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Dear Juan Eugenio Iglesias:
Thanks for the response.
I have a question about T1 and T2 data, whether they must be scanned by
the same patient?
Because I have no T1 sequence data. If i want to get the hippocampal
subfields of T2 data, can I use T1 data of patient A to recon-all and T2 data
of another patient B to segment ?
Thank you very much.
Confused beginner.
Qimo
At 2018-11-26 23:45:17, "Iglesias Gonzalez, Eugenio" <[email protected]>
wrote:
External Email - Use Caution
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,
/E
--
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: <[email protected]> on behalf of qimo601
<[email protected]>
Reply-To: Freesurfer support list <[email protected]>
Date: Monday, 26 November 2018 at 06:49
To: "[email protected]" <[email protected]>
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
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