Sadly, I haven't been able to determine the problem yet. I have tested the exact command that was suggested in both the Mac 5.1.0 version as well as the Windows/Ubuntu 5.1.0 virtual machine version, and neither have seemed to expand correctly when viewed in freeview. I won't have access to a machine running Linux natively until tomorrow. A colleague who runs Freesurfer 5.0 and 5.1.0 on a Linux machine is going to work with me to test if he has this issue as well.
Do you know if there have been any changes to the code of the mris_expand binary since 4.0.2? If not, we may try using the mris_expand from that version on the recon-all results from a 5.1.0 segmentation to see if the issue truly is the expand binary or not.
Any other suggestions you all have would be appreciated.
Thanks, Andrew ________________________________________ From: Alexandre Gramfort [gramfort@nmr.mgh.harvard.edu] Sent: Tuesday, April 24, 2012 3:24 PM To: Andrew C Yourich Subject: Fwd: Fwd: Freesurfer Digest, Vol 98, Issue 29
hi,
have you fixed your problem? I still don't manage to make it work…
thanks Alex
---------- Forwarded message ---------- From: Alexandre Gramfort gramfort@nmr.mgh.harvard.edu Date: Mon, Apr 23, 2012 at 7:10 PM Subject: Re: Fwd: Freesurfer Digest, Vol 98, Issue 29 To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: Nick Schmansky nicks@nmr.mgh.harvard.edu, ayourich@uab.edu, Krish Subramaniam krish@nmr.mgh.harvard.edu, Ruopeng Wang rpwang@nmr.mgh.harvard.edu
not sure about the mac, I'll cc Nick, Krish and Ruopeng so that they can answer.
could be due to my update of XCode this morning but things work fine with freeview -f lh.white -v ../mri/T1.mgz on my mac with lion. sorry for the noise
I built my own in ~fischl/dev/freesurfer/bin/freeview. Sure, put the surfaces somewhere I can look at them and I'll take a look
see the files in :
/homes/6/gramfort/cluster/work/data/MNE-sample-data/subjects/fsaverage/surf/lh.white.expanded
that's the sample data we use for MNE.
the log:
$ mris_expand -thickness lh.white 0.5 lh.white.expanded using distance as a % of thickness expanding surface lh.white by 50.0% of thickness and writing it to lh.white.expanded reading thickness... ending sse = 4485.856144 nrounds = 6 writing expanded surface to lh.white.expanded... writing group avg surface area 822 cm^2 into surface file surface expansion took 27 minutes and 15 seconds.
Alex
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 all,
@bruce : I've just given a try your own binaries in
~fischl/dev/freesurfer/bin/
and it worked fine. It looks like a bug has been fixed since the last stable release.
Alex
On Tue, Apr 24, 2012 at 10:44 PM, Andrew C Yourich ayourich@uab.edu wrote:
Sadly, I haven't been able to determine the problem yet. I have tested the exact command that was suggested in both the Mac 5.1.0 version as well as the Windows/Ubuntu 5.1.0 virtual machine version, and neither have seemed to expand correctly when viewed in freeview. I won't have access to a machine running Linux natively until tomorrow. A colleague who runs Freesurfer 5.0 and 5.1.0 on a Linux machine is going to work with me to test if he has this issue as well.
Do you know if there have been any changes to the code of the mris_expand binary since 4.0.2? If not, we may try using the mris_expand from that version on the recon-all results from a 5.1.0 segmentation to see if the issue truly is the expand binary or not.
Any other suggestions you all have would be appreciated.
Thanks, Andrew ________________________________________ From: Alexandre Gramfort [gramfort@nmr.mgh.harvard.edu] Sent: Tuesday, April 24, 2012 3:24 PM To: Andrew C Yourich Subject: Fwd: Fwd: Freesurfer Digest, Vol 98, Issue 29
hi,
have you fixed your problem? I still don't manage to make it work…
thanks Alex
---------- Forwarded message ---------- From: Alexandre Gramfort gramfort@nmr.mgh.harvard.edu Date: Mon, Apr 23, 2012 at 7:10 PM Subject: Re: Fwd: Freesurfer Digest, Vol 98, Issue 29 To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: Nick Schmansky nicks@nmr.mgh.harvard.edu, ayourich@uab.edu, Krish Subramaniam krish@nmr.mgh.harvard.edu, Ruopeng Wang rpwang@nmr.mgh.harvard.edu
not sure about the mac, I'll cc Nick, Krish and Ruopeng so that they can answer.
could be due to my update of XCode this morning but things work fine with freeview -f lh.white -v ../mri/T1.mgz on my mac with lion. sorry for the noise
I built my own in ~fischl/dev/freesurfer/bin/freeview. Sure, put the surfaces somewhere I can look at them and I'll take a look
see the files in :
/homes/6/gramfort/cluster/work/data/MNE-sample-data/subjects/fsaverage/surf/lh.white.expanded
that's the sample data we use for MNE.
the log:
$ mris_expand -thickness lh.white 0.5 lh.white.expanded using distance as a % of thickness expanding surface lh.white by 50.0% of thickness and writing it to lh.white.expanded reading thickness... ending sse = 4485.856144 nrounds = 6 writing expanded surface to lh.white.expanded... writing group avg surface area 822 cm^2 into surface file surface expansion took 27 minutes and 15 seconds.
Alex
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.
thanks Alex.
If anyone needs a fix before the next release let us know what hardware/software version you are running and we'll send you a binary
cheers Bruce
On Wed, 25 Apr 2012, Alexandre Gramfort wrote:
hi all,
@bruce : I've just given a try your own binaries in
~fischl/dev/freesurfer/bin/
and it worked fine. It looks like a bug has been fixed since the last stable release.
Alex
On Tue, Apr 24, 2012 at 10:44 PM, Andrew C Yourich ayourich@uab.edu wrote:
Sadly, I haven't been able to determine the problem yet. I have tested the exact command that was suggested in both the Mac 5.1.0 version as well as the Windows/Ubuntu 5.1.0 virtual machine version, and neither have seemed to expand correctly when viewed in freeview. I won't have access to a machine running Linux natively until tomorrow. A colleague who runs Freesurfer 5.0 and 5.1.0 on a Linux machine is going to work with me to test if he has this issue as well.
Do you know if there have been any changes to the code of the mris_expand binary since 4.0.2? If not, we may try using the mris_expand from that version on the recon-all results from a 5.1.0 segmentation to see if the issue truly is the expand binary or not.
Any other suggestions you all have would be appreciated.
Thanks, Andrew ________________________________________ From: Alexandre Gramfort [gramfort@nmr.mgh.harvard.edu] Sent: Tuesday, April 24, 2012 3:24 PM To: Andrew C Yourich Subject: Fwd: Fwd: Freesurfer Digest, Vol 98, Issue 29
hi,
have you fixed your problem? I still don't manage to make it work?
thanks Alex
---------- Forwarded message ---------- From: Alexandre Gramfort gramfort@nmr.mgh.harvard.edu Date: Mon, Apr 23, 2012 at 7:10 PM Subject: Re: Fwd: Freesurfer Digest, Vol 98, Issue 29 To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: Nick Schmansky nicks@nmr.mgh.harvard.edu, ayourich@uab.edu, Krish Subramaniam krish@nmr.mgh.harvard.edu, Ruopeng Wang rpwang@nmr.mgh.harvard.edu
not sure about the mac, I'll cc Nick, Krish and Ruopeng so that they can answer.
could be due to my update of XCode this morning but things work fine with freeview -f lh.white -v ../mri/T1.mgz on my mac with lion. sorry for the noise
I built my own in ~fischl/dev/freesurfer/bin/freeview. Sure, put the surfaces somewhere I can look at them and I'll take a look
see the files in :
/homes/6/gramfort/cluster/work/data/MNE-sample-data/subjects/fsaverage/surf/lh.white.expanded
that's the sample data we use for MNE.
the log:
$ mris_expand -thickness lh.white 0.5 lh.white.expanded using distance as a % of thickness expanding surface lh.white by 50.0% of thickness and writing it to lh.white.expanded reading thickness... ending sse = 4485.856144 nrounds = 6 writing expanded surface to lh.white.expanded... writing group avg surface area 822 cm^2 into surface file surface expansion took 27 minutes and 15 seconds.
Alex
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.
If you all have a fixed binary for a Mac Pro running Mac OS 10.6.8 that you would be able to forward me, I would greatly appreciate it.
Thanks, Andrew ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2012 8:56 AM To: Alexandre Gramfort Cc: Andrew C Yourich; Robert C Knowlton; freesurfer@nmr.mgh.harvard.edu Subject: Re: Fwd: Freesurfer Digest, Vol 98, Issue 29
thanks Alex.
If anyone needs a fix before the next release let us know what hardware/software version you are running and we'll send you a binary
cheers Bruce
On Wed, 25 Apr 2012, Alexandre Gramfort wrote:
hi all,
@bruce : I've just given a try your own binaries in
~fischl/dev/freesurfer/bin/
and it worked fine. It looks like a bug has been fixed since the last stable release.
Alex
On Tue, Apr 24, 2012 at 10:44 PM, Andrew C Yourich ayourich@uab.edu wrote:
Sadly, I haven't been able to determine the problem yet. I have tested the exact command that was suggested in both the Mac 5.1.0 version as well as the Windows/Ubuntu 5.1.0 virtual machine version, and neither have seemed to expand correctly when viewed in freeview. I won't have access to a machine running Linux natively until tomorrow. A colleague who runs Freesurfer 5.0 and 5.1.0 on a Linux machine is going to work with me to test if he has this issue as well.
Do you know if there have been any changes to the code of the mris_expand binary since 4.0.2? If not, we may try using the mris_expand from that version on the recon-all results from a 5.1.0 segmentation to see if the issue truly is the expand binary or not.
Any other suggestions you all have would be appreciated.
Thanks, Andrew ________________________________________ From: Alexandre Gramfort [gramfort@nmr.mgh.harvard.edu] Sent: Tuesday, April 24, 2012 3:24 PM To: Andrew C Yourich Subject: Fwd: Fwd: Freesurfer Digest, Vol 98, Issue 29
hi,
have you fixed your problem? I still don't manage to make it work?
thanks Alex
---------- Forwarded message ---------- From: Alexandre Gramfort gramfort@nmr.mgh.harvard.edu Date: Mon, Apr 23, 2012 at 7:10 PM Subject: Re: Fwd: Freesurfer Digest, Vol 98, Issue 29 To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: Nick Schmansky nicks@nmr.mgh.harvard.edu, ayourich@uab.edu, Krish Subramaniam krish@nmr.mgh.harvard.edu, Ruopeng Wang rpwang@nmr.mgh.harvard.edu
not sure about the mac, I'll cc Nick, Krish and Ruopeng so that they can answer.
could be due to my update of XCode this morning but things work fine with freeview -f lh.white -v ../mri/T1.mgz on my mac with lion. sorry for the noise
I built my own in ~fischl/dev/freesurfer/bin/freeview. Sure, put the surfaces somewhere I can look at them and I'll take a look
see the files in :
/homes/6/gramfort/cluster/work/data/MNE-sample-data/subjects/fsaverage/surf/lh.white.expanded
that's the sample data we use for MNE.
the log:
$ mris_expand -thickness lh.white 0.5 lh.white.expanded using distance as a % of thickness expanding surface lh.white by 50.0% of thickness and writing it to lh.white.expanded reading thickness... ending sse = 4485.856144 nrounds = 6 writing expanded surface to lh.white.expanded... writing group avg surface area 822 cm^2 into surface file surface expansion took 27 minutes and 15 seconds.
Alex
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
-
Alexandre Gramfort -
Andrew C Yourich -
Bruce Fischl