Re: [HCP-Users] cluster extent thresholding on surface
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" 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
> Date: Sunday, January 11, 2015 7:38 PM
> To: "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"
> 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" 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
>>>> 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 ${DeltaTE}
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> From: , Gregory
>>>> Date: Friday, January 9, 2015 at 1:26 PM
>>>> To: Matt Glasser ,
>>>> "hcp-users@humanconnectome.org"
>>>> Subject: RE: [HCP-Users] fieldmap processing error
>>>>
>>>> Digging deeper into it, I think the fieldmap voxel sizes may be changed
>>>> or misreported inside the HCP script.
>>>>
>>>> In the analysis/unprocessed directory, the headers look like this:
>>>> [Gbook@compute31 T1w_MPR1]$ fslinfo
>>>> analysis_3T_FieldMap_Magnitude.nii.gz
>>>> data_type INT16
>>>> dim1 80
>>>> dim2 80
>>>> dim3 48
>>>> dim4 2
>>>> datatype 4
Re: [HCP-Users] cluster extent thresholding on surface
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 ${DeltaTE}
Peace,
Matt.
From: , Gregory <gregory.b...@hhchealth.org>
Date: Friday, January 9, 2015 at 1:26 PM
To: Matt Glasser <glass...@wusm.wustl.edu>,
"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: RE: [HCP-Users] fieldmap processing error
Digging deeper into it, I think the fieldmap voxel sizes may be changed
or misreported inside the HCP script.
In the analysis/unprocessed directory, the headers look like this:
[Gbook@compute31 T1w_MPR1]$ fslinfo
analysis_3T_FieldMap_Magnitude.nii.gz
data_type INT16
dim1 80
dim2 80
dim3 48
dim4 2
datatype 4
pixdim1 3.00
pixdim2 3.00
pixdim3 3.00
pixdim4 0.731000
cal_max 0.
cal_min 0.
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 3.00
pixdim2 3.00
pixdim3 3.00
pixdim4 0.731000
cal_max 0.
cal_min 0.
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 3.00 x 3.00 x 3.01 mm
./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log- Magnitude image: 80 x
80 x 48 with dims of 3.00 x 3.00 x 3.00 mm
./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log-Fix this (probably in
reconstruction stage) before re-running this script
From: Glasser, Matthew [mail
[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" 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" 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
>>> 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 ${DeltaTE}
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: , Gregory
>>> Date: Friday, January 9, 2015 at 1:26 PM
>>> To: Matt Glasser ,
>>> "hcp-users@humanconnectome.org"
>>> Subject: RE: [HCP-Users] fieldmap processing error
>>>
>>> Digging deeper into it, I think the fieldmap voxel sizes may be changed
>>> or misreported inside the HCP script.
>>>
>>> In the analysis/unprocessed directory, the headers look like this:
>>> [Gbook@compute31 T1w_MPR1]$ fslinfo
>>> analysis_3T_FieldMap_Magnitude.nii.gz
>>> data_type INT16
>>> dim1 80
>>> dim2 80
>>> dim3 48
>>> dim4 2
>>> datatype 4
>>> pixdim13.00
>>> pixdim23.00
>>> pixdim33.00
>>> pixdim40.731000
>>> cal_max0.
>>> cal_min0.
>>> 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
>>> pixdim13.00
>>> pixdim23.00
>>> pixdim33.00
>>> pixdim40.731000
>>> cal_max0.
>>> cal_min0.
>>> 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 3.00 x 3.00 x 3.01 mm
>>> ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log- Magnitude image: 80 x
>>> 80 x 48 with dims of 3.00 x 3.00 x 3.00 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: , Gregory
>>> Date: Thursday, January 8, 2015 at 12:18 PM
>>> To: "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
