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
>>>
>>>
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>>
>
>
> ________________________________
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