Hi Champe
can you send us the recon-all.log file?
cheers Bruce On Sun, 6 Mar 2016, Champe Barton wrote:
Hi Freesurfer People,
I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced any issues that could have been a result of that function). Everything in FreeSurfer works fine for me—I ran recon-all and successfully processed dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and the pial and white surfaces, and I successfully deleted unnecessary voxels and added a set of control points (in both cases, being careful to make and save the changes on all necessary slices with the brainmask volume highlighted). My only issue is that when I reprocess the data using recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs through the reconstruction without error and then shows no changes at all in freeview when I view the volumes/surfaces. The deleted voxels still appear deleted and I can still load the control points, so why wouldn’t it make the changes?
And just to provide a little extra info: I encounter the same problem when I reprocess the tutorial data for the pial edits tutorial. I delete the voxels as instructed, save the file, reprocess it without error, and then nothing’s changed when I view it all again in freeview.
Any help would be HUGELY appreciated—I’ve stressed over this for weeks trying to get my computer to function properly so that I can begin my work as a research assistant in a neuropsych lab editing and analyzing brain scans with FreeSurfer.
Thanks, Champe
Yeah, my mistake! Here it is:
Thanks! Champe
On Mar 6, 2016, at 9:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Champe
can you send us the recon-all.log file?
cheers Bruce On Sun, 6 Mar 2016, Champe Barton wrote:
Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced any issues that could have been a result of that function). Everything in FreeSurfer works fine for me—I ran recon-all and successfully processed dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and the pial and white surfaces, and I successfully deleted unnecessary voxels and added a set of control points (in both cases, being careful to make and save the changes on all necessary slices with the brainmask volume highlighted). My only issue is that when I reprocess the data using recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs through the reconstruction without error and then shows no changes at all in freeview when I view the volumes/surfaces. The deleted voxels still appear deleted and I can still load the control points, so why wouldn’t it make the changes? And just to provide a little extra info: I encounter the same problem when I reprocess the tutorial data for the pial edits tutorial. I delete the voxels as instructed, save the file, reprocess it without error, and then nothing’s changed when I view it all again in freeview. Any help would be HUGELY appreciated—I’ve stressed over this for weeks trying to get my computer to function properly so that I can begin my work as a research assistant in a neuropsych lab editing and analyzing brain scans with FreeSurfer. Thanks, Champe
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.
Hey Bruce,
I got a notification saying the email my recon-all.log file attachment was too large and had to await moderator approval to be posted to the support list. I was just wondering if you received it or if I should resend it.
Best, Champe
Sent from my iPhone
On Mar 6, 2016, at 9:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Champe
can you send us the recon-all.log file?
cheers Bruce
On Sun, 6 Mar 2016, Champe Barton wrote:
Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced any issues that could have been a result of that function). Everything in FreeSurfer works fine for me—I ran recon-all and successfully processed dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and the pial and white surfaces, and I successfully deleted unnecessary voxels and added a set of control points (in both cases, being careful to make and save the changes on all necessary slices with the brainmask volume highlighted). My only issue is that when I reprocess the data using recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs through the reconstruction without error and then shows no changes at all in freeview when I view the volumes/surfaces. The deleted voxels still appear deleted and I can still load the control points, so why wouldn’t it make the changes? And just to provide a little extra info: I encounter the same problem when I reprocess the tutorial data for the pial edits tutorial. I delete the voxels as instructed, save the file, reprocess it without error, and then nothing’s changed when I view it all again in freeview. Any help would be HUGELY appreciated—I’ve stressed over this for weeks trying to get my computer to function properly so that I can begin my work as a research assistant in a neuropsych lab editing and analyzing brain scans with FreeSurfer. Thanks, Champe
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.
I got it, thanks Bruce On Mon, 7 Mar 2016, Champe Barton wrote:
Hey Bruce,
I got a notification saying the email my recon-all.log file attachment was too large and had to await moderator approval to be posted to the support list. I was just wondering if you received it or if I should resend it.
Best, Champe
Sent from my iPhone
On Mar 6, 2016, at 9:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Champe
can you send us the recon-all.log file?
cheers Bruce
On Sun, 6 Mar 2016, Champe Barton wrote:
Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced any issues that could have been a result of that function). Everything in FreeSurfer works fine for me—I ran recon-all and successfully processed dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and the pial and white surfaces, and I successfully deleted unnecessary voxels and added a set of control points (in both cases, being careful to make and save the changes on all necessary slices with the brainmask volume highlighted). My only issue is that when I reprocess the data using recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs through the reconstruction without error and then shows no changes at all in freeview when I view the volumes/surfaces. The deleted voxels still appear deleted and I can still load the control points, so why wouldn’t it make the changes? And just to provide a little extra info: I encounter the same problem when I reprocess the tutorial data for the pial edits tutorial. I delete the voxels as instructed, save the file, reprocess it without error, and then nothing’s changed when I view it all again in freeview. Any help would be HUGELY appreciated—I’ve stressed over this for weeks trying to get my computer to function properly so that I can begin my work as a research assistant in a neuropsych lab editing and analyzing brain scans with FreeSurfer. Thanks, Champe
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
Hey Bruce,
I recently sent you a log file to look at to determine why reprocessing data wasn’t making any changes in freeview. Have you had a chance to go over it yet? Let me know.
Thanks, Champe
On Mar 7, 2016, at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I got it, thanks Bruce On Mon, 7 Mar 2016, Champe Barton wrote:
Hey Bruce,
I got a notification saying the email my recon-all.log file attachment was too large and had to await moderator approval to be posted to the support list. I was just wondering if you received it or if I should resend it.
Best, Champe
Sent from my iPhone
On Mar 6, 2016, at 9:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Champe
can you send us the recon-all.log file?
cheers Bruce
On Sun, 6 Mar 2016, Champe Barton wrote:
Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced any issues that could have been a result of that function). Everything in FreeSurfer works fine for me—I ran recon-all and successfully processed dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and the pial and white surfaces, and I successfully deleted unnecessary voxels and added a set of control points (in both cases, being careful to make and save the changes on all necessary slices with the brainmask volume highlighted). My only issue is that when I reprocess the data using recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs through the reconstruction without error and then shows no changes at all in freeview when I view the volumes/surfaces. The deleted voxels still appear deleted and I can still load the control points, so why wouldn’t it make the changes? And just to provide a little extra info: I encounter the same problem when I reprocess the tutorial data for the pial edits tutorial. I delete the voxels as instructed, save the file, reprocess it without error, and then nothing’s changed when I view it all again in freeview. Any help would be HUGELY appreciated—I’ve stressed over this for weeks trying to get my computer to function properly so that I can begin my work as a research assistant in a neuropsych lab editing and analyzing brain scans with FreeSurfer. Thanks, Champe
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
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 Champe
it looks like it is not using the control points. How did you create them? They should be stored in a file under in tmp/edit.dat within the subject directory. Does that file exist?
cheers Bruce
On Tue, 15 Mar 2016, Champe Barton wrote:
Hey Bruce,
I recently sent you a log file to look at to determine why reprocessing data wasn’t making any changes in freeview. Have you had a chance to go over it yet? Let me know.
Thanks, Champe
On Mar 7, 2016, at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I got it, thanks Bruce On Mon, 7 Mar 2016, Champe Barton wrote:
Hey Bruce,
I got a notification saying the email my recon-all.log file attachment was too large and had to await moderator approval to be posted to the support list. I was just wondering if you received it or if I should resend it.
Best, Champe
Sent from my iPhone
On Mar 6, 2016, at 9:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Champe
can you send us the recon-all.log file?
cheers Bruce
On Sun, 6 Mar 2016, Champe Barton wrote:
Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced any issues that could have been a result of that function). Everything in FreeSurfer works fine for me—I ran recon-all and successfully processed dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and the pial and white surfaces, and I successfully deleted unnecessary voxels and added a set of control points (in both cases, being careful to make and save the changes on all necessary slices with the brainmask volume highlighted). My only issue is that when I reprocess the data using recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs through the reconstruction without error and then shows no changes at all in freeview when I view the volumes/surfaces. The deleted voxels still appear deleted and I can still load the control points, so why wouldn’t it make the changes? And just to provide a little extra info: I encounter the same problem when I reprocess the tutorial data for the pial edits tutorial. I delete the voxels as instructed, save the file, reprocess it without error, and then nothing’s changed when I view it all again in freeview. Any help would be HUGELY appreciated—I’ve stressed over this for weeks trying to get my computer to function properly so that I can begin my work as a research assistant in a neuropsych lab editing and analyzing brain scans with FreeSurfer. Thanks, Champe
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
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
p.s. sorry, it should be tmp/control.dat On Tue, 15 Mar 2016, Champe Barton wrote:
Hey Bruce,
I recently sent you a log file to look at to determine why reprocessing data wasn’t making any changes in freeview. Have you had a chance to go over it yet? Let me know.
Thanks, Champe
On Mar 7, 2016, at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I got it, thanks Bruce On Mon, 7 Mar 2016, Champe Barton wrote:
Hey Bruce,
I got a notification saying the email my recon-all.log file attachment was too large and had to await moderator approval to be posted to the support list. I was just wondering if you received it or if I should resend it.
Best, Champe
Sent from my iPhone
On Mar 6, 2016, at 9:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Champe
can you send us the recon-all.log file?
cheers Bruce
On Sun, 6 Mar 2016, Champe Barton wrote:
Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced any issues that could have been a result of that function). Everything in FreeSurfer works fine for me—I ran recon-all and successfully processed dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and the pial and white surfaces, and I successfully deleted unnecessary voxels and added a set of control points (in both cases, being careful to make and save the changes on all necessary slices with the brainmask volume highlighted). My only issue is that when I reprocess the data using recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs through the reconstruction without error and then shows no changes at all in freeview when I view the volumes/surfaces. The deleted voxels still appear deleted and I can still load the control points, so why wouldn’t it make the changes? And just to provide a little extra info: I encounter the same problem when I reprocess the tutorial data for the pial edits tutorial. I delete the voxels as instructed, save the file, reprocess it without error, and then nothing’s changed when I view it all again in freeview. Any help would be HUGELY appreciated—I’ve stressed over this for weeks trying to get my computer to function properly so that I can begin my work as a research assistant in a neuropsych lab editing and analyzing brain scans with FreeSurfer. Thanks, Champe
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
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I created them as instructed in the tutorial and called the file “control.dat” so there’s a control.dat file in my subjects directory. Should I have named it tmp/control.dat? Also, would resolving the control points issue also resolve the deleted voxels issue? Cause my it’s not redrawing the pial surface either.
Thanks Champe
On Mar 15, 2016, at 1:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. sorry, it should be tmp/control.dat On Tue, 15 Mar 2016, Champe Barton wrote:
Hey Bruce,
I recently sent you a log file to look at to determine why reprocessing data wasn’t making any changes in freeview. Have you had a chance to go over it yet? Let me know.
Thanks, Champe
On Mar 7, 2016, at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I got it, thanks Bruce On Mon, 7 Mar 2016, Champe Barton wrote:
Hey Bruce,
I got a notification saying the email my recon-all.log file attachment was too large and had to await moderator approval to be posted to the support list. I was just wondering if you received it or if I should resend it.
Best, Champe
Sent from my iPhone
On Mar 6, 2016, at 9:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Champe
can you send us the recon-all.log file?
cheers Bruce
On Sun, 6 Mar 2016, Champe Barton wrote:
Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced any issues that could have been a result of that function). Everything in FreeSurfer works fine for me—I ran recon-all and successfully processed dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and the pial and white surfaces, and I successfully deleted unnecessary voxels and added a set of control points (in both cases, being careful to make and save the changes on all necessary slices with the brainmask volume highlighted). My only issue is that when I reprocess the data using recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs through the reconstruction without error and then shows no changes at all in freeview when I view the volumes/surfaces. The deleted voxels still appear deleted and I can still load the control points, so why wouldn’t it make the changes? And just to provide a little extra info: I encounter the same problem when I reprocess the tutorial data for the pial edits tutorial. I delete the voxels as instructed, save the file, reprocess it without error, and then nothing’s changed when I view it all again in freeview. Any help would be HUGELY appreciated—I’ve stressed over this for weeks trying to get my computer to function properly so that I can begin my work as a research assistant in a neuropsych lab editing and analyzing brain scans with FreeSurfer. Thanks, Champe
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
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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.
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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 Champe
it must be in the tmp subdirectory (that is <subject name>/tmp/control.dat) otherwise we will not find it.
As for the deleted voxel issue - how did you delete them?
Bruce On Tue, 15 Mar 2016, Champe Barton wrote:
I created them as instructed in the tutorial and called the file “control.dat” so there’s a control.dat file in my subjects directory. Should I have named it tmp/control.dat? Also, would resolving the control points issue also resolve the deleted voxels issue? Cause my it’s not redrawing the pial surface either.
Thanks Champe
On Mar 15, 2016, at 1:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. sorry, it should be tmp/control.dat On Tue, 15 Mar 2016, Champe Barton wrote:
Hey Bruce,
I recently sent you a log file to look at to determine why reprocessing data wasn’t making any changes in freeview. Have you had a chance to go over it yet? Let me know.
Thanks, Champe
On Mar 7, 2016, at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I got it, thanks Bruce On Mon, 7 Mar 2016, Champe Barton wrote:
Hey Bruce,
I got a notification saying the email my recon-all.log file attachment was too large and had to await moderator approval to be posted to the support list. I was just wondering if you received it or if I should resend it.
Best, Champe
Sent from my iPhone
On Mar 6, 2016, at 9:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Champe
can you send us the recon-all.log file?
cheers Bruce > On Sun, 6 Mar 2016, Champe Barton wrote: > > Hi Freesurfer People, > I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I > have System Integrity Protection disabled (though I hadn’t experienced any > issues that could have been a result of that function). Everything in > FreeSurfer works fine for me—I ran recon-all and successfully processed > dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and > the pial and white surfaces, and I successfully deleted unnecessary voxels > and added a set of control points (in both cases, being careful to make and > save the changes on all necessary slices with the brainmask volume > highlighted). My only issue is that when I reprocess the data using > recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs > through the reconstruction without error and then shows no changes at all in > freeview when I view the volumes/surfaces. The deleted voxels still appear > deleted and I can still load the control points, so why wouldn’t it make the > changes? > And just to provide a little extra info: I encounter the same problem when I > reprocess the tutorial data for the pial edits tutorial. I delete the voxels > as instructed, save the file, reprocess it without error, and then nothing’s > changed when I view it all again in freeview. > Any help would be HUGELY appreciated—I’ve stressed over this for weeks > trying to get my computer to function properly so that I can begin my work > as a research assistant in a neuropsych lab editing and analyzing brain > scans with FreeSurfer. > Thanks, > Champe _______________________________________________ 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.
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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.
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I used the recon editing tool—I explicitly followed the instructions from the tutorial (even on reprocessing the tutorial data it didn't work), so I had the brainmask.mgz highlighted, checked the recon editing box and held shift and clicked to remove the necessary voxels (they turned black). I removed them on all the necessary slices as well.
Champe
Sent from my iPhone
On Mar 15, 2016, at 1:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Champe
it must be in the tmp subdirectory (that is <subject name>/tmp/control.dat) otherwise we will not find it.
As for the deleted voxel issue - how did you delete them?
Bruce
On Tue, 15 Mar 2016, Champe Barton wrote:
I created them as instructed in the tutorial and called the file “control.dat” so there’s a control.dat file in my subjects directory. Should I have named it tmp/control.dat? Also, would resolving the control points issue also resolve the deleted voxels issue? Cause my it’s not redrawing the pial surface either.
Thanks Champe
On Mar 15, 2016, at 1:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. sorry, it should be tmp/control.dat
On Tue, 15 Mar 2016, Champe Barton wrote:
Hey Bruce,
I recently sent you a log file to look at to determine why reprocessing data wasn’t making any changes in freeview. Have you had a chance to go over it yet? Let me know.
Thanks, Champe
On Mar 7, 2016, at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I got it, thanks Bruce
On Mon, 7 Mar 2016, Champe Barton wrote:
Hey Bruce,
I got a notification saying the email my recon-all.log file attachment was too large and had to await moderator approval to be posted to the support list. I was just wondering if you received it or if I should resend it.
Best, Champe
Sent from my iPhone
> On Mar 6, 2016, at 9:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: > > Hi Champe > > can you send us the recon-all.log file? > > cheers > Bruce >> On Sun, 6 Mar 2016, Champe Barton wrote: >> >> Hi Freesurfer People, >> I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I >> have System Integrity Protection disabled (though I hadn’t experienced any >> issues that could have been a result of that function). Everything in >> FreeSurfer works fine for me—I ran recon-all and successfully processed >> dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and >> the pial and white surfaces, and I successfully deleted unnecessary voxels >> and added a set of control points (in both cases, being careful to make and >> save the changes on all necessary slices with the brainmask volume >> highlighted). My only issue is that when I reprocess the data using >> recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs >> through the reconstruction without error and then shows no changes at all in >> freeview when I view the volumes/surfaces. The deleted voxels still appear >> deleted and I can still load the control points, so why wouldn’t it make the >> changes? >> And just to provide a little extra info: I encounter the same problem when I >> reprocess the tutorial data for the pial edits tutorial. I delete the voxels >> as instructed, save the file, reprocess it without error, and then nothing’s >> changed when I view it all again in freeview. >> Any help would be HUGELY appreciated—I’ve stressed over this for weeks >> trying to get my computer to function properly so that I can begin my work >> as a research assistant in a neuropsych lab editing and analyzing brain >> scans with FreeSurfer. >> Thanks, >> Champe > _______________________________________________ > 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.
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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.
why are you deleting voxels from the brainmask.mgz? That is only used for masking out non-brain tissue. Is that what you are trying to do?
On Tue, 15 Mar 2016, Champe Barton wrote:
I used the recon editing tool—I explicitly followed the instructions from the tutorial (even on reprocessing the tutorial data it didn't work), so I had the brainmask.mgz highlighted, checked the recon editing box and held shift and clicked to remove the necessary voxels (they turned black). I removed them on all the necessary slices as well.
Champe
Sent from my iPhone
On Mar 15, 2016, at 1:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Champe
it must be in the tmp subdirectory (that is <subject name>/tmp/control.dat) otherwise we will not find it.
As for the deleted voxel issue - how did you delete them?
Bruce
On Tue, 15 Mar 2016, Champe Barton wrote:
I created them as instructed in the tutorial and called the file “control.dat” so there’s a control.dat file in my subjects directory. Should I have named it tmp/control.dat? Also, would resolving the control points issue also resolve the deleted voxels issue? Cause my it’s not redrawing the pial surface either.
Thanks Champe
On Mar 15, 2016, at 1:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. sorry, it should be tmp/control.dat
On Tue, 15 Mar 2016, Champe Barton wrote:
Hey Bruce,
I recently sent you a log file to look at to determine why reprocessing data wasn’t making any changes in freeview. Have you had a chance to go over it yet? Let me know.
Thanks, Champe
On Mar 7, 2016, at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I got it, thanks Bruce > On Mon, 7 Mar 2016, Champe Barton wrote: > > > Hey Bruce, > > I got a notification saying the email my recon-all.log file attachment was too large and had to await moderator approval to be posted to the support list. I was just wondering if you received it or if I should resend it. > > Best, > Champe > > Sent from my iPhone > >> On Mar 6, 2016, at 9:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: >> >> Hi Champe >> >> can you send us the recon-all.log file? >> >> cheers >> Bruce >>> On Sun, 6 Mar 2016, Champe Barton wrote: >>> >>> Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X >>> El Capitan version 10.11.2 and I have System Integrity Protection >>> disabled (though I hadn’t experienced any issues that could have >>> been a result of that function). Everything in FreeSurfer works >>> fine for me—I ran recon-all and successfully processed dicom >>> files, I successfully viewed the T1.mgz and brainmask.mgz volumes >>> and the pial and white surfaces, and I successfully deleted >>> unnecessary voxels and added a set of control points (in both >>> cases, being careful to make and save the changes on all >>> necessary slices with the brainmask volume highlighted). My only >>> issue is that when I reprocess the data using recon-all >>> -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs >>> through the reconstruction without error and then shows no >>> changes at all in freeview when I view the volumes/surfaces. The >>> deleted voxels still appear deleted and I can still load the >>> control points, so why wouldn’t it make the changes? And just to >>> provide a little extra info: I encounter the same problem when I >>> reprocess the tutorial data for the pial edits tutorial. I delete >>> the voxels as instructed, save the file, reprocess it without >>> error, and then nothing’s changed when I view it all again in >>> freeview. Any help would be HUGELY appreciated—I’ve stressed over >>> this for weeks trying to get my computer to function properly so >>> that I can begin my work as a research assistant in a neuropsych >>> lab editing and analyzing brain scans with FreeSurfer. Thanks, >>> Champe >> _______________________________________________ >> 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 > > _______________________________________________ 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.
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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.
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Yes, the pial (and white, actually) surface is extending into an area where there is no brain tissue. I'm not sure the anatomical name for it, but it's two cavities, one in the lower half of either hemisphere, where there's no tissue at all. When I process the dicom files I get really erratic surfaces drawn in those areas.
Also, how should I be saving my control points to get them in the tmp folder? I can manually move them there, but I assume it should be done automatically.
Thanks, Champe
Sent from my iPhone
On Mar 15, 2016, at 2:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
why are you deleting voxels from the brainmask.mgz? That is only used for masking out non-brain tissue. Is that what you are trying to do?
On Tue, 15 Mar 2016, Champe Barton wrote:
I used the recon editing tool—I explicitly followed the instructions from the tutorial (even on reprocessing the tutorial data it didn't work), so I had the brainmask.mgz highlighted, checked the recon editing box and held shift and clicked to remove the necessary voxels (they turned black). I removed them on all the necessary slices as well.
Champe
Sent from my iPhone
On Mar 15, 2016, at 1:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Champe
it must be in the tmp subdirectory (that is <subject name>/tmp/control.dat) otherwise we will not find it.
As for the deleted voxel issue - how did you delete them?
Bruce
On Tue, 15 Mar 2016, Champe Barton wrote:
I created them as instructed in the tutorial and called the file “control.dat” so there’s a control.dat file in my subjects directory. Should I have named it tmp/control.dat? Also, would resolving the control points issue also resolve the deleted voxels issue? Cause my it’s not redrawing the pial surface either.
Thanks Champe
On Mar 15, 2016, at 1:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. sorry, it should be tmp/control.dat
On Tue, 15 Mar 2016, Champe Barton wrote:
Hey Bruce,
I recently sent you a log file to look at to determine why reprocessing data wasn’t making any changes in freeview. Have you had a chance to go over it yet? Let me know.
Thanks, Champe > On Mar 7, 2016, at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: > > I got it, thanks > Bruce >> On Mon, 7 Mar 2016, Champe Barton wrote: >> >> >> Hey Bruce, >> >> I got a notification saying the email my recon-all.log file attachment was too large and had to await moderator approval to be posted to the support list. I was just wondering if you received it or if I should resend it. >> >> Best, >> Champe >> >> Sent from my iPhone >> >>> On Mar 6, 2016, at 9:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: >>> >>> Hi Champe >>> >>> can you send us the recon-all.log file? >>> >>> cheers >>> Bruce >>>> On Sun, 6 Mar 2016, Champe Barton wrote: >>>> >>>> Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced any issues that could have been a result of that function). Everything in FreeSurfer works fine for me—I ran recon-all and successfully processed dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and the pial and white surfaces, and I successfully deleted unnecessary voxels and added a set of control points (in both cases, being careful to make and save the changes on all necessary slices with the brainmask volume highlighted). My only issue is that when I reprocess the data using recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs through the reconstruction without error and then shows no changes at all in freeview when I view the volumes/surfaces. The deleted voxels still appear deleted and I can still load the control points, so why wouldn’t it make the changes? And just to provide a little extra info: I encounter the same problem when I reprocess the tutorial data for the pial edits tutorial. I delete the voxels as instructed, save the file, reprocess it without error, and then nothing’s changed when I view it all again in freeview. Any help would be HUGELY appreciated—I’ve stressed over this for weeks trying to get my computer to function properly so that I can begin my work as a research assistant in a neuropsych lab editing and analyzing brain scans with FreeSurfer. Thanks, Champe >>> _______________________________________________ >>> 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 > _______________________________________________ > 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.
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as long as you move the file into the tmp dir recon-all should find it and use it (search for control.dat in the recon-all.log after you have run it).
I'm not sure what's going on with your brainmask.mgz though. You are saying that there are voxels that are deleted (set to 1) in your brainmask.mgz, but still show up inside the surfaces? Are they 0 in the brain.finalsurfs.mgz? The brain.mgz?
On Tue, 15 Mar 2016, Champe Barton wrote:
Yes, the pial (and white, actually) surface is extending into an area where there is no brain tissue. I'm not sure the anatomical name for it, but it's two cavities, one in the lower half of either hemisphere, where there's no tissue at all. When I process the dicom files I get really erratic surfaces drawn in those areas.
Also, how should I be saving my control points to get them in the tmp folder? I can manually move them there, but I assume it should be done automatically.
Thanks, Champe
Sent from my iPhone
On Mar 15, 2016, at 2:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
why are you deleting voxels from the brainmask.mgz? That is only used for masking out non-brain tissue. Is that what you are trying to do?
On Tue, 15 Mar 2016, Champe Barton wrote:
I used the recon editing tool—I explicitly followed the instructions from the tutorial (even on reprocessing the tutorial data it didn't work), so I had the brainmask.mgz highlighted, checked the recon editing box and held shift and clicked to remove the necessary voxels (they turned black). I removed them on all the necessary slices as well.
Champe
Sent from my iPhone
On Mar 15, 2016, at 1:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Champe
it must be in the tmp subdirectory (that is <subject name>/tmp/control.dat) otherwise we will not find it.
As for the deleted voxel issue - how did you delete them?
Bruce
On Tue, 15 Mar 2016, Champe Barton wrote:
I created them as instructed in the tutorial and called the file “control.dat” so there’s a control.dat file in my subjects directory. Should I have named it tmp/control.dat? Also, would resolving the control points issue also resolve the deleted voxels issue? Cause my it’s not redrawing the pial surface either.
Thanks Champe
On Mar 15, 2016, at 1:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. sorry, it should be tmp/control.dat > On Tue, 15 Mar 2016, Champe Barton wrote: > > Hey Bruce, > > I recently sent you a log file to look at to determine why reprocessing data wasn’t making any changes in freeview. Have you had a chance to go over it yet? Let me know. > > Thanks, > Champe >> On Mar 7, 2016, at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: >> >> I got it, thanks >> Bruce >>> On Mon, 7 Mar 2016, Champe Barton wrote: >>> >>> >>> Hey Bruce, >>> >>> I got a notification saying the email my recon-all.log file attachment was too large and had to await moderator approval to be posted to the support list. I was just wondering if you received it or if I should resend it. >>> >>> Best, >>> Champe >>> >>> Sent from my iPhone >>> >>>> On Mar 6, 2016, at 9:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: >>>> >>>> Hi Champe >>>> >>>> can you send us the recon-all.log file? >>>> >>>> cheers >>>> Bruce >>>>> On Sun, 6 Mar 2016, Champe Barton wrote: >>>>> >>>>> Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced any issues that could have been a result of that function). Everything in FreeSurfer works fine for me—I ran recon-all and successfully processed dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and the pial and white surfaces, and I successfully deleted unnecessary voxels and added a set of control points (in both cases, being careful to make and save the changes on all necessary slices with the brainmask volume highlighted). My only issue is that when I reprocess the data using recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs through the reconstruction without error and then shows no changes at all in freeview when I view the volumes/surfaces. The deleted voxels still appear deleted and I can still load the control points, so why wouldn’t it make the changes? And just to provide a little extra info: I encounter the same problem when I reprocess the tutorial data for the pial edits tutorial. I delete the voxels as instructed, save the file, reprocess it without error, and then nothing’s changed when I view it all again in freeview. Any help would be HUGELY appreciated—I’ve stressed over this for weeks trying to get my computer to function properly so that I can begin my work as a research assistant in a neuropsych lab editing and analyzing brain scans with FreeSurfer. Thanks, Champe >>>> _______________________________________________ >>>> 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 >> _______________________________________________ >> 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 _______________________________________________ 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.
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-
Bruce Fischl -
Champe Barton