subject:"\[Freesurfer\] epidewarp.fsl for FSL 5.x"

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

2016-03-22 Thread Douglas Greve

try now

On 3/21/16 10:24 PM, Bharadwaj, Pradyumna - (prad) wrote:
> Hi Doug,
>
> Could you please upload epidewarp.fsl for FSL 5.x once again.
>
> Thanks!
> -Prad
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve 
> <gr...@nmr.mgh.harvard.edu>
> Sent: Tuesday, March 1, 2016 12:39 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] epidewarp.fsl for FSL 5.x
>
> try now
>
> On 03/01/2016 02:16 PM, Versace, Amelia wrote:
>> Hi,
>>
>> I am having the same issue.
>>
>> Can you please upload the updated version of epidewarp.fsl  for FSL 5.x.
>>
>> Thanks a lot, Amelia
>>
>> *From:*freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas
>> Greve
>> *Sent:* Wednesday, February 10, 2016 10:58 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] epidewarp.fsl for FSL 5.x
>>
>> what is your command line? I think there is a rescaling in which it
>> expcts the phase to be 0-2048 (or 4096) as this is how it comes of the
>> (siemens) scanner. Could that be the problem?
>>
>> On 2/10/16 10:40 PM, Joseph Dien wrote:
>>
>>  I ran into the same issue:
>>
>>  FSLVersion 5.0.4
>>
>>  FSLVerMaj 5
>>
>>  FSL Version is 5.0.4, must be 3.X or 4.X
>>
>>  I downloaded the epidewarp.fsl script from the suggested ftp site
>>  and replaced the existing script.  It did indeed fix the version
>>  incompatibility with FSL 5.x.
>>
>>  I ran into a new problem where it was aborting.  After some
>>  trouble shooting and looking over the documentation, I realized
>>  that —-epi is a required input without which the script crashes
>>  (or is it supposed to be optional but there is a bug in the script?).
>>
>>  After including it, it ran much further but then aborted with the
>>  following error:
>>
>>  ERROR: input phase image exceeds allowable phase range.
>>
>>  Allowable range is 6.283 radians.  Image range is: 12.5633 radians.
>>
>>  This is consistent with the documentation.  I’m not sure why the
>>  phase image exceeds the range though.
>>
>>  It ran without problems with SPM’s FieldMap Toolbox and it is from
>>  a standard Siemen’s scanner sequence (two magnitude files and one
>>  phase difference file).
>>
>>  Do I just divide the values by two with something like fslmaths
>>  since it seems to have exactly double the required range?
>>
>>  Joe
>>
>>  On Nov 26, 2014, at 21:36, Douglas Greve
>>  <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
>>  wrote:
>>
>>
>>  It is there again. I don't know what the status if it  is in
>>  terms of the version. Try it and let me know
>>  doug
>>
>>  On 11/25/14 4:34 PM, Morgan Hough wrote:
>>
>>  Hi Doug,
>>
>>  Could you put the epidewarp.fsl script back on your ftp
>>  site? I don’t see it at the link in the archives:
>>
>>  
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
>>
>>  BTW, is the script updated in some way for 5.x or can I
>>  can the old script just be changed to accept 5.x version
>>  numbers.
>>
>>  Cheers,
>>
>>  -Morgan
>>
>>  ___
>>  Freesurfer mailing list
>>  Freesurfer@nmr.mgh.harvard.edu
>>  <mailto: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] epidewarp.fsl for FSL 5.x

2016-03-21 Thread Bharadwaj, Pradyumna - (prad)

Hi Doug,

Could you please upload epidewarp.fsl for FSL 5.x once again. 

Thanks!
-Prad

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve 
<gr...@nmr.mgh.harvard.edu>
Sent: Tuesday, March 1, 2016 12:39 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] epidewarp.fsl for FSL 5.x

try now

On 03/01/2016 02:16 PM, Versace, Amelia wrote:
>
> Hi,
>
> I am having the same issue.
>
> Can you please upload the updated version of epidewarp.fsl  for FSL 5.x.
>
> Thanks a lot, Amelia
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas
> Greve
> *Sent:* Wednesday, February 10, 2016 10:58 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] epidewarp.fsl for FSL 5.x
>
> what is your command line? I think there is a rescaling in which it
> expcts the phase to be 0-2048 (or 4096) as this is how it comes of the
> (siemens) scanner. Could that be the problem?
>
> On 2/10/16 10:40 PM, Joseph Dien wrote:
>
> I ran into the same issue:
>
> FSLVersion 5.0.4
>
> FSLVerMaj 5
>
> FSL Version is 5.0.4, must be 3.X or 4.X
>
> I downloaded the epidewarp.fsl script from the suggested ftp site
> and replaced the existing script.  It did indeed fix the version
> incompatibility with FSL 5.x.
>
> I ran into a new problem where it was aborting.  After some
> trouble shooting and looking over the documentation, I realized
> that —-epi is a required input without which the script crashes
> (or is it supposed to be optional but there is a bug in the script?).
>
> After including it, it ran much further but then aborted with the
> following error:
>
> ERROR: input phase image exceeds allowable phase range.
>
> Allowable range is 6.283 radians.  Image range is: 12.5633 radians.
>
> This is consistent with the documentation.  I’m not sure why the
> phase image exceeds the range though.
>
> It ran without problems with SPM’s FieldMap Toolbox and it is from
> a standard Siemen’s scanner sequence (two magnitude files and one
> phase difference file).
>
> Do I just divide the values by two with something like fslmaths
> since it seems to have exactly double the required range?
>
> Joe
>
> On Nov 26, 2014, at 21:36, Douglas Greve
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
> wrote:
>
>
> It is there again. I don't know what the status if it  is in
> terms of the version. Try it and let me know
> doug
>
> On 11/25/14 4:34 PM, Morgan Hough wrote:
>
> Hi Doug,
>
> Could you put the epidewarp.fsl script back on your ftp
> site? I don’t see it at the link in the archives:
>
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
>
> BTW, is the script updated in some way for 5.x or can I
> can the old script just be changed to accept 5.x version
> numbers.
>
> Cheers,
>
> -Morgan
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> <mailto: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.
>
> 
> 
>
> Joseph Dien, PhD
>
> Senior Research Scientist
>
> Maryland Neuroimaging Center
>
> University of Maryland, College Park
>
> E-mail: jdie...@mac.com <mailto:jdie...@mac.com>
> Cell Phone: 202-297-8117
> http://joedien.com
>
>
>
>
>
> ___
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/f

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

2016-03-01 Thread Douglas N Greve

try now

On 03/01/2016 02:16 PM, Versace, Amelia wrote:
>
> Hi,
>
> I am having the same issue.
>
> Can you please upload the updated version of epidewarp.fsl  for FSL 5.x.
>
> Thanks a lot, Amelia
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas 
> Greve
> *Sent:* Wednesday, February 10, 2016 10:58 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] epidewarp.fsl for FSL 5.x
>
> what is your command line? I think there is a rescaling in which it 
> expcts the phase to be 0-2048 (or 4096) as this is how it comes of the 
> (siemens) scanner. Could that be the problem?
>
> On 2/10/16 10:40 PM, Joseph Dien wrote:
>
> I ran into the same issue:
>
> FSLVersion 5.0.4
>
> FSLVerMaj 5
>
> FSL Version is 5.0.4, must be 3.X or 4.X
>
> I downloaded the epidewarp.fsl script from the suggested ftp site
> and replaced the existing script.  It did indeed fix the version
> incompatibility with FSL 5.x.
>
> I ran into a new problem where it was aborting.  After some
> trouble shooting and looking over the documentation, I realized
> that —-epi is a required input without which the script crashes
> (or is it supposed to be optional but there is a bug in the script?).
>
> After including it, it ran much further but then aborted with the
> following error:
>
> ERROR: input phase image exceeds allowable phase range.
>
> Allowable range is 6.283 radians.  Image range is: 12.5633 radians.
>
> This is consistent with the documentation.  I’m not sure why the
> phase image exceeds the range though.
>
> It ran without problems with SPM’s FieldMap Toolbox and it is from
> a standard Siemen’s scanner sequence (two magnitude files and one
> phase difference file).
>
> Do I just divide the values by two with something like fslmaths
> since it seems to have exactly double the required range?
>
> Joe
>
> On Nov 26, 2014, at 21:36, Douglas Greve
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
> wrote:
>
>
> It is there again. I don't know what the status if it  is in
> terms of the version. Try it and let me know
> doug
>
> On 11/25/14 4:34 PM, Morgan Hough wrote:
>
> Hi Doug,
>
> Could you put the epidewarp.fsl script back on your ftp
> site? I don’t see it at the link in the archives:
>
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
>
> BTW, is the script updated in some way for 5.x or can I
> can the old script just be changed to accept 5.x version
> numbers.
>
> Cheers,
>
> -Morgan
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> <mailto: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.
>
> 
> 
>
> Joseph Dien, PhD
>
> Senior Research Scientist
>
> Maryland Neuroimaging Center
>
> University of Maryland, College Park
>
> E-mail: jdie...@mac.com <mailto:jdie...@mac.com>
> Cell Phone: 202-297-8117
> http://joedien.com
>
>
>
>
>
> ___
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> 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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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

2016-03-01 Thread Versace, Amelia

Hi,
I am having the same issue.
Can you please upload the updated version of epidewarp.fsl  for FSL 5.x.
Thanks a lot, Amelia

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Wednesday, February 10, 2016 10:58 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] epidewarp.fsl for FSL 5.x

what is your command line? I think there is a rescaling in which it expcts the 
phase to be 0-2048 (or 4096) as this is how it comes of the (siemens) scanner. 
Could that be the problem?

On 2/10/16 10:40 PM, Joseph Dien wrote:
I ran into the same issue:

FSLVersion 5.0.4
FSLVerMaj 5
FSL Version is 5.0.4, must be 3.X or 4.X

I downloaded the epidewarp.fsl script from the suggested ftp site and replaced 
the existing script.  It did indeed fix the version incompatibility with FSL 
5.x.

I ran into a new problem where it was aborting.  After some trouble shooting 
and looking over the documentation, I realized that --epi is a required input 
without which the script crashes (or is it supposed to be optional but there is 
a bug in the script?).

After including it, it ran much further but then aborted with the following 
error:

ERROR: input phase image exceeds allowable phase range.
Allowable range is 6.283 radians.  Image range is: 12.5633 radians.

This is consistent with the documentation.  I'm not sure why the phase image 
exceeds the range though.

It ran without problems with SPM's FieldMap Toolbox and it is from a standard 
Siemen's scanner sequence (two magnitude files and one phase difference file).

Do I just divide the values by two with something like fslmaths since it seems 
to have exactly double the required range?

Joe

On Nov 26, 2014, at 21:36, Douglas Greve 
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> wrote:

It is there again. I don't know what the status if it  is in terms of the 
version. Try it and let me know
doug
On 11/25/14 4:34 PM, Morgan Hough wrote:
Hi Doug,

Could you put the epidewarp.fsl script back on your ftp site? I don't see it at 
the link in the archives:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl

BTW, is the script updated in some way for 5.x or can I can the old script just 
be changed to accept 5.x version numbers.

Cheers,

-Morgan

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto: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.

Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com<mailto:jdie...@mac.com>
Cell Phone: 202-297-8117
http://joedien.com

___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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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] epidewarp.fsl for FSL 5.x

2016-02-11 Thread Joseph Dien

MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag 
/Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-1-01-01.nii
 --dph 
/Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii
 --tediff 2.46 --esp 0.51 --epi fMRI/RPA003/bold/001/f.nii.gz --vsm 
fMRI/RPA003/bold/b0dcmap.nii.gz



> On Feb 10, 2016, at 22:58, Douglas Greve  wrote:
> 
> what is your command line? I think there is a rescaling in which it expcts 
> the phase to be 0-2048 (or 4096) as this is how it comes of the (siemens) 
> scanner. Could that be the problem?
> 
> 
> On 2/10/16 10:40 PM, Joseph Dien wrote:
>> I ran into the same issue:
>> 
>> FSLVersion 5.0.4
>> FSLVerMaj 5
>> FSL Version is 5.0.4, must be 3.X or 4.X
>> 
>> I downloaded the epidewarp.fsl script from the suggested ftp site and 
>> replaced the existing script.  It did indeed fix the version incompatibility 
>> with FSL 5.x.
>> 
>> I ran into a new problem where it was aborting.  After some trouble shooting 
>> and looking over the documentation, I realized that —-epi is a required 
>> input without which the script crashes (or is it supposed to be optional but 
>> there is a bug in the script?).
>> 
>> After including it, it ran much further but then aborted with the following 
>> error:
>> 
>> ERROR: input phase image exceeds allowable phase range.
>> Allowable range is 6.283 radians.  Image range is: 12.5633 radians.
>> 
>> This is consistent with the documentation.  I’m not sure why the phase image 
>> exceeds the range though.
>> 
>> It ran without problems with SPM’s FieldMap Toolbox and it is from a 
>> standard Siemen’s scanner sequence (two magnitude files and one phase 
>> difference file).
>> 
>> Do I just divide the values by two with something like fslmaths since it 
>> seems to have exactly double the required range?
>> 
>> Joe
>> 
>>> On Nov 26, 2014, at 21:36, Douglas Greve < 
>>> gr...@nmr.mgh.harvard.edu 
>>> > wrote:
>>> 
>>> 
>>> It is there again. I don't know what the status if it  is in terms of the 
>>> version. Try it and let me know
>>> doug
>>> 
>>> On 11/25/14 4:34 PM, Morgan Hough wrote:
 Hi Doug,
 
 Could you put the epidewarp.fsl script back on your ftp site? I don’t see 
 it at the link in the archives:
 
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
  
 
 
 BTW, is the script updated in some way for 5.x or can I can the old script 
 just be changed to accept 5.x version numbers. 
 
 Cheers,
 
 -Morgan
>>> 
>>> ___
>>> 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.
>> 
>> 
>> 
>> Joseph Dien, PhD
>> Senior Research Scientist
>> Maryland Neuroimaging Center
>> University of Maryland, College Park
>> E-mail: jdie...@mac.com 
>> Cell Phone: 202-297-8117
>> http://joedien.com 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> 
> ___
> 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.



Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

2016-02-11 Thread Douglas N Greve

How was the phase nii created?

On 02/11/2016 11:12 AM, Joseph Dien wrote:
> MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag 
> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-1-01-01.nii
>  
> --dph 
> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii
>  
> --tediff 2.46 --esp 0.51 --epi fMRI/RPA003/bold/001/f.nii.gz --vsm 
> fMRI/RPA003/bold/b0dcmap.nii.gz
>
>
>
>> On Feb 10, 2016, at 22:58, Douglas Greve > > wrote:
>>
>> what is your command line? I think there is a rescaling in which it 
>> expcts the phase to be 0-2048 (or 4096) as this is how it comes of 
>> the (siemens) scanner. Could that be the problem?
>>
>>
>> On 2/10/16 10:40 PM, Joseph Dien wrote:
>>> I ran into the same issue:
>>>
>>> FSLVersion 5.0.4
>>> FSLVerMaj 5
>>> FSL Version is 5.0.4, must be 3.X or 4.X
>>>
>>> I downloaded the epidewarp.fsl script from the suggested ftp site 
>>> and replaced the existing script.  It did indeed fix the version 
>>> incompatibility with FSL 5.x.
>>>
>>> I ran into a new problem where it was aborting.  After some trouble 
>>> shooting and looking over the documentation, I realized that —-epi 
>>> is a required input without which the script crashes (or is it 
>>> supposed to be optional but there is a bug in the script?).
>>>
>>> After including it, it ran much further but then aborted with the 
>>> following error:
>>>
>>> ERROR: input phase image exceeds allowable phase range.
>>> Allowable range is 6.283 radians.  Image range is: 12.5633 radians.
>>>
>>> This is consistent with the documentation.  I’m not sure why the 
>>> phase image exceeds the range though.
>>>
>>> It ran without problems with SPM’s FieldMap Toolbox and it is from a 
>>> standard Siemen’s scanner sequence (two magnitude files and one 
>>> phase difference file).
>>>
>>> Do I just divide the values by two with something like fslmaths 
>>> since it seems to have exactly double the required range?
>>>
>>> Joe
>>>
 On Nov 26, 2014, at 21:36, Douglas Greve 
  wrote:


 It is there again. I don't know what the status if it  is in terms 
 of the version. Try it and let me know
 doug

 On 11/25/14 4:34 PM, Morgan Hough wrote:
> Hi Doug,
>
> Could you put the epidewarp.fsl script back on your ftp site? I 
> don’t see it at the link in the archives:
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
>
> BTW, is the script updated in some way for 5.x or can I can the 
> old script just be changed to accept 5.x version numbers.
>
> Cheers,
>
> -Morgan

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 The information in this e-mail is intended only for the person to 
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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.
>>>
>>> 
>>>
>>> Joseph Dien, PhD
>>> Senior Research Scientist
>>> Maryland Neuroimaging Center
>>> University of Maryland, College Park
>>> E-mail: jdie...@mac.com 
>>> Cell Phone: 202-297-8117
>>> http://joedien.com 
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
>> 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.
>
> 
>
> Joseph Dien, PhD
> Senior Research Scientist
> Maryland Neuroimaging Center
> University of Maryland, College Park
> E-mail: jdie...@mac.com 
> Cell Phone: 202-297-8117
> http://joedien.com
>
>
>
>

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

2016-02-11 Thread Joseph Dien

using spm_read_vols I confirmed that the min and max of the phase difference 
file is indeed -4096 and 4092 respectively.

Further troubleshooting epidewarp.fsl indicates that the script is correctly 
branching to "# Input is phase difference and magnitude”

It then executes the following commands:

  # Rescale the delta phase to be between -pi and pi. Starts out
  # at 0 - 4095. Make sure the phase is float precision with _32R
  set cmd = ($FSLToFloat $dph -sub 2047.5 -mul 0.00153435539 $tmpdir/dph 
$FSLToFloatFlag )
  echo $cmd |& tee -a $LF
  $cmd |& tee -a $LF
  if($status) exit 1;

what echoes to the screen is:

fslmaths 
/Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii
 -sub 2047.5 -mul 0.00153435539 fMRI/RPA003/bold/tmp-epidewarp.90814.fsl/dph 
-odt float

it then aborts at the next section:

  cp $tmpdir/dph.$ext $tmpdir/dph.preprelude.$ext
  set dph = $tmpdir/dph
  if($#epimat) cp $epimat `dirname $dph`/`basename $dph .$ext`.mat # Copy 
matfile

  # Do the phase unwrapping (-f for 3D, -v for verbose)
  set cmd = (prelude -p $dph -a $mag -o $dph -f -v -m $head);
  echo $cmd |& tee -a $LF
  $cmd |& tee -a $LF
  if($status) exit 1;

So apparently this rescaling command is not doing so correctly?  The script 
comment says it expects the values to be between 0 and 4095 whereas the file 
goes to -4096 so perhaps that was a bit more negative than it was expecting?

Joe


> On Feb 11, 2016, at 11:12, Joseph Dien  wrote:
> 
> MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag 
> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-1-01-01.nii
>  --dph 
> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii
>  --tediff 2.46 --esp 0.51 --epi fMRI/RPA003/bold/001/f.nii.gz --vsm 
> fMRI/RPA003/bold/b0dcmap.nii.gz
> 
> 
> 
>> On Feb 10, 2016, at 22:58, Douglas Greve > > wrote:
>> 
>> what is your command line? I think there is a rescaling in which it expcts 
>> the phase to be 0-2048 (or 4096) as this is how it comes of the (siemens) 
>> scanner. Could that be the problem?
>> 
>> 
>> On 2/10/16 10:40 PM, Joseph Dien wrote:
>>> I ran into the same issue:
>>> 
>>> FSLVersion 5.0.4
>>> FSLVerMaj 5
>>> FSL Version is 5.0.4, must be 3.X or 4.X
>>> 
>>> I downloaded the epidewarp.fsl script from the suggested ftp site and 
>>> replaced the existing script.  It did indeed fix the version 
>>> incompatibility with FSL 5.x.
>>> 
>>> I ran into a new problem where it was aborting.  After some trouble 
>>> shooting and looking over the documentation, I realized that —-epi is a 
>>> required input without which the script crashes (or is it supposed to be 
>>> optional but there is a bug in the script?).
>>> 
>>> After including it, it ran much further but then aborted with the following 
>>> error:
>>> 
>>> ERROR: input phase image exceeds allowable phase range.
>>> Allowable range is 6.283 radians.  Image range is: 12.5633 radians.
>>> 
>>> This is consistent with the documentation.  I’m not sure why the phase 
>>> image exceeds the range though.
>>> 
>>> It ran without problems with SPM’s FieldMap Toolbox and it is from a 
>>> standard Siemen’s scanner sequence (two magnitude files and one phase 
>>> difference file).
>>> 
>>> Do I just divide the values by two with something like fslmaths since it 
>>> seems to have exactly double the required range?
>>> 
>>> Joe
>>> 
 On Nov 26, 2014, at 21:36, Douglas Greve < 
 gr...@nmr.mgh.harvard.edu 
 > wrote:
 
 
 It is there again. I don't know what the status if it  is in terms of the 
 version. Try it and let me know
 doug
 
 On 11/25/14 4:34 PM, Morgan Hough wrote:
> Hi Doug,
> 
> Could you put the epidewarp.fsl script back on your ftp site? I don’t see 
> it at the link in the archives:
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
>  
> 
> 
> BTW, is the script updated in some way for 5.x or can I can the old 
> script just be changed to accept 5.x version numbers. 
> 
> Cheers,
> 
> -Morgan
 
 ___
 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

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

2016-02-11 Thread Douglas N Greve

yes, that is the problem. Where did that phase image come from? You can 
use fslmaths to simply rescale it to 0-4095, then it should work

On 02/11/2016 11:34 AM, Joseph Dien wrote:
> using spm_read_vols I confirmed that the min and max of the phase 
> difference file is indeed -4096 and 4092 respectively.
>
> Further troubleshooting epidewarp.fsl indicates that the script is 
> correctly branching to "# Input is phase difference and magnitude”
>
> It then executes the following commands:
>
>   # Rescale the delta phase to be between -pi and pi. Starts out
>   # at 0 - 4095. Make sure the phase is float precision with _32R
>   set cmd = ($FSLToFloat $dph -sub 2047.5 -mul 0.00153435539 
> $tmpdir/dph $FSLToFloatFlag )
>   echo $cmd |& tee -a $LF
>   $cmd |& tee -a $LF
>   if($status) exit 1;
>
> what echoes to the screen is:
>
> fslmaths 
> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii
>  
> -sub 2047.5 -mul 0.00153435539 
> fMRI/RPA003/bold/tmp-epidewarp.90814.fsl/dph -odt float
>
> it then aborts at the next section:
>
>   cp $tmpdir/dph.$ext $tmpdir/dph.preprelude.$ext
>   set dph = $tmpdir/dph
>   if($#epimat) cp $epimat `dirname $dph`/`basename $dph .$ext`.mat # 
> Copy matfile
>
>   # Do the phase unwrapping (-f for 3D, -v for verbose)
>   set cmd = (prelude -p $dph -a $mag -o $dph -f -v -m $head);
>   echo $cmd |& tee -a $LF
>   $cmd |& tee -a $LF
>   if($status) exit 1;
>
> So apparently this rescaling command is not doing so correctly?  The 
> script comment says it expects the values to be between 0 and 4095 
> whereas the file goes to -4096 so perhaps that was a bit more negative 
> than it was expecting?
>
> Joe
>
>
>> On Feb 11, 2016, at 11:12, Joseph Dien > > wrote:
>>
>> MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag 
>> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-1-01-01.nii
>>  
>> --dph 
>> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii
>>  
>> --tediff 2.46 --esp 0.51 --epi fMRI/RPA003/bold/001/f.nii.gz --vsm 
>> fMRI/RPA003/bold/b0dcmap.nii.gz
>>
>>
>>
>>> On Feb 10, 2016, at 22:58, Douglas Greve >> > wrote:
>>>
>>> what is your command line? I think there is a rescaling in which it 
>>> expcts the phase to be 0-2048 (or 4096) as this is how it comes of 
>>> the (siemens) scanner. Could that be the problem?
>>>
>>>
>>> On 2/10/16 10:40 PM, Joseph Dien wrote:
 I ran into the same issue:

 FSLVersion 5.0.4
 FSLVerMaj 5
 FSL Version is 5.0.4, must be 3.X or 4.X

 I downloaded the epidewarp.fsl script from the suggested ftp site 
 and replaced the existing script.  It did indeed fix the version 
 incompatibility with FSL 5.x.

 I ran into a new problem where it was aborting.  After some trouble 
 shooting and looking over the documentation, I realized that —-epi 
 is a required input without which the script crashes (or is it 
 supposed to be optional but there is a bug in the script?).

 After including it, it ran much further but then aborted with the 
 following error:

 ERROR: input phase image exceeds allowable phase range.
 Allowable range is 6.283 radians. Image range is: 12.5633 radians.

 This is consistent with the documentation.  I’m not sure why the 
 phase image exceeds the range though.

 It ran without problems with SPM’s FieldMap Toolbox and it is from 
 a standard Siemen’s scanner sequence (two magnitude files and one 
 phase difference file).

 Do I just divide the values by two with something like fslmaths 
 since it seems to have exactly double the required range?

 Joe

> On Nov 26, 2014, at 21:36, Douglas Greve 
>  wrote:
>
>
> It is there again. I don't know what the status if it  is in terms 
> of the version. Try it and let me know
> doug
>
> On 11/25/14 4:34 PM, Morgan Hough wrote:
>> Hi Doug,
>>
>> Could you put the epidewarp.fsl script back on your ftp site? I 
>> don’t see it at the link in the archives:
>>
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
>>
>> BTW, is the script updated in some way for 5.x or can I can the 
>> old script just be changed to accept 5.x version numbers.
>>
>> Cheers,
>>
>> -Morgan
>
> ___
> 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

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

2016-02-10 Thread Douglas Greve

what is your command line? I think there is a rescaling in which it 
expcts the phase to be 0-2048 (or 4096) as this is how it comes of the 
(siemens) scanner. Could that be the problem?



On 2/10/16 10:40 PM, Joseph Dien wrote:

I ran into the same issue:

FSLVersion 5.0.4
FSLVerMaj 5
FSL Version is 5.0.4, must be 3.X or 4.X

I downloaded the epidewarp.fsl script from the suggested ftp site and 
replaced the existing script.  It did indeed fix the version 
incompatibility with FSL 5.x.


I ran into a new problem where it was aborting.  After some trouble 
shooting and looking over the documentation, I realized that —-epi is 
a required input without which the script crashes (or is it supposed 
to be optional but there is a bug in the script?).


After including it, it ran much further but then aborted with the 
following error:


ERROR: input phase image exceeds allowable phase range.
Allowable range is 6.283 radians.  Image range is: 12.5633 radians.

This is consistent with the documentation.  I’m not sure why the phase 
image exceeds the range though.


It ran without problems with SPM’s FieldMap Toolbox and it is from a 
standard Siemen’s scanner sequence (two magnitude files and one phase 
difference file).


Do I just divide the values by two with something like fslmaths since 
it seems to have exactly double the required range?


Joe

On Nov 26, 2014, at 21:36, Douglas Greve > wrote:



It is there again. I don't know what the status if it  is in terms of 
the version. Try it and let me know

doug

On 11/25/14 4:34 PM, Morgan Hough wrote:

Hi Doug,

Could you put the epidewarp.fsl script back on your ftp site? I 
don’t see it at the link in the archives:


ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl

BTW, is the script updated in some way for 5.x or can I can the old 
script just be changed to accept 5.x version numbers.


Cheers,

-Morgan


___
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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.




Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com 
Cell Phone: 202-297-8117
http://joedien.com



___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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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] epidewarp.fsl for FSL 5.x

2016-02-10 Thread Joseph Dien

I ran into the same issue:

FSLVersion 5.0.4
FSLVerMaj 5
FSL Version is 5.0.4, must be 3.X or 4.X

I downloaded the epidewarp.fsl script from the suggested ftp site and replaced 
the existing script.  It did indeed fix the version incompatibility with FSL 
5.x.

I ran into a new problem where it was aborting.  After some trouble shooting 
and looking over the documentation, I realized that —-epi is a required input 
without which the script crashes (or is it supposed to be optional but there is 
a bug in the script?).

After including it, it ran much further but then aborted with the following 
error:

ERROR: input phase image exceeds allowable phase range.
Allowable range is 6.283 radians.  Image range is: 12.5633 radians.

This is consistent with the documentation.  I’m not sure why the phase image 
exceeds the range though.

It ran without problems with SPM’s FieldMap Toolbox and it is from a standard 
Siemen’s scanner sequence (two magnitude files and one phase difference file).

Do I just divide the values by two with something like fslmaths since it seems 
to have exactly double the required range?

Joe

> On Nov 26, 2014, at 21:36, Douglas Greve  wrote:
> 
> 
> It is there again. I don't know what the status if it  is in terms of the 
> version. Try it and let me know
> doug
> 
> On 11/25/14 4:34 PM, Morgan Hough wrote:
>> Hi Doug,
>> 
>> Could you put the epidewarp.fsl script back on your ftp site? I don’t see it 
>> at the link in the archives:
>> 
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl 
>> 
>> 
>> BTW, is the script updated in some way for 5.x or can I can the old script 
>> just be changed to accept 5.x version numbers. 
>> 
>> Cheers,
>> 
>> -Morgan
> 
> ___
> 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.

Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com
Cell Phone: 202-297-8117
http://joedien.com

___
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

2014-11-26 Thread Douglas Greve



It is there again. I don't know what the status if it  is in terms of 
the version. Try it and let me know

doug

On 11/25/14 4:34 PM, Morgan Hough wrote:

Hi Doug,

Could you put the epidewarp.fsl script back on your ftp site? I don’t 
see it at the link in the archives:


ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl

BTW, is the script updated in some way for 5.x or can I can the old 
script just be changed to accept 5.x version numbers.


Cheers,

-Morgan


___
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] epidewarp.fsl for FSL 5.x

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

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