Hi users, For cluster extent thresholding on surface I am using wb_command -cifti-find-clusters. How to find surface area to have corrected p value of 0.05?
Thanks, _______________ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons On Jan 9, 2015, at 3:24 PM, "Glasser, Matthew" <glass...@wusm.wustl.edu> wrote: > This line in the pipelines deals with either case: > > ${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude > > > On 1/9/15, 2:17 PM, "Greg Burgess" <gcburg...@gmail.com> wrote: > >> I think (but am not 100% certain) that the magnitude image should be a >> single volume (dim4 = 1), whereas your magnitude image appears to be two >> volumes (dim4 = 2). That could be the mismatching dimension. >> >> --Greg >> >> ____________________________________________________________________ >> Greg Burgess, Ph.D. >> Staff Scientist, Human Connectome Project >> Washington University School of Medicine >> Department of Anatomy and Neurobiology >> Phone: 314-362-7864 >> Email: gburg...@wustl.edu >> >>> On Jan 9, 2015, at 1:59 PM, Glasser, Matthew <glass...@wusm.wustl.edu> >>> wrote: >>> >>> Can you check that the headers of these files look okay: >>> >>> >>> ${StudyFolder}/${Subject}/${fMRIName}/DistortionCorrectionAndEPIToT1wReg_ >>> FLIRTBBRAndFreeSurferBBRbased/FieldMap/Phase.nii.gz >>> >>> ${StudyFolder}/${Subject}/${fMRIName}/DistortionCorrectionAndEPIToT1wReg_ >>> FLIRTBBRAndFreeSurferBBRbased/FieldMap/Magnitude_brain >>> >>> The first file is directly copied from the input location >>> >>> ${FSLDIR}/bin/imcp ${PhaseInputName} ${WD}/Phase >>> >>> And the second one has had the following done to it (initial fslmaths >>> command reads from input location): >>> >>> ${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude >>> ${FSLDIR}/bin/bet ${WD}/Magnitude ${WD}/Magnitude_brain -f 0.35 -m >>> #Brain extract the magnitude image >>> >>> If all those files look okay, then the issue is with the >>> fsl_prepare_fieldmap script, which is a part of the FSL distribution and >>> is supported by the FSL team: >>> >>> ${FSLDIR}/bin/fsl_prepare_fieldmap SIEMENS ${WD}/Phase >>> ${WD}/Magnitude_brain ${WD}/FieldMap ${DeltaTE} >>> >>> Peace, >>> >>> Matt. >>> >>> From: <Book>, Gregory <gregory.b...@hhchealth.org> >>> Date: Friday, January 9, 2015 at 1:26 PM >>> To: Matt Glasser <glass...@wusm.wustl.edu>, >>> "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> Subject: RE: [HCP-Users] fieldmap processing error >>> >>> Digging deeper into it, I think the fieldmap voxel sizes may be changed >>> or misreported inside the HCP script. >>> >>> In the analysis/unprocessed directory, the headers look like this: >>> [Gbook@compute31 T1w_MPR1]$ fslinfo >>> analysis_3T_FieldMap_Magnitude.nii.gz >>> data_type INT16 >>> dim1 80 >>> dim2 80 >>> dim3 48 >>> dim4 2 >>> datatype 4 >>> pixdim1 3.000000 >>> pixdim2 3.000000 >>> pixdim3 3.000000 >>> pixdim4 0.731000 >>> cal_max 0.0000 >>> cal_min 0.0000 >>> file_type NIFTI-1+ >>> [Gbook@compute31 T1w_MPR1]$ fslinfo analysis_3T_FieldMap_Phase.nii.gz >>> data_type INT16 >>> dim1 80 >>> dim2 80 >>> dim3 48 >>> dim4 1 >>> datatype 4 >>> pixdim1 3.000000 >>> pixdim2 3.000000 >>> pixdim3 3.000000 >>> pixdim4 0.731000 >>> cal_max 0.0000 >>> cal_min 0.0000 >>> file_type NIFTI-1+ >>> >>> Then, when running the HCP pipeline, it reports this error (found >>> through grep): >>> >>> ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log:Phase and Magnitude images >>> must have the same number of voxels and voxel dimensions >>> ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log-Current dimensions are: >>> ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log- Phase image: 80 x >>> 80 x 48 with dims of 3.000000 x 3.000000 x 3.000001 mm >>> ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log- Magnitude image: 80 x >>> 80 x 48 with dims of 3.000000 x 3.000000 x 3.000000 mm >>> ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log-Fix this (probably in >>> reconstruction stage) before re-running this script >>> >>> From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] >>> Sent: Thursday, January 08, 2015 2:07 PM >>> To: Book, Gregory; hcp-users@humanconnectome.org >>> Subject: Re: [HCP-Users] fieldmap processing error >>> >>> Probably the easiest thing to do would be to fix the outlying image >>> dimension by editing the NIFTI header. What program are you using to >>> convert from scanner format to NIFTI? We use dcm2nii in the HCP. >>> >>> Peace, >>> >>> Matt. >>> >>> From: <Book>, Gregory <gregory.b...@hhchealth.org> >>> Date: Thursday, January 8, 2015 at 12:18 PM >>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> Subject: [HCP-Users] fieldmap processing error >>> >>> We¹ve noticed an error while processing some fMRI data through the HCP >>> pipeline. Several series are failing with the following message: >>> >>> Phase and Magnitude images must have the same number of voxels and >>> voxel dimensions >>> Current dimensions are: >>> Phase image: 80 x 80 x 48 with dims of 3.000000 x 3.000000 x >>> 3.000000 mm >>> Magnitude image: 80 x 80 x 48 with dims of 3.000000 x 3.000000 x >>> 3.000001 mm >>> Fix this (probably in reconstruction stage) before re-running this >>> script >>> >>> Is there any way we can bypass this error? The voxel sizes are only off >>> by 0.000001 mm >>> It¹s also weird, because the pipeline contains 5 runs of the same task, >>> and all use the same fieldmap files. The first task processes fine, but >>> the next 4 fail with this error message. >>> >>> -G >>> >>> _________________________________________________ >>> Gregory Book >>> Senior Technology Manager >>> Olin Neuropsychiatry Research Center, Institute of Living, Hartford >>> Hospital >>> 200 Retreat Avenue >>> Hartford, CT 06106 >>> Tel: 860-545-7267 Fax: 860-545-7797 >>> gregory.b...@hhchealth.org >>> http://nidb.sourceforge.net >>> >>> >>> This e-mail message, including any attachments, is for the sole use of >>> the intended recipient(s) and may contain confidential and privileged >>> information. Any unauthorized review, use, disclosure, or distribution >>> is prohibited. If you are not the intended recipient, or an employee or >>> agent responsible for delivering the message to the intended recipient, >>> please contact the sender by reply e-mail and destroy all copies of the >>> original message, including any attachments. >>> _______________________________________________ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> 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. If >>> you are not the intended recipient, be advised that any unauthorized >>> use, disclosure, copying or the taking of any action in reliance on the >>> contents of this information is strictly prohibited. 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