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
-----------------------------------------------------------
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
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
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" <[email protected]> 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: [email protected]
On Jan 9, 2015, at 1:59 PM, Glasser, Matthew <[email protected]>
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 ${DeltaTE}
Peace,
Matt.
From: <Book>, Gregory <[email protected]>
Date: Friday, January 9, 2015 at 1:26 PM
To: Matt Glasser <[email protected]>,
"[email protected]" <[email protected]>
Subject: RE: [HCP-Users] fieldmap processing error
Digging deeper into it, I think the fieldmap voxel sizes may be changed
or misreported inside the HCP script.
In the analysis/unprocessed directory, the headers look like this:
[Gbook@compute31 T1w_MPR1]$ 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:glasserm@wusm.wustl.edu]
Sent: Thursday, January 08, 2015 2:07 PM
To: Book, Gregory; [email protected]
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 <[email protected]>
Date: Thursday, January 8, 2015 at 12:18 PM
To: "[email protected]" <[email protected]>
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
[email protected]
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
[email protected]
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. If you have
received this email in error, please immediately notify the sender via
telephone or return mail.
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. If you have
received this email in error, please immediately notify the sender via
telephone or return mail.
_______________________________________________
HCP-Users mailing list
[email protected]
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. If you have received this email in error, please immediately notify the sender via telephone or return mail.
_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
_______________________________________________
HCP-Users mailing list
[email protected]
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. If you have received this email in error, please immediately notify the sender via telephone
or return mail.
_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
|
