Do you see a filed called dwi-ec.nii.gz? That should be the output of eddy_correct. The log file says it is running it. Two min does seem a little fast for 60 directions; I have another case that does 340 in about 40min. Try running eddy_correct outside of dt_recon and see what happens.,
On 10/26/2022 5:53 AM, Ward Deferm wrote:
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Dear Freesurfer Developers,
I am trying to perform the dt_recon command for a single participant of my dataset. The original data comes from a philips scanner and was in the PAR/REC format. I converted these files to nifti’s using dcm2niix. This seemed to have worked as I got my nifti files and .bval and .bvec.
However, when I run the dt_recon command it does not give me a hard error, but the output is not how it should be. Instead of taking 1-2 hours to complete the command, the command is done in about 3 minutes and I’m doubting if the eddy corrections are actually performed (fsl seems to be installed properly and is recognized when sourcing freesurfer. When trying to view the output with freeview I get 2 outcomes. Sometimes all of the file's work but there is no eddy correction performed and the FA volume is spread all over the brain when looking at this volume using freeview. But other times certain volumes either refuse to load or come up as a blank rectangle. In the freeview command line I then get the error:
WARNING: 37103 NaNs found in volume /home/ward/freesurfer/subjects/testdtrecon/dti/ra.nii.gz
In the attached files you can find the dt_recon log file. As for version and operating system I am running:
- freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
2)Ubuntu 22.04.1 LTS
Kind regards,
Ward Deferm
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