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_surf er/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
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: 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
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
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 e.iglesias@ucl.ac.uk :
External Email - Use CautionDear 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
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 Freesurfer@nmr.mgh.harvard.edu 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.
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: 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 09:29 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu 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 <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk>:
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: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 오진영 <jinyoung.oh555@gmail.commailto:jinyoung.oh555@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, 30 July 2018 at 06:41 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: JongHyun Lee <jonghyunlee1993@gmail.commailto:jonghyunlee1993@gmail.com> 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 Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu 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.
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 e.iglesias@ucl.ac.uk :
External Email - Use CautionDear 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
*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 09:29 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *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:
noneMatrix:
-3.00003 8.73125e-11 2.22045e-16 -8.4821e-14 -2.67186e-12 -3.00003 5.55112e-16 3.00003 1.97674e-10Offset: [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-13Singular: 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 < e.iglesias@ucl.ac.uk>:
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
*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
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 Freesurfer@nmr.mgh.harvard.edu 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 Freesurfer@nmr.mgh.harvard.edu 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@nmr.mgh.harvard.edu
-
Iglesias Gonzalez, Eugenio -
오진영