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

2016-03-22 Thread Douglas Greve
Douglas N Greve > > 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.

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

2016-03-21 Thread Bharadwaj, Pradyumna - (prad)
: [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:*freesurf

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

2016-03-01 Thread Douglas N Greve
urfer-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

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

2016-03-01 Thread Versace, Amelia
: 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

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 respe

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-

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:

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 f

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

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 wa

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.h