[Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3
Hi Folks, I am running recon-all with -autorecon1 -autorecon2, -nomotioncor -notal-check -nonuintensitycor (this is with fs version 5.3) it almost runs through but toward the end, when mri_segstats is called I get the error message: .../mri/ribbon.mgz, -1): could not open file any ideas why this could be occurring ? Thanks Mehul ___ 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] error while running autorecon1 and autorecon2 in fs-v5.3
ps: i believe my error is the same as the one in this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html Mehul On Thu, May 30, 2013 at 12:13 AM, Mehul Sampat mpsam...@gmail.com wrote: Hi Folks, I am running recon-all with -autorecon1 -autorecon2, -nomotioncor -notal-check -nonuintensitycor (this is with fs version 5.3) it almost runs through but toward the end, when mri_segstats is called I get the error message: .../mri/ribbon.mgz, -1): could not open file any ideas why this could be occurring ? Thanks Mehul ___ 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] error loading volume brainmask.gcut.mgz
Hi Freesurfers, I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia ___ 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] Problem with recon-all
Dear FS experts, I have a problem with the command recon-all. In many cases when I use it on the same brain's MRI, on the CLUSTER COMPUTING INFRASTRUCTURE, about 40% of my jobs finish without erros while the other are killed at the command nu_currect, as you can see from the file.log in attachment. Do you have any suggestions? Thanks a lot for your help. Best regardes, Andrea Thu May 23 13:58:52 CEST 2013 /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001 /opt/exp_soft/mag/freesurfer/bin/recon-all -debug -s 001 -autorecon-all subjid 001 setenv SUBJECTS_DIR /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16 FREESURFER_HOME /opt/exp_soft/mag/freesurfer Actual FREESURFER_HOME /opt/exp_soft/mag/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux pccms114.ba.infn.it 2.6.18-348.1.1.el5 #1 SMP Thu Jan 24 13:25:42 CET 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize10240 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 32768 memorylocked 32 kbytes maxproc 386293 total used free sharedbuffers cached Mem: 49448428 462321603216268 0 900488 29561664 -/+ buffers/cache: 15770008 33678420 Swap: 16779884 613964 16165920 program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22
[Freesurfer] Exporting surface coordinates to Nifti header space
Hi Freesurfers! I'd like to load my original Nifti T1 image data (subject.nii) and the wm/gm-surface coordinate data (for instance lh.pial) in matlab as vectors in the same coordinate system. If I do it in the naive way, i.e. [x,y,z,1]=[i,j,k,1]*sform' for the Nifti coordinates resp. freesurfer_read_surf(...) for the surface nodes, then surface and Nifti appear not to be coregisterred. It looks as though there would be a spacial shift missing. Although having tried several matrices I cant figure out which is the one to choose. Inspecting the Data by Freeviewer I observe the same spacial shift, inspecting it by 'tkmedit subject_id brainmask.mgz lh.pial' everything is fine. Could you tell me, which transform I have to apply to the surface coordinates? That would be really nice. Thanks and best Regards, Max ___ 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] error loading volume brainmask.gcut.mgz
did you run out of disk space? Can you run mri_info on it? On Thu, 30 May 2013, Claudia Dacquino wrote: Hi Freesurfers,I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia ___ 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] error loading volume brainmask.gcut.mgz
Yes I did run mri_info, these are the results: Volume information for brainmask.gcuts.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.92 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = -0., c_r = 8.4909 : x_a = -0., y_a = 0., z_a = 1., c_a = -0.4031 : x_s = 0., y_s = -1., z_s = -0., c_s = -34.1638 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. -0. 136.4909 -0. 0. 1. -128.4031 0. -1. -0.93.8362 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 136.4909 -0. -0. -1.93.8362 -0. 1. -0. 128.4031 0. 0. 0. 1. Cheers 2013/5/30 Claudia Dacquino claudia.dacqu...@gmail.com Yes I did run mri_info, these are the results: Volume information for brainmask.gcuts.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.92 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = -0., c_r = 8.4909 : x_a = -0., y_a = 0., z_a = 1., c_a = -0.4031 : x_s = 0., y_s = -1., z_s = -0., c_s = -34.1638 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. -0. 136.4909 -0. 0. 1. -128.4031 0. -1. -0.93.8362 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 136.4909 -0. -0. -1.93.8362 -0. 1. -0. 128.4031 0. 0. 0. 1. Cheers 2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu did you run out of disk space? Can you run mri_info on it? On Thu, 30 May 2013, Claudia Dacquino wrote: Hi Freesurfers,I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia 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/**compliancelinehttp://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.
Re: [Freesurfer] error loading volume brainmask.gcut.mgz
is your disk partition full? And please cc the list so others can answer Bruce On Thu, 30 May 2013, Claudia Dacquino wrote: Yes I did run mri_info, these are the results: Volume information for brainmask.gcuts.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.92 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = -0., c_r = 8.4909 : x_a = -0., y_a = 0., z_a = 1., c_a = -0.4031 : x_s = 0., y_s = -1., z_s = -0., c_s = -34.1638 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. -0. 136.4909 -0. 0. 1. -128.4031 0. -1. -0. 93.8362 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 136.4909 -0. -0. -1. 93.8362 -0. 1. -0. 128.4031 0. 0. 0. 1. Cheers 2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu did you run out of disk space? Can you run mri_info on it? On Thu, 30 May 2013, Claudia Dacquino wrote: Hi Freesurfers,I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia 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.
Re: [Freesurfer] error loading volume brainmask.gcut.mgz
yes I did answer again to the list. no it is no full at all. 2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu is your disk partition full? And please cc the list so others can answer Bruce On Thu, 30 May 2013, Claudia Dacquino wrote: Yes I did run mri_info, these are the results: Volume information for brainmask.gcuts.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.92 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = -0., c_r = 8.4909 : x_a = -0., y_a = 0., z_a = 1., c_a = -0.4031 : x_s = 0., y_s = -1., z_s = -0., c_s = -34.1638 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. -0. 136.4909 -0. 0. 1. -128.4031 0. -1. -0.93.8362 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 136.4909 -0. -0. -1.93.8362 -0. 1. -0. 128.4031 0. 0. 0. 1. Cheers 2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu did you run out of disk space? Can you run mri_info on it? On Thu, 30 May 2013, Claudia Dacquino wrote: Hi Freesurfers,I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia 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/**compliancelinehttp://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.
Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3
Does 5.3 assume recon-all -all will always run first? Since ribbon.mgz will not get created till autorecon3. In V4, that is part of autorecon2 though. Gen On Thu, May 30, 2013 at 12:24 AM, Mehul Sampat mpsam...@gmail.com wrote: ps: i believe my error is the same as the one in this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html Mehul On Thu, May 30, 2013 at 12:13 AM, Mehul Sampat mpsam...@gmail.com wrote: Hi Folks, I am running recon-all with -autorecon1 -autorecon2, -nomotioncor -notal-check -nonuintensitycor (this is with fs version 5.3) it almost runs through but toward the end, when mri_segstats is called I get the error message: .../mri/ribbon.mgz, -1): could not open file any ideas why this could be occurring ? Thanks Mehul ___ 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.
Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3
Could you provide the recon-all.log file? -Zeke On 05/30/2013 10:24 AM, Gennan Chen wrote: Does 5.3 assume recon-all -all will always run first? Since ribbon.mgz will not get created till autorecon3. In V4, that is part of autorecon2 though. Gen On Thu, May 30, 2013 at 12:24 AM, Mehul Sampat mpsam...@gmail.com mailto:mpsam...@gmail.com wrote: ps: i believe my error is the same as the one in this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html Mehul On Thu, May 30, 2013 at 12:13 AM, Mehul Sampat mpsam...@gmail.com mailto:mpsam...@gmail.com wrote: Hi Folks, I am running recon-all with -autorecon1 -autorecon2, -nomotioncor -notal-check -nonuintensitycor (this is with fs version 5.3) it almost runs through but toward the end, when mri_segstats is called I get the error message: .../mri/ribbon.mgz, -1): could not open file any ideas why this could be occurring ? Thanks Mehul ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error loading volume brainmask.gcut.mgz
and my freesurfer version is 5.1. 2013/5/30 Claudia Dacquino claudia.dacqu...@gmail.com yes I did answer again to the list. no it is no full at all. 2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu is your disk partition full? And please cc the list so others can answer Bruce On Thu, 30 May 2013, Claudia Dacquino wrote: Yes I did run mri_info, these are the results: Volume information for brainmask.gcuts.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.92 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = -0., c_r = 8.4909 : x_a = -0., y_a = 0., z_a = 1., c_a = -0.4031 : x_s = 0., y_s = -1., z_s = -0., c_s = -34.1638 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. -0. 136.4909 -0. 0. 1. -128.4031 0. -1. -0.93.8362 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 136.4909 -0. -0. -1.93.8362 -0. 1. -0. 128.4031 0. 0. 0. 1. Cheers 2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu did you run out of disk space? Can you run mri_info on it? On Thu, 30 May 2013, Claudia Dacquino wrote: Hi Freesurfers,I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia 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/**compliancelinehttp://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.
Re: [Freesurfer] mris_divide_parcellation color table error
I am running version 5.3- the latest version. I also tried running the codes on v5.0 and got the same result. Is there any way I can change the color table so that the colors of the parcellation are unique? Thanks, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, May 29, 2013 8:41 PM To: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error Sure On May 29, 2013, at 9:36 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: The colors are visually different by a shade then loop every 4 or so colors. I think the color table may be running on a loop? I can send the annot and surface file if you need that as well. Best, Tina From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, May 29, 2013 8:02 PM To: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error p.s. can you send me the splittable text file ? I seem to have deleted it. I'll try to test it out tomorrow On Thu, 30 May 2013, Tina Jeon wrote: Yes same result as with freeview. Sent from my iPhone On May 29, 2013, at 7:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg$FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010 -03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center ‘14 _ ___ UT Southwestern Medical Center The future of medicine, today. neonate_buckner40_atlas.png splittable.txt ___ 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. splittable.txt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] white matter volume per lobe...
It is probably the region that is more than 5mm away from cortex. In the wmparc it should be labeled as wm-lh-unknown doug On 05/30/2013 11:27 AM, Gonzalo Rojas Costa wrote: Hi Doug: I used the instructions that you told me to get the white matter per each lobule... But, I got the grey colored region (red arrow)... Which neuroanatomical area is ?... Sincerely, Gonzalo Rojas Costa Message: 15 Date: Mon, 27 May 2013 22:41:41 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl -- 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.
Re: [Freesurfer] volume and mean value of a custom made white matter ROI
Hi Subha, use mri_segstats, something like mri_segstats --i norm.mgz -seg arcfas.mgz -id 1 -sum arcfas.summary.dat Look at the --help for more info doug On 05/30/2013 07:04 AM, Subhabrata Chaudhury wrote: Hello Everyone, Greetings. I am learning freesurfer tricks. I am stuck and have a question. I have run 10 subjects through freesurfer. I have made custom volume regions for arcuate fasciculus for 10 subjects. Now I want to get some measurements inside this region. How do I get the volume of the region ? How do I get the mean T1 intensity in this region ? Can somebody share some script or point me to some script ? Will be very thankful. Subha ___ 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.
Re: [Freesurfer] Exporting surface coordinates to Nifti header space
Hi Max, does this page give you what you need to know? http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 05/30/2013 08:29 AM, schre...@informatik.hu-berlin.de wrote: Hi Freesurfers! I'd like to load my original Nifti T1 image data (subject.nii) and the wm/gm-surface coordinate data (for instance lh.pial) in matlab as vectors in the same coordinate system. If I do it in the naive way, i.e. [x,y,z,1]=[i,j,k,1]*sform' for the Nifti coordinates resp. freesurfer_read_surf(...) for the surface nodes, then surface and Nifti appear not to be coregisterred. It looks as though there would be a spacial shift missing. Although having tried several matrices I cant figure out which is the one to choose. Inspecting the Data by Freeviewer I observe the same spacial shift, inspecting it by 'tkmedit subject_id brainmask.mgz lh.pial' everything is fine. Could you tell me, which transform I have to apply to the surface coordinates? That would be really nice. Thanks and best Regards, Max ___ 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.
Re: [Freesurfer] Correction for multiple comparisons error
Hey Doug, I was wondering whether you had a chance to give this a look! Thanks again, Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis Sent: Tuesday, May 28, 2013 1:38 PM To: Douglas Greve; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error Hi Doug, 1) My cmd line is: mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir lh.Diseased_gender_age.glmdir 2) The FS version that I am using is the stable 5.0.0, 3) I have attached the full terminal output in this email. Thank you for your time! Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, May 27, 2013 10:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error what is your cmd line? What version of FS are you using? What is the full terminal output? doug On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote: Hi! I have been running the mri_glmfit-sim command to do the correction for multiple comparisons for my group analysis and for some voxel-based thresholds (not all) there is an error that comes up when reading the colortable from the annotation file: reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** and then it gets stuck. Do you happen to know what might be causing this issue? Thank you for your time, Panos ___ 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 ___ 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] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
Hi all, This is a follow-up on my question so that people can know what I've tried and how it works. I added control points in the white matter and the delineation of the temporal lobe has improved to a satisfying level. We also find what Michael has suggested very interesting. But it seems that if we change the parameters for certain subjects, we would have to rerun all of the other subjects with the same set of parameters, which may not be desirable at the moment. Thanks for all the help, Cherry On Wed, May 22, 2013 at 4:46 PM, Yizhou Ma ym...@nyu.edu wrote: Hi Michael, This method seems cool. I'll try to implement it. Thank you so much. Best, Cherry On Wed, May 22, 2013 at 4:17 PM, Harms, Michael mha...@wustl.edu wrote: I've also posted in the past on a set of expert options that helped our surfaces in the temporal lobe considerably. You should be able to locate that post in the archives. -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Yizhou Ma ym...@nyu.edu Date: Wednesday, May 22, 2013 2:30 PM To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu, Chris Watson christopher.wat...@childrens.harvard.edu Subject: Re: [Freesurfer] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz? Ok. I'll give it a try. Thanks, Chris Bruce! On Wed, May 22, 2013 at 3:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Cherry Chris is right. Putting control points in the WM will help the pial surface as well. cheers Bruce On Wed, 22 May 2013, Yizhou Ma wrote: Hi Chris, Thanks a lot. I agree that control points should actually only be put in white matter. I'm just not sure if I can expand the pial surface to a satisfactory extend if I only do edits in the white matter. It seems to me that the problem here is that the signal weakened in the lower part of the brain so that the gray matter doesn't have adequate intensity to be included in the pial surface (the values are around 30). Thanks, Cherry On Wed, May 22, 2013 at 3:14 PM, Chris Watson Christopher.Watson@childrens.**harvard.educhristopher.wat...@childrens.harvard.edu wrote: You need to place the control points in the white matter, not around it. On 05/22/2013 03:04 PM, Yizhou Ma wrote: Dear FS experts, I have a subject where large portions of temporal lobe is not included in the pial surface. A member in my lab has suggested edits on brain.finalsurfs.mgz. However, in the following page it is indicated that edits on brain.finalsurfs.mgz is only intended for cases regarding inclusion of cerebellum. Can anyone please let me know which volume I should be working on in this case? http://ftp.nmr.mgh.harvard.**edu/fswiki/FsTutorial/**PialEditshttp://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Thanks, Cherry __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail. -- The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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.
Re: [Freesurfer] tkmedit on ssh remote machine error
Jon, I have not seen or heard of this error before... are both machines Mac OSX 10.6.8? Also, will the same command will produce a brain image when not logged in remotely? -Zeke On 05/30/2013 12:43 PM, Jon Wieser wrote: hi freesurfer folks I'm ssh'ing to from one MAc to another X11 is on both machines MAC OS X 10.6.8 When I start TKmedit with: (freesurfer files are in the freesurfer directory) tkmedit freesurfer brainmask.mgz -aux T1.mgz I get the errors: Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] Error: kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 349 Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] Error: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] Error: kCGErrorIllegalArgument: CGSSetWindowSendExposed: Invalid window 0x15d Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] Error: unknown error code: invalid drawable error: xp_attach_gl_context returned: 2 tkmedit GUI opens and the image window opens, but the image window is blank (white) , (no image of the brain) i have set X11forwarding to yes in the /etc/sshd_config file so xeyes works ok remotely Jon ___ 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] WARNING: tcsh v6.17.06 has an exit code bug!
Hello everyone, I just updated to Freesurfer 5.3.0, my OS is Ubuntu 12.04. When I run 'recon-all -i T1 image -subjid subject name' I receive the following error: WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! The directory structure appears to be set up correctly, and the command finishes without error. I do not receive this error when using Freesurfer 5.1.0. I have yet to run 'recon-all -all -subjid subject name' in 5.3.0. Any ideas on what produces this error? is it safe to ignore? Thanks in advance, 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.
[Freesurfer] Download difficulty
Hello all, I seem to be having some difficulty downloading the freesurfer software to my MAC computers. I have tried my laptop (MacBook pro, I don't remember the version but it is approx. 10.3) as well as a desktop (imac, mac osx version 10.8.3) and also tried two different networks. I have tried just clicking on the link (on your download page) as well as the curl -O command line. I get an NSURL error everytime, prior to any significant downloading. I have not have this difficulty with other freeware downloading to the same computers or on these networks. Any thoughts? Thanks Mike ___ 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] WARNING: tcsh v6.17.06 has an exit code bug!
Hi Andrew, It is expected that you would not see this warning with Freesurfer version 5.1. Its just a warning, but tcsh v6.17.06 on Ubuntu always returns exit code 0. This can be problematic for instances where recon-all encounters and error and should fail. If you ran recon-all and have all the expected files than you should be all set. I believe you can use the Ubuntu Update Manager tool to install the latest version tcsh. -Zeke On 05/30/2013 01:19 PM, Andrew Bock wrote: Hello everyone, I just updated to Freesurfer 5.3.0, my OS is Ubuntu 12.04. When I run 'recon-all -i T1 image -subjid subject name' I receive the following error: WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! The directory structure appears to be set up correctly, and the command finishes without error. I do not receive this error when using Freesurfer 5.1.0. I have yet to run 'recon-all -all -subjid subject name' in 5.3.0. Any ideas on what produces this error? is it safe to ignore? Thanks in advance, Andrew ___ 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.
Re: [Freesurfer] Download difficulty
Mike, I just tested the links on this page the download page and they work for me: http://surfer.nmr.mgh.harvard.edu/fswiki/Download What happens when you type this command into your terminal: curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg Both techniques work from my location. -Zeke On 05/30/2013 01:46 PM, Michael Paldino wrote: Hello all, I seem to be having some difficulty downloading the freesurfer software to my MAC computers. I have tried my laptop (MacBook pro, I don't remember the version but it is approx. 10.3) as well as a desktop (imac, mac osx version 10.8.3) and also tried two different networks. I have tried just clicking on the link (on your download page) as well as the curl -O command line. I get an NSURL error everytime, prior to any significant downloading. I have not have this difficulty with other freeware downloading to the same computers or on these networks. Any thoughts? Thanks Mike ___ 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.
Re: [Freesurfer] WARNING: tcsh v6.17.06 has an exit code bug!
Thanks Zeke. To my knowledge tcsh v6.17.06 is the latest version of tcsh for Ubuntu 12.04 LTS, but I just discovered tcsh v6.18.01 is available for more recent versions of Ubuntu (e.g. Ubuntu 12.10, 13.04). If you (or anyone else) knows of any issues with tcsh v6.18.01 please let me know, otherwise I'll update to that version. Andrew On Thu, May 30, 2013 at 10:51 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Hi Andrew, It is expected that you would not see this warning with Freesurfer version 5.1. Its just a warning, but tcsh v6.17.06 on Ubuntu always returns exit code 0. This can be problematic for instances where recon-all encounters and error and should fail. If you ran recon-all and have all the expected files than you should be all set. I believe you can use the Ubuntu Update Manager tool to install the latest version tcsh. -Zeke On 05/30/2013 01:19 PM, Andrew Bock wrote: Hello everyone, I just updated to Freesurfer 5.3.0, my OS is Ubuntu 12.04. When I run 'recon-all -i T1 image -subjid subject name' I receive the following error: WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! The directory structure appears to be set up correctly, and the command finishes without error. I do not receive this error when using Freesurfer 5.1.0. I have yet to run 'recon-all -all -subjid subject name' in 5.3.0. Any ideas on what produces this error? is it safe to ignore? Thanks in advance, Andrew __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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.
[Freesurfer] mprage flag in recon-all
Hi! Is there more documentation on what settings the mprage flag enables in recon-all? Specifically, I would be interested which individual steps it affects and what the parameters are for each of the steps. Thanks! Caspar ___ 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] white matter volume per lobe...
Hi Doug: But, in the mri_aparc2aseg command, I test with the --wmparc-dmax 200 option... I put that big value to test it, but I got the image that I sent you... Sincerely, Gonzalo Rojas Costa On Thu, May 30, 2013 at 12:06 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It is probably the region that is more than 5mm away from cortex. In the wmparc it should be labeled as wm-lh-unknown doug On 05/30/2013 11:27 AM, Gonzalo Rojas Costa wrote: Hi Doug: I used the instructions that you told me to get the white matter per each lobule... But, I got the grey colored region (red arrow)... Which neuroanatomical area is ?... Sincerely, Gonzalo Rojas Costa Message: 15 Date: Mon, 27 May 2013 22:41:41 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl -- 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/ 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. -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit on ssh remote machine error
both machines have Mac OS X 10.6.8 the tkmedit works fine when not logged in remotely there is no error and the brain image is there Jon - Original Message - From: Z K zkauf...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 30, 2013 12:16:55 PM Subject: Re: [Freesurfer] tkmedit on ssh remote machine error Jon, I have not seen or heard of this error before... are both machines Mac OSX 10.6.8? Also, will the same command will produce a brain image when not logged in remotely? -Zeke On 05/30/2013 12:43 PM, Jon Wieser wrote: hi freesurfer folks I'm ssh'ing to from one MAc to another X11 is on both machines MAC OS X 10.6.8 When I start TKmedit with: (freesurfer files are in the freesurfer directory) tkmedit freesurfer brainmask.mgz -aux T1.mgz I get the errors: Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] Error: kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 349 Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] Error: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] Error: kCGErrorIllegalArgument: CGSSetWindowSendExposed: Invalid window 0x15d Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] Error: unknown error code: invalid drawable error: xp_attach_gl_context returned: 2 tkmedit GUI opens and the image window opens, but the image window is blank (white) , (no image of the brain) i have set X11forwarding to yes in the /etc/sshd_config file so xeyes works ok remotely Jon ___ 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. -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How to determine a smoothing kernel size for surface that is approx. equal to 4mm in volumetric data?
Hello Freesurfer users I'm trying to replicate my earlier findings in 3D space by warping the data into surface using freesurfer. Previously, the 3D data were smoothed using 4mm FWHM kernel and I'm wondering what size of smoothing kernel for 2D would be equivalent to 4mm for volumes. Any help would be greatly appreciated. Glen ___ 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] How to determine a smoothing kernel size for surface that is approx. equal to 4mm in volumetric data?
there is no equivalent. I'd start with 4 and move up. doug On 05/30/2013 02:51 PM, Glen Lee wrote: Hello Freesurfer users I'm trying to replicate my earlier findings in 3D space by warping the data into surface using freesurfer. Previously, the 3D data were smoothed using 4mm FWHM kernel and I'm wondering what size of smoothing kernel for 2D would be equivalent to 4mm for volumes. Any help would be greatly appreciated. Glen ___ 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.
Re: [Freesurfer] mris_divide_parcellation color table error (fwd)
Yes it worked. Thank you that is exactly what I needed. Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 12:36 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error (fwd) Hi Tina is this (attached) more what you wanted? If so, then I think you want to use mris_make_face_parcellation instead of mris_divide_parcellation. I can't remember what they used in that paper, but in mris_divide_parcellation I try to have the different units within a parcel have similar colors (which evidentally fails when you split it so finely) Bruce On Thu, 30 May 2013, Tina Jeon wrote: I am running version 5.3- the latest version. I also tried running the codes on v5.0 and got the same result. Is there any way I can change the color table so that the colors of the parcellation are unique? Thanks, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, May 29, 2013 8:41 PM To: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error Sure On May 29, 2013, at 9:36 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: The colors are visually different by a shade then loop every 4 or so colors. I think the color table may be running on a loop? I can send the annot and surface file if you need that as well. Best, Tina From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, May 29, 2013 8:02 PM To: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error p.s. can you send me the splittable text file ? I seem to have deleted it. I'll try to test it out tomorrow On Thu, 30 May 2013, Tina Jeon wrote: Yes same result as with freeview. Sent from my iPhone On May 29, 2013, at 7:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg$FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010 -03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center ‘14 _ ___ UT Southwestern Medical Center The future of medicine, today. neonate_buckner40_atlas.png splittable.txt ___ 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. splittable.txt ___ 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] How to determine a smoothing kernel size for surface that is approx. equal to 4mm in volumetric data?
Hi Glen there is no way to get an equivalent 2D kernel to the 3D one. sorry Bruce On Thu, 30 May 2013, Glen Lee wrote: Hello Freesurfer users I'm trying to replicate my earlier findings in 3D space by warping the data into surface using freesurfer. Previously, the 3D data were smoothed using 4mm FWHM kernel and I'm wondering what size of smoothing kernel for 2D would be equivalent to 4mm for volumes. Any help would be greatly appreciated. Glen ___ 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] Correction for multiple comparisons error
hmm, can't tell from that what is going on. Can you tar up lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at the end of this email)? doug On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote: Hey Doug, Of course, I attached it in txt format in this email! Best, Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 2:55 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error Can you send me the terminal output in a text file? A word doc is very inconvenient:). doug On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote: Hi Doug, 1) My cmd line is: mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir lh.Diseased_gender_age.glmdir 2) The FS version that I am using is the stable 5.0.0, 3) I have attached the full terminal output in this email. Thank you for your time! Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, May 27, 2013 10:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error what is your cmd line? What version of FS are you using? What is the full terminal output? doug On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote: Hi! I have been running the mri_glmfit-sim command to do the correction for multiple comparisons for my group analysis and for some voxel-based thresholds (not all) there is an error that comes up when reading the colortable from the annotation file: reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** and then it gets stuck. Do you happen to know what might be causing this issue? Thank you for your time, Panos ___ 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 -- 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/ -- 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.
Re: [Freesurfer] white matter volume per lobe...
can you send me your full command line as well as the terminal output? On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote: Hi Doug: But, in the mri_aparc2aseg command, I test with the --wmparc-dmax 200 option... I put that big value to test it, but I got the image that I sent you... Sincerely, Gonzalo Rojas Costa On Thu, May 30, 2013 at 12:06 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It is probably the region that is more than 5mm away from cortex. In the wmparc it should be labeled as wm-lh-unknown doug On 05/30/2013 11:27 AM, Gonzalo Rojas Costa wrote: Hi Doug: I used the instructions that you told me to get the white matter per each lobule... But, I got the grey colored region (red arrow)... Which neuroanatomical area is ?... Sincerely, Gonzalo Rojas Costa Message: 15 Date: Mon, 27 May 2013 22:41:41 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl -- 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/ 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. -- 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] Correction for multiple comparisons error
Definitely, just uploaded it! Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:10 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error hmm, can't tell from that what is going on. Can you tar up lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at the end of this email)? doug On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote: Hey Doug, Of course, I attached it in txt format in this email! Best, Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 2:55 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error Can you send me the terminal output in a text file? A word doc is very inconvenient:). doug On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote: Hi Doug, 1) My cmd line is: mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir lh.Diseased_gender_age.glmdir 2) The FS version that I am using is the stable 5.0.0, 3) I have attached the full terminal output in this email. Thank you for your time! Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, May 27, 2013 10:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error what is your cmd line? What version of FS are you using? What is the full terminal output? doug On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote: Hi! I have been running the mri_glmfit-sim command to do the correction for multiple comparisons for my group analysis and for some voxel-based thresholds (not all) there is an error that comes up when reading the colortable from the annotation file: reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** and then it gets stuck. Do you happen to know what might be causing this issue? Thank you for your time, Panos ___ 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 -- 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/ -- 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.
Re: [Freesurfer] tkmedit on ssh remote machine error
On Thu, May 30, 2013 at 2:37 PM, Jon Wieser wie...@uwm.edu wrote: both machines have Mac OS X 10.6.8 the tkmedit works fine when not logged in remotely there is no error and the brain image is there Did you do ssh -Y or have ForwardX11Trusted yes in your ssh.config? Richard ___ 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] Correction for multiple comparisons error
This is a problem with version 5.0 when you set the clusterwise pvalue to something close to 1. I re-rand it with .995 and it work. This is fixed in 5.3 doug On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote: Definitely, just uploaded it! Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:10 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error hmm, can't tell from that what is going on. Can you tar up lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at the end of this email)? doug On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote: Hey Doug, Of course, I attached it in txt format in this email! Best, Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 2:55 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error Can you send me the terminal output in a text file? A word doc is very inconvenient:). doug On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote: Hi Doug, 1) My cmd line is: mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir lh.Diseased_gender_age.glmdir 2) The FS version that I am using is the stable 5.0.0, 3) I have attached the full terminal output in this email. Thank you for your time! Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, May 27, 2013 10:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error what is your cmd line? What version of FS are you using? What is the full terminal output? doug On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote: Hi! I have been running the mri_glmfit-sim command to do the correction for multiple comparisons for my group analysis and for some voxel-based thresholds (not all) there is an error that comes up when reading the colortable from the annotation file: reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** and then it gets stuck. Do you happen to know what might be causing this issue? Thank you for your time, Panos ___ 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 -- 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/ -- 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/ -- 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.
Re: [Freesurfer] white matter volume per lobe...
Hi Doug: The command is: mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax 200 and the terminal output is: mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200 SUBJECTS_DIR /usr/local/freesurfer/subjects subject OAS1_0001_MR1 outvol mri/lobulitos_2.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 200.00 RipUnknown 1 Reading lh white surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot reading colortable from annotation file... colortable with 8 entries read (originally none) Reading rh white surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot reading colortable from annotation file... colortable with 8 entries read (originally none) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz Loading filled from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7659 vertices from left hemi Ripped 7544 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz ASeg Vox2RAS: --- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; - Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 688931 Used brute-force search on 139 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to mri/lobulitos_2.mgz Sincerely, Gonzalo Rojas Costa On Thu, May 30, 2013 at 4:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: can you send me your full command line as well as the terminal output? On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote: Hi Doug: But, in the mri_aparc2aseg command, I test with the --wmparc-dmax 200 option... I put that big value to test it, but I got the image that I sent you... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Average for each voxel across all conditions
Hi, I have an experiment where I have 3 conditions in a FIR event related analysis (running FS 4.5). I need to get the mean activity level for each voxel across all conditions across the run, so that I can calculate percent signal change for each individual voxel. Is this available (I have analyzed each run separately) somewhere? Katie ___ 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 weights from FS-Fast analysis
Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things: 1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest. The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that. So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest. Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram? This would suffice to give me the %age signal change? I would be doing these computations in Matlab using MRIread. 2) A results table with the headings: Cluster p (FWE corrected) Cluster size Peak Voxel p (FWE corrected) Peak Voxel T Peak Voxel Coords BA Anatomical Landmark I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files from the group level analysis. I can get the peak voxel coordinates from the summary files as well. I can use this to get the peak voxel p from the group level sig.nii.gz file. Is this FWE corrected? If not, how can I get this information? I can use these coordinates to get the peak voxel T by getting the value from the group level F.nii.gz file and taking its square root. How can I get the sign of the T statistic? I can use the Lancaster transform to convert the MNI305 peak voxel coordinates into the Atlas coordinates to look up the putative BA and landmarks (unless there is a better way with Freesurfer? I'm seeing some references to some BA labels in the forum but it doesn't look like this is a complete set yet?). Sorry for all these questions! I got some nice results from FSFAST and would like to get them written up. Cheers! Joe On May 29, 2013, at 10:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: On 5/29/13 10:42 PM, Joseph Dien wrote: On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Joe, On 05/29/2013 01:00 AM, Joseph Dien wrote: I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? For the first level analysis, the first N beta weights correspond to the N conditions in the paradigm file. The rest are nuisance variables. Ah, very good! In order to compute the percent signal change statistic (I'm following the MarsBaR approach: http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated) I'm also going to need the beta weights for the session mean regressors. How are the nuisance regressors organized? You can just use the meanfunc.nii.gz. Also, each contrasts is computed as the simple contrast (ces) and as a percent of the baseline at the voxel (cespct, cesvarpct). 2) In order to extract the cluster, it looks like I would use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged with the number of the corresponding cluster. Is that from a group analysis? Yes, that's right. I could then use that to generate masks to extract the information I need for each cluster from beta.nii.gz. If this is from a group analysis, then there should already be a file there (something.y.ocn.dat) that has a value for each subject in the rows and a value for each cluster in the columns. I see it. Are these values already scaled as percent signal change? If so, that would be wonderful! :) Only if you specified it when you ran isxconcat-sess. Note that the non-scaled values are actually scaled to percent of grand mean intensity. Is that correct? 3) The final information that I would need is the canonical hrf shape generated by FSFAST for a single event. I guess I could generate that by setting up a dummy analysis run with a single event of the desired duration and then look in the X variable in the resulting X.mat file? try this plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf) Perfect! :) Sorry for all the questions! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ Freesurfer mailing list
Re: [Freesurfer] Correction for multiple comparisons error
Great, thanks!! In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) analysis on each hemisphere separately (lh.**.glmfit and rh.**.glmfit) do I still need to apply the correction over the two hemispheres (that is divide by 2 the cluster wise threshold since in FS 5.0.0 the --2spaces flag does not apply)? Best, Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:29 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error This is a problem with version 5.0 when you set the clusterwise pvalue to something close to 1. I re-rand it with .995 and it work. This is fixed in 5.3 doug On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote: Definitely, just uploaded it! Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:10 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error hmm, can't tell from that what is going on. Can you tar up lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at the end of this email)? doug On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote: Hey Doug, Of course, I attached it in txt format in this email! Best, Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 2:55 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error Can you send me the terminal output in a text file? A word doc is very inconvenient:). doug On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote: Hi Doug, 1) My cmd line is: mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir lh.Diseased_gender_age.glmdir 2) The FS version that I am using is the stable 5.0.0, 3) I have attached the full terminal output in this email. Thank you for your time! Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, May 27, 2013 10:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error what is your cmd line? What version of FS are you using? What is the full terminal output? doug On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote: Hi! I have been running the mri_glmfit-sim command to do the correction for multiple comparisons for my group analysis and for some voxel-based thresholds (not all) there is an error that comes up when reading the colortable from the annotation file: reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** and then it gets stuck. Do you happen to know what might be causing this issue? Thank you for your time, Panos ___ 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 -- 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/ -- 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/ -- 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/
Re: [Freesurfer] Correction for multiple comparisons error
yes On 05/30/2013 04:43 PM, Fotiadis, Panagiotis wrote: Great, thanks!! In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) analysis on each hemisphere separately (lh.**.glmfit and rh.**.glmfit) do I still need to apply the correction over the two hemispheres (that is divide by 2 the cluster wise threshold since in FS 5.0.0 the --2spaces flag does not apply)? Best, Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:29 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error This is a problem with version 5.0 when you set the clusterwise pvalue to something close to 1. I re-rand it with .995 and it work. This is fixed in 5.3 doug On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote: Definitely, just uploaded it! Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:10 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error hmm, can't tell from that what is going on. Can you tar up lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at the end of this email)? doug On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote: Hey Doug, Of course, I attached it in txt format in this email! Best, Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 2:55 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error Can you send me the terminal output in a text file? A word doc is very inconvenient:). doug On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote: Hi Doug, 1) My cmd line is: mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir lh.Diseased_gender_age.glmdir 2) The FS version that I am using is the stable 5.0.0, 3) I have attached the full terminal output in this email. Thank you for your time! Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, May 27, 2013 10:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error what is your cmd line? What version of FS are you using? What is the full terminal output? doug On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote: Hi! I have been running the mri_glmfit-sim command to do the correction for multiple comparisons for my group analysis and for some voxel-based thresholds (not all) there is an error that comes up when reading the colortable from the annotation file: reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** and then it gets stuck. Do you happen to know what might be causing this issue? Thank you for your time, Panos ___ 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 -- 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/ -- 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/ -- 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
Re: [Freesurfer] Average for each voxel across all conditions
Hi Katie, I don't remember what 4.5 outputs. Is there a meanfunc volume there? Itwould be much easier to support you if you were using version 5.x:) doug On 05/30/2013 04:36 PM, Katie Bettencourt wrote: Hi, I have an experiment where I have 3 conditions in a FIR event related analysis (running FS 4.5). I need to get the mean activity level for each voxel across all conditions across the run, so that I can calculate percent signal change for each individual voxel. Is this available (I have analyzed each run separately) somewhere? Katie ___ 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.
Re: [Freesurfer] Correction for multiple comparisons error
Great, thanks! Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:47 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error yes On 05/30/2013 04:43 PM, Fotiadis, Panagiotis wrote: Great, thanks!! In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) analysis on each hemisphere separately (lh.**.glmfit and rh.**.glmfit) do I still need to apply the correction over the two hemispheres (that is divide by 2 the cluster wise threshold since in FS 5.0.0 the --2spaces flag does not apply)? Best, Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:29 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error This is a problem with version 5.0 when you set the clusterwise pvalue to something close to 1. I re-rand it with .995 and it work. This is fixed in 5.3 doug On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote: Definitely, just uploaded it! Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:10 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error hmm, can't tell from that what is going on. Can you tar up lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at the end of this email)? doug On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote: Hey Doug, Of course, I attached it in txt format in this email! Best, Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 2:55 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error Can you send me the terminal output in a text file? A word doc is very inconvenient:). doug On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote: Hi Doug, 1) My cmd line is: mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir lh.Diseased_gender_age.glmdir 2) The FS version that I am using is the stable 5.0.0, 3) I have attached the full terminal output in this email. Thank you for your time! Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, May 27, 2013 10:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error what is your cmd line? What version of FS are you using? What is the full terminal output? doug On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote: Hi! I have been running the mri_glmfit-sim command to do the correction for multiple comparisons for my group analysis and for some voxel-based thresholds (not all) there is an error that comes up when reading the colortable from the annotation file: reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** and then it gets stuck. Do you happen to know what might be causing this issue? Thank you for your time, Panos ___ 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 -- 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/ -- 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/
Re: [Freesurfer] tkmedit on ssh remote machine error
yes, I have ForwardX11Trusted yes in ssh_config and I do ssh -Y Jon - Original Message - From: R Edgar freesurfer@gmail.com To: Jon Wieser wie...@uwm.edu Cc: Z K zkauf...@nmr.mgh.harvard.edu, freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 30, 2013 3:26:05 PM Subject: Re: [Freesurfer] tkmedit on ssh remote machine error On Thu, May 30, 2013 at 2:37 PM, Jon Wieser wie...@uwm.edu wrote: both machines have Mac OS X 10.6.8 the tkmedit works fine when not logged in remotely there is no error and the brain image is there Did you do ssh -Y or have ForwardX11Trusted yes in your ssh.config? Richard -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ 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] MRIread generating one dimensional vector
I tried using MRIread to look at the contents of the analysis files (using
Fressurfer 5.2.0 under OS X 10.8.3 and Matlab 2013a):
mri = MRIread('ces.nii.gz',0);
but I'm getting one-dimensional vectors:
mri
mri =
srcbext: ''
analyzehdr: []
bhdr: []
vol: [1x163842 double]
niftihdr: [1x1 struct]
fspec: 'ces.nii.gz'
pwd: '/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/CS-v-OTHERS'
flip_angle: 0
tr: 2000
te: 0
ti: 0
vox2ras0: [4x4 double]
volsize: [1 163842 1]
height: 1
width: 163842
depth: 1
nframes: 1
vox2ras: [4x4 double]
nvoxels: 163842
xsize: 1.
ysize: 1.
zsize: 1.
x_r: -0.
x_a: 0.0067
x_s: -0.0150
y_r: 4.1714e-08
y_a: 0.9131
y_s: 0.4078
z_r: -0.0164
z_a: -0.4077
z_s: 0.9130
c_r: -6.8259e+04
c_a: 465.0319
c_s: -995.9002
vox2ras1: [4x4 double]
Mdc: [3x3 double]
volres: [1. 1. 1.]
tkrvox2ras: [4x4 double]
It's fine when I read one of the functional files (f.nii.gz).
Am I doing something wrong? Or if it is supposed to be like this, how do I
convert to XYZ coordinates? The vox2ras fields are expecting a
four-dimensional matrix.
Thanks!
Joe
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//
___
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] Correction for multiple comparisons error
Sorry for the follow up email. If for instance I want to see any clusters that have a p value of 0.05 or less, I need to set the cluster wise p value in the mri_glmfit-sim command to 0.025 (to account for the correction over the two hemispheres). Then, suppose that a cluster is shown in the summary that has a p value of 0.015. Is that its actual p value, or is its actual p value (that is the value reported to the paper) 0.03? Thanks, Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis Sent: Thursday, May 30, 2013 4:50 PM To: Douglas N Greve Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error Great, thanks! Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:47 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error yes On 05/30/2013 04:43 PM, Fotiadis, Panagiotis wrote: Great, thanks!! In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) analysis on each hemisphere separately (lh.**.glmfit and rh.**.glmfit) do I still need to apply the correction over the two hemispheres (that is divide by 2 the cluster wise threshold since in FS 5.0.0 the --2spaces flag does not apply)? Best, Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:29 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error This is a problem with version 5.0 when you set the clusterwise pvalue to something close to 1. I re-rand it with .995 and it work. This is fixed in 5.3 doug On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote: Definitely, just uploaded it! Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:10 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error hmm, can't tell from that what is going on. Can you tar up lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at the end of this email)? doug On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote: Hey Doug, Of course, I attached it in txt format in this email! Best, Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 2:55 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error Can you send me the terminal output in a text file? A word doc is very inconvenient:). doug On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote: Hi Doug, 1) My cmd line is: mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir lh.Diseased_gender_age.glmdir 2) The FS version that I am using is the stable 5.0.0, 3) I have attached the full terminal output in this email. Thank you for your time! Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, May 27, 2013 10:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error what is your cmd line? What version of FS are you using? What is the full terminal output? doug On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote: Hi! I have been running the mri_glmfit-sim command to do the correction for multiple comparisons for my group analysis and for some voxel-based thresholds (not all) there is an error that comes up when reading the colortable from the annotation file: reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** and then it gets stuck. Do you happen to know what might be causing this issue? Thank you for your time, Panos ___ 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
[Freesurfer] combining masks in freesurfer ??
Hi All, Is there a way to combine multiple binary volumetric masks into a single binary volumetric mask in freesurfer ? Please let me know. Thankyou Subha ___ 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] MRIread generating one dimensional vector
That is a surface file. Each of the 163842 values corresponds to a
vertex in the surface. If you want xyz, you need to load in the surface.
You can also analyze the data in the native space if that would make it
easier (but you can't surface smooth).
doug
On 05/30/2013 05:08 PM, Joseph Dien wrote:
I tried using MRIread to look at the contents of the analysis files
(using Fressurfer 5.2.0 under OS X 10.8.3 and Matlab 2013a):
mri = MRIread('ces.nii.gz',0);
but I'm getting one-dimensional vectors:
mri
mri =
srcbext: ''
analyzehdr: []
bhdr: []
vol: [1x163842 double]
niftihdr: [1x1 struct]
fspec: 'ces.nii.gz'
pwd: '/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/CS-v-OTHERS'
flip_angle: 0
tr: 2000
te: 0
ti: 0
vox2ras0: [4x4 double]
volsize: [1 163842 1]
height: 1
width: 163842
depth: 1
nframes: 1
vox2ras: [4x4 double]
nvoxels: 163842
xsize: 1.
ysize: 1.
zsize: 1.
x_r: -0.
x_a: 0.0067
x_s: -0.0150
y_r: 4.1714e-08
y_a: 0.9131
y_s: 0.4078
z_r: -0.0164
z_a: -0.4077
z_s: 0.9130
c_r: -6.8259e+04
c_a: 465.0319
c_s: -995.9002
vox2ras1: [4x4 double]
Mdc: [3x3 double]
volres: [1. 1. 1.]
tkrvox2ras: [4x4 double]
It's fine when I read one of the functional files (f.nii.gz).
Am I doing something wrong? Or if it is supposed to be like this, how
do I convert to XYZ coordinates? The vox2ras fields are expecting a
four-dimensional matrix.
Thanks!
Joe
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com mailto:jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//
--
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
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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] Correction for multiple comparisons error
you would report .03 doug On 05/30/2013 05:10 PM, Fotiadis, Panagiotis wrote: Sorry for the follow up email. If for instance I want to see any clusters that have a p value of 0.05 or less, I need to set the cluster wise p value in the mri_glmfit-sim command to 0.025 (to account for the correction over the two hemispheres). Then, suppose that a cluster is shown in the summary that has a p value of 0.015. Is that its actual p value, or is its actual p value (that is the value reported to the paper) 0.03? Thanks, Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis Sent: Thursday, May 30, 2013 4:50 PM To: Douglas N Greve Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error Great, thanks! Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:47 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error yes On 05/30/2013 04:43 PM, Fotiadis, Panagiotis wrote: Great, thanks!! In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) analysis on each hemisphere separately (lh.**.glmfit and rh.**.glmfit) do I still need to apply the correction over the two hemispheres (that is divide by 2 the cluster wise threshold since in FS 5.0.0 the --2spaces flag does not apply)? Best, Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:29 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error This is a problem with version 5.0 when you set the clusterwise pvalue to something close to 1. I re-rand it with .995 and it work. This is fixed in 5.3 doug On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote: Definitely, just uploaded it! Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:10 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error hmm, can't tell from that what is going on. Can you tar up lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at the end of this email)? doug On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote: Hey Doug, Of course, I attached it in txt format in this email! Best, Panos From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 2:55 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error Can you send me the terminal output in a text file? A word doc is very inconvenient:). doug On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote: Hi Doug, 1) My cmd line is: mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir lh.Diseased_gender_age.glmdir 2) The FS version that I am using is the stable 5.0.0, 3) I have attached the full terminal output in this email. Thank you for your time! Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, May 27, 2013 10:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error what is your cmd line? What version of FS are you using? What is the full terminal output? doug On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote: Hi! I have been running the mri_glmfit-sim command to do the correction for multiple comparisons for my group analysis and for some voxel-based thresholds (not all) there is an error that comes up when reading the colortable from the annotation file: reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** and then it gets stuck. Do you happen to know what might be causing this issue? Thank you for your time, Panos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] combining masks in freesurfer ??
you can use fscalc mask1.mgh and mask2.mgh -o mask1-and-mask2.mgz assuming you want to use an AND function doug On 05/30/2013 05:18 PM, Subhabrata Chaudhury wrote: Hi All, Is there a way to combine multiple binary volumetric masks into a single binary volumetric mask in freesurfer ? Please let me know. Thankyou Subha ___ 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.
Re: [Freesurfer] MRIread generating one dimensional vector
Oh duh. Okay, thanks!
Joe
On May 30, 2013, at 5:38 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
That is a surface file. Each of the 163842 values corresponds to a vertex in
the surface. If you want xyz, you need to load in the surface. You can also
analyze the data in the native space if that would make it easier (but you
can't surface smooth).
doug
On 05/30/2013 05:08 PM, Joseph Dien wrote:
I tried using MRIread to look at the contents of the analysis files (using
Fressurfer 5.2.0 under OS X 10.8.3 and Matlab 2013a):
mri = MRIread('ces.nii.gz',0);
but I'm getting one-dimensional vectors:
mri
mri =
srcbext: ''
analyzehdr: []
bhdr: []
vol: [1x163842 double]
niftihdr: [1x1 struct]
fspec: 'ces.nii.gz'
pwd: '/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/CS-v-OTHERS'
flip_angle: 0
tr: 2000
te: 0
ti: 0
vox2ras0: [4x4 double]
volsize: [1 163842 1]
height: 1
width: 163842
depth: 1
nframes: 1
vox2ras: [4x4 double]
nvoxels: 163842
xsize: 1.
ysize: 1.
zsize: 1.
x_r: -0.
x_a: 0.0067
x_s: -0.0150
y_r: 4.1714e-08
y_a: 0.9131
y_s: 0.4078
z_r: -0.0164
z_a: -0.4077
z_s: 0.9130
c_r: -6.8259e+04
c_a: 465.0319
c_s: -995.9002
vox2ras1: [4x4 double]
Mdc: [3x3 double]
volres: [1. 1. 1.]
tkrvox2ras: [4x4 double]
It's fine when I read one of the functional files (f.nii.gz).
Am I doing something wrong? Or if it is supposed to be like this, how do I
convert to XYZ coordinates? The vox2ras fields are expecting a
four-dimensional matrix.
Thanks!
Joe
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com mailto:jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//
--
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/
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.
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//
___
Freesurfer mailing list
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] combining masks in freesurfer ??
Hello Doug, Thank you. Will fscalc work with volume mask ? You wrote .mgh. mgh is surface data, right ? Best wishes Subha - Original Message - From: Douglas N Greve Sent: 05/30/13 05:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] combining masks in freesurfer ?? you can use fscalc mask1.mgh and mask2.mgh -o mask1-and-mask2.mgz assuming you want to use an AND function doug On 05/30/2013 05:18 PM, Subhabrata Chaudhury wrote: Hi All, Is there a way to combine multiple binary volumetric masks into a single binary volumetric mask in freesurfer ? Please let me know. Thankyou Subha___ 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 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] combining masks in freesurfer ??
mgh format can be volume or surface. fscalc will work with either. it will also work with nifti or analize formats On 05/30/2013 05:44 PM, Subhabrata Chaudhury wrote: Hello Doug, Thank you. Will fscalc work with volume mask ? You wrote .mgh. mgh is surface data, right ? Best wishes Subha - Original Message - From: Douglas N Greve Sent: 05/30/13 05:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] combining masks in freesurfer ?? you can use fscalc mask1.mgh and mask2.mgh -o mask1-and-mask2.mgz assuming you want to use an AND function doug On 05/30/2013 05:18 PM, Subhabrata Chaudhury wrote: Hi All, Is there a way to combine multiple binary volumetric masks into a single binary volumetric mask in freesurfer ? Please let me know. Thankyou Subha ___ 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. -- 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] Download difficulty
Mike, I have tested the download from multiple computers on multiple different networks, including my home network. It is successful everytime. I dont know if you have a a system administrator who can help resolve the situation on your end but everything seems to be running correctly on our side. -Zeke Hello all, I seem to be having some difficulty downloading the freesurfer software to my MAC computers. I have tried my laptop (MacBook pro, I don't remember the version but it is approx. 10.3) as well as a desktop (imac, mac osx version 10.8.3) and also tried two different networks. I have tried just clicking on the link (on your download page) as well as the curl -O command line. I get an NSURL error everytime, prior to any significant downloading. I have not have this difficulty with other freeware downloading to the same computers or on these networks. Any thoughts? Thanks Mike ___ 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.
Re: [Freesurfer] combining masks in freesurfer ??
Hi Subha you could use mri_and to do the job cheers Bruce On Thu, 30 May 2013, Subhabrata Chaudhury wrote: Hi All, Is there a way to combine multiple binary volumetric masks into a single binary volumetric mask in freesurfer ? Please let me know. Thankyou Subha ___ 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] recon-all error
Hi Mia That's a very large defect. Can you visualize it and see if you can figure out where it comes from? Bruce On May 30, 2013, at 2:39 PM, Borzello, Mia mborze...@partners.org wrote: Hi freesurfers, I encountered an error using recon-all for a scan series of 177 slices. I'm not sure exactly why it errorred, but I included the error log. Thanks so much, Mia recon-all.log ___ 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] CUDA install; libcudart; 64-bit detection
Hi all, probably mostly Bruce and co., I've just got a new linux box set up and am able to run all graphical tools and recon-all OK. Linux Mint 15 x64 RC (based on Ubuntu 13) Intel i5 Ivy Bridge nVidia GTX 650 Ti nVidia drivers: Selected from System Device Drivers; nvidia-313-updates; automatically installed. Freesurfer 5.3 Centos 6 version Now I'm hoping to get CUDA working. The proximate problem is that when I run Freesurfer's cudadetect I get: error while loading shared libraries: libcudart.so.5: cannot open shared object file: No such file or directory Indeed, searching the file system, there appears to be no libcudart.* anywhere. But there do appear to be CUDA components installed with the installation of the nvidia video driver: /usr/lib/nvidia-313-updates/libcuda.so 10.4 MB (plus some version-named links to same) So, my current model is that nvidia has installed what it considers to be the necessary components for an application to use to operate the CUDA hardware. Googling around, there seem to be some mentions that libcudart.so.* is something that would be supplied with a particular application (in this case Freesurfer). I'm not sure I believe that, but... The only other alternative I see is to download the nvidia CUDA developer kit and install that. However I'm very loath to do that because it replaces the video driver along with installing a lot of other unneeded apparatus. I have no idea the extent to which that installation works with or against the Ubuntu/Mint installation scheme, and what would happen on next video driver update. Not to mention that the latest Ubuntu-compatible package nvidia has is for 11.10, while my Mint is based on Ubuntu 13. Any idea how to proceed? Any chance of getting libcudart.so.5 a la carte? SIDE NOTE ON 64-bit detection in cuda_setup I see that in script cuda_setup there's a section which detects 64-bit by looking for directory: /usr/lib64 However, on Mint (so I assume Ubuntu and Debian) 64-bit, there is no such directory. Instead, there are: /usr/lib /usr/lib32 Suggestions for other ways to detect 64-bit: http://stackoverflow.com/questions/246007/how-to-determine-whether-a-given-linux-is-32-bit-or-64-bit I'm pretty sure this is not pertinent to the hunt for missing libcudart.so, but seems like that needs to be fixed too for Ubuntu/Mint. Thanks, -- Graham ___ 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 weights from FS-Fast analysis
I was able to make more progress so I'm mostly good at this point but I have a remaining question: I assume the contents of sig.nii.gz (which I assume are the vertex p-values) are not FWE corrected. Is it possible to get FWE-corrected vertex p-values? Or are only clusterwise corrections available? Thanks again for your patience! Joe On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com wrote: Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things: 1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest. The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that. So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest. Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram? This would suffice to give me the %age signal change? I would be doing these computations in Matlab using MRIread. 2) A results table with the headings: Cluster p (FWE corrected) Cluster size Peak Voxel p (FWE corrected) Peak Voxel T Peak Voxel Coords BA Anatomical Landmark I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files from the group level analysis. I can get the peak voxel coordinates from the summary files as well. I can use this to get the peak voxel p from the group level sig.nii.gz file. Is this FWE corrected? If not, how can I get this information? I can use these coordinates to get the peak voxel T by getting the value from the group level F.nii.gz file and taking its square root. How can I get the sign of the T statistic? I can use the Lancaster transform to convert the MNI305 peak voxel coordinates into the Atlas coordinates to look up the putative BA and landmarks (unless there is a better way with Freesurfer? I'm seeing some references to some BA labels in the forum but it doesn't look like this is a complete set yet?). Sorry for all these questions! I got some nice results from FSFAST and would like to get them written up. Cheers! Joe On May 29, 2013, at 10:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: On 5/29/13 10:42 PM, Joseph Dien wrote: On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Joe, On 05/29/2013 01:00 AM, Joseph Dien wrote: I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? For the first level analysis, the first N beta weights correspond to the N conditions in the paradigm file. The rest are nuisance variables. Ah, very good! In order to compute the percent signal change statistic (I'm following the MarsBaR approach: http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated) I'm also going to need the beta weights for the session mean regressors. How are the nuisance regressors organized? You can just use the meanfunc.nii.gz. Also, each contrasts is computed as the simple contrast (ces) and as a percent of the baseline at the voxel (cespct, cesvarpct). 2) In order to extract the cluster, it looks like I would use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged with the number of the corresponding cluster. Is that from a group analysis? Yes, that's right. I could then use that to generate masks to extract the information I need for each cluster from beta.nii.gz. If this is from a group analysis, then there should already be a file there (something.y.ocn.dat) that has a value for each subject in the rows and a value for each cluster in the columns. I see it. Are these values already scaled as percent signal change? If so, that would be wonderful! :) Only if you specified it when you ran isxconcat-sess. Note that the non-scaled values are actually scaled to percent of grand mean intensity. Is that correct? 3) The final information that I would need is the canonical hrf shape generated by FSFAST for a single event. I guess I could generate that by setting up a dummy analysis run with a single event of the desired duration and then look in the X variable in the resulting X.mat file? try this plot(X.runflac(1).flac.ev(2).tirf,
