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
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 greve@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 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: jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com
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 <greve@nmr.mgh.harvard.edu mailto:greve@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: jdien07@mac.com mailto:jdien07@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
MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-00001-000001-01.nii --dph /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-00001-000001-02.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 greve@nmr.mgh.harvard.edu 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 < mailto:greve@nmr.mgh.harvard.edugreve@nmr.mgh.harvard.edu mailto:greve@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 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 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 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: jdien07@mac.com mailto:jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com 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 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: jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com
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/sRPA003-0005-00001-000001-02.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 jdien07@mac.com wrote:
MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-00001-000001-01.nii --dph /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-00001-000001-02.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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 < mailto:greve@nmr.mgh.harvard.edugreve@nmr.mgh.harvard.edu mailto:greve@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 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 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 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: jdien07@mac.com mailto:jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: jdien07@mac.com mailto:jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com http://joedien.com/ _______________________________________________ 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: jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com
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/sRPA003-0005-00001-000001-02.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 <jdien07@mac.com mailto:jdien07@mac.com> wrote:
MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-00001-000001-01.nii --dph /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-00001-000001-02.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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 greve@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: jdien07@mac.com mailto:jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com 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 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: jdien07@mac.com mailto:jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com 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
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: jdien07@mac.com mailto:jdien07@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
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/sRPA003-0004-00001-000001-01.nii --dph /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-00001-000001-02.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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 greve@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: jdien07@mac.com mailto:jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com 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 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: jdien07@mac.com mailto:jdien07@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
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 <greve@nmr.mgh.harvard.edumailto:greve@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.edumailto: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: jdien07@mac.commailto:jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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: jdien07@mac.com <mailto:jdien07@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
Hi Doug,
Could you please upload epidewarp.fsl for FSL 5.x once again.
Thanks! -Prad ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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: jdien07@mac.com <mailto:jdien07@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 greve@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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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: jdien07@mac.com <mailto:jdien07@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 greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bharadwaj, Pradyumna - (prad) -
Douglas Greve -
Douglas N Greve
-
Joseph Dien -
Versace, Amelia