External Email - Use Caution Dear Eugenio
Thank you for your help. As I need to segment the nuclei of amygdala, I'll try to download the development version. Thanks!! Jinyoung 2018-07-30 17:39 GMT+09:00 Iglesias Gonzalez, Eugenio <[email protected]> : > 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]>: > > * 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]> on behalf of 오진영 < > [email protected]> > *Reply-To: *Freesurfer support list <[email protected]> > *Date: *Monday, 30 July 2018 at 06:41 > *To: *"[email protected]" <[email protected]> > *Cc: *JongHyun Lee <[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] > 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. > > > > _______________________________________________ > Freesurfer mailing list > [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. > >
_______________________________________________ Freesurfer mailing list [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.
