Mark,
My apologies for not including additional information.
Here is a link to the de-identified data that I am running. https://app.box.com/s/fvcnes91m0v2zigz9fxfdp1206f8zyjk
There are three subfolders
1) nifti - contains files converted directly from the DICOM files
2) fmap - contains the preprocessing of the field map
3) bold - contains the data and processing for FEAT images.
a) bold directory contains rfmri_original.nii.gz, This is the original data, and rfmri.nii.gz which is the unwrapped data.
In addition, I have copied the fieldmap2edges.png for your convenience to this top directory that shows the edges floating above the brain. I believe all the images have bold directory have been processed properly. I have down sampled the original T1w image and skull stripped images using ANTs using the identity transform. This allows me to display all the images in fslview in the bold directory with the command fslview *fmap*.gz &. I believe this shows that all the images are originally aligned (but not registered).
I have tried numerous things to remove this artifact but to no avail. I have tried the same procedure of removing the aliasing on another data set and it worked fine.
There is also a problem further down in the processing pipeline that produces a FATAL ERROR. The error is reported in bold/rfmri.feat/logs/feat1b_reg.e22757 (contents included in email below). I don’t know if the two problems are related.
Thanks for your help,
Bob
[bkraft@aging1a logs]$ cat feat1b_reg.e22757
Option -w ( highres dof ) selected with argument "BBR"
while executing
"if { [ catch {
for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
switch -- [ lindex $argv $argindex ] {
-I {
incr argin..."
(file "/aging1/software/fsl/bin/feat" line 119)
[bkraft@aging1a logs]$
On May 21, 2015, at 6:41 PM, Mark Jenkinson <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi,
Can you send us a link to some example illustrations of the problem?
It is hard to know what is going wrong from this description, as it all sounds fine in general.
Hopefully just seeing some examples will make it clearer.
All the best,
Mark
From: Robert Kraft <[log in to unmask]<mailto:[log in to unmask]>>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>>
Date: Wednesday, 20 May 2015 14:45
To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>>
Subject: [FSL] Distortion Correction
I am trying to apply distortion correction using FEAT GUI on an fMRI data set. I have done this many times with very few problems. However, my last study used a tighter FOV. The whole brain was acquired but there was some aliasing along the phase encode direction for both the fMRI data and the Field Map. As a result of this aliasing I am having trouble using the FEAT GUI without some manual processing of the data.
Here is what I have tries so far
1) Remove the aliasing with fslroi and fslmerge from the fieldmap and fmri data set. This procedure has been described in the tutorials and on the discussion board. It seems to work well. It does modify the shift the qto_xyz:2 by 34.375, which equals to the 11 pixels I shifted times the pixel dimension of 3.125.
2) Skull strip the fieldmap (magnitude image) with bet2 to create fmap_mag_brain.nii.gz This works great and I haven't encountered any problems.
3) Skull strip the first volume of the fMRI data with bet2, create a mask, and then apply the mask to the 4D fmri data set.
4) Use FEAT GUI to setup my Prestats processing of the fMRI data. I have turned off Brain Extraction. BBR is selected - although it doesn't allow me to select another option.
5) Verify that all the images are in the same orientation in fslview. I also load the images into Freeview so I can see that the images overlay one another in physical space. Everything looks great. The fMRI data set has very little motion and images (except for the distortion) are almost perfectly registered.
6) Run feat from the command line. ( feat rfmri.fsf )
During the registration process the brain is shifted. This is most obvious in the fieldmap2edges.png. Where the field map and white matter edges have been shifted in the inferior to superior direction by almost 3/4 of the brain.
At this point, I have no idea what to do. Any suggestion or advice on debugging would be extremely helpful.
Thanks
Bob
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