[HCP-Users] what is behind the spin-echo based bias field correction
Hello, I am trying to understand how the “- - biascorrection=SEBASED” option in the GenericfMRIVolumeProcessingPipeline.sh works. Could someone refer me to a paper on how the bias field can be estimated from a spin echo and a gradient echo? Which images are used for the gradient echo? Many thanks Olivia Olivia Viessmann, PhD A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School Building 75, Third Ave Charlestown, MA 02129 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] path to bbregister .dat file for REST call
csv>);
do
RESOURCE=$(echo ${RESOURCEROW} | cut -d, -f2)
#
# DOWNLOAD FILES FROM FMRI PREPROC RESOURCES
#
if [[ $RESOURCE =~ ^.*fMRI.*_preproc ]]; then
SERIES=$(echo "$RESOURCE" | sed -e
"s/_preproc//")
echo $SUBJ $LABEL $URI $RESOURCE
$SERIES
DIRECTORY="$SUBJ/MNINonLinear/Results/${SERIES}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased"
mkdir -p $DIRECTORY/FieldMap
curl -s -k --cookie
JSESSIONID=$JSESSIONID
https://db.humanconnectome.org${URI}/resources/${RESOURCE}/files/${SERIES}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/fMRI2str.mat<https://db.humanconnectome.org${uri}/resources/$%7BRESOURCE%7D/files/$%7BSERIES%7D/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/fMRI2str.mat>
-o $DIRECTORY/fMRI2str.mat
curl -s -k --cookie
JSESSIONID=$JSESSIONID
https://db.humanconnectome.org${URI}/resources/${RESOURCE}/files/${SERIES}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef_dc_jac.nii.gz<https://db.humanconnectome.org${uri}/resources/$%7BRESOURCE%7D/files/$%7BSERIES%7D/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef_dc_jac.nii.gz>
-o $DIRECTORY/FieldMap/SBRef_dc_jac.nii.gz
fi
done
done
You can set the JSESSIONID with this call:
read -s -p "ENTER PASSWORD: " PW;JSESSIONID=`curl -s -k -u
YOUR_USERNAME_HERE:$PW
https://db.humanconnectome.org/REST/JSESSIONID`;export<https://db.humanconnectome.org/REST/JSESSIONID%60;export>
JSESSIONID;echo $JSESSIONID
I hope this helps. Note, I didn’t include the file Tim mentioned that you
would already in your download folders.
Regards,
Mike
From:
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
[mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Viessmann, Olivia
M.
Sent: Tuesday, February 27, 2018 9:48 AM
To: NEUROSCIENCE tim mailto:tsc...@mst.edu>>
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] path to bbregister .dat file for REST call
Dear Tim,
thanks a lot for the detailed explanation, this is all tremendously helpful and
is indeed what I am looking for.
I hope someone on this list knows where the transforms are stored. As soon as I
know from where to download it I will give it a try and let you know if it
worked.
Thanks
Olivia
On 26 Feb 2018, at 18:22, Timothy Coalson
mailto:tsc...@mst.edu>> wrote:
0307_3T/RESOURCES/rfMRI_REST1_LR_preproc/rfMR
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Re: [HCP-Users] ERROR: Unexpected parameter: -local-affine-method in PostFreeSurferPipeLineBatch.sh
The dev_latest version worked.
Thanks a lot,
Olivia
Olivia Viessmann, PhD
A.A. Martinos Center for Biomedical Imaging
Harvard Medical School
Massachusetts General Hospital
Building 75, Third Ave
Charlestown, MA 02129
On 12 Mar 2018, at 19:05, Timothy Coalson
mailto:tsc...@mst.edu>> wrote:
Yes, the newest pipelines used an option that isn't in the 1.2.3 release. Grab
the "dev_latest" zip file that matches your OS from here:
http://brainvis.wustl.edu/workbench/
Tim
On Mon, Mar 12, 2018 at 5:57 PM, Viessmann, Olivia M.
mailto:oviessm...@mgh.harvard.edu>> wrote:
Hello,
I am running the PostFreeSurferPipeLineBatch.sh script from the
Pipelines/Examples/Scripts/ on the example subject 100307. I've successfully
tun the PreFreeSurfer and FreeSurfer scripts, but ran into the following
problem with the PostFreeSurfer script when it calls wb_command
I get the following error
While running:
${HOME}/HCPData/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command
-surface-distortion
${HOME}/HCPData/Pipelines_ExampleData/100307/MNINonLinear/Native/100307.L.sphere.native.surf.gii
${HOME}/HCPData/Pipelines_ExampleData/100307/MNINonLinear/Native/100307.L.sphere.reg.reg_LR.native.surf.gii
${HOME}/HCPData/Pipelines_ExampleData/100307/MNINonLinear/Native/100307.L.Strain_FS.native.shape.gii
-local-affine-method
ERROR: Unexpected parameter: -local-affine-method
Is the script relying on a newer version of wb_command? I downloaded the
binaries for workbench from here
https://www.humanconnectome.org/software/get-connectome-workbench
Thanks a lot in advance
Olivia
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[HCP-Users] ERROR: Unexpected parameter: -local-affine-method in PostFreeSurferPipeLineBatch.sh
Hello,
I am running the PostFreeSurferPipeLineBatch.sh script from the
Pipelines/Examples/Scripts/ on the example subject 100307. I've successfully
tun the PreFreeSurfer and FreeSurfer scripts, but ran into the following
problem with the PostFreeSurfer script when it calls wb_command
I get the following error
While running:
${HOME}/HCPData/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command
-surface-distortion
${HOME}/HCPData/Pipelines_ExampleData/100307/MNINonLinear/Native/100307.L.sphere.native.surf.gii
${HOME}/HCPData/Pipelines_ExampleData/100307/MNINonLinear/Native/100307.L.sphere.reg.reg_LR.native.surf.gii
${HOME}/HCPData/Pipelines_ExampleData/100307/MNINonLinear/Native/100307.L.Strain_FS.native.shape.gii
-local-affine-method
ERROR: Unexpected parameter: -local-affine-method
Is the script relying on a newer version of wb_command? I downloaded the
binaries for workbench from here
https://www.humanconnectome.org/software/get-connectome-workbench
Thanks a lot in advance
Olivia
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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Re: [HCP-Users] path to bbregister .dat file for REST call
Dear Tim, thanks a lot for the detailed explanation, this is all tremendously helpful and is indeed what I am looking for. I hope someone on this list knows where the transforms are stored. As soon as I know from where to download it I will give it a try and let you know if it worked. Thanks Olivia On 26 Feb 2018, at 18:22, Timothy Coalson mailto:tsc...@mst.edu>> wrote: 0307_3T/RESOURCES/rfMRI_REST1_LR_preproc/rfMR The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] path to bbregister .dat file for REST call
Hi Matt,
I would like to transform the surfaces from native space to the EPI run, i.e.
to the head position of the subject during the rs-fMRI acquisition. My final
aim is to calculate surface orientations to the main B0 field and relate them
to the rs-fmri data, so I need to rotate the surface to the exact head
orientation during the EPI acquisition. I already noticed that the T1w image is
rigidly transformed before the freeSurfer recon-all is run.
My plan was to use the inverse of the acpc.mat file (that I understand to be
the 6 DOF transform used to align the subject rigidly to MNI) and the inverse
of the EPItoT1w.dat to transform the surfaces.
But you mention the FSLBBR preregistration - what do you think is the correct
transformation file for me?
Thanks a lot,
Olivia
On 26 Feb 2018, at 16:42, Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
That will contain an incomplete EPI to T1w registration because we preregister
with FSLBBR. Why do you need this transform in this format?
Peace,
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Viessmann, Olivia M."
mailto:oviessm...@mgh.harvard.edu>>
Date: Monday, February 26, 2018 at 3:36 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] path to bbregister .dat file for REST call
Hello,
I would like to retrieve the bbregister .dat file from the EPI to T1w
registration but don't know its exact path.
>From the shell scripts on github
>(Pipelines/fMRIVolume.scripts/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh)
I found out that the file I am looking for is named EPItoT1w.dat. However the
path in the script is ${WD}, so I don't know what to put into my curl call, eg:
curl -u myUserName:myPassWord -O
https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/200109/experiments/200109_CREST/resources/200109_CREST/files//EPItoT1w.dat<https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/200109/experiments/200109_CREST/resources/200109_CREST/files/%3C??%3E/EPItoT1w.dat>
I'd very much appreciate if someone who knows the naming of this path could let
me know.
Many thanks
Olivia Viessmann
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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dispose of the e-mail.
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[HCP-Users] path to bbregister .dat file for REST call
Hello,
I would like to retrieve the bbregister .dat file from the EPI to T1w
registration but don't know its exact path.
>From the shell scripts on github
>(Pipelines/fMRIVolume.scripts/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh)
I found out that the file I am looking for is named EPItoT1w.dat. However the
path in the script is ${WD}, so I don't know what to put into my curl call, eg:
curl -u myUserName:myPassWord -O
https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/200109/experiments/200109_CREST/resources/200109_CREST/files//EPItoT1w.dat
I'd very much appreciate if someone who knows the naming of this path could let
me know.
Many thanks
Olivia Viessmann
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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