Re: [Freesurfer] mprage flag in recon-all

[Caspar M. Schwiedrzik]

thanks!
caspar


2013/5/31 Bruce Fischl :
> oh, my mistake. I thought it called them with specific parms. Sorry:
>
> for mri_segment:
>
> gray_hi = 99 ;   (same as --ghi 99)
> wm_low = 89 ;(same as -wlo 89)
>
>
> for mri_normalize:
>
> intensity_below = 15 ; (same as -b 15)
>
> cheers
> Bruce
>
>
>
> On Fri, 31 May 2013, Caspar M. Schwiedrzik wrote:
>
>> yes, but recon-all just calls mri_segment with -mprage and mri_normalize
>> with -mprage.
>> I would like to know what -mprage does in these two functions, but i
>> cannot
>> search them because they are executables, not scripts.
>> Caspar
>>
>> 2013/5/31 Harms, Michael 
>>
>> Use any editor (even Word) with a search capacity, and search for the
>> string 'mprage'.
>> That will lead to you the variable internal to recon-all called
>> "IsMPRAGE".  Searching for "IsMPRAGE" will then show you all in the
>> stages that the -mprage flag affects.
>>
>> 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: "Caspar M. Schwiedrzik" 
>> Date: Friday, May 31, 2013 2:14 PM
>> To: "Freesurfer@nmr.mgh.harvard.edu" 
>> Subject: Re: [Freesurfer] mprage flag in recon-all
>>
>> I only find flags for mri_normalize and mri_segment in recon-all, and
>> I have trouble reading the contents mri_normalize with a regular text
>> editor.
>> caspar
>>
>>
>> 2013/5/31 Bruce Fischl 
>>   Hi Caspar
>>
>>   it changes some parameters to the intensity normalization
>>   and segmentation to account for the lower SNR and
>>   increased CNR in the mprage. You'll need to look in the
>>   recon-all script for the details
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:
>>
>> Hi!
>> Is there more documentation on what settings
>> the mprage flag enables in
>> recon-all?
>> Specifically, I would be interested which
>> individual steps it affects and
>> what  the parameters are for each of the
>> steps.
>> Thanks!
>> Caspar
>>
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>>
>>
>> 
>>
>>
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If
>> you are not the intended recipient, be advised that any unauthorized
>> use, disclosure, copying or the taking of any action in reliance on
>> the contents of this information is strictly prohibited. If you have
>> received this email in error, please immediately notify the sender via
>> telephone or return mail.
>>
>>
>>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mprage flag in recon-all

[Bruce Fischl]

oh, my mistake. I thought it called them with specific parms. Sorry:

for mri_segment:

gray_hi = 99 ;   (same as --ghi 99)
wm_low = 89 ;(same as -wlo 89)


for mri_normalize:

intensity_below = 15 ; (same as -b 15)

cheers
Bruce


On Fri, 
31 May 2013, Caspar M. Schwiedrzik wrote:



yes, but recon-all just calls mri_segment with -mprage and mri_normalize
with -mprage.
I would like to know what -mprage does in these two functions, but i cannot
search them because they are executables, not scripts.
Caspar

2013/5/31 Harms, Michael 

Use any editor (even Word) with a search capacity, and search for the
string 'mprage'.
That will lead to you the variable internal to recon-all called
"IsMPRAGE".  Searching for "IsMPRAGE" will then show you all in the
stages that the -mprage flag affects.

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: "Caspar M. Schwiedrzik" 
Date: Friday, May 31, 2013 2:14 PM
To: "Freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] mprage flag in recon-all

I only find flags for mri_normalize and mri_segment in recon-all, and
I have trouble reading the contents mri_normalize with a regular text
editor.
caspar


2013/5/31 Bruce Fischl 
  Hi Caspar

  it changes some parameters to the intensity normalization
  and segmentation to account for the lower SNR and
  increased CNR in the mprage. You'll need to look in the
  recon-all script for the details

  cheers
  Bruce


  On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:

Hi!
Is there more documentation on what settings
the mprage flag enables in
recon-all?
Specifically, I would be interested which
individual steps it affects and
what  the parameters are for each of the
steps.
Thanks!
Caspar





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.


 





The materials in this message are private and may contain Protected
Healthcare Information or other information of a sensitive nature. If
you are not the intended recipient, be advised that any unauthorized
use, disclosure, copying or the taking of any action in reliance on
the contents of this information is strictly prohibited. If you have
received this email in error, please immediately notify the sender via
telephone or return mail.



___
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.

Re: [Freesurfer] mprage flag in recon-all

[Bruce Fischl]

mri_normalize is a binary so you can't, just recon-all.

On Fri, 31 May 2013, Caspar M. Schwiedrzik wrote:


I only find flags for mri_normalize and mri_segment in recon-all, and I have
trouble reading the contents mri_normalize with a regular text editor.
caspar


2013/5/31 Bruce Fischl 
  Hi Caspar

  it changes some parameters to the intensity normalization and
  segmentation to account for the lower SNR and increased CNR in
  the mprage. You'll need to look in the recon-all script for the
  details

  cheers
  Bruce


  On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:

Hi!
Is there more documentation on what settings the
mprage flag enables in
recon-all?
Specifically, I would be interested which individual
steps it affects and
what  the parameters are for each of the steps.
Thanks!
Caspar





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 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.

Re: [Freesurfer] mprage flag in recon-all

[Harms, Michael]

Sorry, I misinterpreted your question.  In that case, if you want more than the broad-brush description that Bruce provided, you'll likely need to download the source code and scour the c-code yourself to find the exact specifics.


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: "Caspar M. Schwiedrzik" <cschwie...@mail.rockefeller.edu>
Date: Friday, May 31, 2013 2:50 PM
To: "Harms, Michael" <mha...@wustl.edu>, "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mprage flag in recon-all




yes, but recon-all just calls mri_segment with -mprage and mri_normalize with -mprage.

I would like to know what -mprage does in these two functions, but i cannot search them because they are executables, not scripts.

Caspar

2013/5/31 Harms, Michael <mha...@wustl.edu>






Use any editor (even Word) with a search capacity, and search for the string 'mprage'.
That will lead to you the variable internal to recon-all called "IsMPRAGE".  Searching for "IsMPRAGE" will then show you all in the stages that the -mprage flag affects.


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: "Caspar M. Schwiedrzik" <cschwie...@mail.rockefeller.edu>
Date: Friday, May 31, 2013 2:14 PM
To: "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mprage flag in recon-all






I only find flags for mri_normalize and mri_segment in recon-all, and I have trouble reading the contents mri_normalize with a regular text editor.

caspar


2013/5/31 Bruce Fischl <fis...@nmr.mgh.harvard.edu>

Hi Caspar

it changes some parameters to the intensity normalization and segmentation to account for the lower SNR and increased CNR in the mprage. You'll need to look in the recon-all script for the details

cheers
Bruce




On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:


Hi!
Is there more documentation on what settings the mprage flag enables in
recon-all?
Specifically, I would be interested which individual steps it affects and
what  the parameters are for each of the steps.
Thanks!
Caspar








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.










 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient,
 be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return
 mail.









 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


___
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.

Re: [Freesurfer] mprage flag in recon-all

[Caspar M. Schwiedrzik]

yes, but recon-all just calls mri_segment with -mprage and mri_normalize
with -mprage.
I would like to know what -mprage does in these two functions, but i cannot
search them because they are executables, not scripts.
Caspar

2013/5/31 Harms, Michael 

>
>  Use any editor (even Word) with a search capacity, and search for the
> string 'mprage'.
> That will lead to you the variable internal to recon-all called
> "IsMPRAGE".  Searching for "IsMPRAGE" will then show you all in the stages
> that the -mprage flag affects.
>
>  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: "Caspar M. Schwiedrzik" 
> Date: Friday, May 31, 2013 2:14 PM
> To: "Freesurfer@nmr.mgh.harvard.edu" 
> Subject: Re: [Freesurfer] mprage flag in recon-all
>
>  I only find flags for mri_normalize and mri_segment in recon-all, and I
> have trouble reading the contents mri_normalize with a regular text editor.
> caspar
>
>
> 2013/5/31 Bruce Fischl 
>
>> Hi Caspar
>>
>> it changes some parameters to the intensity normalization and
>> segmentation to account for the lower SNR and increased CNR in the mprage.
>> You'll need to look in the recon-all script for the details
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:
>>
>>  Hi!
>>> Is there more documentation on what settings the mprage flag enables in
>>> recon-all?
>>> Specifically, I would be interested which individual steps it affects and
>>> what  the parameters are for each of the steps.
>>> Thanks!
>>> Caspar
>>>
>>>
>>>
>>>
>>
>>  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<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.
>>
>
>
>  --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
___
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.

Re: [Freesurfer] mprage flag in recon-all

[Caspar M. Schwiedrzik]

I only find flags for mri_normalize and mri_segment in recon-all, and I
have trouble reading the contents mri_normalize with a regular text editor.
caspar


2013/5/31 Bruce Fischl 

> Hi Caspar
>
> it changes some parameters to the intensity normalization and segmentation
> to account for the lower SNR and increased CNR in the mprage. You'll need
> to look in the recon-all script for the details
>
> cheers
> Bruce
>
>
>
> On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:
>
>  Hi!
>> Is there more documentation on what settings the mprage flag enables in
>> recon-all?
>> Specifically, I would be interested which individual steps it affects and
>> what  the parameters are for each of the steps.
>> Thanks!
>> Caspar
>>
>>
>>
>>
>
> 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 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.

Re: [Freesurfer] mprage flag in recon-all

[Bruce Fischl]

Hi Caspar

it changes some parameters to the intensity normalization and segmentation 
to account for the lower SNR and increased CNR in the mprage. You'll need 
to look in the recon-all script for the details


cheers
Bruce


On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:


Hi!
Is there more documentation on what settings the mprage flag enables in
recon-all?
Specifically, I would be interested which individual steps it affects and
what  the parameters are for each of the steps.
Thanks!
Caspar


___
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.

[Freesurfer] mprage flag in recon-all

[Caspar M. Schwiedrzik]

Hi!
Is there more documentation on what settings the mprage flag enables in
recon-all?
Specifically, I would be interested which individual steps it affects and
what  the parameters are for each of the steps.
Thanks!
Caspar
___
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.