Did you look in the last volume (z)? Peace,
Matt. From: "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>> Date: Friday, July 8, 2016 at 6:36 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? 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]<mailto:[email protected]>] Sent: Thursday, July 07, 2016 4:53 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? 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. ________________________________ 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
