1) In T2wToT1wDistortionCorrect code, fugue fsl command has been used to
preprocess the fieldmap into a shiftmap and the output is e.g
FieldMap_ShiftMapT1w.nii.gz. In the next step, shiftmap is used to warp field
as followes:
${FSLDIR}/bin/convertwarp --relout --rel --ref=${WD}/Magnitude
--shiftmap=${WD}/FieldMap_ShiftMap${TXw}.nii.gz --shiftdir=${UnwarpDir}
--out=${WD}/FieldMap_Warp${TXw}.nii.gz
The output of above i.e. FieldMap_Warp${TXw}.nii.gz is zero for both T1w and
T2w data!
2) Because the value that dicom field(0019,1018) shows is 1/2 of
1/(BW/BaseRes); (I compared by just dividing).
forexample in prefreesurferBatch code we have: T2wSampleSpacing="0.0000021"
#DICOM field (0019,1018) in s or "NONE" if not used. but of
Structurals\T2w_SPC1 protocol of HCP, 1/(BW=744/BaseRes=320) would result in
~0.0000043. It was also the same for my case.
Thanks,
Zahra
________________________________
From: Glasser, Matthew [[email protected]]
Sent: Thursday, July 07, 2016 4:53 AM
To: Shams, Z. (Zahra); [email protected]
Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
Perhaps I’m a bit muddled this evening, but I’m not understanding the field map
issue you are having. Can you be more specific about what file is all zeros?
As for the sample spacing, how do you know that it is off by a factor of 2?
Peace,
Matt.
From: "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>>
Date: Wednesday, July 6, 2016 at 8:25 AM
To: Matt Glasser <[email protected]<mailto:[email protected]>>
Subject: RE: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
Dear Matt,
You already gave me a hint on how to solve the problem of brain extraction and
it's now perfect.
Currently, I have problem with T1 and T2 distortion correction using
Gradient-echo field map and the problem is that the output of convertwarp which
is FieldMap-Warp is zero. I applied that to my T1w, T2w and UNI (from mp2rage
sequence) images and have the same problem for all of them. I'd appreciate if
you could help me to get over that.
The other thing I'd like to mention is that for T1w&T2wsamplespacing, the dicom
field (0019,1018) has been used in the code which is 1/2*(BW/# of pixels
equivalent to base resolution). Should't it(dicom field (0019,1018)) be
multiplied by 2 to have the right dwell time of BW/Base Res.?
Thank you in advance for your taking time to answer my email.
Best regards,
Zahra
________________________________
From: Glasser, Matthew [[email protected]<mailto:[email protected]>]
Sent: Sunday, June 19, 2016 10:17 PM
To: Shams, Z. (Zahra)
Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain
extraction?
Did you go ahead and try running FreeSurfer? It may be able to recover as the
brain masked data are only used to improve FreeSurfer’s internal registration.
It uses its own brain masking algorithm.
Peace,
Matt.
From: "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>>
Date: Sunday, June 19, 2016 at 3:14 PM
To: Matt Glasser <[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 on it.
Best regards,
Xara
________________________________
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
