Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29
I've replaced my old mris_expand file with the one downloaded from the link below, and now it is working perfectly. Thank you so much to all of you who helped me resolve this issue. I really appreciate it. - Andrew From: Nick Schmansky [ni...@nmr.mgh.harvard.edu] Sent: Thursday, April 26, 2012 10:18 AM To: Andrew C Yourich Cc: Bruce Fischl; gramf...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29 i've posted a build for the mac here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/ n. On Wed, 2012-04-25 at 15:02 +, Andrew C Yourich wrote: 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 [fis...@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 ayour...@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 [gramf...@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 gramf...@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 fis...@nmr.mgh.harvard.edu Cc: Nick Schmansky ni...@nmr.mgh.harvard.edu, ayour...@uab.edu, Krish Subramaniam kr...@nmr.mgh.harvard.edu, Ruopeng Wang rpw...@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 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
Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29
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 [fis...@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 ayour...@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 [gramf...@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 gramf...@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 fis...@nmr.mgh.harvard.edu Cc: Nick Schmansky ni...@nmr.mgh.harvard.edu, ayour...@uab.edu, Krish Subramaniam kr...@nmr.mgh.harvard.edu, Ruopeng Wang rpw...@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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_expand not working since upgrading to v.5.1.0
I have encountered this issue running Freesurfer 5.1.0 on both a Mac Pro running Mac OS 10.6.8 as well as a Dell PC running Freesurfer using the Ubuntu virtual machine package provided for Windows (OS was Windows XP). I'm going to attempt run the command exactly as you wrote it in the e-mail to Alex and then view it in freeview to see if anything has changed. Thanks, Andrew From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, April 22, 2012 9:10 AM To: Andrew C Yourich Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_expand not working since upgrading to v.5.1.0 Hi Andrew, I just tried this and it worked fine for me. If you tell me what os/hardware you are running on I'll send you a current binary and you can see if that works. cheers Bruce p.s. do you look at the surfaces via: freeview -f lh.white lh.white.expanded On Fri, 20 Apr 2012, Andrew C Yourich wrote: Hello, I have recently upgraded from running version 4.0.2 of Freesurfer to the most current version (v.5.1.0), and have encountered a problem. I used to be able to expand the recon-all generated white matter volume by a percentage of the grey matter thickness using mris_expand, but ever since changing to the most current version, the mris_expand command is not returning correct results. The command I use is: mris_expand -thickness ./lh.white $1 lh.white.expanded where $1 is a variable indicating the percentage I wish to expand by. Since the version change, mris_expand does not seem to actually change the volume of lh.white, with the output file lh.white.expanded looking identical to lh.white after running the command. This occurs regardless of the value I enter for $1 (be it very large, very small, or even negative) The command appears to run normally as it did in v.4.0.2 and does not give any error message, but the output volume appears unchanged from the input volume. Have the parameters or flags for this command changed between the versions, or has mris_expand been deprecated? If so, what flags or command should I use instead? Thanks, - Andrew 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
Re: [Freesurfer] mris_expand not working since upgrading to v.5.1.0
I personally do not have access to a Linux machine, but I do know someone in our department that does run freesurfer on one. I had e-mailed him on Friday to see if he encountered this issue as well, so let me follow up with him and see if he is able to check mris_expand results on his computer. - Andrew From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, April 23, 2012 9:44 AM To: Andrew C Yourich Cc: freesurfer@nmr.mgh.harvard.edu; Robert C Knowlton; gramf...@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] mris_expand not working since upgrading to v.5.1.0 can you try it on a linux machine? On Mon, 23 Apr 2012, Andrew C Yourich wrote: I have encountered this issue running Freesurfer 5.1.0 on both a Mac Pro running Mac OS 10.6.8 as well as a Dell PC running Freesurfer using the Ubuntu virtual machine package provided for Windows (OS was Windows XP). I'm going to attempt run the command exactly as you wrote it in the e-mail to Alex and then view it in freeview to see if anything has changed. Thanks, Andrew From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, April 22, 2012 9:10 AM To: Andrew C Yourich Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_expand not working since upgrading to v.5.1.0 Hi Andrew, I just tried this and it worked fine for me. If you tell me what os/hardware you are running on I'll send you a current binary and you can see if that works. cheers Bruce p.s. do you look at the surfaces via: freeview -f lh.white lh.white.expanded On Fri, 20 Apr 2012, Andrew C Yourich wrote: Hello, I have recently upgraded from running version 4.0.2 of Freesurfer to the most current version (v.5.1.0), and have encountered a problem. I used to be able to expand the recon-all generated white matter volume by a percentage of the grey matter thickness using mris_expand, but ever since changing to the most current version, the mris_expand command is not returning correct results. The command I use is: mris_expand -thickness ./lh.white $1 lh.white.expanded where $1 is a variable indicating the percentage I wish to expand by. Since the version change, mris_expand does not seem to actually change the volume of lh.white, with the output file lh.white.expanded looking identical to lh.white after running the command. This occurs regardless of the value I enter for $1 (be it very large, very small, or even negative) The command appears to run normally as it did in v.4.0.2 and does not give any error message, but the output volume appears unchanged from the input volume. Have the parameters or flags for this command changed between the versions, or has mris_expand been deprecated? If so, what flags or command should I use instead? Thanks, - Andrew 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] mris_expand not working since upgrading to v.5.1.0
Hello, I have recently upgraded from running version 4.0.2 of Freesurfer to the most current version (v.5.1.0), and have encountered a problem. I used to be able to expand the recon-all generated white matter volume by a percentage of the grey matter thickness using mris_expand, but ever since changing to the most current version, the mris_expand command is not returning correct results. The command I use is: mris_expand -thickness ./lh.white $1 lh.white.expanded where $1 is a variable indicating the percentage I wish to expand by. Since the version change, mris_expand does not seem to actually change the volume of lh.white, with the output file lh.white.expanded looking identical to lh.white after running the command. This occurs regardless of the value I enter for $1 (be it very large, very small, or even negative) The command appears to run normally as it did in v.4.0.2 and does not give any error message, but the output volume appears unchanged from the input volume. Have the parameters or flags for this command changed between the versions, or has mris_expand been deprecated? If so, what flags or command should I use instead? Thanks, - Andrew ___ 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.
