External Email - Use Caution
Hello FreeSurfer Developers,
I am trying to analyze the subfields of the hippocampus using FreeSurfer 6.0 based on the tutorial, "Segmentation of hippocampal subfields". However, several errors come up when I run:
recon-all -s 102 -hippocampal-subfields-T1
#@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18 PDT 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18 PDT 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
I have searched through the list to see if anyone else has had this issue but to no avail.
Version:
freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
OS: X V 10.9.5
Thanks! Jasmin
External Email - Use Caution
Dear Jasmin, The script segmentSF_T1.sh does not seem to be able to find basic commands like pwd and dirname. Are these in your path? 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 Jasmin Alves jalves@usc.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 11 July 2018 at 16:26 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
External Email - Use Caution Hello FreeSurfer Developers,
I am trying to analyze the subfields of the hippocampus using FreeSurfer 6.0 based on the tutorial, "Segmentation of hippocampal subfields". However, several errors come up when I run:
recon-all -s 102 -hippocampal-subfields-T1
#@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18 PDT 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18 PDT 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
I have searched through the list to see if anyone else has had this issue but to no avail.
Version:
freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
OS: X V 10.9.5
Thanks! Jasmin
-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edumailto:jalves@usc.edu
External Email - Use Caution
Hello Eugenio,
Thank you for the reply. The script, segmentSF_T1.sh is found in
/Users/PageLab/Documents/freesurfer/bin
The freesurfer environment has been set to
/Users/PageLab/Documents/freesurfer
So, I am not sure why the script is inaccessible. Recon-all works great.
Thanks, Jasmin On Wed, Jul 11, 2018 at 9:08 AM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:
External Email - Use CautionDear Jasmin,
The script segmentSF_T1.sh does not seem to be able to find basic commands like pwd and dirname. Are these in your path?
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 Jasmin Alves jalves@usc.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Wednesday, 11 July 2018 at 16:26 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
External Email - Use Caution *Hello FreeSurfer Developers,
I am trying to analyze the subfields of the hippocampus using FreeSurfer 6.0 based on the tutorial, "Segmentation of hippocampal subfields". However, several errors come up when I run:
recon-all -s 102 -hippocampal-subfields-T1
#@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18 PDT 2018
dirname: Command not found.
pwd: Command not found.
pwd: Command not found.
/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
#--------------------------------------------
#@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18 PDT 2018
dirname: Command not found.
pwd: Command not found.
pwd: Command not found.
/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
I have searched through the list to see if anyone else has had this issue but to no avail.
Version:
freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
OS: X V 10.9.5
Thanks!
Jasmin
--
Jasmin Alves
Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail. nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c= clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m= w4MGsgIqoYbSnHHZCr8GnKo65Vd50Pdt3Ha1YYG4Rw8&s=JWFtZN0TxhbF- szDNVVAGtRlTVerKBV7GCF0cFlu-_w&e=
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www. partners.org_complianceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN 0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=w4MGsgIqoYbSnHHZCr8GnKo65Vd50P dt3Ha1YYG4Rw8&s=2mrR0Thpt73B1ran6vJjkbnFjoZ7wovDcNc23JUxZLY&e= . 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
Sorry, I meant pwd, dirname, etc
-- 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 Jasmin Alves jalves@usc.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 11 July 2018 at 17:16 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
External Email - Use Caution Hello Eugenio,
Thank you for the reply. The script, segmentSF_T1.sh is found in
/Users/PageLab/Documents/freesurfer/bin
The freesurfer environment has been set to
/Users/PageLab/Documents/freesurfer
So, I am not sure why the script is inaccessible. Recon-all works great.
Thanks, Jasmin On Wed, Jul 11, 2018 at 9:08 AM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:
External Email - Use Caution Dear Jasmin, The script segmentSF_T1.sh does not seem to be able to find basic commands like pwd and dirname. Are these in your path? 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 Jasmin Alves <jalves@usc.edumailto:jalves@usc.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 11 July 2018 at 16:26 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
External Email - Use Caution Hello FreeSurfer Developers,
I am trying to analyze the subfields of the hippocampus using FreeSurfer 6.0 based on the tutorial, "Segmentation of hippocampal subfields". However, several errors come up when I run:
recon-all -s 102 -hippocampal-subfields-T1
#@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18 PDT 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18 PDT 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
I have searched through the list to see if anyone else has had this issue but to no avail.
Version:
freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
OS: X V 10.9.5
Thanks! Jasmin
-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edumailto:jalves@usc.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edumailto:jalves@usc.edu
External Email - Use Caution
And yes, pwd and dirname are both in my path.
m-100205:bin PageLab$ pwd
/Users/PageLab/Documents/freesurfer/bin
m-100205:bin PageLab$ dirname
usage: dirname path
m-100205:bin PageLab$ dirname path
.
On Wed, Jul 11, 2018 at 9:25 AM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:
External Email - Use CautionSorry, I meant pwd, dirname, etc
--
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 Jasmin Alves jalves@usc.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Wednesday, 11 July 2018 at 17:16 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
External Email - Use Caution *Hello Eugenio,
Thank you for the reply. The script, segmentSF_T1.sh is found in
/Users/PageLab/Documents/freesurfer/bin
The freesurfer environment has been set to
/Users/PageLab/Documents/freesurfer
So, I am not sure why the script is inaccessible. Recon-all works great.
Thanks, Jasmin
On Wed, Jul 11, 2018 at 9:08 AM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:
External Email - Use Caution *Dear Jasmin,
The script segmentSF_T1.sh does not seem to be able to find basic commands like pwd and dirname. Are these in your path?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jeiglesias.com&d=DwMGaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=uVoTt2lUUI3lPCTLL4_m3xXKcQAIY7CvMjUHkiqxFVM&s=b3vNs9mm-UmTB5bTPc3gp4k8a2SJTV-z-VfU-ANEdUk&e=
http://cmictig.cs.ucl.ac.uk/ https://urldefense.proofpoint.com/v2/url?u=http-3A__cmictig.cs.ucl.ac.uk_&d=DwMGaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=uVoTt2lUUI3lPCTLL4_m3xXKcQAIY7CvMjUHkiqxFVM&s=QturHXAvxSxNX-kZlXqIqw-HhIKq9k9ygwb5etQh0d0&e=
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jasmin Alves jalves@usc.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Wednesday, 11 July 2018 at 16:26 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
External Email - Use Caution *Hello FreeSurfer Developers,
I am trying to analyze the subfields of the hippocampus using FreeSurfer 6.0 based on the tutorial, "Segmentation of hippocampal subfields". However, several errors come up when I run:
recon-all -s 102 -hippocampal-subfields-T1
#@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18 PDT 2018
dirname: Command not found.
pwd: Command not found.
pwd: Command not found.
/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
#--------------------------------------------
#@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18 PDT 2018
dirname: Command not found.
pwd: Command not found.
pwd: Command not found.
/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
I have searched through the list to see if anyone else has had this issue but to no avail.
Version:
freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
OS: X V 10.9.5
Thanks!
Jasmin
--
Jasmin Alves
Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail. nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c= clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m= w4MGsgIqoYbSnHHZCr8GnKo65Vd50Pdt3Ha1YYG4Rw8&s=JWFtZN0TxhbF- szDNVVAGtRlTVerKBV7GCF0cFlu-_w&e=
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www. partners.org_complianceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN 0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=w4MGsgIqoYbSnHHZCr8GnKo65Vd50P dt3Ha1YYG4Rw8&s=2mrR0Thpt73B1ran6vJjkbnFjoZ7wovDcNc23JUxZLY&e= . 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.
--
Jasmin Alves
Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail. nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c= clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m= uVoTt2lUUI3lPCTLL4_m3xXKcQAIY7CvMjUHkiqxFVM&s= aCD9YXVaLEQPHlwxNffpxqU41dBZYS5tbIyn4A_o6LE&e=
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www. partners.org_complianceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN 0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=uVoTt2lUUI3lPCTLL4_ m3xXKcQAIY7CvMjUHkiqxFVM&s=ZNP-IbNxBbHy68ce1SNMRD2bIJmwPOfgdEvDfD6dltM&e= . 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
Hello Eugenio,
I noticed Matlab doesn't open when I run the hippocampal analysis, so when I tried to click on the file, segmentSubjectT1_autoEstimateAlveusML,
I encountered the following error:
Check with the developer to make sure segmentSubjectT1_autoEstimateAlveusML works with this version of OS X. You may need to reinstall the application. Be sure to install any available updates for the application and OS X.
Thanks, Jasmin
On Wed, Jul 11, 2018 at 9:15 AM, Jasmin Alves jalves@usc.edu wrote:
Hello Eugenio,
Thank you for the reply. The script, segmentSF_T1.sh is found in
/Users/PageLab/Documents/freesurfer/bin
The freesurfer environment has been set to
/Users/PageLab/Documents/freesurfer
So, I am not sure why the script is inaccessible. Recon-all works great.
Thanks, Jasmin On Wed, Jul 11, 2018 at 9:08 AM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:
External Email - Use CautionDear Jasmin,
The script segmentSF_T1.sh does not seem to be able to find basic commands like pwd and dirname. Are these in your path?
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 Jasmin Alves jalves@usc.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Wednesday, 11 July 2018 at 16:26 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
External Email - Use Caution *Hello FreeSurfer Developers,
I am trying to analyze the subfields of the hippocampus using FreeSurfer 6.0 based on the tutorial, "Segmentation of hippocampal subfields". However, several errors come up when I run:
recon-all -s 102 -hippocampal-subfields-T1
#@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18 PDT 2018
dirname: Command not found.
pwd: Command not found.
pwd: Command not found.
/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
#--------------------------------------------
#@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18 PDT 2018
dirname: Command not found.
pwd: Command not found.
pwd: Command not found.
/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
I have searched through the list to see if anyone else has had this issue but to no avail.
Version:
freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
OS: X V 10.9.5
Thanks!
Jasmin
--
Jasmin Alves
Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nm r.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c=clK 7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rN RHLug&m=w4MGsgIqoYbSnHHZCr8GnKo65Vd50Pdt3Ha1YYG4Rw8&s= JWFtZN0TxhbF-szDNVVAGtRlTVerKBV7GCF0cFlu-_w&e=
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.part ners.org_complianceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BO UHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=w4MGsgIqoYbSnH HZCr8GnKo65Vd50Pdt3Ha1YYG4Rw8&s=2mrR0Thpt73B1ran6vJjkbnFjoZ7 wovDcNc23JUxZLY&e= . 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.
-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu
freesurfer@nmr.mgh.harvard.edu
-
Iglesias Gonzalez, Eugenio -
Jasmin Alves