Is this a problem for only a single subject, or have you had issues with other
subjects? If it is an isolated case, I might be inclined to recommend you:
1. Resample the T2w brain mask to T1w space using applywarp and
${StudyFolder}/${Subject}/T1w/xfms/T2w_reg_dc.nii.gz and nearest neighbor
interpolation
2. Apply it to the unmasked images to generate properly brain masked data:
${StudyFolder}/${Subject}/T1w/T1w_acpc_dc.nii.gz
${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore.nii.gz
${StudyFolder}/${Subject}/T1w/T2w_acpc_dc.nii.gz
${StudyFolder}/${Subject}/T1w/T2w_acpc_dc_restore.nii.gz
3. Rerun the module that does the final alignment to MNI space:
${GitRepo}/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh
--workingdir=${StudyFolder}/${Subject}/MNINonLinear
--t1=${StudyFolder}/${Subject}/T1w/T1w_acpc_dc \
--t1rest=${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore \
--t1restbrain=${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore_brain \
--t2=${StudyFolder}/${Subject}/T1w/T2w_acpc_dc \
--t2rest=${StudyFolder}/${Subject}/T1w/T2w_acpc_dc_restore \
--t2restbrain=${StudyFolder}/${Subject}/T1w/T2w_acpc_dc_restore_brain \
--ref=${GitRepo}/global/templates/MNI152_T1_0.8mm.nii.gz \
--refbrain=${GitRepo}/global/templates/MNI152_T1_0.8mm_brain.nii.gz \
--refmask=${GitRepo}/global/templates/MNI152_T1_0.8mm_brain_mask.nii.gz \
--ref2mm=${GitRepo}/global/templates/MNI152_T1_2mm.nii.gz \
--ref2mmmask=${GitRepo}/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz \
--owarp=${StudyFolder}/${Subject}/MNINonLinear/xfms/acpc_dc2standard.nii.gz
\
--oinvwarp=${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz \
--ot1=${StudyFolder}/${Subject}/MNINonLinear/T1w \
--ot1rest=${StudyFolder}/${Subject}/MNINonLinear/T1w_restore \
--ot1restbrain=${StudyFolder}/${Subject}/MNINonLinear/T1w_restore_brain \
--ot2=${StudyFolder}/${Subject}/MNINonLinear/T2w \
--ot2rest=${StudyFolder}/${Subject}/MNINonLinear/T2w_restore \
--ot2restbrain=${StudyFolder}/${Subject}/MNINonLinear/T2w_restore_brain \
--fnirtconfig=${GitRepo}/global/config/T1_2_MNI152_2mm.cnf
Matt.
From: "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>>
Date: Tuesday, March 1, 2016 at 5:06 PM
To: Matt Glasser <[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: RE: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
Yes, it looks totally fine; the problem is just with T1w data.
Xahra
________________________________
From: Glasser, Matthew [[email protected]<mailto:[email protected]>]
Sent: Tuesday, March 01, 2016 11:13 PM
To: Shams, Z. (Zahra);
[email protected]<mailto:[email protected]>
Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
Out of curiosity, does the T2w brain extraction look better?
Matt.
From: "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>>
Date: Tuesday, March 1, 2016 at 3:31 PM
To: Matt Glasser <[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: RE: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
I attached both MNI template and T1w_acpc nii.gz files with the image of
overlaying one on the other.
Thanks,
Xahra
________________________________
From: Glasser, Matthew [[email protected]<mailto:[email protected]>]
Sent: Tuesday, March 01, 2016 6:35 PM
To: Shams, Z. (Zahra);
[email protected]<mailto:[email protected]>
Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
I need to be able to see the alignment with the template.
Matt.
From: "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>>
Date: Tuesday, March 1, 2016 at 2:54 AM
To: Matt Glasser <[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: RE: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
T1 rigid alignment has been attached, but I can't see anything wrong with that.
________________________________
From: Glasser, Matthew [[email protected]<mailto:[email protected]>]
Sent: Tuesday, March 01, 2016 12:25 AM
To: Shams, Z. (Zahra);
[email protected]<mailto:[email protected]>
Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
What does the rigid alignment that precedes the brain extraction look like (i.e
${StudyFolder}/${Subject}/T1w/T1w_acpc.nii.gz
Thanks,
Matt.
From: "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>>
Date: Monday, February 29, 2016 at 10:22 AM
To: Matt Glasser <[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: RE: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
Hi Matthew,
Sorry for the long silence. I attached the raw T1w and T2w data as well as the
one you asked for.
and my call to PreFreeSurfer script is as follows:
T1wInputImages=${StudyFolder}/${Subject}/T1w/T1w.nii.gz
T2wInputImages=${StudyFolder}/${Subject}/T2w/T2w.nii.gz
SpinEchoPhaseEncodePositive="NONE"
DwellTime="NONE"
SEUnwarpDir="NONE"
TopupConfig="NONE"
GEB0InputName="NONE"
T1wSampleSpacing="0.0000092" #DICOM field (0019,1018) in s or "NONE" if not used
T2wSampleSpacing="0.0000027" #DICOM field (0019,1018) in s or "NONE" if not used
UnwarpDir="NONE"
BrainSize="150" #BrainSize in mm, 150 for humans
FNIRTConfig="${HCPPIPEDIR_Config}/T1_2_MNI152_2mm.cnf"
GradientDistortionCoeffs="NONE"
##
AtlasSpaceFolder="${StudyFolder}/${Subject}/MNINonLinear"
######
# template folders
T1wTemplate="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm.nii.gz"
T1wTemplateBrain="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm_brain.nii.gz"
T1wTemplate2mm="${HCPPIPEDIR_Templates}/MNI152_T1_2mm.nii.gz"
T2wTemplate="${HCPPIPEDIR_Templates}/MNI152_T2_0.8mm.nii.gz"
T2wTemplateBrain="${HCPPIPEDIR_Templates}/MNI152_T2_0.8mm_brain.nii.gz"
T2wTemplate2mm="${HCPPIPEDIR_Templates}/MNI152_T2_2mm.nii.gz"
TemplateMask="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm_brain_mask.nii.gz"
Template2mmMask="${HCPPIPEDIR_Templates}/MNI152_T1_2mm_brain_mask_dil.nii.gz"
sh ${HCPPIPEDIR}/PreFreeSurfer/PreFreeSurferPipeline_19022016.sh \
--path="$StudyFolder" \
--subject="$Subject" \
--t1="$T1wInputImages" \
--t2="$T2wInputImages" \
--t1template="$T1wTemplate" \
--t1templatebrain="$T1wTemplateBrain" \
--t1template2mm="$T1wTemplate2mm" \
--t2template="$T2wTemplate" \
--t2templatebrain="$T2wTemplateBrain" \
--t2template2mm="$T2wTemplate2mm" \
--templatemask="$TemplateMask" \
--template2mmmask="$Template2mmMask" \
--brainsize="$BrainSize" \
--fnirtconfig="$FNIRTConfig" \
--fmapmag="NONE" \
--fmapphase="NONE" \
--fmapgeneralelectric="NONE" \
--echodiff="NONE" \
--SEPhaseNeg="NONE" \
--SEPhasePos="NONE" \
--echospacing="$DwellTime" \
--seunwarpdir="$SEUnwarpDir" \
--t1samplespacing="$T1wSampleSpacing" \
--t2samplespacing="$T2wSampleSpacing" \
--unwarpdir="$UnwarpDir" \
--gdcoeffs="$GradientDistortionCoeffs" \
--avgrdcmethod="$AvgrdcSTRING" \
--topupconfig="$TopupConfig" \
--printcom=$PRINTCOM
Thanks again,
Xahra
________________________________
From: Glasser, Matthew [[email protected]<mailto:[email protected]>]
Sent: Friday, February 26, 2016 8:17 PM
To: Shams, Z. (Zahra);
[email protected]<mailto:[email protected]>
Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
We’ve not seen this particular issue before. Can you post some images of your
raw data? Also, what does the registration look like for this file to the
template:
${StudyFolder}/${Subject}/T1w/BrainExtraction_FNIRTbased/T1w_acpc_to_MNI_nonlin.nii.gz
Also post your call to PreFreeSurfer.
Peace,
Matt.
From:
<[email protected]<mailto:[email protected]>>
on behalf of "Shams, Z. (Zahra)"
<[email protected]<mailto:[email protected]>>
Date: Friday, February 26, 2016 at 4:21 AM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
Hi Matthew,
Thanks, I used the 0.8 template, but the problem still persists!
I attached PreFreeSurfer T1 output to this post, I would appreciate any help or
guide.
Best regards,
Xahra
________________________________
From: Glasser, Matthew [[email protected]<mailto:[email protected]>]
Sent: Thursday, February 25, 2016 12:54 AM
To: Shams, Z. (Zahra);
[email protected]<mailto:[email protected]>
Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
Yes there are. Have a look at the ${GitRepo}/global/templates directory. See
if using the 0.8mm templates helps.
Peace,
Matt.
From:
<[email protected]<mailto:[email protected]>>
on behalf of "Shams, Z. (Zahra)"
<[email protected]<mailto:[email protected]>>
Date: Wednesday, February 24, 2016 at 5:10 AM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
Dear all,
I’ve just started working with HCP structural pipeline. I’ve got two questions!
1) In PreFreeSurfer step for processing my 0.8mm T1w and T2w images, I’m
wondering if there are 0.8mm templates (in order to prevent upsampling my
output to 0.7mm) I can use instead of those 0.7mm templates.
2) Output of the brain extraction step missed some small parts of the
cortex, how can I improve the results?
Many thanks for your time,
Xara
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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.
________________________________
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.
________________________________
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.
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