Re: [Freesurfer] WM/Pial surfs Problem with SPGRs from 3T GE

[Thomas Fink]

Hey experts,

Thank you very much for your advice!

So I guess my best guess would be to use recon-all with -nuintensitycor-3T
and add an expert option file for "-b 20" and "-n 5".
These flags belong to the "mri_normalize" binary?

Best regards
Thomas


On Thu, Jul 26, 2012 at 4:12 PM, Bruce Fischl wrote:

> Hi Michael
>
> that's a good thought. Let me talk to Nick, and see if we should default
> to it and have a 1.5T flag instead
>
> Bruce
>
> On Thu, 26 Jul 2012, Michael Waskom wrote:
>
>  Yes, that flag still works in 5.1.
>> Bruce, think these parameters could be default in 5.2?  It's a long extra
>> flag (that is, I imagine, someone arcane knowledge) for what has to be the
>> overwhelmingly modal field strength these days.
>>
>> Sorry to hijack, but this would be nice!
>>
>> Cheers,
>> Michael
>>
>> On Wed, Jul 25, 2012 at 10:29 PM, Mehul Sampat 
>> wrote:
>>   Hi Thomas,
>> The following message posted by Michael Harms
>> http://www.mail-archive.com/**freesur...@nmr.mgh.harvard.**
>> edu/msg20991.html
>> has some very useful options. I recently noticed that they help us
>> with a very similar problem...
>>
>> Also, I recall that for FS v5.0 there was a flag -nuintensitycor-3T
>> for "optimal parameters for nu_correct for 3T scans"
>> (as described in release notes for v5.0.)
>>
>> Bruce, the -nuintensitycor-3T is still available in v5.1 right?
>> If yes, then we could combine the options the two set of options and
>> run recon-all with "-b 20 -n 5 and  -nuintensitycor-3T"  for
>> the 3T scans? Would this be reasonable or does this combination not
>> recommended ?
>>
>> Thanks
>> Mehul
>>
>>
>>
>>
>>
>>
>> On Tue, Jul 24, 2012 at 12:47 AM, Thomas Fink
>>  wrote:
>>   Hey Experts,
>>
>>   As you can see from the picture, the autorecon does not
>>   work properly (for WM/Pial surfs) with my files:
>>   Especially in the temporal lobes.
>>
>>   I am working with the SPGR files of a 3T GE Machine.
>>   Is there any way to optimize the autorecon results for
>>   SPGRs?
>>   (Except the lavish application of CPs.)
>>
>>   Best regards
>>   Thomas
>>
>
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Re: [Freesurfer] WM/Pial surfs Problem with SPGRs from 3T GE

[Bruce Fischl]

Hi Michael

that's a good thought. Let me talk to Nick, and see if we should default 
to it and have a 1.5T flag instead


Bruce
On Thu, 26 Jul 2012, Michael Waskom 
wrote:



Yes, that flag still works in 5.1.
Bruce, think these parameters could be default in 5.2?  It's a long extra
flag (that is, I imagine, someone arcane knowledge) for what has to be the
overwhelmingly modal field strength these days.

Sorry to hijack, but this would be nice!

Cheers,
Michael

On Wed, Jul 25, 2012 at 10:29 PM, Mehul Sampat 
wrote:
  Hi Thomas, 
The following message posted by Michael Harms
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20991.html
has some very useful options. I recently noticed that they help us
with a very similar problem...

Also, I recall that for FS v5.0 there was a flag -nuintensitycor-3T
for "optimal parameters for nu_correct for 3T scans"
(as described in release notes for v5.0.)

Bruce, the -nuintensitycor-3T is still available in v5.1 right? 
If yes, then we could combine the options the two set of options and
run recon-all with "-b 20 -n 5 and  -nuintensitycor-3T"  for 
the 3T scans? Would this be reasonable or does this combination not
recommended ?

Thanks
Mehul 

 




On Tue, Jul 24, 2012 at 12:47 AM, Thomas Fink
 wrote:
  Hey Experts,

  As you can see from the picture, the autorecon does not
  work properly (for WM/Pial surfs) with my files:
  Especially in the temporal lobes.

  I am working with the SPGR files of a 3T GE Machine.
  Is there any way to optimize the autorecon results for
  SPGRs?
  (Except the lavish application of CPs.)

  Best regards
  Thomas



  On Mon, Jul 23, 2012 at 6:00 PM,
   wrote:
Send Freesurfer mailing list submissions to
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To subscribe or unsubscribe via the World Wide
Web, visit
       
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or, via email, send a message with subject or
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When replying, please edit your Subject line
so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Re: Questions about correction over 2
hemispheres and MCC
      (Reem Jan)
   2. More than two time-points in
longitudinal base = Memory
      allocation error? (Liz Bowman)
   3. Re: Talairach registration (Mojdeh
Zamyadi)
   4. Subcortical segmentations (Jordan
Pierce)



--

Message: 1
Date: Sun, 22 Jul 2012 21:12:44 +
From: Reem Jan 
Subject: Re: [Freesurfer] Questions about
correction over 2
        hemispheres and MCC
To: "Watson, Christopher"

Cc: Freesurfer Mailinglist

Message-ID:
       

<3375b664d4a0834fb7d0c15d590a9ef11825d...@fmhs-mbx1.fmhs.auckland.ac.nz>

Content-Type: text/plain; charset="iso-8859-1"

Hi Bruce, J?rgen and Chris

Thank you for elaborating further. I've gone
with a Bonferroni correction as I had a
limited number of tests (a-priori hypothesis).
But just out of interest Chris, you mentioned
you found correlations between subcortical
structures, do you have a reference I could
look at? The tool that J?rgen suggested
requires we enter a correlation coefficient,
so I wondered if I could use published values
or whether I'd need to calculate my own (if
so, could you please recommend a way of doing
that in Freesurfer or FSL?)

Many thanks in advance

Kind regards
Reem

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu]
On Behalf Of J?rgen H?nggi
Sent: Sunday, 22 July 2012 7:47 p.m.
To: Watson, Christopher
Cc: Freesurfer Mailinglist
Subject: Re: [Freesurfer] Questions about
correction over 2 hemispheres and MCC

Hi Chris

Yes there are such tools. Bonferroni oder
Sidak test that take into account the
correlated measures. Here you can find these
tools

http://www.quantitativeskills.com/sisa/calculations/bonfer.htm

Cheers
J?rgen


On [DATE], "Wats

Re: [Freesurfer] WM/Pial surfs Problem with SPGRs from 3T GE

[Bruce Fischl]

Hi Mehul

it's really all empirical. You just don't want the intensity 
normalization to erode the gray/white boundary.


cheers
Bruce
On Wed, 25 Jul 2012, Mehul 
Sampat wrote:



Hi Thomas, 
The following message posted by Michael Harms
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20991.html
has some very useful options. I recently noticed that they help us with a
very similar problem...

Also, I recall that for FS v5.0 there was a flag -nuintensitycor-3T for
"optimal parameters for nu_correct for 3T scans"
(as described in release notes for v5.0.)

Bruce, the -nuintensitycor-3T is still available in v5.1 right? 
If yes, then we could combine the options the two set of options and run
recon-all with "-b 20 -n 5 and  -nuintensitycor-3T"  for 
the 3T scans? Would this be reasonable or does this combination not
recommended ?

Thanks
Mehul 

 




On Tue, Jul 24, 2012 at 12:47 AM, Thomas Fink
 wrote:
  Hey Experts,

  As you can see from the picture, the autorecon does not work
  properly (for WM/Pial surfs) with my files:
  Especially in the temporal lobes.

  I am working with the SPGR files of a 3T GE Machine.
  Is there any way to optimize the autorecon results for SPGRs?
  (Except the lavish application of CPs.)

  Best regards
  Thomas



  On Mon, Jul 23, 2012 at 6:00 PM,
   wrote:
Send Freesurfer mailing list submissions to
        freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web,
visit
       
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body
'help' to
        freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
        freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it
is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Re: Questions about correction over 2
hemispheres and MCC
      (Reem Jan)
   2. More than two time-points in longitudinal base
= Memory
      allocation error? (Liz Bowman)
   3. Re: Talairach registration (Mojdeh Zamyadi)
   4. Subcortical segmentations (Jordan Pierce)



--

Message: 1
Date: Sun, 22 Jul 2012 21:12:44 +
From: Reem Jan 
Subject: Re: [Freesurfer] Questions about correction
over 2
        hemispheres and MCC
To: "Watson, Christopher"

Cc: Freesurfer Mailinglist

Message-ID:
       

<3375b664d4a0834fb7d0c15d590a9ef11825d...@fmhs-mbx1.fmhs.auckland.ac.nz>

Content-Type: text/plain; charset="iso-8859-1"

Hi Bruce, J?rgen and Chris

Thank you for elaborating further. I've gone with a
Bonferroni correction as I had a limited number of
tests (a-priori hypothesis). But just out of
interest Chris, you mentioned you found correlations
between subcortical structures, do you have a
reference I could look at? The tool that J?rgen
suggested requires we enter a correlation
coefficient, so I wondered if I could use published
values or whether I'd need to calculate my own (if
so, could you please recommend a way of doing that
in Freesurfer or FSL?)

Many thanks in advance

Kind regards
Reem

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On
Behalf Of J?rgen H?nggi
Sent: Sunday, 22 July 2012 7:47 p.m.
To: Watson, Christopher
Cc: Freesurfer Mailinglist
Subject: Re: [Freesurfer] Questions about correction
over 2 hemispheres and MCC

Hi Chris

Yes there are such tools. Bonferroni oder Sidak test
that take into account the correlated measures. Here
you can find these tools

http://www.quantitativeskills.com/sisa/calculations/bonfer.htm

Cheers
J?rgen


On [DATE], "Watson, Christopher" <[ADDRESS]> wrote:

> What about, for example, the correlations I've
seen in a cohort of subjects.
>
> In 158 subjects aged 10-19 (both controls and
patients), the
> correlation between L & R thalamus is 0.91, and
the correlations
> between L & R of caudate, putamen, pallidum,

Re: [Freesurfer] WM/Pial surfs Problem with SPGRs from 3T GE

[Mehul Sampat]

Hi Thomas,

The following message posted by Michael Harms
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20991.html
has some very useful options. I recently noticed that they help us with a
very similar problem...

Also, I recall that for FS v5.0 there was a flag -nuintensitycor-3T for
"optimal parameters for nu_correct for 3T scans"
(as described in release notes for v5.0.)

Bruce, the -nuintensitycor-3T is still available in v5.1 right?
If yes, then we could combine the options the two set of options and run
recon-all with "-b 20 -n 5 and  -nuintensitycor-3T"  for
the 3T scans? Would this be reasonable or does this combination not
recommended ?

Thanks
Mehul






On Tue, Jul 24, 2012 at 12:47 AM, Thomas Fink  wrote:

> Hey Experts,
>
> As you can see from the picture, the autorecon does not work properly (for
> WM/Pial surfs) with my files:
> Especially in the temporal lobes.
>
> I am working with the SPGR files of a 3T GE Machine.
> Is there any way to optimize the autorecon results for SPGRs?
> (Except the lavish application of CPs.)
>
> Best regards
> Thomas
>
>
>
> On Mon, Jul 23, 2012 at 6:00 PM, 
> wrote:
>
>> Send Freesurfer mailing list submissions to
>> freesurfer@nmr.mgh.harvard.edu
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> or, via email, send a message with subject or body 'help' to
>> freesurfer-requ...@nmr.mgh.harvard.edu
>>
>> You can reach the person managing the list at
>> freesurfer-ow...@nmr.mgh.harvard.edu
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Freesurfer digest..."
>>
>>
>> Today's Topics:
>>
>>1. Re: Questions about correction over 2 hemispheres and MCC
>>   (Reem Jan)
>>2. More than two time-points in longitudinal base = Memory
>>   allocation error? (Liz Bowman)
>>3. Re: Talairach registration (Mojdeh Zamyadi)
>>4. Subcortical segmentations (Jordan Pierce)
>>
>>
>> --
>>
>> Message: 1
>> Date: Sun, 22 Jul 2012 21:12:44 +
>> From: Reem Jan 
>> Subject: Re: [Freesurfer] Questions about correction over 2
>> hemispheres and MCC
>> To: "Watson, Christopher" 
>> Cc: Freesurfer Mailinglist 
>> Message-ID:
>> <
>> 3375b664d4a0834fb7d0c15d590a9ef11825d...@fmhs-mbx1.fmhs.auckland.ac.nz>
>>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi Bruce, J?rgen and Chris
>>
>> Thank you for elaborating further. I've gone with a Bonferroni correction
>> as I had a limited number of tests (a-priori hypothesis). But just out of
>> interest Chris, you mentioned you found correlations between subcortical
>> structures, do you have a reference I could look at? The tool that J?rgen
>> suggested requires we enter a correlation coefficient, so I wondered if I
>> could use published values or whether I'd need to calculate my own (if so,
>> could you please recommend a way of doing that in Freesurfer or FSL?)
>>
>> Many thanks in advance
>>
>> Kind regards
>> Reem
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
>> freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of J?rgen H?nggi
>> Sent: Sunday, 22 July 2012 7:47 p.m.
>> To: Watson, Christopher
>> Cc: Freesurfer Mailinglist
>> Subject: Re: [Freesurfer] Questions about correction over 2 hemispheres
>> and MCC
>>
>> Hi Chris
>>
>> Yes there are such tools. Bonferroni oder Sidak test that take into
>> account the correlated measures. Here you can find these tools
>>
>> http://www.quantitativeskills.com/sisa/calculations/bonfer.htm
>>
>> Cheers
>> J?rgen
>>
>>
>> On [DATE], "Watson, Christopher" <[ADDRESS]> wrote:
>>
>> > What about, for example, the correlations I've seen in a cohort of
>> subjects.
>> >
>> > In 158 subjects aged 10-19 (both controls and patients), the
>> > correlation between L & R thalamus is 0.91, and the correlations
>> > between L & R of caudate, putamen, pallidum, hippocampus, and amygdala
>> were all 0.75 or higher.
>> >
>> > I would think that a Bonferroni correction would be incredibly
>> > conservative and, in my opinion, just plain wrong because true
>> > significant diff's would be missed. Is there any principled way of
>> > dealing with multiple tests that are correlated?
>> >
>> > Thanks,
>> > Chris
>> > 
>> > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> > Sent: Saturday, July 21, 2012 12:01 PM
>> > To: Watson, Christopher
>> > Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
>> > Subject: Re: [Freesurfer] Questions about correction over 2
>> > hemispheres and MCC
>> >
>> > Hi Chris,
>> >
>> > bonferroni will be overly conservative in that case, but we rarely
>> > really know the true covariance structure of the data, so we would
>> > rather err on the side of being conservative.
>> >
>> > cheers
>> > Bruce
>> > On Fri, 20 Jul 2012