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hi,FreeSurfer experts. I am trying to use segmentHA_T2.sh command to segment the T2 FLAIR Sequence MRI Data. Also I am now only having T2 Data. But there was a mistake in the first step. Sincerely ask for help.
(1)First I use recon-all command to generate the subject file from my nii file.But it stop in Correct Defect step. I have run three times after 48 hours. It also stop there. I dont't know why. Can you help me?
my command: recon-all -all -i nii-004/ADNI_004_3D_FLAIR.nii.gz -s Subj004 -itkthreads 4
The output of the terminal is as follows： CORRECTING DEFECT 45 (vertices=24, convex hull=53, v0=135114) After retessellation of defect 45 (v0=135114), euler #=96 (83072,238273,155297) : difference with theory (-19) = -115 CORRECTING DEFECT 46 (vertices=97, convex hull=30, v0=136402) After retessellation of defect 46 (v0=136402), euler #=97 (83078,238301,155320) : difference with theory (-18) = -115 CORRECTING DEFECT 47 (vertices=74, convex hull=24, v0=138982) After retessellation of defect 47 (v0=138982), euler #=98 (83088,238338,155348) : difference with theory (-17) = -115 CORRECTING DEFECT 48 (vertices=83, convex hull=55, v0=139717) After retessellation of defect 48 (v0=139717), euler #=99 (83098,238391,155392) : difference with theory (-16) = -115 CORRECTING DEFECT 49 (vertices=141431, convex hull=17606, v0=149662)
(2)Because of the above mistakes, I haven't tried the next step yet. segmentHA_T2.sh subject004 ADNI_004_3D_FLAIR.nii.gz T2 0
(3)Attached is the log(recon-all.log).
(4)My envientment as follows: Ubuntu 16.04 amd_x64 freesurfer-linux-centos6_x86_64-dev.tar.gz(21-Nov-2018) My data type: 3D-FLAIR (Pixel Spacing X=1.0 mm; Pixel Spacing Y=1.0 mm; Pulse Sequence=SE/IR; Slice Thickness=1.2000000476837158 mm; TE=441.0 ms; TI=1650.0 ms; TR=4800.0 ms; Weighting=T2;)
Thanks, Qimo