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 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
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
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 ${DeltaTE}
Peace,
Matt.
From: Book, Gregory gregory.b...@hhchealth.org
Date: Friday, January 9, 2015 at 1:26 PM
To: Matt Glasser glass...@wusm.wustl.edu,
hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: RE: [HCP-Users] fieldmap processing error
Digging deeper into it, I think the fieldmap voxel sizes may be changed
or misreported inside the HCP script.
In the analysis/unprocessed directory, the headers look like this:
[Gbook@compute31 T1w_MPR1]$ fslinfo
analysis_3T_FieldMap_Magnitude.nii.gz
data_type INT16
dim1 80
dim2 80
dim3 48
dim4 2
datatype 4
pixdim1 3.00
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 [mailto:glasserm@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
[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
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: 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
