Dear Freesurfer community, Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and the following command line: trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tracula.config It stops, giving me errors like these: niiRead(): error opening file /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz ERROR: reading /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz While setting "dob0 = 0" everything runs smoothly. Can you help me please? I'll attach the log + dmrirc (tracula.config) Best,Elia. -------------------------------------------------------------------------------------------------------------- Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Hi Elia - It looks like this file didn't get created: /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
The command that was supposed to create it was epidewarp.fsl. You can find the command line that begins with "epidewarp.fsl" in the log file that you sent me. When you run that whole line directly from the unix command line, do you get any errors?
a.y
On Thu, 12 Jun 2014, Elia S. wrote:
Dear Freesurfer community, Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and the following command line:
trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tracula.config
It stops, giving me errors like these:
niiRead(): error opening file /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
ERROR: reading /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz
While setting "dob0 = 0" everything runs smoothly.
Can you help me please? I'll attach the log + dmrirc (tracula.config)
Best, Elia.
Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS
Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Hi Anastasia, Yes, launching the same command line from terminal produced the same error, but at the same time we realized we were using the wrong magnetic/phase dicoms.....which weren't magnetic/phase images at all.Could that be the cause of the failure? I would answer the question myself but right now I don't have the correct images to test it. Best,Elia.
Date: Sun, 15 Jun 2014 07:21:28 -0400 From: ayendiki@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Hi Elia - It looks like this file didn't get created: /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
The command that was supposed to create it was epidewarp.fsl. You can find the command line that begins with "epidewarp.fsl" in the log file that you sent me. When you run that whole line directly from the unix command line, do you get any errors?
a.y
On Thu, 12 Jun 2014, Elia S. wrote:
Dear Freesurfer community, Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and the following command line:
trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tracula.config
It stops, giving me errors like these:
niiRead(): error opening file /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
ERROR: reading /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz
While setting "dob0 = 0" everything runs smoothly.
Can you help me please? I'll attach the log + dmrirc (tracula.config)
Best, Elia.
Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS
Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
_______________________________________________ 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.
Hi Elia - This could very well be the case. Does the epidewarp.fsl command give you any specific error message, or does it just not create an output?
a.y
On Tue, 17 Jun 2014, Elia S. wrote:
Hi Anastasia, Yes, launching the same command line from terminal produced the same error, but at the same time we realized we were using the wrong magnetic/phase dicoms.....which weren't magnetic/phase images at all. Could that be the cause of the failure? I would answer the question myself but right now I don't have the correct images to test it.
Best, Elia.
Date: Sun, 15 Jun 2014 07:21:28 -0400 From: ayendiki@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Hi Elia - It looks like this file didn't get created: /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
The command that was supposed to create it was epidewarp.fsl. You can find the command line that begins with "epidewarp.fsl" in the log file that you sent me. When you run that whole line directly from the unix command line, do you get any errors?
a.y
On Thu, 12 Jun 2014, Elia S. wrote:
Dear Freesurfer community, Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and the follow
ing command
line:
trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/trac
ula.config
It stops, giving me errors like these:
niiRead(): error opening file /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
ERROR: reading /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.g
z
While setting "dob0 = 0" everything runs smoothly.
Can you help me please? I'll attach the log + dmrirc (tracula.config)
Best, Elia.
Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS
Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:4
5 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
_______________________________________________ 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.
Hi Anastasia, The epidewarp.fsl gives me the following output: FSLVersion 5.0.6FSLVerMaj 5FSL Version is 5.0.6, must be 3.X or 4.X Either from script or command line. Best,Elia.
Date: Tue, 17 Jun 2014 09:17:58 -0400 From: ayendiki@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Hi Elia - This could very well be the case. Does the epidewarp.fsl command give you any specific error message, or does it just not create an output?
a.y
On Tue, 17 Jun 2014, Elia S. wrote:
Hi Anastasia, Yes, launching the same command line from terminal produced the same error, but at the same time we realized we were using the wrong magnetic/phase dicoms.....which weren't magnetic/phase images at all. Could that be the cause of the failure? I would answer the question myself but right now I don't have the correct images to test it.
Best, Elia.
Date: Sun, 15 Jun 2014 07:21:28 -0400 From: ayendiki@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Hi Elia - It looks like this file didn't get created: /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
The command that was supposed to create it was epidewarp.fsl. You can find the command line that begins with "epidewarp.fsl" in the log file that you sent me. When you run that whole line directly from the unix command line, do you get any errors?
a.y
On Thu, 12 Jun 2014, Elia S. wrote:
Dear Freesurfer community, Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and the follow
ing command
line:
trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/trac
ula.config
It stops, giving me errors like these:
niiRead(): error opening file /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
ERROR: reading /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.g
z
While setting "dob0 = 0" everything runs smoothly.
Can you help me please? I'll attach the log + dmrirc (tracula.config)
Best, Elia.
Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS
Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:4
5 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
_______________________________________________ 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.
Check the email archives for a recent message about epidewarp.fsl from Doug, there is a newer version that works with FSL 5.
On Tue, 17 Jun 2014, Elia S. wrote:
Hi Anastasia, The epidewarp.fsl gives me the following output:
FSLVersion 5.0.6 FSLVerMaj 5 FSL Version is 5.0.6, must be 3.X or 4.X
Either from script or command line.
Best, Elia.
Date: Tue, 17 Jun 2014 09:17:58 -0400 From: ayendiki@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Hi Elia - This could very well be the case. Does the epidewarp.fsl command give you any specific error message, or does it just not create an output?
a.y
On Tue, 17 Jun 2014, Elia S. wrote:
Hi Anastasia, Yes, launching the same command line from terminal produced the same error, but at the sa
me
time we realized we were using the wrong magnetic/phase dicoms.....which weren't magnetic/phase images at all. Could that be the cause of the failure? I would answer the question myself but right now
I
don't have the correct images to test it.
Best, Elia.
Date: Sun, 15 Jun 2014 07:21:28 -0400 From: ayendiki@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Hi Elia - It looks like this file didn't get created: /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
The command that was supposed to create it was epidewarp.fsl. You can find the command line that begins with "epidewarp.fsl" in the log file that you sent me. When you run that whole line directly from the unix command line, do you get any errors?
a.y
On Thu, 12 Jun 2014, Elia S. wrote:
Dear Freesurfer community, Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and the foll
ow
ing command
line:
trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tr
ac
ula.config
It stops, giving me errors like these:
niiRead(): error opening file /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
ERROR: reading /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii
.g
z
While setting "dob0 = 0" everything runs smoothly.
Can you help me please? I'll attach the log + dmrirc (tracula.config)
Best, Elia.
--
Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS
Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20
:4
5 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf
er
The information in this e-mail is intended only for the person to whom it is addressed. I
f
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.
Hi Anastasia, Found it, I'll replace it right away, thanks :) Best,Elia.
Date: Tue, 17 Jun 2014 09:29:14 -0400 From: ayendiki@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Check the email archives for a recent message about epidewarp.fsl from Doug, there is a newer version that works with FSL 5.
On Tue, 17 Jun 2014, Elia S. wrote:
Hi Anastasia, The epidewarp.fsl gives me the following output:
FSLVersion 5.0.6 FSLVerMaj 5 FSL Version is 5.0.6, must be 3.X or 4.X
Either from script or command line.
Best, Elia.
Date: Tue, 17 Jun 2014 09:17:58 -0400 From: ayendiki@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Hi Elia - This could very well be the case. Does the epidewarp.fsl command give you any specific error message, or does it just not create an output?
a.y
On Tue, 17 Jun 2014, Elia S. wrote:
Hi Anastasia, Yes, launching the same command line from terminal produced the same error, but at the sa
me
time we realized we were using the wrong magnetic/phase dicoms.....which weren't magnetic/phase images at all. Could that be the cause of the failure? I would answer the question myself but right now
I
don't have the correct images to test it.
Best, Elia.
Date: Sun, 15 Jun 2014 07:21:28 -0400 From: ayendiki@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Hi Elia - It looks like this file didn't get created: /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
The command that was supposed to create it was epidewarp.fsl. You can find the command line that begins with "epidewarp.fsl" in the log file that you sent me. When you run that whole line directly from the unix command line, do you get any errors?
a.y
On Thu, 12 Jun 2014, Elia S. wrote:
Dear Freesurfer community, Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and the foll
ow
ing command
line:
trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tr
ac
ula.config
It stops, giving me errors like these:
niiRead(): error opening file /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
ERROR: reading /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii
.g
z
While setting "dob0 = 0" everything runs smoothly.
Can you help me please? I'll attach the log + dmrirc (tracula.config)
Best, Elia.
--
Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS
Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20
:4
5 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf
er
The information in this e-mail is intended only for the person to whom it is addressed. I
f
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 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
-
Anastasia Yendiki -
Elia S.