Are you sure you removed a *slice* (e.g., via 'fslroi' on the NIFTI) and
not a frame (i.e., gradient direction). The fact that you mentioned you
did something before running 'dcm2nii' would suggest that you did the
latter.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: [log in to unmask]
On 12/3/15 8:46 AM, "Frederik Geissler" <[log in to unmask]> wrote:
Dear Jesper; dear all,
I just tried to run my topup script after removing the bottom respectively
top slice (as well as bottom and top slice at the same time) before
running dcm2nii but unfortunately it did not work out yet. The error I
receive is the same as before. This is the command I am using in my script:
fslroi AP.nii.gz APb0.nii.gz 0 1
fslroi PA.nii.gz PAb0.nii.gz 0 1
fslmerge -t all_b0.nii.gz APb0.nii.gz PAb0.nii.gz
rm APb0.nii.gz
rm PAb0.nii.gz
topup --imain=all_b0.nii.gz
--datain=/home/nr199144/Frederik/NEW/Data/datain.txt --config=b02b0.cnf
--out=topup_results --fout=topup_field --iout=topup_unwarped_b0s
applytopup --imain=AP.nii.gz,PA.nii.gz
--datain=/home/nr199144/Frederik/NEW/Data/datain.txt --inindex=1,2
--topup=topup_results --out=posttu.nii.gz
As you already mentioned I use the common config that might cause me
trouble. I searched the .cnf file, created a copy of it in which I removed
the subsample command and started a new topup run with my new config cmd.
Like this:
... topup --imain=all_b0.nii.gz
--datain=/home/nr199144/Frederik/NEW/Data/datain.txt
--config=/home/nr199144/Frederik/NEW/Data/formerknownasb02b0.cnf
--out=topup_results --fout=topup_field --iout=topup_unwarped_b0s ...
Its running at the moment and giving me no error so far. My question -
since I am not that familiar with the topup architecture respectively
Subsampling - is:
Can I just remove the Subsampling command without any trouble later on or
will it affect my data quality by any means?
Thank you very much for your help already!
Best regards,
Frederik
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