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WorldToImageTransform after cropping:
AffineTransform (0x128c17790)
RTTI typeinfo: itk::AffineTransform<double, 3u>
Reference Count: 1
Modified Time: 377450804
Debug: Off
Object Name:
Observers:
none
Matrix:
-3.00003 8.73125e-11 2.22045e-16
-8.4821e-14 -2.67186e-12 -3.00003
5.55112e-16 3.00003 1.97674e-10
Offset: [15.4608, 101.71, 117.525]
Center: [0, 0, 0]
Translation: [15.4608, 101.71, 117.525]
Inverse:
-0.33333 4.85723e-17 9.7012e-12
8.32667e-17 2.19633e-11 0.33333
9.42996e-15 -0.33333 -2.96735e-13
Singular: 0
I am WriteImage and I'm running!
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does not contain MRI parameters
numberOfLabels: 25
Rasterizing mesh...here: 25
here2: 25
done
mri_convert.bin discreteLabels.mgz discreteLabelsResampledT1.mgz -rt nearest -odt float -rl /Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from discreteLabels.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 2.84217e-14)
j_ras = (0, 6.58905e-11, -1)
k_ras = (2.91038e-11, 1, -8.90815e-13)
reading template info from volume /Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz...
Reslicing using nearest
writing to discreteLabelsResampledT1.mgz...
mv: rename volumesAmygdala.txt to /Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt: No such file or directory
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Dear Jinyoung,
Can you please send us the log, or at least the last few lines before the error?
Also, which exact version are you using? 6.0 or dev?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.
harvard.edu > on behalf of 오진영 <jinyoung.oh555@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Date: Monday, 30 July 2018 at 06:41
To: "freesurfer@nmr.mgh.harvard.edu " <freesurfer@nmr.mgh.harvard.edu >
Cc: JongHyun Lee <jonghyunlee1993@gmail.com>
Subject: [Freesurfer] hippocampal subfields segmentation error
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Hello, freesurfer experts
I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala by using "segmentSF_T1.sh" command.
I have downloaded the newest development version(freesurfer v.6.0) and license, as well as the required matlab runtime.
However, I am getting the following error:
mv: rename volumesAmygdala.txt to /Users/mnd_mac/Desktop/JY_
surfer/T1_data/Jinyoung_T1/ Jinyoung_test/mri/lh. hippoSfVolumes-T1.amygdala. v10.txt: No such file or directory
and I have no idea how to find the text file and solve this problem out.
If you have any idea or recommends, please send me the e-mail back.
Thanks!
Jinyoung
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