I agree that is very strange. If you were to rerun fMRIVolume and fMRISurface do you get the same issue? You could also try extracting the first volume and feeding it in as an SBRef manually to see if that fixes things.
Matt. From: Qunjun Liang <[email protected]<mailto:[email protected]>> Date: Tuesday, April 9, 2019 at 10:38 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] An error about subcortical processinginHCPfMRI-surface pipeline Hi Matt, Sorry to bother you again. Followed your recommend, I have checked the header of those two error image. I found that the space dimension of FunTask_AP.nii.gz is 91X108X91 while it is 91X109X91 of that in ROIs.2.nii.gz. Then I had compared this parameter to our other dataset preprocessing by HCP pipeline and confirmed that the y dimension of 108 in FunTask_AP.nii.gz is a wrong number. For now, I still have no idea about what caused this error. Could you give me a cue? Sincerely, Qunjun ------------------ Original ------------------ From: "Glasser, Matthew"<[email protected]<mailto:[email protected]>>; Date: Sat, Apr 6, 2019 12:13 PM To: "Qunjun Liang"<[email protected]<mailto:[email protected]>>; Cc: "[email protected]<mailto:[email protected]>"<[email protected]<mailto:[email protected]>>; Subject: Re: [HCP-Users] An error about subcortical processinginHCPfMRI-surface pipeline The files in the error message. Matt. From: Qunjun Liang <[email protected]<mailto:[email protected]>> Date: Friday, April 5, 2019 at 11:10 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] An error about subcortical processing inHCPfMRI-surface pipeline Hi Matt, Yes, we don't have an SBRef image. Because at the beginning of this experiment, the sequence was set referring to the UK Biobank Project. BTW, the scanner is Siemens 3T trio. Sorry I don't know clearly about what files you mean... But I searched the MNINonLinear/ directory and found an file named {task name}_SBRef.nii.gz, so I used fslhd with this file. The result showed: #----------------------- filename /media/LQJ/Social_Navigation/Social_nifti/201806138_hrw/MNINonLinear/Results/FunTask_AP/FunTask_AP_SBRef.nii.gz size of header 348 data_type FLOAT32 dim0 3 dim1 91 dim2 108 dim3 91 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 16 nbyper 4 bitpix 32 pixdim0 -1.000000 pixdim1 2.000000 pixdim2 2.000000 pixdim3 2.000000 pixdim4 1.200000 pixdim5 0.000000 pixdim6 0.000000 pixdim7 0.000000 vox_offset 352 cal_max 0.000000 cal_min 0.000000 scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 toffset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name MNI_152 qform_code 4 qto_xyz:1 -2.000000 0.000000 -0.000000 90.000000 qto_xyz:2 0.000000 2.000000 -0.000000 -126.000000 qto_xyz:3 0.000000 0.000000 2.000000 -72.000000 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Right-to-Left qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name MNI_152 sform_code 4 sto_xyz:1 -2.000000 0.000000 0.000000 90.000000 sto_xyz:2 0.000000 2.000000 0.000000 -126.000000 sto_xyz:3 0.000000 0.000000 2.000000 -72.000000 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior file_type NIFTI-1+ file_code 1 descrip FSL5.0 aux_file #------------------- If this file is the file you have mention about or I got an wrong one? Sincerely, Qunjun ------------------ Original ------------------ From: "Glasser, Matthew"<[email protected]<mailto:[email protected]>>; Date: Sat, Apr 6, 2019 11:32 AM To: "Qunjun Liang"<[email protected]<mailto:[email protected]>>; Cc: "[email protected]<mailto:[email protected]>"<[email protected]<mailto:[email protected]>>; Subject: Re: [HCP-Users] An error about subcortical processing inHCPfMRI-surface pipeline Do you not have an SBRef image? I wonder if that feature is not working. You could paste in fslhd from those two files. Matt. From: Qunjun Liang <[email protected]<mailto:[email protected]>> Date: Friday, April 5, 2019 at 10:23 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] An error about subcortical processing in HCPfMRI-surface pipeline Hi Matt, Thank you for the prompt reply. I have packed the batch script I used to call PreFreeSufer, PostFreeSufer, fMRIVolume and fMRISurface, as well as the log file (.o and .e) after running the pipelines. The zip file is placed in the attachment. Sincerely, Qunjun ------------------ Original ------------------ From: "Glasser, Matthew"<[email protected]<mailto:[email protected]>>; Date: Sat, Apr 6, 2019 10:39 AM To: "Qunjun Liang"<[email protected]<mailto:[email protected]>>;"[email protected]<mailto:[email protected]>"<[email protected]<mailto:[email protected]>>; Subject: Re: [HCP-Users] An error about subcortical processing in HCPfMRI-surface pipeline Please post how you called PreFreeSurfer, PostFreeSurfer, fMRIVolume, and fMRISurface. Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Qunjun Liang <[email protected]<mailto:[email protected]>> Date: Friday, April 5, 2019 at 9:37 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] An error about subcortical processing in HCP fMRI-surface pipeline Dear HCP experts, An error was occurred when I used fMRI surface generation pipeline: #---------------------------------- While running: wb_command -cifti-create-dense-timeseries /{PATH to subject}/MNINonLinear/Results/{task name}/{task name}_temp_subject.dtseries.nii -volume /{PATH to subject}/MNINonLinear/Results/{task name}/{task name}.nii.gz /{PATH to subject}/MNINonLinear/ROIs/ROIs.2.nii.gz ERROR: label volume has a different volume space than data volume #---------------------------------- I used GenericfMRISurfaceProcessingPipelineBatch.sh in Example/ directory to call the pipeline. The parameters (LowResMesh, FinalfMRIResolution and GrayordinatesResolution) were set in accord with that inPostFreesurferPipeline and fMRIVolume pipeline. Given than my fMRI data were acquired by multiband sequence, so I wonder if the pipeline was expected to do some extra modifications to fit multiband image? Environment: 1. Ubuntu 14.04 LTS 2. HCP pipeline 4.0.0 3. Workbench 1.3.2 4. FreeSurfer 6.0 5. FSL 5.0.9 Sincerely, ------------------ Qunjun Liang, Ph.D. School of psychology South China Normal University Zhongshan Avenue West 55, Tianhe District Guangzhou 510631 P. R. China _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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