Dear Qimo,

You do need a T1 volume to run the main recon-all; sorry if the wiki wasn’t clear enough. It is true that segmenta_T2.sh only uses the intensities of the FLAIR scan, but a recon-all processed T1 is still necessary.

Cheers,

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London, and

Research Affiliate

Computer Science and Artificial Intelligence Laboratory (CSAIL)

Massachusetts Institute of Technology

http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of qimo601 <qimo601@126.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 26 November 2018 at 06:49
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] segmentHA_T2.sh: amygdala recon-all command stoped.

External Email - Use Caution

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