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<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu<mailto:juan.sanc...@nyspi.columbia.edu>> Date: Thursday, March 29, 2018 at 10:23 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
