Hello, I am running into a tracula error very early in the preprocessing steps. I have data that was already somewhat preprocessed (reconstruction, eddy correction and magnetic field inhomogeneity correction) that I'm trying to use as an input. I have turned off those steps in the tracula configuration file. Tracula seems to find these files and starts making a few of the dwi output files in the subject's freesurfer/dmri folder. However, it then says something about not having the correct "frames" and it can't find the file dwi_frames.nii.gz. I'm not sure what this error is referring to. I attempted to run the same subject's data from their raw dicoms instead of the slightly-preprocessed file and also ran into errors. If it makes a difference, the subject had recon-all performed with freesurfer version 5.0 and I am now using version 5.3. Perhaps the subject is missing some necessary recon-all output that is only created with 5.3? Any advice?
Thanks, Mike Datko
Hi Mike - I'll need to see the configuration file and trac-all.log.
Thanks, a.y
On Mon, 21 Oct 2013, Michael Datko wrote:
Hello,I am running into a tracula error very early in the preprocessing steps. I have data that was already somewhat preprocessed (reconstruction, eddy correction and magnetic field inhomogeneity correction) that I'm trying to use as an input. I have turned off those steps in the tracula configuration file. Tracula seems to find these files and starts making a few of the dwi output files in the subject's freesurfer/dmri folder. However, it then says something about not having the correct "frames" and it can't find the file dwi_frames.nii.gz. I'm not sure what this error is referring to. I attempted to run the same subject's data from their raw dicoms instead of the slightly-preprocessed file and also ran into errors. If it makes a difference, the subject had recon-all performed with freesurfer version 5.0 and I am now using version 5.3. Perhaps the subject is missing some necessary recon-all output that is only created with 5.3? Any advice?
Thanks, Mike Datko
Hi Anastasia, I've attached my configuration file, and below is pasted the contents of the error log. Below that, I've pasted the last few lines of the trac-all log (not the error log), because it says something about a "dyld" that cannot be loaded...might be related to the problem.
Thanks, Mike
from error log:
------------------------------ SUBJECT 226A DATE Tue Oct 15 18:38:18 PDT 2013 USER mdatko HOST captain-cosine.local PROCESSOR i386 OS Darwin Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 $Id: trac-preproc,v 1.17.2.8 2013/02/16 20:57:05 ayendiki Exp $ /Applications/freesurfer/bin/trac-preproc PWD /Users/mdatko/Desktop CMD mri_probedicom --i /Users/mdatko/Desktop/226A/dti/i00001.CFMRI.1
Last few lines from non-error log:
mri_probedicom --i /Users/mdatko/Desktop/226A/dti/i00001.CFMRI.1 > /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dcminfo.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/mri_probedicom Reason: image not found Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
trac-preproc exited with ERRORS at Tue Oct 15 18:38:18 PDT 2013
On Tue, Oct 22, 2013 at 8:04 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Mike - I'll need to see the configuration file and trac-all.log.
Thanks, a.y
On Mon, 21 Oct 2013, Michael Datko wrote:
Hello,I am running into a tracula error very early in the preprocessing
steps.
I have data that was already somewhat preprocessed (reconstruction, eddy correction and magnetic field inhomogeneity correction) that I'm trying to use as an input. I have turned off those steps in the tracula configuration file. Tracula seems to find these files and starts making a few of the dwi output files in the subject's freesurfer/dmri folder. However, it then says something about not having the correct "frames" and it can't find the file dwi_frames.nii.gz. I'm not sure what this error is referring to. I attempted to run the same subject's data from their raw dicoms instead of the slightly-preprocessed file and also ran into errors. If it makes a difference, the subject had recon-all performed with freesurfer version 5.0 and I am now using version 5.3. Perhaps the subject is missing some necessary recon-all output that is only created with 5.3? Any advice?
Thanks, Mike Datko
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/**compliancelinehttp://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.
Mike,
You need to install XQuartz: http://xquartz.macosforge.org/landing/
Also see the following troubleshooting page: http://ftp.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting
-Zeke
On 10/28/2013 03:17 PM, Michael Datko wrote:
Hi Anastasia, I've attached my configuration file, and below is pasted the contents of the error log. Below that, I've pasted the last few lines of the trac-all log (not the error log), because it says something about a "dyld" that cannot be loaded...might be related to the problem.
Thanks, Mike
from error log:
SUBJECT 226A DATE Tue Oct 15 18:38:18 PDT 2013 USER mdatko HOST captain-cosine.local PROCESSOR i386 OS Darwin Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 $Id: trac-preproc,v 1.17.2.8 2013/02/16 20:57:05 ayendiki Exp $ /Applications/freesurfer/bin/trac-preproc PWD /Users/mdatko/Desktop CMD mri_probedicom --i /Users/mdatko/Desktop/226A/dti/i00001.CFMRI.1
Last few lines from non-error log:
mri_probedicom --i /Users/mdatko/Desktop/226A/dti/i00001.CFMRI.1 > /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dcminfo.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/mri_probedicom Reason: image not found Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
trac-preproc exited with ERRORS at Tue Oct 15 18:38:18 PDT 2013
On Tue, Oct 22, 2013 at 8:04 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu mailto:ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Mike - I'll need to see the configuration file and trac-all.log. Thanks, a.y On Mon, 21 Oct 2013, Michael Datko wrote: Hello,I am running into a tracula error very early in the preprocessing steps. I have data that was already somewhat preprocessed (reconstruction, eddy correction and magnetic field inhomogeneity correction) that I'm trying to use as an input. I have turned off those steps in the tracula configuration file. Tracula seems to find these files and starts making a few of the dwi output files in the subject's freesurfer/dmri folder. However, it then says something about not having the correct "frames" and it can't find the file dwi_frames.nii.gz. I'm not sure what this error is referring to. I attempted to run the same subject's data from their raw dicoms instead of the slightly-preprocessed file and also ran into errors. If it makes a difference, the subject had recon-all performed with freesurfer version 5.0 and I am now using version 5.3. Perhaps the subject is missing some necessary recon-all output that is only created with 5.3? Any advice? Thanks, Mike Datko 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 <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 XQuartz website you linked makes it sound like it is identical to X11, is it different in some way? I have X11 already and it works flawlessly with other applications such as AFNI and FSL.
On Mon, Oct 28, 2013 at 12:36 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Mike,
You need to install XQuartz: http://xquartz.macosforge.org/**landing/http://xquartz.macosforge.org/landing/
Also see the following troubleshooting page: http://ftp.nmr.mgh.harvard.**edu/fswiki/freesurfer_GUIs_**troubleshootinghttp://ftp.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting
-Zeke
On 10/28/2013 03:17 PM, Michael Datko wrote:
Hi Anastasia, I've attached my configuration file, and below is pasted the contents of the error log. Below that, I've pasted the last few lines of the trac-all log (not the error log), because it says something about a "dyld" that cannot be loaded...might be related to the problem.
Thanks, Mike
from error log:
SUBJECT 226A DATE Tue Oct 15 18:38:18 PDT 2013 USER mdatko HOST captain-cosine.local PROCESSOR i386 OS Darwin Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_**I386 i386 $Id: trac-preproc,v 1.17.2.8 2013/02/16 20:57:05 ayendiki Exp $ /Applications/freesurfer/bin/**trac-preproc PWD /Users/mdatko/Desktop CMD mri_probedicom --i /Users/mdatko/Desktop/226A/**dti/i00001.CFMRI.1
Last few lines from non-error log:
mri_probedicom --i /Users/mdatko/Desktop/226A/**dti/i00001.CFMRI.1 > /Users/mdatko/Desktop/tracula_**tutorial/data/freesurfer/226A/** dmri/dcminfo.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/**mri_probedicom Reason: image not found Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_**I386 i386
trac-preproc exited with ERRORS at Tue Oct 15 18:38:18 PDT 2013
On Tue, Oct 22, 2013 at 8:04 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.eduayendiki@nmr.mgh.harvard.edu>> wrote:
Hi Mike - I'll need to see the configuration file and trac-all.log. Thanks, a.y On Mon, 21 Oct 2013, Michael Datko wrote: Hello,I am running into a tracula error very early in the preprocessing steps. I have data that was already somewhat preprocessed (reconstruction, eddy correction and magnetic field inhomogeneity correction) that I'm trying to use as an input. I have turned off those steps in the tracula configuration file. Tracula seems to find these files and starts making a few of the dwi output files in the subject's freesurfer/dmri folder. However, it then says something about not having the correct "frames" and it can't find the file dwi_frames.nii.gz. I'm not sure what this error is referring to. I attempted to run the same subject's data from their raw dicoms instead ofthe slightly-preprocessed file and also ran into errors. If it makes a difference, the subject had recon-all performed with freesurfer version 5.0 and I am now using version 5.3. Perhaps the subject is missing some necessary recon-all output that is only created with 5.3? Any advice?
Thanks, Mike Datko 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<http://www.partners.org/__complianceline> <http://www.partners.org/**complianceline<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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello, I installed XQuartz and the processing gets a little bit farther than it did before. However, I now run into an error about not being able to move the bvecs file. To my knowledge I specified the bvecs file correctly (in the same log file I attached previously), and it is in a format that has worked with other FSL programs in the past. Just in case, I have attached my bvecs and bvals files here if you want to verify. Any advice? Here are the last few lines of the log file before it quits:
fslswapdim /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig.nii.gz x -y -z /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig_flip.nii.gz mv -f /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig_flip.mghdti.bvecs /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/bvecs mv: rename /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig_flip.mghdti.bvecs to /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/bvecs: No such file or directory Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
trac-preproc exited with ERRORS at Mon Oct 28 14:13:00 PDT 2013
On Mon, Oct 28, 2013 at 12:52 PM, Michael Datko mikedatko@gmail.com wrote:
The XQuartz website you linked makes it sound like it is identical to X11, is it different in some way? I have X11 already and it works flawlessly with other applications such as AFNI and FSL.
On Mon, Oct 28, 2013 at 12:36 PM, Z K zkaufman@nmr.mgh.harvard.eduwrote:
Mike,
You need to install XQuartz: http://xquartz.macosforge.org/**landing/http://xquartz.macosforge.org/landing/
Also see the following troubleshooting page: http://ftp.nmr.mgh.harvard.**edu/fswiki/freesurfer_GUIs_**troubleshootinghttp://ftp.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting
-Zeke
On 10/28/2013 03:17 PM, Michael Datko wrote:
Hi Anastasia, I've attached my configuration file, and below is pasted the contents of the error log. Below that, I've pasted the last few lines of the trac-all log (not the error log), because it says something about a "dyld" that cannot be loaded...might be related to the problem.
Thanks, Mike
from error log:
SUBJECT 226A DATE Tue Oct 15 18:38:18 PDT 2013 USER mdatko HOST captain-cosine.local PROCESSOR i386 OS Darwin Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_**I386 i386 $Id: trac-preproc,v 1.17.2.8 2013/02/16 20:57:05 ayendiki Exp $ /Applications/freesurfer/bin/**trac-preproc PWD /Users/mdatko/Desktop CMD mri_probedicom --i /Users/mdatko/Desktop/226A/**dti/i00001.CFMRI.1
Last few lines from non-error log:
mri_probedicom --i /Users/mdatko/Desktop/226A/**dti/i00001.CFMRI.1 > /Users/mdatko/Desktop/tracula_**tutorial/data/freesurfer/226A/** dmri/dcminfo.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/**mri_probedicom Reason: image not found Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_**I386 i386
trac-preproc exited with ERRORS at Tue Oct 15 18:38:18 PDT 2013
On Tue, Oct 22, 2013 at 8:04 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.eduayendiki@nmr.mgh.harvard.edu>> wrote:
Hi Mike - I'll need to see the configuration file and trac-all.log. Thanks, a.y On Mon, 21 Oct 2013, Michael Datko wrote: Hello,I am running into a tracula error very early in the preprocessing steps. I have data that was already somewhat preprocessed (reconstruction, eddy correction and magnetic field inhomogeneity correction) that I'm trying to use as an input. I have turned off those steps in the tracula configuration file. Tracula seems to find these files and starts making a few of the dwi output files in the subject's freesurfer/dmri folder. However, it then says something about not having the correct "frames" and it can't find the file dwi_frames.nii.gz. I'm not sure what this error is referring to. I attempted to run the same subject's data from their raw dicoms instead ofthe slightly-preprocessed file and also ran into errors. If it makes a difference, the subject had recon-all performed with freesurfer version 5.0 and I am now using version 5.3. Perhaps the subject is missing some necessary recon-all output that is only created with 5.3? Any advice?
Thanks, Mike Datko 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<http://www.partners.org/__complianceline> <http://www.partners.org/**complianceline<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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Michael - Two things: First, in the dmrirc that you attached previously, the bvecfile and bvalfile lines are commented out. Second, these files need to be in column, not row format, as shown in the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps, a.y
On Mon, 28 Oct 2013, Michael Datko wrote:
Hello,I installed XQuartz and the processing gets a little bit farther than it did before. However, I now run into an error about not being able to move the bvecs file. To my knowledge I specified the bvecs file correctly (in the same log file I attached previously), and it is in a format that has worked with other FSL programs in the past. Just in case, I have attached my bvecs and bvals files here if you want to verify. Any advice? Here are the last few lines of the log file before it quits:
fslswapdim /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig.nii.gz x -y -z /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig_flip.nii.gz mv -f /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig_flip.mghdti.bvecs /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/bvecs mv: rename /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig_flip.mghdti.bvecs to /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/bvecs: No such file or directory Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
trac-preproc exited with ERRORS at Mon Oct 28 14:13:00 PDT 2013
On Mon, Oct 28, 2013 at 12:52 PM, Michael Datko mikedatko@gmail.com wrote: The XQuartz website you linked makes it sound like it is identical to X11, is it different in some way? I have X11 already and it works flawlessly with other applications such as AFNI and FSL.
On Mon, Oct 28, 2013 at 12:36 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote: Mike,
You need to install XQuartz: http://xquartz.macosforge.org/landing/ Also see the following troubleshooting page: http://ftp.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting -Zeke On 10/28/2013 03:17 PM, Michael Datko wrote: Hi Anastasia, I've attached my configuration file, and below is pasted the contents of the error log. Below that, I've pasted the last few lines of the trac-all log (not the error log), because it says something about a "dyld" that cannot be loaded...might be related to the problem. Thanks, Mike from error log: ------------------------------ SUBJECT 226A DATE Tue Oct 15 18:38:18 PDT 2013 USER mdatko HOST captain-cosine.local PROCESSOR i386 OS Darwin Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 $Id: trac-preproc,v 1.17.2.8 2013/02/16 20:57:05 ayendiki Exp $ /Applications/freesurfer/bin/trac-preproc PWD /Users/mdatko/Desktop CMD mri_probedicom --i /Users/mdatko/Desktop/226A/dti/i00001.CFMRI.1 Last few lines from non-error log: mri_probedicom --i /Users/mdatko/Desktop/226A/dti/i00001.CFMRI.1 > /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dcminfo.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/mri_probedicom Reason: image not found Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Tue Oct 15 18:38:18 PDT 2013 On Tue, Oct 22, 2013 at 8:04 AM, Anastasia Yendiki<ayendiki@nmr.mgh.harvard.edu mailto:ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Mike - I'll need to see the configuration file and trac-all.log.
Thanks, a.y
On Mon, 21 Oct 2013, Michael Datko wrote:
Hello,I am running into a tracula error very early in the preprocessing steps.
I have data that was already somewhat preprocessed (reconstruction, eddy correction and magnetic field inhomogeneity correction) that I'm trying to use as an input. I have turned off those steps in the tracula configuration file. Tracula seems to find these files and starts making a few of the dwi output files in the subject's freesurfer/dmri folder. However, it then says something about not having the correct "frames" and it can't find the file dwi_frames.nii.gz. I'm not sure what this error is referring to. I attempted to run the same subject's data from their raw dicoms instead of the slightly-preprocessed file and also ran into errors. If it makes a difference, the subject had recon-all performed with freesurfer version 5.0 and I am now using version 5.3. Perhaps the subject is missing some necessary recon-all output that is only created with 5.3? Any advice?
Thanks, Mike Datko
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 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
Im of the understanding that X11 and XQuartz will not conflict. Many users running Mac OSX Snow Leopard have both applications installed on their systems. But if you are extremely weary of potential issues than I suppose you could create a symbolic link from /opt/X11 to /usr/X11. Additional symlinks may be required tho, which should be easily determined based on the error message obtained.
-Zeke
On 10/28/2013 03:52 PM, Michael Datko wrote:
The XQuartz website you linked makes it sound like it is identical to X11, is it different in some way? I have X11 already and it works flawlessly with other applications such as AFNI and FSL.
On Mon, Oct 28, 2013 at 12:36 PM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
Mike, You need to install XQuartz: http://xquartz.macosforge.org/__landing/ <http://xquartz.macosforge.org/landing/> Also see the following troubleshooting page: http://ftp.nmr.mgh.harvard.__edu/fswiki/freesurfer_GUIs___troubleshooting <http://ftp.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting> -Zeke On 10/28/2013 03:17 PM, Michael Datko wrote: Hi Anastasia, I've attached my configuration file, and below is pasted the contents of the error log. Below that, I've pasted the last few lines of the trac-all log (not the error log), because it says something about a "dyld" that cannot be loaded...might be related to the problem. Thanks, Mike from error log: ------------------------------ SUBJECT 226A DATE Tue Oct 15 18:38:18 PDT 2013 USER mdatko HOST captain-cosine.local PROCESSOR i386 OS Darwin Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE___I386 i386 $Id: trac-preproc,v 1.17.2.8 2013/02/16 20:57:05 ayendiki Exp $ /Applications/freesurfer/bin/__trac-preproc PWD /Users/mdatko/Desktop CMD mri_probedicom --i /Users/mdatko/Desktop/226A/__dti/i00001.CFMRI.1 Last few lines from non-error log: mri_probedicom --i /Users/mdatko/Desktop/226A/__dti/i00001.CFMRI.1 > /Users/mdatko/Desktop/tracula___tutorial/data/freesurfer/226A/__dmri/dcminfo.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/__mri_probedicom Reason: image not found Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE___I386 i386 trac-preproc exited with ERRORS at Tue Oct 15 18:38:18 PDT 2013 On Tue, Oct 22, 2013 at 8:04 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>> wrote: Hi Mike - I'll need to see the configuration file and trac-all.log. Thanks, a.y On Mon, 21 Oct 2013, Michael Datko wrote: Hello,I am running into a tracula error very early in the preprocessing steps. I have data that was already somewhat preprocessed (reconstruction, eddy correction and magnetic field inhomogeneity correction) that I'm trying to use as an input. I have turned off those steps in the tracula configuration file. Tracula seems to find these files and starts making a few of the dwi output files in the subject's freesurfer/dmri folder. However, it then says something about not having the correct "frames" and it can't find the file dwi_frames.nii.gz. I'm not sure what this error is referring to. I attempted to run the same subject's data from their raw dicoms instead of the slightly-preprocessed file and also ran into errors. If it makes a difference, the subject had recon-all performed with freesurfer version 5.0 and I am now using version 5.3. Perhaps the subject is missing some necessary recon-all output that is only created with 5.3? Any advice? Thanks, Mike Datko 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 <http://www.partners.org/__complianceline> <http://www.partners.org/__complianceline <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.__edu/mailman/listinfo/__freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
freesurfer@nmr.mgh.harvard.edu
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Anastasia Yendiki -
Michael Datko -
Z K