FYI: The images released from the HCP with the names "SpinEchoFieldMap"
ARE the SE EPI images that topup needs as input for distortion correction
of the fMRI data.
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 63110 Email: [log in to unmask]
On 12/12/13 5:18 AM, "Jesper Andersson" <[log in to unmask]>
wrote:
>Dear Martin,
>
>> I'm trying to use topup for phase distortion correction of the EPI scans
>> from the Human Connectome Project. However, for some reason topup gives
>> a segmentation fault. Here is what I tried:
>>
>> 1) Combine LR and RL field map files
>>
>> fslmerge -t 100307_3T_SpinEchoFieldMap_LRRL.nii.gz \
>> 100307_3T_SpinEchoFieldMap_LR.nii.gz \
>> 100307_3T_SpinEchoFieldMap_RL.nii.gz
>
>topup takes (differently distorted) EPI images as input. Not field maps.
>>
>> this results in 100307_3T_SpinEchoFieldMap_LRRL.nii.gz with a total of 6
>> volumes. The first three have L->R phase encoding, the last three R->L.
>>
>> 2) Run topup:
>>
>> topup --imain=100307_3T_SpinEchoFieldMap_LRRL.nii \
>>--datain=topup_lrrl.txt
>
>You need to use a configuration file for running topup. There should be a
>file b02b0.cnf with the FSL distribution.
>
>Hence, swap your field maps for regular b=0 EPI images, and add
>--config=b02b0.cnf to the command line.
>
>Good luck Jesper
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