External Email - Use Caution Dear Jin, 6.0 does not segment the nuclei of the amygdala; you can ignore that line, assuming the code runs to completion (I am assuming it does?) If you want to segment the nuclei of the amygdala, you’ll have to download the development version: http://freesurfer.net/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <[email protected]> on behalf of 오진영 <[email protected]> Reply-To: Freesurfer support list <[email protected]> Date: Monday, 30 July 2018 at 09:29 To: Freesurfer support list <[email protected]> Subject: Re: [Freesurfer] hippocampal subfields segmentation error External Email - Use Caution Dear Eugenio, Thanks for your reply. I am running version "freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" of freesurfer. As the log is so long, I attached whole log as a text file and I just copied few lines before the error below: 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 Thank you so much. Hope to hear you soon! Jin Young 2018-07-30 17:01 GMT+09:00 Iglesias Gonzalez, Eugenio <[email protected]<mailto:[email protected]>>: External Email - Use Caution 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 http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <[email protected]<mailto:[email protected]>> on behalf of 오진영 <[email protected]<mailto:[email protected]>> Reply-To: Freesurfer support list <[email protected]<mailto:[email protected]>> Date: Monday, 30 July 2018 at 06:41 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Cc: JongHyun Lee <[email protected]<mailto:[email protected]>> Subject: [Freesurfer] hippocampal subfields segmentation error External Email - Use Caution 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 _______________________________________________ Freesurfer mailing list [email protected]<mailto:[email protected]> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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