners Compliance
 HelpLine at http://www.partners.org/complianceline . If the e-mail was
 sent to you in error but does not contain patient information, please
 contact the sender and properly dispose of the e-mail.




-- 
--
Laura M. Tully, MA
Social Neuroscience  Psychopathology, Harvard University
Center for the Assessment and Prevention of Prodromal States, UCLA Semel
Institute of Neuroscience
ltu...@mednet.ucla.edu
ltu...@fas.harvard.edu
310-267-0170
--
My musings as a young

Re: [Freesurfer] mean thickness covariate, mean area covariate, mri_anatomical_stats for multiple subjects

[Michael Harms]

Hi Laura,
If you're looking for another reference that has used this approach, you
could see our 2010 paper:
http://www.ncbi.nlm.nih.gov/pubmed/20118463

cheers,
-MH

-- 
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From:  Laura M. Tully tully.la...@googlemail.com
Date:  Saturday, March 9, 2013 5:58 PM
To:  Anderson M. Winkler wink...@fmrib.ox.ac.uk
Cc:  free freesurfer@nmr.mgh.harvard.edu
Subject:  Re: [Freesurfer] mean thickness covariate, mean area covariate, 
mri_anatomical_stats for multiple subjects

Hi Anderson, 

Thanks, that reference is particularly helpful.

Re: the usage of the white versus pial area question - I believe that the
default area calculation in freesurfer is the white surface area, so unless
one specifies the pial in calculations, the standard surface area output for
surface area by parcellation will be white. This suggests the use of the
global measurement of white surface area as a covariate would be an
appropriate, whereas if one was specifically using pial surface area in the
aparc calculations, it may make more sense to use the global measure of pial
surface area as a covariate, correct? As for which one to use in analysis,
I'm not sure - conceptually it might be that the pial surface area is more
sensitive to atrophy but I don't know if that is born out in the data...

Laura. 


On Sat, Mar 9, 2013 at 11:49 AM, Anderson M. Winkler
wink...@fmrib.ox.ac.uk wrote:
 Hi Laura,
 
 
 1. Is there a paper that I could cite that recommends using mean cortical
 thickness rather than ICV?
  
 If it helps, we used cortical thickness and area as covariate for the
 respective analysis of regional thickness and area. Brain volume, which is
 more closely related to ICV, correlates well with area, but not with
 thickness. We computed a global thickness average by weighting the thickness
 of each region by their respective areas. The paper is this:
 http://surfer.nmr.mgh.harvard.edu/ftp/articles/Winkler2010_Neuroimage.pdf
  
 1. Would the same logic be applied to surface area analyses? i.e. would it
 make more sense to use mean surface area as a covariate in surface area
 analyses? If so, which mean surface area calculation should be used?
 mri_anatomical_stats can produce both pial and white matter mean surface area
 stats. 
 
 Yes, I think so. It seems more logical to have a global measurement of area in
 the model than a measurement of brain volume. On the other hand, area and
 thickness are not correlated one to another (as shown in the paper above and
 also in Panizzon et al, 2009, in Cereb Cortex). I don't think there is a clear
 answer on which, pial or white, should be used. I'd probably go with the
 white, as I think it may be more robust to image quality, but I admit this is
 a rather weak justification and if the images are good, perhaps the pial could
 be just as good, despite the fact that it somewhat depends on the white for
 its construction.
 
  
 1. Is there a way to run mri_anatomical_stats on multiple subjects at once
 and write to a tablefile (similar to asegstats2table output)?
 
 I think you can use aparcstats2table, then add up all regions in a spreadsheet
 (or even with awk/gawk). Alternatively, you can use grep to pick the
 WhiteSurfArea for each hemisphere from the ?h.aparc.stats file for each
 subject.
 
 Hope this helps!
 
 All the best,
 
 Anderson
 



-- 
--
Laura M. Tully, MA
Social Neuroscience  Psychopathology, Harvard University
Center for the Assessment and Prevention of Prodromal States, UCLA Semel
Institute of Neuroscience
ltu...@mednet.ucla.edu
ltu...@fas.harvard.edu
310-267-0170
--
My musings as a young clinical scientist:
http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura
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[Freesurfer] mean thickness covariate, mean area covariate, mri_anatomical_stats for multiple subjects

[Laura M. Tully]

Hello freesurfers,

It appears that prior discussions on the listserv have recommended using
mean cortical thickness (rather than ICV) as a covariate for thickness
analyses (predominantly recommended by Michael Harms). I have three
questions about this:


   1. Is there a paper that I could cite that recommends using mean
   cortical thickness rather than ICV?
   2. Would the same logic be applied to surface area analyses? i.e. would
   it make more sense to use mean surface area as a covariate in surface area
   analyses? If so, which mean surface area calculation should be used?
   mri_anatomical_stats can produce both pial and white matter mean surface
   area stats.
   3. Is there a way to run mri_anatomical_stats on multiple subjects at
   once and write to a tablefile (similar to asegstats2table output)?

Thanks!

Laura.

-- 
--
Laura M. Tully, MA
Social Neuroscience  Psychopathology, Harvard University
Center for the Assessment and Prevention of Prodromal States, UCLA Semel
Institute of Neuroscience
ltu...@mednet.ucla.edu
ltu...@fas.harvard.edu
310-267-0170
--
Follow me on Twitter: @tully_laura
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] mean thickness covariate, mean area covariate, mri_anatomical_stats for multiple subjects

[Anderson M. Winkler]

Hi Laura,


1. Is there a paper that I could cite that recommends using mean
cortical thickness rather than ICV?


If it helps, we used cortical thickness and area as covariate for the
respective analysis of regional thickness and area. Brain volume, which is
more closely related to ICV, correlates well with area, but not with
thickness. We computed a global thickness average by weighting the
thickness of each region by their respective areas. The paper is this:
http://surfer.nmr.mgh.harvard.edu/ftp/articles/Winkler2010_Neuroimage.pdf



1. Would the same logic be applied to surface area analyses? i.e.
would it make more sense to use mean surface area as a covariate in surface
area analyses? If so, which mean surface area calculation should be used?
mri_anatomical_stats can produce both pial and white matter mean surface
area stats.


Yes, I think so. It seems more logical to have a global measurement of area
in the model than a measurement of brain volume. On the other hand, area
and thickness are not correlated one to another (as shown in the paper
above and also in Panizzon et al, 2009, in Cereb Cortex). I don't think
there is a clear answer on which, pial or white, should be used. I'd
probably go with the white, as I think it may be more robust to image
quality, but I admit this is a rather weak justification and if the images
are good, perhaps the pial could be just as good, despite the fact that it
somewhat depends on the white for its construction.




1. Is there a way to run mri_anatomical_stats on multiple subjects at
once and write to a tablefile (similar to asegstats2table output)?


I think you can use aparcstats2table, then add up all regions in a
spreadsheet (or even with awk/gawk). Alternatively, you can use grep to
pick the WhiteSurfArea for each hemisphere from the ?h.aparc.stats file for
each subject.

Hope this helps!

All the best,

Anderson
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] mean thickness covariate, mean area covariate, mri_anatomical_stats for multiple subjects

[Laura M. Tully]

Hi Anderson,

Thanks, that reference is particularly helpful.

Re: the usage of the white versus pial area question - I believe that the
default area calculation in freesurfer is the white surface area, so unless
one specifies the pial in calculations, the standard surface area output
for surface area by parcellation will be white. This suggests the use of
the global measurement of white surface area as a covariate would be an
appropriate, whereas if one was specifically using pial surface area in the
aparc calculations, it may make more sense to use the global measure of
pial surface area as a covariate, correct? As for which one to use in
analysis, I'm not sure - conceptually it might be that the pial surface
area is more sensitive to atrophy but I don't know if that is born out in
the data...

Laura.


On Sat, Mar 9, 2013 at 11:49 AM, Anderson M. Winkler wink...@fmrib.ox.ac.uk
 wrote:

 Hi Laura,



1. Is there a paper that I could cite that recommends using mean
cortical thickness rather than ICV?


 If it helps, we used cortical thickness and area as covariate for the
 respective analysis of regional thickness and area. Brain volume, which is
 more closely related to ICV, correlates well with area, but not with
 thickness. We computed a global thickness average by weighting the
 thickness of each region by their respective areas. The paper is this:
 http://surfer.nmr.mgh.harvard.edu/ftp/articles/Winkler2010_Neuroimage.pdf



1. Would the same logic be applied to surface area analyses? i.e.
would it make more sense to use mean surface area as a covariate in 
 surface
area analyses? If so, which mean surface area calculation should be used?
mri_anatomical_stats can produce both pial and white matter mean surface
area stats.


 Yes, I think so. It seems more logical to have a global measurement of
 area in the model than a measurement of brain volume. On the other hand,
 area and thickness are not correlated one to another (as shown in the paper
 above and also in Panizzon et al, 2009, in Cereb Cortex). I don't think
 there is a clear answer on which, pial or white, should be used. I'd
 probably go with the white, as I think it may be more robust to image
 quality, but I admit this is a rather weak justification and if the images
 are good, perhaps the pial could be just as good, despite the fact that it
 somewhat depends on the white for its construction.




1. Is there a way to run mri_anatomical_stats on multiple subjects at
once and write to a tablefile (similar to asegstats2table output)?


 I think you can use aparcstats2table, then add up all regions in a
 spreadsheet (or even with awk/gawk). Alternatively, you can use grep to
 pick the WhiteSurfArea for each hemisphere from the ?h.aparc.stats file for
 each subject.

 Hope this helps!

 All the best,

 Anderson




-- 
--
Laura M. Tully, MA
Social Neuroscience  Psychopathology, Harvard University
Center for the Assessment and Prevention of Prodromal States, UCLA Semel
Institute of Neuroscience
ltu...@mednet.ucla.edu
ltu...@fas.harvard.edu
310-267-0170
--
My musings as a young clinical scientist:
http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mean thickness covariate, mean area covariate, mri_anatomical_stats for multiple subjects

[Anderson M. Winkler]

Hi Laura,
I think yes, sounds right. Maybe run both ways and see if the results agree
or differ.
All the best,
Anderson


2013/3/9 Laura M. Tully tully.la...@googlemail.com

 Hi Anderson,

 Thanks, that reference is particularly helpful.

 Re: the usage of the white versus pial area question - I believe that the
 default area calculation in freesurfer is the white surface area, so unless
 one specifies the pial in calculations, the standard surface area output
 for surface area by parcellation will be white. This suggests the use of
 the global measurement of white surface area as a covariate would be an
 appropriate, whereas if one was specifically using pial surface area in the
 aparc calculations, it may make more sense to use the global measure of
 pial surface area as a covariate, correct? As for which one to use in
 analysis, I'm not sure - conceptually it might be that the pial surface
 area is more sensitive to atrophy but I don't know if that is born out in
 the data...

 Laura.


 On Sat, Mar 9, 2013 at 11:49 AM, Anderson M. Winkler 
 wink...@fmrib.ox.ac.uk wrote:

 Hi Laura,



1. Is there a paper that I could cite that recommends using mean
cortical thickness rather than ICV?


 If it helps, we used cortical thickness and area as covariate for the
 respective analysis of regional thickness and area. Brain volume, which is
 more closely related to ICV, correlates well with area, but not with
 thickness. We computed a global thickness average by weighting the
 thickness of each region by their respective areas. The paper is this:
 http://surfer.nmr.mgh.harvard.edu/ftp/articles/Winkler2010_Neuroimage.pdf



1. Would the same logic be applied to surface area analyses? i.e.
would it make more sense to use mean surface area as a covariate in 
 surface
area analyses? If so, which mean surface area calculation should be used?
mri_anatomical_stats can produce both pial and white matter mean surface
area stats.


 Yes, I think so. It seems more logical to have a global measurement of
 area in the model than a measurement of brain volume. On the other hand,
 area and thickness are not correlated one to another (as shown in the paper
 above and also in Panizzon et al, 2009, in Cereb Cortex). I don't think
 there is a clear answer on which, pial or white, should be used. I'd
 probably go with the white, as I think it may be more robust to image
 quality, but I admit this is a rather weak justification and if the images
 are good, perhaps the pial could be just as good, despite the fact that it
 somewhat depends on the white for its construction.




1. Is there a way to run mri_anatomical_stats on multiple subjects
at once and write to a tablefile (similar to asegstats2table output)?


 I think you can use aparcstats2table, then add up all regions in a
 spreadsheet (or even with awk/gawk). Alternatively, you can use grep to
 pick the WhiteSurfArea for each hemisphere from the ?h.aparc.stats file for
 each subject.

 Hope this helps!

 All the best,

 Anderson




 --
 --
 Laura M. Tully, MA
 Social Neuroscience  Psychopathology, Harvard University
 Center for the Assessment and Prevention of Prodromal States, UCLA Semel
 Institute of Neuroscience
 ltu...@mednet.ucla.edu
 ltu...@fas.harvard.edu
 310-267-0170
 --
 My musings as a young clinical scientist:
 http://theclinicalbrain.blogspot.com/
 Follow me on Twitter: @tully_laura

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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mean thickness difference maps

[Kirk, Gregory]

Hi All,  I wanted to clarify a point. Publications of cortical thickness
differences are usually produced with maps called mean thickness
difference maps.
 
I dug through the mail archive but did not find an answer
 
(Q1)
These statistical parametric maps are I assume produced by computing a
mri_glmfit with doss, and a contrast (1 -1 0)  i.e. each class is
fit to a linear model but both have the same slope and the offsets are
different and the inference is on the difference in the intercepts. The
resulting maps are the maps commonly referred to as mean thickness
difference maps ?
 
(Q2) I seem to remember a conversation about how this is done. First
each group is fit to an optimal line, i.e. each group gets a line with
the intercept
and slope to minimize the data fit error, then the average of the slopes
is computed and this average slope is used for each of two new lines,
one for each group, then an intercept is computed for each group such
that with the nonoptimal slope the data fit error is minimized, am I
correct that this is in fact
the procedure.
 
(Q3) Does this in fact give an intercept that is the mean of the
thickness values for each group , the thought experiments I have cooked
say yes but
I have not made a proof ?
 
Thanks
 
Greg
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