Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of our newer macs and it seemed to work fine. I was running it on an older linux version of freesurfer. Still couldnt figure the issue on the linux though for the config file. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:35 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
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 Andrew - The files should be one row per DWI volume. See example here, under "Specify the diffusion-encoding gradient table" and "Specify the b-value table": http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps, a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of our newer macs and it seemed to work fine. I was running it on an older linux version of freesurfer. Still couldnt figure the issue on the linux though for the config file. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:35 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
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.
Awesome. I overlooked that. It worked but now I get this error/image not found. Should I attach something else?
fslswapdim /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz x z -y /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz fslorient -forceradiological /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz tkregister2 --mov /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz --targ /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anatorig2anat.mat --reg /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anat2anatorig.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer//tktools/tkregister2.bin Reason: image not found Trace/BPT trap ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:19 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - The files should be one row per DWI volume. See example here, under "Specify the diffusion-encoding gradient table" and "Specify the b-value table": http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps, a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of our newer macs and it seemed to work fine. I was running it on an older linux version of freesurfer. Still couldnt figure the issue on the linux though for the config file. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:35 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
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.
Can you tell us which build of freesurfer you're using (should be in trac-all.log) and what version of OSX you have this installed in?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
Awesome. I overlooked that. It worked but now I get this error/image not found. Should I attach something else?
fslswapdim /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz x z -y /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz fslorient -forceradiological /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz tkregister2 --mov /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz --targ /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anatorig2anat.mat --reg /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anat2anatorig.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer//tktools/tkregister2.bin Reason: image not found Trace/BPT trap ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:19 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - The files should be one row per DWI volume. See example here, under "Specify the diffusion-encoding gradient table" and "Specify the b-value table": http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps, a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of our newer macs and it seemed to work fine. I was running it on an older linux version of freesurfer. Still couldnt figure the issue on the linux though for the config file. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:35 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
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.
From the log I found this
Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
And mac osx 10.6.8 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:51 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you tell us which build of freesurfer you're using (should be in trac-all.log) and what version of OSX you have this installed in?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
Awesome. I overlooked that. It worked but now I get this error/image not found. Should I attach something else?
fslswapdim /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz x z -y /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz fslorient -forceradiological /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz tkregister2 --mov /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz --targ /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anatorig2anat.mat --reg /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anat2anatorig.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer//tktools/tkregister2.bin Reason: image not found Trace/BPT trap ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:19 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - The files should be one row per DWI volume. See example here, under "Specify the diffusion-encoding gradient table" and "Specify the b-value table": http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps, a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of our newer macs and it seemed to work fine. I was running it on an older linux version of freesurfer. Still couldnt figure the issue on the linux though for the config file. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:35 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
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.
Can you please check for a line that says "build-stamp" in the log that tells you which freesurfer build you used?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
From the log I found this
Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
And mac osx 10.6.8 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:51 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you tell us which build of freesurfer you're using (should be in trac-all.log) and what version of OSX you have this installed in?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
Awesome. I overlooked that. It worked but now I get this error/image not found. Should I attach something else?
fslswapdim /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz x z -y /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz fslorient -forceradiological /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz tkregister2 --mov /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz --targ /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anatorig2anat.mat --reg /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anat2anatorig.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer//tktools/tkregister2.bin Reason: image not found Trace/BPT trap ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:19 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - The files should be one row per DWI volume. See example here, under "Specify the diffusion-encoding gradient table" and "Specify the b-value table": http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps, a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of our newer macs and it seemed to work fine. I was running it on an older linux version of freesurfer. Still couldnt figure the issue on the linux though for the config file. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:35 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
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.
build-stamp.txt: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 5:20 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you please check for a line that says "build-stamp" in the log that tells you which freesurfer build you used?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
From the log I found this
Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
And mac osx 10.6.8 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:51 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you tell us which build of freesurfer you're using (should be in trac-all.log) and what version of OSX you have this installed in?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
Awesome. I overlooked that. It worked but now I get this error/image not found. Should I attach something else?
fslswapdim /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz x z -y /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz fslorient -forceradiological /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz tkregister2 --mov /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz --targ /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anatorig2anat.mat --reg /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anat2anatorig.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer//tktools/tkregister2.bin Reason: image not found Trace/BPT trap ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:19 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - The files should be one row per DWI volume. See example here, under "Specify the diffusion-encoding gradient table" and "Specify the b-value table": http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps, a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of our newer macs and it seemed to work fine. I was running it on an older linux version of freesurfer. Still couldnt figure the issue on the linux though for the config file. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:35 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
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 Andrew - Try installing XQuartz: http://xquartz.macosforge.org/landing/
a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
build-stamp.txt: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 5:20 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you please check for a line that says "build-stamp" in the log that tells you which freesurfer build you used?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
From the log I found this
Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
And mac osx 10.6.8 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:51 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you tell us which build of freesurfer you're using (should be in trac-all.log) and what version of OSX you have this installed in?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
Awesome. I overlooked that. It worked but now I get this error/image not found. Should I attach something else?
fslswapdim /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz x z -y /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz fslorient -forceradiological /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz tkregister2 --mov /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz --targ /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anatorig2anat.mat --reg /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anat2anatorig.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer//tktools/tkregister2.bin Reason: image not found Trace/BPT trap ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:19 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - The files should be one row per DWI volume. See example here, under "Specify the diffusion-encoding gradient table" and "Specify the b-value table": http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps, a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of our newer macs and it seemed to work fine. I was running it on an older linux version of freesurfer. Still couldnt figure the issue on the linux though for the config file. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:35 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
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.
Should I rerun recon-all after I install it? ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Tuesday, July 16, 2013 11:28 AM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - Try installing XQuartz: http://xquartz.macosforge.org/landing/
a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
build-stamp.txt: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 5:20 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you please check for a line that says "build-stamp" in the log that tells you which freesurfer build you used?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
From the log I found this
Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
And mac osx 10.6.8 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:51 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you tell us which build of freesurfer you're using (should be in trac-all.log) and what version of OSX you have this installed in?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
Awesome. I overlooked that. It worked but now I get this error/image not found. Should I attach something else?
fslswapdim /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz x z -y /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz fslorient -forceradiological /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz tkregister2 --mov /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz --targ /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anatorig2anat.mat --reg /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anat2anatorig.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer//tktools/tkregister2.bin Reason: image not found Trace/BPT trap ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:19 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - The files should be one row per DWI volume. See example here, under "Specify the diffusion-encoding gradient table" and "Specify the b-value table": http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps, a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of our newer macs and it seemed to work fine. I was running it on an older linux version of freesurfer. Still couldnt figure the issue on the linux though for the config file. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:35 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
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.
No, just run the trac-all command that failed with that library error.
On Tue, 16 Jul 2013, Gundran, Andrew wrote:
Should I rerun recon-all after I install it? ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Tuesday, July 16, 2013 11:28 AM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - Try installing XQuartz: http://xquartz.macosforge.org/landing/
a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
build-stamp.txt: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 5:20 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you please check for a line that says "build-stamp" in the log that tells you which freesurfer build you used?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
From the log I found this
Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
And mac osx 10.6.8 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:51 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you tell us which build of freesurfer you're using (should be in trac-all.log) and what version of OSX you have this installed in?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
Awesome. I overlooked that. It worked but now I get this error/image not found. Should I attach something else?
fslswapdim /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz x z -y /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz fslorient -forceradiological /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz tkregister2 --mov /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz --targ /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anatorig2anat.mat --reg /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anat2anatorig.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer//tktools/tkregister2.bin Reason: image not found Trace/BPT trap ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:19 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - The files should be one row per DWI volume. See example here, under "Specify the diffusion-encoding gradient table" and "Specify the b-value table": http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps, a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of our newer macs and it seemed to work fine. I was running it on an older linux version of freesurfer. Still couldnt figure the issue on the linux though for the config file. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:35 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
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.
And that worked. Great news...another error this time with FSL's flirt. I'm a bit confused on that one since I use FSL a bit within a terminal. I didnt think I had to setenv for it?
flirt.fsl -ref /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bbregister.34704/fslregister/refvol.fslregister.nii -in /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bbregister.34704/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bbregister.34704/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bbregister.34704/reg.init.dat.fsl.mat0 flirt.fsl: Command not found. ERROR: flirt
Thanks so much for your patience!
________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Tuesday, July 16, 2013 11:28 AM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - Try installing XQuartz: http://xquartz.macosforge.org/landing/
a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
build-stamp.txt: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 5:20 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you please check for a line that says "build-stamp" in the log that tells you which freesurfer build you used?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
From the log I found this
Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
And mac osx 10.6.8 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:51 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you tell us which build of freesurfer you're using (should be in trac-all.log) and what version of OSX you have this installed in?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
Awesome. I overlooked that. It worked but now I get this error/image not found. Should I attach something else?
fslswapdim /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz x z -y /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz fslorient -forceradiological /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz tkregister2 --mov /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz --targ /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anatorig2anat.mat --reg /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anat2anatorig.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer//tktools/tkregister2.bin Reason: image not found Trace/BPT trap ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:19 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - The files should be one row per DWI volume. See example here, under "Specify the diffusion-encoding gradient table" and "Specify the b-value table": http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps, a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of our newer macs and it seemed to work fine. I was running it on an older linux version of freesurfer. Still couldnt figure the issue on the linux though for the config file. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:35 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
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You're very welcome. The error is for flirt.fsl, which is a copy of flirt included in the freesurfer distribution. So if you want to use that, you'll need to source the freesurfer setup script as usual. (You wouldn't need to if you were using flirt from the fsl distribution.)
On Tue, 16 Jul 2013, Gundran, Andrew wrote:
And that worked. Great news...another error this time with FSL's flirt. I'm a bit confused on that one since I use FSL a bit within a terminal. I didnt think I had to setenv for it?
flirt.fsl -ref /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bbregister.34704/fslregister/refvol.fslregister.nii -in /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bbregister.34704/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bbregister.34704/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bbregister.34704/reg.init.dat.fsl.mat0 flirt.fsl: Command not found. ERROR: flirt
Thanks so much for your patience!
From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Tuesday, July 16, 2013 11:28 AM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - Try installing XQuartz: http://xquartz.macosforge.org/landing/
a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
build-stamp.txt: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 5:20 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you please check for a line that says "build-stamp" in the log that tells you which freesurfer build you used?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
From the log I found this
Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
And mac osx 10.6.8 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:51 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you tell us which build of freesurfer you're using (should be in trac-all.log) and what version of OSX you have this installed in?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
Awesome. I overlooked that. It worked but now I get this error/image not found. Should I attach something else?
fslswapdim /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz x z -y /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz fslorient -forceradiological /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz tkregister2 --mov /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz --targ /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anatorig2anat.mat --reg /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anat2anatorig.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer//tktools/tkregister2.bin Reason: image not found Trace/BPT trap ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:19 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - The files should be one row per DWI volume. See example here, under "Specify the diffusion-encoding gradient table" and "Specify the b-value table": http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps, a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of our newer macs and it seemed to work fine. I was running it on an older linux version of freesurfer. Still couldnt figure the issue on the linux though for the config file. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:35 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
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 -
Gundran, Andrew