Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul
Hi Paul
you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically something big is wrong like skull attached to brain or something
cheers Bruce
On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul
Hello Bruce, Yes, the skull is still attached. Should I remove the skull for all the slices and re-run it again? Best, Paul
On Fri, May 19, 2017 at 10:28 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Paul
you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically something big is wrong like skull attached to brain or something
cheers Bruce
On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Freesurfer expert, While running recon-all on one of my subjects, the
pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul
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yes, or try rerunning watershed with different parameters. YOu don't have to remove the entire skull that was left - just the connection between it and wm On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Bruce, Yes, the skull is still attached. Should I remove the skull for all the slices and re-run it again? Best, Paul
On Fri, May 19, 2017 at 10:28 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Paul
you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically something big is wrong like skull attached to brain or something cheers Bruce On Fri, 19 May 2017, miracle ozzoude wrote: Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul
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Hello Bruce, Is 2 or 3 slices ok? Also, after that I should run the rest of recon-all stage from autorecon2. Best, Paul
On Fri, May 19, 2017 at 11:32 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
yes, or try rerunning watershed with different parameters. YOu don't have to remove the entire skull that was left - just the connection between it and wm
On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Bruce, Yes, the skull is still attached. Should I remove the skull
for all the slices and re-run it again? Best, Paul
On Fri, May 19, 2017 at 10:28 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Paul
you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically something big is wrong like skull attached to brain or something cheers Bruce On Fri, 19 May 2017, miracle ozzoude wrote: Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul
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it depends on how many connections there are On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Bruce, Is 2 or 3 slices ok? Also, after that I should run the rest of recon-all stage from autorecon2. Best, Paul
On Fri, May 19, 2017 at 11:32 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: yes, or try rerunning watershed with different parameters. YOu don't have to remove the entire skull that was left - just the connection between it and wm On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Bruce, Yes, the skull is still attached. Should I remove the skull for all the slices and re-run it again? Best, Paul On Fri, May 19, 2017 at 10:28 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Paul you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically something big is wrong like skull attached to brain or something cheers Bruce On Fri, 19 May 2017, miracle ozzoude wrote: Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul _______________________________________________ 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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Hello Bruce, Thank you. Also, I don't need to run the entire pipeline again just autorecon2 and autorecon3 Best, Paul
On Fri, May 19, 2017 at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
it depends on how many connections there are
On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Bruce, Is 2 or 3 slices ok? Also, after that I should run the rest of
recon-all stage from autorecon2. Best, Paul
On Fri, May 19, 2017 at 11:32 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: yes, or try rerunning watershed with different parameters. YOu don't have to remove the entire skull that was left - just the connection between it and wm On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Bruce, Yes, the skull is still attached. Should I remove the skull for all the slices and re-run it again? Best, Paul On Fri, May 19, 2017 at 10:28 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Paul you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically something big is wrong like skull attached to brain or something cheers Bruce On Fri, 19 May 2017, miracle ozzoude wrote: Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul _______________________________________________ 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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it depends what you do. If you edit the wm.mgz to remove the connection you only need to run autorecon2-wm and autorecon3, which is a lot faster
cheers Bruce
On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Bruce, Thank you. Also, I don't need to run the entire pipeline again just autorecon2 and autorecon3 Best, Paul
On Fri, May 19, 2017 at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: it depends on how many connections there are On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Bruce, Is 2 or 3 slices ok? Also, after that I should run the rest of recon-all stage from autorecon2. Best, Paul On Fri, May 19, 2017 at 11:32 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: yes, or try rerunning watershed with different parameters. YOu don't have to remove the entire skull that was left - just the connection between it and wm On Fri, 19 May 2017, miracle ozzoude wrote: Hello Bruce, Yes, the skull is still attached. Should I remove the skull for all the slices and re-run it again? Best, Paul On Fri, May 19, 2017 at 10:28 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Paul you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically something big is wrong like skull attached to brain or something cheers Bruce On Fri, 19 May 2017, miracle ozzoude wrote: Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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I edited the brainmask not the wm.mgz. Best, Paul
On Fri, May 19, 2017 at 11:49 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
it depends what you do. If you edit the wm.mgz to remove the connection you only need to run autorecon2-wm and autorecon3, which is a lot faster
cheers Bruce
On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Bruce, Thank you. Also, I don't need to run the entire pipeline again
just autorecon2 and autorecon3 Best, Paul
On Fri, May 19, 2017 at 11:41 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: it depends on how many connections there are On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Bruce, Is 2 or 3 slices ok? Also, after that I should run the rest of recon-all stage from autorecon2. Best, Paul On Fri, May 19, 2017 at 11:32 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: yes, or try rerunning watershed with different parameters. YOu don't have to remove the entire skull that was left - just the connection between it and wm On Fri, 19 May 2017, miracle ozzoude wrote: Hello Bruce, Yes, the skull is still attached. Should I remove the skull for all the slices and re-run it again? Best, Paul On Fri, May 19, 2017 at 10:28 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Paul you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically something big is wrong like skull attached to brain or something cheers Bruce On Fri, 19 May 2017, miracle ozzoude wrote: Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Hi Paul, are you using version 6? Is this happening on more than one subject or is this subject an outlier?
On 05/19/2017 10:28 AM, Bruce Fischl wrote:
Hi Paul
you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically something big is wrong like skull attached to brain or something
cheers Bruce
On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Bruce, So far, I have only encountered this error in 2/147 of my subjects. Best, Paul
On Mon, May 22, 2017 at 11:00 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Paul, are you using version 6? Is this happening on more than one subject or is this subject an outlier?
On 05/19/2017 10:28 AM, Bruce Fischl wrote:
Hi Paul
you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically something big is wrong like skull attached to brain or something
cheers Bruce
On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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And is this version 6 or 5.3?
On 05/23/2017 08:21 AM, miracle ozzoude wrote:
Hello Bruce, So far, I have only encountered this error in 2/147 of my subjects. Best, Paul
On Mon, May 22, 2017 at 11:00 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Paul, are you using version 6? Is this happening on more than one subject or is this subject an outlier? On 05/19/2017 10:28 AM, Bruce Fischl wrote: > Hi Paul > > you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically > something big is wrong like skull attached to brain or something > > cheers > Bruce > > > On Fri, 19 May 2017, miracle ozzoude wrote: > >> Hello Freesurfer expert, While running recon-all on one of my >> subjects, the >> pipeline got stuck during the "fix topology rh" stage for almost >> 12hrs. How >> do I diagnosis the problem and fix it? I have attached the recon-all.log >> file. Thank you >> Best, >> Paul >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Version 6
On Tue, May 23, 2017 at 11:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
And is this version 6 or 5.3?
On 05/23/2017 08:21 AM, miracle ozzoude wrote:
Hello Bruce, So far, I have only encountered this error in 2/147 of my subjects. Best, Paul
On Mon, May 22, 2017 at 11:00 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Paul, are you using version 6? Is this happening on more than one subject or is this subject an outlier? On 05/19/2017 10:28 AM, Bruce Fischl wrote: > Hi Paul > > you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically > something big is wrong like skull attached to brain or something > > cheers > Bruce > > > On Fri, 19 May 2017, miracle ozzoude wrote: > >> Hello Freesurfer expert, While running recon-all on one of my >> subjects, the >> pipeline got stuck during the "fix topology rh" stage for almost >> 12hrs. How >> do I diagnosis the problem and fix it? I have attached the recon-all.log >> file. Thank you >> Best, >> Paul >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Doug and Bruce,
I have encountered the same issue with 2 other subjects. I checked the ?h.orig.nofix and find nothing wrong (like attached skull). How do I proceed with solving these problems? I have attached each subject's recon.log file.
Thanks, Paul
On Tue, May 23, 2017 at 11:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
And is this version 6 or 5.3?
On 05/23/2017 08:21 AM, miracle ozzoude wrote:
Hello Bruce, So far, I have only encountered this error in 2/147 of my subjects. Best, Paul
On Mon, May 22, 2017 at 11:00 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Paul, are you using version 6? Is this happening on more than one subject or is this subject an outlier? On 05/19/2017 10:28 AM, Bruce Fischl wrote: > Hi Paul > > you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically > something big is wrong like skull attached to brain or something > > cheers > Bruce > > > On Fri, 19 May 2017, miracle ozzoude wrote: > >> Hello Freesurfer expert, While running recon-all on one of my >> subjects, the >> pipeline got stuck during the "fix topology rh" stage for almost >> 12hrs. How >> do I diagnosis the problem and fix it? I have attached the recon-all.log >> file. Thank you >> Best, >> Paul >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Douglas N Greve -
miracle ozzoude