The command you ran locally is using the Jacobian as the bias field, which
is incorrect, and the "-div Jacobian -mul Jacobian" is just cancelling out
any effect (output has same bias as input fMRI). It should instead be "-div
BiasField.2 -mul Jacobian_MNI.2".
That said, your original output looks like the bias field was incorrectly
estimated. Did you use --biascorrection=SEBASED in your call to
GenericfMRIVolumeProcessingPipeline? If you used --biascorrection=LEGACY
(might be the default?) you may also want to check if your
MNINonLinear/T1w_restore and MNINonLinear/T2w_restore look properly bias
corrected.
-Keith
On Thu, Mar 29, 2018 at 11:55 AM, Glasser, Matthew <glass...@wustl.edu>
wrote:
> I think that might be an old version of the pipelines. If you run on the
> latest version is it better?
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of "Sanchez, Juan
> (NYSPI)" <juan.sanc...@nyspi.columbia.edu>
> Date: Thursday, March 29, 2018 at 10:23 AM
> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: [HCP-Users] Intensity Normalization 3_22
>
> Dear all
>
> We are using the 3_22 Pipelines to process out data.
>
> We noticed that the processed fMRI results had an unusual intensity
> inhomogeneity for ALL of our runs. (first attachment)
>
> We found that the error occurued during intensity normalization
>
> Here:
>
> ${FSLDIR}/bin/fslmaths ${InputfMRI} $biascom $jacobiancom -mas
> ${BrainMask} -mas ${InputfMRI}_mask -thr 0 -ing 10000 ${OutputfMRI} -odt
> float
>
>
> I copied the relevant files and ran the fslmaths command localy
>
> (InputfMRI = Task_fMRI_emomo_1)
>
> fslmaths Task_fMRI_emomo_1_nonlin.nii.gz -div Jacobian_MNI.2.nii.gz -mul
> Jacobian_MNI.2.nii.gz -mas Task_fMRI_emomo_1_nonlin_mask.nii.gz -thr 0
> -ing 1000 output -odt float
> The output (second attachment) looked correct.
>
>
> I have tried to replicate the error and have not been able to
> Can anyone suggest a possible explenation?
> Thanks
> J
>
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