[Freesurfer] recon-all error
Hi, We're getting the following error from recon-all: command line: pbsubmit -m etanski -c 'recon-all -s DODASD012 -all -i /cluster/archive/300/siemens/TrioTim-35006-20120718-151622-227000/391000-15-01.dcm -mail etan...@nmr.mgh.harvard.edu' output: ... ... mri_binarize --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14699/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/manoach/dod/subjects/DODASD012/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14699/ones.mgz sysname Linux hostname compute-0-88 machine x86_64 user etanski input ./tmp.mri_nu_correct.mni.14699/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.14699/ones.mgz Binarizing based on threshold min-1 max+infinity binval1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/input.mean.dat $Id: mri_segstats.c,v 1.75.2.3 2012/07/16 14:41:02 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/input.mean.dat sysname Linux hostname compute-0-88 machine x86_64 user etanski Loading ./tmp.mri_nu_correct.mni.14699/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0 Reporting on 0 segmentations Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.14699/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/output.mean.dat $Id: mri_segstats.c,v 1.75.2.3 2012/07/16 14:41:02 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/output.mean.dat sysname Linux hostname compute-0-88 machine x86_64 user etanski Loading ./tmp.mri_nu_correct.mni.14699/ones.mgz Loading ./tmp.mri_nu_correct.mni.14699/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0 Reporting on 0 segmentations Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.14699/output.mean.dat (standard_in) 1: syntax error mris_calc -o ./tmp.mri_nu_correct.mni.14699/nu2.mnc ./tmp.mri_nu_correct.mni.14699/nu2.mnc mul Linux compute-0-88 2.6.32-220.23.1.el6.x86_64 #1 SMP Mon Jun 18 18:58:52 BST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s DODASD012 exited with ERRORS at Wed Jul 25 12:27:28 EDT 2012 For more details, see the log file /autofs/cluster/manoach/dod/subjects/DODASD012/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any suggestions? Thanks, Yigal ___ 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] Freesurfer Command in Matlab
Hi, I'm trying to run the following command in through matlab: system(['mri_surf2surf --srcsubject average7 --trgsubject average7 --srcsurfval /space/schnook/1/users/yigal/projects/dti/data/old_recons/results/control_vs_sch_rh_average7_2mm_ttest.mgz --trgsurfval /space/schnook/1/users/yigal/projects/dti/data/old_recons/results/control_vs_sch_rh_average7_2mm_ttest.mgz --hemi rh --nsmooth-out 3']) And get the following error message mri_surf2surf: /usr/pubsw/common/matlab/7.4/sys/os/glnxa64/libgcc_s.so.1: version `GCC_4.2.0' not found (required by /usr/lib64/libstdc++.so.6) When I run the command from a terminal window, there's no problem. Any ideas? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Output of selxavg3
Hi, Of all the files that selxavg3 generates inside the contrast folder, only three are described in the wiki: ces.nii, cesvar.nii, and sig.nii. Does anyone know the other files below represent? Also, which files are used for subsequent group analyses? cesmag.nii fsig.nii minsig.nii cesmagpct.nii cespct.nii cesvarpct.nii iminsig.nii ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer ftimepoint variable
Hi, I'm trying to use a TCL script that runs through every time point in a surface. I'm using the following commands: set gaLinkedVars(ftimepoint) 0 (or 1, 2, etc) SendLinkedVarGroup overlay But tksurfer is always showing point 0 (doesn't advance in time). Similar TCL commands for fthresh and fslope work fine. Any ideas? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_vol2surf - MNI subject
Hi, If I have volume data in MNI subject space (produced using --tal option in mri_vol2vol), how do I project it onto the surface in the same subject space? There does not seem to be an equivalent tal option in mri_vol2surf. Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem running tksurfer
tksurfer fsaverage lh inflated surfer: current subjects dir: /autofs/space/ventzl_001/users/SUBJECTS_DIR surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/schnook_001/users/yigal/projects/functional surfer: Reading header info from /autofs/space/ventzl_001/users/SUBJECTS_DIR/fsaverage/mri/T1.mgz reading group avg surface area 822 cm^2 from file surfer: vertices=163842, faces=327680 Loading /usr/local/freesurfer/stable4/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /usr/local/freesurfer/stable4/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/stable4/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/stable4/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/stable4/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/stable4/lib/tcl/tkUtils.tcl Error loading icon_disk_multiview: couldn't open "/usr/local/freesurfer/stable4/lib/images/icon_disk_multiview.gif": no such file or directory Error sourcing /usr/local/freesurfer/stable4/lib/tcl/tksurfer.tcl: image "icon_disk_multiview" doesn't exist reading white matter vertex locations... ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cortical thickness conversion
Hi, I'm trying to convert corical thickness maps into a common space and getting this error. Any ideas? mri_surf2surf --srcsubject mano002_new --trgsubject fsaverage --hemi lh --srcsurfval lh.thickness --trgsurfval /space/schnook/1/users/yigal/projects/dti/data/new_recons/mano002_new/surf/lh.thickness_fsaverage.nii --nsmooth-in 3 --nsmooth-out 3 srcsubject = mano002_new srcval = lh.thickness srctype= trgsubject = fsaverage trgval = /space/schnook/1/users/yigal/projects/dti/data/new_recons/mano002_new/surf/lh.thickness_fsaverage.nii trgtype= surfreg= sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 Reading source surface reg /autofs/space/ventzl_001/users/SUBJECTS_DIR/mano002_new/surf/lh.sphere.reg Loading source data ERROR: dimesion inconsitency in source data Number of surface vertices = 115532 Number of value vertices = 118209 mri_surf2surf --srcsubject mano002_new --trgsubject fsaverage --hemi rh --srcsurfval rh.thickness --trgsurfval /space/schnook/1/users/yigal/projects/dti/data/new_recons/mano002_new/surf/rh.thickness_fsaverage.nii --nsmooth-in 3 --nsmooth-out 3 srcsubject = mano002_new srcval = rh.thickness srctype= trgsubject = fsaverage trgval = /space/schnook/1/users/yigal/projects/dti/data/new_recons/mano002_new/surf/rh.thickness_fsaverage.nii trgtype= surfreg= sphere.reg srchemi= rh trghemi= rh frame = 0 fwhm-in= 0 fwhm-out = 0 Reading source surface reg /autofs/space/ventzl_001/users/SUBJECTS_DIR/mano002_new/surf/rh.sphere.reg Loading source data ERROR: dimesion inconsitency in source data Number of surface vertices = 116029 Number of value vertices = 120919 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_surfcluster
Hi, When I run mri_surfcluster on a surface with 12 timepoints, how do I know when each of the reported clusters occurred? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_fwhm problem
Hi, I'm getting an NAN value for some surfaces but not for others. Any ideas? Both surfaces below were generated using an identical process. [yi...@schnook sph_sm20]$ pwd /autofs/space/ventzl_001/users/SUBJECTS_DIR/mano010/bold/EMexec3/sph_sm20 [yi...@schnook sph_sm20]$ mris_fwhm --i e001-rh.bhdr --subject average7 --hemi rh average7 rh white Number of vertices 163842 Number of faces327680 Total area 65350.234375 GroupSurface 0 FIX_VERTEX_AREA 1 AvgVtxArea 0.398861 AvgVtxDist 0.724276 StdVtxDist 0.238694 INFO: bvolumeRead: min = -0.473817, max = 0.363422 Polynomial detrending, order = 0 Computing spatial AR1 ar1mn = 0.995086, ar1std = 0.00271769, ar1max = 0.999702 avg vertex dist 0.724276 avg vertex dist 0.724276 fwhm = 12.150420 [yi...@schnook sph_sm20]$ pwd /autofs/space/ventzl_001/users/SUBJECTS_DIR/mano016/bold/EMexec3/sph_sm20 [yi...@schnook sph_sm20]$ mris_fwhm --i e001-rh.bhdr --subject average7 --hemi rh average7 rh white Number of vertices 163842 Number of faces327680 Total area 65350.234375 GroupSurface 0 FIX_VERTEX_AREA 1 AvgVtxArea 0.398861 AvgVtxDist 0.724276 StdVtxDist 0.238694 INFO: bvolumeRead: min = -0.749406, max = 1.43625 Polynomial detrending, order = 0 Computing spatial AR1 ar1mn = inf, ar1std = nan, ar1max = inf avg vertex dist 0.724276 avg vertex dist 0.724276 fwhm = nan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mni152.register.dat
Hi, Does mni152.register.dat map from fsaverage to mni152 or vice versa? Specifically, I'm using an fsaverage surface that I want to project onto mni152 volume using surf2vol. Should I invert the matrix? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mni152.register.dat
How about when viewing an mni152 volume in tkmedit - what should I use as overlay-reg? Douglas N Greve wrote: you don't need to invert it, just use as is. doug Yigal Agam wrote: Hi, Does mni152.register.dat map from fsaverage to mni152 or vice versa? Specifically, I'm using an fsaverage surface that I want to project onto mni152 volume using surf2vol. Should I invert the matrix? Thanks, Yigal ___ 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] [Fwd: fsaverage to average7]
Hi all, Is there a way to convert results that I have on fsaverage to average7? I need to do that to be compatible with some average7 results that go into the same paper. When I use mri_surf2surf, activation is displaced. Any advice would be appreciated. This is what I've done: mri_surf2surf --srcsubject fsaverage --trgsubject average7 --sval [fsaverage file]--hemi lh --tval [average7 file] Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fsaverage to mni152
Hi, What's the best way to convert an fsaverage volume into an MNI152 volume that can be viewed on top of a standard brain (MNI152_T1_2mm_brain.nii.gz) in fslview? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fsaverage to mni152
Thanks, Doug. Also, how can this be done from an individual brain to mni152? Do I need to use fsaverage as an intermediate? Yigal Douglas N Greve wrote: > Use $FREESURFER_HOME/average/mni152.register.dat and mri_vol2vol with > --inv > > Yigal Agam wrote: >> Hi, >> >> What's the best way to convert an fsaverage volume into an MNI152 >> volume that can be viewed on top of a standard brain >> (MNI152_T1_2mm_brain.nii.gz) in fslview? >> >> Thanks, >> Yigal >> ___ >> 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] Circle around vertex
Hi, In surface-based analysis, is it possible to create an ROI label that is a circle of a certain radius around a given vertex? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Comments in paradigm files
Hi, Can you add comments to a paradigm file? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fsaverage to mni152
Hi Doug, Returning to this old thread: I'm doing what you said and getting weird results (activation not where I think it should be): mri_vol2vol --mov --targ --inv --reg $FREESURFER_HOME/average/mni152.register.dat --o --no-save-reg Can you give an example of the command you would use? Thanks, Yigal Douglas N Greve wrote: > Use $FREESURFER_HOME/average/mni152.register.dat and mri_vol2vol with > --inv > > Yigal Agam wrote: >> Hi, >> >> What's the best way to convert an fsaverage volume into an MNI152 >> volume that can be viewed on top of a standard brain >> (MNI152_T1_2mm_brain.nii.gz) in fslview? >> >> Thanks, >> Yigal >> ___ >> 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] w file conversion
Hi, Is it possible to convert a .w file to another format? Thanks, Yigal ___ 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] Tutorial Files
Hi, We're having problems untarring the tutorial data. Are the uncompressed data available anywhere? Thanks, Yigal ___ 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] Getting Talairach Coordinates
Hi, Is there a way to get the Tal and MNI coordinates of a given fsaverage vertex through matlab or the unix command line, without opening tksurfer? Thanks, Yigal ___ 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] MNI305 to MNI152
How do I convert between the two coordinate systems? Yigal ___ 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] aparc.a2005s.annot errors?
Hi, There are some "holes" in fsaverage lh cingulate labels in the a2005s annotation. For example, vertex 16631, between the cingulate gyrus and sulcus is part of the superior frontal gyrus label. Same with vertices 20390 and 141081. Is that an error? This is a problem for us because it creates holes in our ACC labels. Thanks, Yigal ___ 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] MNI152
Hi, Is it possible to export a functional volume from individual brain space to mni152, so it can be overlaid on the standard mni152 brain in fslview? Thanks, Yigal ___ 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] FDR in gray matter
Hi, Is it possible to restrict FDR correction to gray matter in tkmedit? Thanks ___ 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] mni coordinates to volume index
Hi, Is it possible in matlab to get the volume index coordinates corresponding to specific MNI coordiates? Thanks, Yigal ___ 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.
