Re: [Freesurfer] mri_vol2surf --projopt
Allright, if the option --interp nearest is used the output is as given in a previous post (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35148.html). After applying --interp trilin the output is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --interp trilin --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map.gm.mgz reading wm volume fraction from /.../map.wm.mgz reading csf volume fraction from /.../map.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --interp trilin --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault If the option --interp is dissmissed completely the output is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map.gm.mgz reading wm volume fraction from /.../map.wm.mgz reading csf volume fraction from /.../map.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault Voxel size of the epi and the map data from mri_compute_volume_fractions is 1.5 x 1.5 x 2 mm^3 and of the t1 image is 1 x 1 x 1 mm^3. On Mon, 14 Apr 2014 12:24:37 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you send your commandline with --interp as well as the terminal output? On 04/14/2014 06:54 AM, Joerg Pfannmoeller wrote: Well, there is no difference between trilin or nearest. mri_vol2surf displays segfault regardless which option I use (trilin or nearest). On Thu, 10 Apr 2014 11:30:38 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I don't understand what the question is. If you need to interpolate, then use --interp trilinear doug On 04/10/2014 04:36 AM, Joerg Pfannmoeller wrote: Allright! The only point I would like to emphasize is: Regardless if option trilin or nearest is used I need to interpolate the functional data to the structural image of the subject. This might be due to a feature of the function build_sample_array in the mri_vol2surf source code. In this function there are some constant values (din = 1.0, dout = 0.1, nsamples = 10), which might be the reason why I need to interpolate the functional data to the structural image. Currently I can not investigate the code any further. Do you have enough experience with the source code to clarify this question? On Wed, 09 Apr 2014 09:31:57 -0400 Douglas Greve gr...@nmr.mgh.harvard.edu wrote: You can use --projfrac (which can perform an interpolation with --interp trilinear) On 4/9/14 2:44 AM, Joerg Pfannmoeller wrote: Sorry for this question, but now I am confused. Do you mean that I should not use projopt and just use the interpolation? If so why should I not use projfrac? On Tue, 08 Apr 2014 15:02:36 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to do without it for now and just do the interpolation On 04/08/2014 03:32 AM, Joerg Pfannmoeller wrote: Well, I need to use that option. In this case I will just interpolate to the 1 mm grid and proceed this way. On Mon, 07 Apr 2014 12:14:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Sorry, I don't understand. You mean it still segfaults without --projopt or that you have to use projopt? On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote: Unfortunately that is no option for me. On Fri, 04 Apr 2014 15:33:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Don't use --projopt and it won't segfault On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote: The command is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex The output is the follwoing: srcvol = /.../f001
Re: [Freesurfer] mri_vol2surf --projopt
Well, there is no difference between trilin or nearest. mri_vol2surf displays segfault regardless which option I use (trilin or nearest). On Thu, 10 Apr 2014 11:30:38 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I don't understand what the question is. If you need to interpolate, then use --interp trilinear doug On 04/10/2014 04:36 AM, Joerg Pfannmoeller wrote: Allright! The only point I would like to emphasize is: Regardless if option trilin or nearest is used I need to interpolate the functional data to the structural image of the subject. This might be due to a feature of the function build_sample_array in the mri_vol2surf source code. In this function there are some constant values (din = 1.0, dout = 0.1, nsamples = 10), which might be the reason why I need to interpolate the functional data to the structural image. Currently I can not investigate the code any further. Do you have enough experience with the source code to clarify this question? On Wed, 09 Apr 2014 09:31:57 -0400 Douglas Greve gr...@nmr.mgh.harvard.edu wrote: You can use --projfrac (which can perform an interpolation with --interp trilinear) On 4/9/14 2:44 AM, Joerg Pfannmoeller wrote: Sorry for this question, but now I am confused. Do you mean that I should not use projopt and just use the interpolation? If so why should I not use projfrac? On Tue, 08 Apr 2014 15:02:36 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to do without it for now and just do the interpolation On 04/08/2014 03:32 AM, Joerg Pfannmoeller wrote: Well, I need to use that option. In this case I will just interpolate to the 1 mm grid and proceed this way. On Mon, 07 Apr 2014 12:14:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Sorry, I don't understand. You mean it still segfaults without --projopt or that you have to use projopt? On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote: Unfortunately that is no option for me. On Fri, 04 Apr 2014 15:33:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Don't use --projopt and it won't segfault On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote: The command is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex The output is the follwoing: srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = subjid surfreg = sphere.reg reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map001.gm.mgz reading wm volume fraction from /.../map001.wm.mgz reading csf volume fraction from /.../map001.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault Do you have an idea about the cause of the error? On Wed, 02 Apr 2014 17:28:14 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is your command line that is seg faulting? What is the terminal output? On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote: Please help me with this issue: If I apply mri_surf2vol to a single volume of unprocessed epi-data, it results in a segmentation fault. It works if I apply mri_vol2vol for registration of epi and anatomy, but than an interpolation is involved. I would like to avoid the interpolation and apply mri_surf2vol directly to the unprocessed data in order to minimize the number of interpolations. At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote: This is something BF added Sept 1 2009: added --projopt switch to do optimal linear estimation of gray matter values given a set of precomputed gray matter densities. I don't know what it would mean beyond that doug On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote: Hello, I found an option in mri_vol2surf for which I could not find a documentation. The option is called: --projopt It would be nice if somebody could give a description of this option. Respectfully yours pfannmoe
Re: [Freesurfer] mri_vol2surf --projopt
However, let's forget about this question. I need to address something else and until that is finished it does not matter. On Mon, 14 Apr 2014 12:54:30 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Well, there is no difference between trilin or nearest. mri_vol2surf displays segfault regardless which option I use (trilin or nearest). On Thu, 10 Apr 2014 11:30:38 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I don't understand what the question is. If you need to interpolate, then use --interp trilinear doug On 04/10/2014 04:36 AM, Joerg Pfannmoeller wrote: Allright! The only point I would like to emphasize is: Regardless if option trilin or nearest is used I need to interpolate the functional data to the structural image of the subject. This might be due to a feature of the function build_sample_array in the mri_vol2surf source code. In this function there are some constant values (din = 1.0, dout = 0.1, nsamples = 10), which might be the reason why I need to interpolate the functional data to the structural image. Currently I can not investigate the code any further. Do you have enough experience with the source code to clarify this question? On Wed, 09 Apr 2014 09:31:57 -0400 Douglas Greve gr...@nmr.mgh.harvard.edu wrote: You can use --projfrac (which can perform an interpolation with --interp trilinear) On 4/9/14 2:44 AM, Joerg Pfannmoeller wrote: Sorry for this question, but now I am confused. Do you mean that I should not use projopt and just use the interpolation? If so why should I not use projfrac? On Tue, 08 Apr 2014 15:02:36 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to do without it for now and just do the interpolation On 04/08/2014 03:32 AM, Joerg Pfannmoeller wrote: Well, I need to use that option. In this case I will just interpolate to the 1 mm grid and proceed this way. On Mon, 07 Apr 2014 12:14:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Sorry, I don't understand. You mean it still segfaults without --projopt or that you have to use projopt? On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote: Unfortunately that is no option for me. On Fri, 04 Apr 2014 15:33:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Don't use --projopt and it won't segfault On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote: The command is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex The output is the follwoing: srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = subjid surfreg = sphere.reg reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map001.gm.mgz reading wm volume fraction from /.../map001.wm.mgz reading csf volume fraction from /.../map001.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault Do you have an idea about the cause of the error? On Wed, 02 Apr 2014 17:28:14 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is your command line that is seg faulting? What is the terminal output? On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote: Please help me with this issue: If I apply mri_surf2vol to a single volume of unprocessed epi-data, it results in a segmentation fault. It works if I apply mri_vol2vol for registration of epi and anatomy, but than an interpolation is involved. I would like to avoid the interpolation and apply mri_surf2vol directly to the unprocessed data in order to minimize the number of interpolations. At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote: This is something BF added Sept 1 2009: added --projopt switch to do optimal linear estimation of gray matter values given a set of precomputed gray matter densities. I don't know what it would mean beyond that doug On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote: Hello, I found an option in mri_vol2surf for which I could not find
Re: [Freesurfer] mri_vol2surf --projopt
Allright! The only point I would like to emphasize is: Regardless if option trilin or nearest is used I need to interpolate the functional data to the structural image of the subject. This might be due to a feature of the function build_sample_array in the mri_vol2surf source code. In this function there are some constant values (din = 1.0, dout = 0.1, nsamples = 10), which might be the reason why I need to interpolate the functional data to the structural image. Currently I can not investigate the code any further. Do you have enough experience with the source code to clarify this question? On Wed, 09 Apr 2014 09:31:57 -0400 Douglas Greve gr...@nmr.mgh.harvard.edu wrote: You can use --projfrac (which can perform an interpolation with --interp trilinear) On 4/9/14 2:44 AM, Joerg Pfannmoeller wrote: Sorry for this question, but now I am confused. Do you mean that I should not use projopt and just use the interpolation? If so why should I not use projfrac? On Tue, 08 Apr 2014 15:02:36 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to do without it for now and just do the interpolation On 04/08/2014 03:32 AM, Joerg Pfannmoeller wrote: Well, I need to use that option. In this case I will just interpolate to the 1 mm grid and proceed this way. On Mon, 07 Apr 2014 12:14:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Sorry, I don't understand. You mean it still segfaults without --projopt or that you have to use projopt? On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote: Unfortunately that is no option for me. On Fri, 04 Apr 2014 15:33:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Don't use --projopt and it won't segfault On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote: The command is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex The output is the follwoing: srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = subjid surfreg = sphere.reg reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map001.gm.mgz reading wm volume fraction from /.../map001.wm.mgz reading csf volume fraction from /.../map001.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault Do you have an idea about the cause of the error? On Wed, 02 Apr 2014 17:28:14 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is your command line that is seg faulting? What is the terminal output? On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote: Please help me with this issue: If I apply mri_surf2vol to a single volume of unprocessed epi-data, it results in a segmentation fault. It works if I apply mri_vol2vol for registration of epi and anatomy, but than an interpolation is involved. I would like to avoid the interpolation and apply mri_surf2vol directly to the unprocessed data in order to minimize the number of interpolations. At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote: This is something BF added Sept 1 2009: added --projopt switch to do optimal linear estimation of gray matter values given a set of precomputed gray matter densities. I don't know what it would mean beyond that doug On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote: Hello, I found an option in mri_vol2surf for which I could not find a documentation. The option is called: --projopt It would be nice if somebody could give a description of this option. Respectfully yours pfannmoe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Re: [Freesurfer] mri_vol2surf --projopt
Sorry for this question, but now I am confused. Do you mean that I should not use projopt and just use the interpolation? If so why should I not use projfrac? On Tue, 08 Apr 2014 15:02:36 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to do without it for now and just do the interpolation On 04/08/2014 03:32 AM, Joerg Pfannmoeller wrote: Well, I need to use that option. In this case I will just interpolate to the 1 mm grid and proceed this way. On Mon, 07 Apr 2014 12:14:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Sorry, I don't understand. You mean it still segfaults without --projopt or that you have to use projopt? On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote: Unfortunately that is no option for me. On Fri, 04 Apr 2014 15:33:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Don't use --projopt and it won't segfault On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote: The command is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex The output is the follwoing: srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = subjid surfreg = sphere.reg reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map001.gm.mgz reading wm volume fraction from /.../map001.wm.mgz reading csf volume fraction from /.../map001.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault Do you have an idea about the cause of the error? On Wed, 02 Apr 2014 17:28:14 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is your command line that is seg faulting? What is the terminal output? On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote: Please help me with this issue: If I apply mri_surf2vol to a single volume of unprocessed epi-data, it results in a segmentation fault. It works if I apply mri_vol2vol for registration of epi and anatomy, but than an interpolation is involved. I would like to avoid the interpolation and apply mri_surf2vol directly to the unprocessed data in order to minimize the number of interpolations. At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote: This is something BF added Sept 1 2009: added --projopt switch to do optimal linear estimation of gray matter values given a set of precomputed gray matter densities. I don't know what it would mean beyond that doug On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote: Hello, I found an option in mri_vol2surf for which I could not find a documentation. The option is called: --projopt It would be nice if somebody could give a description of this option. Respectfully yours pfannmoe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@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 mailto: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
Re: [Freesurfer] mri_surcluster and centroid option
On Mon, 07 Apr 2014 12:02:24 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Is this group data? Or otherwise on fsaverage? Or on the subject's surface? It is on a single subject on its on anatomy (self). How are you determining that the centroid is outside of the cluster? The coordinates are outside the cluster, there is nothing to worry about that. It should give you a vertex number for the centroid (I think). As you told in your last mail it gives Tal-coordinates and not vertices. I opted not to use the centroid by default for this reason. This can happen because the centroid is irregular. I don not understand this: What do you mean by irregular? ___ 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.
Re: [Freesurfer] mri_surcluster and centroid option
Hi, I am sorry to disappoint you. I wrote another srcipt to compute the centroid in order to clarify whats happening. The centroid computed by the script is in the center of the cluster. However, the differences could be due to details of the computation. I was not able to unriddle all the details in the freesurfer code. Probably I am going to keep this script since it fits what I would like to compute. Before I forget about it, I use freesurfer 5.3. Greetings pfannmoe On Wed, 9 Apr 2014 08:33:26 -0400 (EDT) Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jeorg if the cluster is non-convex, the centroid is not guaranteed to be in the interior. Think of a C or U shape. cheers Bruce On Wed, 9 Apr 2014, Joerg Pfannmoeller wrote: On Mon, 07 Apr 2014 12:02:24 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Is this group data? Or otherwise on fsaverage? Or on the subject's surface? It is on a single subject on its on anatomy (self). How are you determining that the centroid is outside of the cluster? The coordinates are outside the cluster, there is nothing to worry about that. It should give you a vertex number for the centroid (I think). As you told in your last mail it gives Tal-coordinates and not vertices. I opted not to use the centroid by default for this reason. This can happen because the centroid is irregular. I don not understand this: What do you mean by irregular? ___ 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
Re: [Freesurfer] mri_vol2surf --projopt
Well, I need to use that option. In this case I will just interpolate to the 1 mm grid and proceed this way. On Mon, 07 Apr 2014 12:14:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Sorry, I don't understand. You mean it still segfaults without --projopt or that you have to use projopt? On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote: Unfortunately that is no option for me. On Fri, 04 Apr 2014 15:33:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Don't use --projopt and it won't segfault On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote: The command is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex The output is the follwoing: srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = subjid surfreg = sphere.reg reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map001.gm.mgz reading wm volume fraction from /.../map001.wm.mgz reading csf volume fraction from /.../map001.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault Do you have an idea about the cause of the error? On Wed, 02 Apr 2014 17:28:14 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is your command line that is seg faulting? What is the terminal output? On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote: Please help me with this issue: If I apply mri_surf2vol to a single volume of unprocessed epi-data, it results in a segmentation fault. It works if I apply mri_vol2vol for registration of epi and anatomy, but than an interpolation is involved. I would like to avoid the interpolation and apply mri_surf2vol directly to the unprocessed data in order to minimize the number of interpolations. At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote: This is something BF added Sept 1 2009: added --projopt switch to do optimal linear estimation of gray matter values given a set of precomputed gray matter densities. I don't know what it would mean beyond that doug On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote: Hello, I found an option in mri_vol2surf for which I could not find a documentation. The option is called: --projopt It would be nice if somebody could give a description of this option. Respectfully yours pfannmoe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@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 mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617
Re: [Freesurfer] mri_vol2surf --projopt
Unfortunately that is no option for me. On Fri, 04 Apr 2014 15:33:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Don't use --projopt and it won't segfault On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote: The command is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex The output is the follwoing: srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = subjid surfreg = sphere.reg reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map001.gm.mgz reading wm volume fraction from /.../map001.wm.mgz reading csf volume fraction from /.../map001.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault Do you have an idea about the cause of the error? On Wed, 02 Apr 2014 17:28:14 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is your command line that is seg faulting? What is the terminal output? On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote: Please help me with this issue: If I apply mri_surf2vol to a single volume of unprocessed epi-data, it results in a segmentation fault. It works if I apply mri_vol2vol for registration of epi and anatomy, but than an interpolation is involved. I would like to avoid the interpolation and apply mri_surf2vol directly to the unprocessed data in order to minimize the number of interpolations. At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote: This is something BF added Sept 1 2009: added --projopt switch to do optimal linear estimation of gray matter values given a set of precomputed gray matter densities. I don't know what it would mean beyond that doug On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote: Hello, I found an option in mri_vol2surf for which I could not find a documentation. The option is called: --projopt It would be nice if somebody could give a description of this option. Respectfully yours pfannmoe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@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 mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
Re: [Freesurfer] mri_surcluster and centroid option
Hi, you are right! The Talairach ccordinates change. Unfortunately, the centroid coordinate of my data are outside the cluster. Do you have any suggestions about that? I also tried your version of the script. The following message appeared: mri_surfcluster: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory Since I use Ubuntu it is not so simple to switch from my current version libnetcdf.so.7 back to libnetcdf.so.6. Do you know a workaround? Respectfully yours pfannmoe On Fri, 04 Apr 2014 15:38:09 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I'm not sure, when I run it it results in different xyz. What version are you using? I've put a copy of my version (for linux) here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfcluster doug On 04/03/2014 03:56 AM, Joerg Pfannmoeller wrote: Hi, I am trying to compute centroid coordinates of maps for functional activation obtained from fsfast with mri_surfcluster. The command is: mri_surfcluster --in /.../sig.nii.gz --thmin 3 --thmax infinity--sign pos --subject subjid --hemi rh --surf white --annot aparc --frame 0 --minarea 0 --sum ./tabular_surfcluster.txt -- centroid Unfortunately, the centroid option has no effect. Results in tabular_surfcluster.txt with and without centroid option are identical. What am I doing wrong? Respectfully yours pfannmoe ___ 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 gr...@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 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] mri_vol2surf --projopt
Hello, I found an option in mri_vol2surf for which I could not find a documentation. The option is called: --projopt It would be nice if somebody could give a description of this option. Respectfully yours pfannmoe ___ 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.
Re: [Freesurfer] tkmedit edit voxel tcl script
This topic has been discussed previously without a conclusive answer. After some www inquests I realized that it is easily possible to process nii-images using spm functions for matlab. The functions for loading and saving images are: V = spm_vol(angio_corrected_marked); [Y, XYZ] = spm_read_vols(V); spm_write_vol(V,Y); After the images are loaded they can be processed using matlab functionality. Thus, tcl scripting for those purposes is not necessary. On Fri, 7 Mar 2014 16:37:33 -0500 (EST) Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Pfannmoe, I don't believe it is possible to edit a voxel via tcl scripts. If so the command would be listed on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkMeditScripting -Louis On Wed, 5 Mar 2014, Joerg Pfannmoeller wrote: Hello, if I have selected a voxel in a volume with tkmedit with a tcl script, how can I set the voxel value to 0. Sincerely yours pfannmoe ___ 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] TkmEdit Scripting SetBrushInfo Error
Hi, I am getting tzhe following an error if I use the following command in a tcl-script: SetBrushInfo 3 1 2000 1 The error is: Error: Parsing script file This error was encountered while running the script specified with the -tcl option. What is wrong? Sincerely yours pfannmoe ___ 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] tkmedit edit voxel tcl script
Hello, if I have selected a voxel in a volume with tkmedit with a tcl script, how can I set the voxel value to 0. Sincerely yours pfannmoe ___ 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.
Re: [Freesurfer] TkmEdit Scripting SetBrushInfo Error
Allright, it works if I use those commands:
UpdateBrushInfo { inBrush inLow inHigh inNewValue inMode inCloneSource }
SetEditBrushConfiguration
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[Freesurfer] tkmedit and masking
Hello, I am using tkmedit to display functional data as an overlay on anatomical data. I am asking myself if there is a feature in tkmedit which allows to apply a mask to the functional. Ideally would be a cortex mask to remove all non-cortex voxels. Regards Joerg -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ 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.
Re: [Freesurfer] Dura Correction, Surface Based Stream and FS-Fast
Hi, I corrected my proceeding and separated the echoes using the pipeline: recon-all -s subj_name -i /.../dicom_images.dcm recon-all -s subj_name -use-gpu -mprage -all mri_convert -odt float -f 0 ./... .dcm $SUBJECTS_DIR/subj_name/mri/000.mgz mri_convert -odt float -f 1 ./... .dcm $SUBJECTS_DIR/subj_name/mri/001.mgz mri_convert -odt float -f 2 ./... .dcm $SUBJECTS_DIR/subj_name/mri/002.mgz mri_convert -odt float -f 3 ./... .dcm $SUBJECTS_DIR/subj_name/mri/003.mgz mris_make_surfaces -dura %03d.mgz 4 subj_name lh mris_make_surfaces -dura %03d.mgz 4 subj_name rh recon-all -autorecon-pial -subjid subj_name -use-gpu -mprage . I see a difference in the cortical atlas after doing recon-all -autorecon-pial, but if I take a look at the 3D-Volume I still find pieces of the dura included in the cortex. Please check the figure attached to this mail. The red cross signals the location. Regards Joerg On Wed, 12 Jun 2013 09:03:21 -0400 (EDT) Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Joerg you need to convert the individual echoes to be in conformed space without scaling the intensities, then run it with something like mris_make_surfaces -dura echo%d.mgz 4 subj_name lh otherwise it will just load 001.mgz 4 times and think it is the different echoes. That is, name the echoes echo0.mgz echo1.mgz echo2.mgz and echo3.mgz cheers Bruce On Wed, 12 Jun 2013, Joerg Pfannmoeller wrote: Hello FSexperts, I used the mgh memprage and the dura correction scheme described in: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28479.html . Afterwards I applied recon-all -autorecon-pial -subjid subj_name to the subjects in order to include the changes in the subsequent FS-Fast analysis. Currently I do not see any effect in tksurfer if I proceed like this. Please correct me if I am wrong with my effect size expectation. For completeness I add the command pipeline used: recon-all -s subj_name -i /.../dicom_images.dcm recon-all -s subj_name -use-gpu -mprage -all mri_convert -odt float ./... .dcm $SUBJECTS_DIR/subj_name/mri/001.mgz mris_make_surfaces -dura 001.mgz 4 subj_name lh mris_make_surfaces -dura 001.mgz 4 subj_name rh recon-all -autorecon-pial -subjid subj_name ___ 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. -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de attachment: corrected.jpeg___ 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] Dura Correction, Surface Based Stream and FS-Fast
Hello FSexperts, I used the mgh memprage and the dura correction scheme described in: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28479.html . Afterwards I applied recon-all -autorecon-pial -subjid subj_name to the subjects in order to include the changes in the subsequent FS-Fast analysis. Currently I do not see any effect in tksurfer if I proceed like this. Please correct me if I am wrong with my effect size expectation. For completeness I add the command pipeline used: recon-all -s subj_name -i /.../dicom_images.dcm recon-all -s subj_name -use-gpu -mprage -all mri_convert -odt float ./... .dcm $SUBJECTS_DIR/subj_name/mri/001.mgz mris_make_surfaces -dura 001.mgz 4 subj_name lh mris_make_surfaces -dura 001.mgz 4 subj_name rh recon-all -autorecon-pial -subjid subj_name ___ 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.
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Found a fix for that problem: http://www.mathworks.com/matlabcentral/newsreader/view_thread/284776 On Tue, 14 May 2013 14:14:31 -0400 Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Joerg, I'm guessing you have some matlab setup script that has run prior to the freesurfer setup. I see this output: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6 which is not something freesurfer would link against or require. normally it should use /usr/lib64/libstdc++.so.6. try running this prior to sourcing the freesurfer setup: setenv LD_LIBRARY_PATH Glad to see 5.3 works otherwise. Thanks for testing it. Nick On Tue, 2013-05-14 at 15:17 +0200, Joerg Pfannmoeller wrote: Unfortunately encountered a problem in fs-fast stream during execution of selxavg3-sess. Added a relevant part of the log file below: sxa3pwd = /home/...removed... sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./session02 -analysis harm.sm0.mni305 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# session02 ### /home/...removed.../freesurfer_fMRT/session02 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m - outtop = /home/...removed.../freesurfer_fMRT Extension format = nii.gz 1 stim-v-base.mat nruns = 1 autostimdur = outanadir = /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305 Found 45239/537168 ( 8.4) voxels in mask Creating Design Matrix ... creation time = 0.009 sec DoMCFit = 1 ntptot = 100, nX = 8, DOF = 92 Saving X matrix to /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/Xtmp.mat XCond = 444.207 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.493933(t=0.004964) 2 -0.25 -0.269463(t=0.00648) 3 0 -0.0514275(t=0.00734) 4 0.25 0.155364(t=0.008221) 5 0.5 0.337574(t=0.009058) AR1 Correction M: 0.0769642 1.19552 Computing contrast matrices OLS Beta Pass run 1t= 0.0 Global Mean 725.29 Global In-Mask Mean = 725.295 (694.97) Rescale Target = 100 RescaleFactor = 0.137875 OLS Residual Pass run 1t= 0.0 Saving rho1 Smoothing ACF /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer/bin/mri_fwhm) /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /usr/local/freesurfer/bin/mri_fwhm) ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only -- ERROR: fast_selxavg3() failed\n Seemingly a problem with GLIBCXX_3.4.11. My OS is Lubuntu 13.04. On Tue, 14 May 2013 08:28:05 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems. Also freeview runs without an error for the subject bert. On Mon, 13 May 2013 14:40:10 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Just for completeness, I refer to my first contribution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html On Mon, 13 May 2013 13:58:30 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems. Also freeview runs without an error for the subject bert. On Mon, 13 May 2013 14:40:10 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Just for completeness, I refer to my first contribution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html On Mon, 13 May 2013 13:58:30 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick 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. -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Unfortunately encountered a problem in fs-fast stream during execution of selxavg3-sess. Added a relevant part of the log file below: sxa3pwd = /home/...removed... sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./session02 -analysis harm.sm0.mni305 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# session02 ### /home/...removed.../freesurfer_fMRT/session02 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m - outtop = /home/...removed.../freesurfer_fMRT Extension format = nii.gz 1 stim-v-base.mat nruns = 1 autostimdur = outanadir = /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305 Found 45239/537168 ( 8.4) voxels in mask Creating Design Matrix ... creation time = 0.009 sec DoMCFit = 1 ntptot = 100, nX = 8, DOF = 92 Saving X matrix to /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/Xtmp.mat XCond = 444.207 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.493933(t=0.004964) 2 -0.25 -0.269463(t=0.00648) 3 0 -0.0514275(t=0.00734) 4 0.25 0.155364(t=0.008221) 5 0.5 0.337574(t=0.009058) AR1 Correction M: 0.0769642 1.19552 Computing contrast matrices OLS Beta Pass run 1t= 0.0 Global Mean 725.29 Global In-Mask Mean = 725.295 (694.97) Rescale Target = 100 RescaleFactor = 0.137875 OLS Residual Pass run 1t= 0.0 Saving rho1 Smoothing ACF /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer/bin/mri_fwhm) /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /usr/local/freesurfer/bin/mri_fwhm) ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only -- ERROR: fast_selxavg3() failed\n Seemingly a problem with GLIBCXX_3.4.11. My OS is Lubuntu 13.04. On Tue, 14 May 2013 08:28:05 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems. Also freeview runs without an error for the subject bert. On Mon, 13 May 2013 14:40:10 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Just for completeness, I refer to my first contribution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html On Mon, 13 May 2013 13:58:30 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick 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. -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick 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. -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
