Ok, thanks for the answer.
_______________
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 11, 2015, at 10:20 PM, "Harms, Michael" <mha...@wustl.edu> wrote:
>
> We are working on developing a script that will use randomise and permutation
> testing to accomplish that, but don't have anything to share at this time.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> -----------------------------------------------------------
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From: Marta Moreno <mmorenoort...@icloud.com>
> Date: Sunday, January 11, 2015 7:38 PM
> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: [HCP-Users] cluster extent thresholding on surface
>
> 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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