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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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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