Re: [Freesurfer] mri_surfcluster problem
It cannot read the .w file as input. There is no need to use .w files (despite what it might say). On 12/03/2014 12:22 AM, wangzhiwei3233 wrote: *The command I used is* /mri_surfcluster --in sig.w --subject fsaverage --hemi lh --annot aparc --sign pos --minarea 30 --sum area100.pos.cluster.summary --o area100.pos.cluster.w --thmin 1.3/ *Teriminal output is * /thsign = pos, id = 1/ /version $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $/ /hemi = lh/ /srcid = sig.w / /srcsubjid = fsaverage/ /srcsurf= white/ /srcframe = 0/ /thsign = pos/ /thmin = 1.3/ /thmax = -1/ /fdr= -1/ /minarea= 30/ /xfmfile= talairach.xfm/ /nth = -1/ /outid= area100.pos.cluster.w paint/ /sumfile = area100.pos.cluster.summary/ /subjectsdir= /isilon/work/FBIP/0_projects/freesurfer/subjects/ /FixMNI = 1/ /- XFM matrix (RAS2RAS) ---/ //isilon/work/FBIP/0_projects/Pinna/freesurfer/subjects/fsaverage/mri/transforms/talairach.xfm/ / 1.000 0.000 0.000 0.000;/ / 0.000 1.000 0.000 0.000;/ / 0.000 0.000 1.000 0.000;/ / 0.000 0.000 0.000 1.000;/ // /Reading source surface /isilon/work/FBIP/0_projects/freesurfer/subjects/fsaverage/surf/lh.white/ /Done reading source surface/ /Reading annotation /isilon/work/FBIP/0_projects/freesurfer/subjects/fsaverage/label/lh.aparc.annot/ /reading colortable from annotation file.../ /colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)/ /Computing metric properties/ /Loading source values/ /mri_read(): couldn't determine type of file /isilon/work/FBIP/0_projects/PROJECT/GROUP_27SUB/fsaverage.lh/c1/g2v0.weight/high+low/sig.w/ /ERROR: could not read sig.w as type / At 2014-12-03 13:03:45, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: That is the right command line. What is the terminal output? On 12/2/14 8:01 AM, wangzhiwei3233 wrote: Hi Freesurfer experts, I just want to try cluster level threshold by cluster size, but not by mc simulation. So I tried the command like : mri_surfcluster --in sig.nii.gz --subject fsaverage --hemi lh --annot aparc --sign pos --minarea 50 --sum area50.pos.cluster.summary --o area50.pos.cluster.nii.gz --thmin 1.3 However, I found that the command did not set the non-cluster vertices to zero. The help of mri_surfcluster says that this command currently only supports paint (or w) format for input and output. I converted the sig.nii.gz to sig.w using / mri_surf2surf --s fsaverage --hemi lh --sval sig.nii.gz --tval sig.w --trg_type paint./ But command mri_surfcluster could not read the paint file. Could anyone help me? Thanks! Zhiwei ___ 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/ ___ 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] mri_surfcluster problem
Hi Freesurfer experts, I just want to try cluster level threshold by cluster size, but not by mc simulation. So I tried the command like : mri_surfcluster --in sig.nii.gz --subject fsaverage --hemi lh --annot aparc --sign pos --minarea 50 --sum area50.pos.cluster.summary --o area50.pos.cluster.nii.gz --thmin 1.3 However, I found that the command did not set the non-cluster vertices to zero. The help of mri_surfcluster says that this command currently only supports paint (or w) format for input and output. I converted the sig.nii.gz to sig.w using mri_surf2surf --s fsaverage --hemi lh --sval sig.nii.gz --tval sig.w --trg_type paint. But command mri_surfcluster could not read the paint file. Could anyone help me? Thanks! Zhiwei___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_surfcluster problem
That is the right command line. What is the terminal output? On 12/2/14 8:01 AM, wangzhiwei3233 wrote: Hi Freesurfer experts, I just want to try cluster level threshold by cluster size, but not by mc simulation. So I tried the command like : mri_surfcluster --in sig.nii.gz --subject fsaverage --hemi lh --annot aparc --sign pos --minarea 50 --sum area50.pos.cluster.summary --o area50.pos.cluster.nii.gz --thmin 1.3 However, I found that the command did not set the non-cluster vertices to zero. The help of mri_surfcluster says that this command currently only supports paint (or w) format for input and output. I converted the sig.nii.gz to sig.w using / mri_surf2surf --s fsaverage --hemi lh --sval sig.nii.gz --tval sig.w --trg_type paint./ But command mri_surfcluster could not read the paint file. Could anyone help me? Thanks! Zhiwei ___ 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] mri_surfcluster problem
The command I used is mri_surfcluster --in sig.w --subject fsaverage --hemi lh --annot aparc --sign pos --minarea 30 --sum area100.pos.cluster.summary --o area100.pos.cluster.w --thmin 1.3 Teriminal output is thsign = pos, id = 1 version $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ hemi = lh srcid = sig.w srcsubjid = fsaverage srcsurf= white srcframe = 0 thsign = pos thmin = 1.3 thmax = -1 fdr= -1 minarea= 30 xfmfile= talairach.xfm nth = -1 outid= area100.pos.cluster.w paint sumfile = area100.pos.cluster.summary subjectsdir= /isilon/work/FBIP/0_projects/freesurfer/subjects FixMNI = 1 - XFM matrix (RAS2RAS) --- /isilon/work/FBIP/0_projects/Pinna/freesurfer/subjects/fsaverage/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Reading source surface /isilon/work/FBIP/0_projects/freesurfer/subjects/fsaverage/surf/lh.white Done reading source surface Reading annotation /isilon/work/FBIP/0_projects/freesurfer/subjects/fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Computing metric properties Loading source values mri_read(): couldn't determine type of file /isilon/work/FBIP/0_projects/PROJECT/GROUP_27SUB/fsaverage.lh/c1/g2v0.weight/high+low/sig.w ERROR: could not read sig.w as type At 2014-12-03 13:03:45, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: That is the right command line. What is the terminal output? On 12/2/14 8:01 AM, wangzhiwei3233 wrote: Hi Freesurfer experts, I just want to try cluster level threshold by cluster size, but not by mc simulation. So I tried the command like : mri_surfcluster --in sig.nii.gz --subject fsaverage --hemi lh --annot aparc --sign pos --minarea 50 --sum area50.pos.cluster.summary --o area50.pos.cluster.nii.gz --thmin 1.3 However, I found that the command did not set the non-cluster vertices to zero. The help of mri_surfcluster says that this command currently only supports paint (or w) format for input and output. I converted the sig.nii.gz to sig.w using mri_surf2surf --s fsaverage --hemi lh --sval sig.nii.gz --tval sig.w --trg_type paint. But command mri_surfcluster could not read the paint file. Could anyone help me? Thanks! Zhiwei ___ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://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] mri_surfcluster problem?
Kara and Lauren, I think Doug has fixed this problem. i had similar problem but it is working now. pratap Hi Lauren (and Doug), I'm having the same issue. I ran montecarlo simulations on Friday and then tried to use the results in mri_surfcluster. It ran, but I also got the same CWP values (-0.1) for each cluster in the sum file. Also, when it runs, it gives a CEPHES ERROR. Here is what I get: INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release. thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39.2.2 2008/12/31 16:06:00 greve Exp $ hemi = rh srcid = ./group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.mgh srcsubjid = average7 srcsurf= white srcframe = 0 thsign = abs thmin = 3 thmax = inf fdr= -1 minarea= 0 xfmfile= talairach.xfm nth = -1 outid= /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii nii ocnid= /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii nii sumfile = /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.sum subjectsdir= /space/ventzl/1/users/SUBJECTS_DIR FixMNI = 1 - XFM matrix (RAS2RAS) --- /space/ventzl/1/users/SUBJECTS_DIR/average7/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Reading source surface /space/ventzl/1/users/SUBJECTS_DIR/average7/surf/rh.white Done reading source surface Reading annotation /space/ventzl/1/users/SUBJECTS_DIR/average7/label/rh.aparc.annot reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 9.2406 at vertex 150454 overall min = -4.29783 at vertex 159827 surface nvertices 163842 surface area 98024.702210 surface area 65349.801473 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=3.00 (3.00), thmax=inf (inf), thsignid=0, minarea=0.00 Found 23 clusters Max cluster size 2791.366699 INFO: fixing MNI talairach coordinates *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** Saving thresholded output to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software. Saving cluster numbers to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software. Kara Lauren LaCount wrote: Hi Everyone, I'm having a bit of a problem with mri_surfcluster. I ran it
Re: [Freesurfer] mri_surfcluster problem?
Thanks Pratap, I'll try it again. Kara Pratap Kunwar wrote: Kara and Lauren, I think Doug has fixed this problem. i had similar problem but it is working now. pratap Hi Lauren (and Doug), I'm having the same issue. I ran montecarlo simulations on Friday and then tried to use the results in mri_surfcluster. It ran, but I also got the same CWP values (-0.1) for each cluster in the sum file. Also, when it runs, it gives a CEPHES ERROR. Here is what I get: INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release. thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39.2.2 2008/12/31 16:06:00 greve Exp $ hemi = rh srcid = ./group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.mgh srcsubjid = average7 srcsurf= white srcframe = 0 thsign = abs thmin = 3 thmax = inf fdr= -1 minarea= 0 xfmfile= talairach.xfm nth = -1 outid= /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii nii ocnid= /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii nii sumfile = /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.sum subjectsdir= /space/ventzl/1/users/SUBJECTS_DIR FixMNI = 1 - XFM matrix (RAS2RAS) --- /space/ventzl/1/users/SUBJECTS_DIR/average7/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Reading source surface /space/ventzl/1/users/SUBJECTS_DIR/average7/surf/rh.white Done reading source surface Reading annotation /space/ventzl/1/users/SUBJECTS_DIR/average7/label/rh.aparc.annot reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 9.2406 at vertex 150454 overall min = -4.29783 at vertex 159827 surface nvertices 163842 surface area 98024.702210 surface area 65349.801473 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=3.00 (3.00), thmax=inf (inf), thsignid=0, minarea=0.00 Found 23 clusters Max cluster size 2791.366699 INFO: fixing MNI talairach coordinates *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** Saving thresholded output to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software. Saving cluster numbers to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software. Kara Lauren LaCount wrote: Hi Everyone, I'm having a bit of a problem with mri_surfcluster. I ran it alright last week on the right hemisphere, and now am unable to get
Re: [Freesurfer] mri_surfcluster problem?
Looks like it's working again! Thanks for fixing it, Doug, and for pointing out that it was fixed, Pratap! -Lauren On Fri, Jan 9, 2009 at 3:54 PM, Kara Dyckman k...@nmr.mgh.harvard.edu wrote: Thanks Pratap, I'll try it again. Kara Pratap Kunwar wrote: Kara and Lauren, I think Doug has fixed this problem. i had similar problem but it is working now. pratap Hi Lauren (and Doug), I'm having the same issue. I ran montecarlo simulations on Friday and then tried to use the results in mri_surfcluster. It ran, but I also got the same CWP values (-0.1) for each cluster in the sum file. Also, when it runs, it gives a CEPHES ERROR. Here is what I get: INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release. thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39.2.2 2008/12/31 16:06:00 greve Exp $ hemi = rh srcid = ./group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.mgh srcsubjid = average7 srcsurf= white srcframe = 0 thsign = abs thmin = 3 thmax = inf fdr= -1 minarea= 0 xfmfile= talairach.xfm nth = -1 outid= /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii nii ocnid= /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii nii sumfile = /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.sum subjectsdir= /space/ventzl/1/users/SUBJECTS_DIR FixMNI = 1 - XFM matrix (RAS2RAS) --- /space/ventzl/1/users/SUBJECTS_DIR/average7/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Reading source surface /space/ventzl/1/users/SUBJECTS_DIR/average7/surf/rh.white Done reading source surface Reading annotation /space/ventzl/1/users/SUBJECTS_DIR/average7/label/rh.aparc.annot reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 9.2406 at vertex 150454 overall min = -4.29783 at vertex 159827 surface nvertices 163842 surface area 98024.702210 surface area 65349.801473 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=3.00 (3.00), thmax=inf (inf), thsignid=0, minarea=0.00 Found 23 clusters Max cluster size 2791.366699 INFO: fixing MNI talairach coordinates *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** Saving thresholded output to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software. Saving cluster numbers to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So
Re: [Freesurfer] mri_surfcluster problem?
Hi Lauren (and Doug), I'm having the same issue. I ran montecarlo simulations on Friday and then tried to use the results in mri_surfcluster. It ran, but I also got the same CWP values (-0.1) for each cluster in the sum file. Also, when it runs, it gives a CEPHES ERROR. Here is what I get: INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release. thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39.2.2 2008/12/31 16:06:00 greve Exp $ hemi = rh srcid = ./group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.mgh srcsubjid = average7 srcsurf= white srcframe = 0 thsign = abs thmin = 3 thmax = inf fdr= -1 minarea= 0 xfmfile= talairach.xfm nth = -1 outid= /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii nii ocnid= /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii nii sumfile = /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.sum subjectsdir= /space/ventzl/1/users/SUBJECTS_DIR FixMNI = 1 - XFM matrix (RAS2RAS) --- /space/ventzl/1/users/SUBJECTS_DIR/average7/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Reading source surface /space/ventzl/1/users/SUBJECTS_DIR/average7/surf/rh.white Done reading source surface Reading annotation /space/ventzl/1/users/SUBJECTS_DIR/average7/label/rh.aparc.annot reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 9.2406 at vertex 150454 overall min = -4.29783 at vertex 159827 surface nvertices 163842 surface area 98024.702210 surface area 65349.801473 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=3.00 (3.00), thmax=inf (inf), thsignid=0, minarea=0.00 Found 23 clusters Max cluster size 2791.366699 INFO: fixing MNI talairach coordinates *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** *** CEPHES ERROR: bdtr (p 0.0) domain error *** Saving thresholded output to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software. Saving cluster numbers to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software. Kara Lauren LaCount wrote: Hi Everyone, I'm having a bit of a problem with mri_surfcluster. I ran it alright last week on the right hemisphere, and now am unable to get it to run through with the left. First I'm running mri_glmfit to get .csd files with 1 iterations (split into 10 runs to speed things up), and then I'm running mri_surfcluster with
[Freesurfer] mri_surfcluster problem?
Hi Everyone, I'm having a bit of a problem with mri_surfcluster. I ran it alright last week on the right hemisphere, and now am unable to get it to run through with the left. First I'm running mri_glmfit to get .csd files with 1 iterations (split into 10 runs to speed things up), and then I'm running mri_surfcluster with something like: mri_surfcluster --in ../SENS/xrun_gavg/lh.osgm.0.5frac.mfx/osgm/sig.mgh --subject average --hemi lh --surf white --annot aparc.a2005s --csd ../csdfiles/mcz_SENS_lh_1_ mfx_0.5frac_th01_1of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_1_mfx_0.5frac_th01_2of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_1_mfx_0.5frac_th01_3of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_1_mfx_0.5frac_th01_4of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_1_mfx_0.5frac_th01_5of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_1_mfx_0.5frac_th01_6of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_1_mfx_0.5frac_th01_7of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_1_mfx_0.5frac_th01_8of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_1_mfx_0.5frac_th01_9of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_1_mfx_0.5frac_th01_10of10-osgm.csd --sum ./clusters_mcz_SENS_lh_1_mfx_0.5frac_th01/sum_mcz_SENS_lh_1_m fx_0.5frac_th01 --csdpdf ./clusters_mcz_SENS_lh_1_mfx_0.5frac_th01/csdpdf_mcz_SENS_lh_1_m fx_0.5frac_th01 --vwsig ./clusters_mcz_SENS_lh_1_mfx_0.5frac_th01/vwsig_mcz_SENS_lh_1_mfx_0.5frac_th01.mgh --cwsig /clusters_mcz_SENS_lh_1_mfx_0.5frac_th01/cwsig_mcz_SENS_lh_1_mfx_0.5frac_th01.mgh --o ./clusters_mcz_SENS_lh_1_mfx_0.5frac_th01/out_mcz_SENS_lh_1_mfx_0.5frac_th01 --ocn ./clusters_mcz_SENS_lh_1_mfx_0.5frac_th01/ocn_mcz_SENS_lh_1_mfx_0.5frac_th01 --olab ./clusters_mcz_SENS_lh_1_mfx_0.5frac_th01/labels/labels_mcz_SENS_lh_1_mfx_0.5frac_th01 (in summary: mri_surfcluster --in x --subject average --hemi lh --surf white --annot aparc.a2005s --csd x1 --csd x2 ... --csd x10 --sum x --csdpdf x --vwsig x.mgh --cwsig x.mgh --o x --ocn x --olab x) When I try to run this I get a segmentation fault. If i take out --csdpdf it will run, but the cluster-wise probabilities in the sum file are all the same (-0.1 for one time I tried it, and something like -17 the other time), and the nrep in the sum file is -2 (or -10 the other time I tried) instead of 1. Does anyone have any idea what I could be doing wrong? I think everything was recently updated (probably because of the cluster size bug?) because I can no longer re-run last week's right hemisphere analysis using the same csd files (tried this for troubleshooting), so maybe I have to start doing something differently with the new version of this command with the left hemisphere? Thank you! -Lauren -- ~ Lauren LaCount Martinos Center for Biomedical Imaging Massachusetts General Hospital CNY 149, 13th St. Charlestown, MA 02129 llaco...@nmr.mgh.harvard.edu ~ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_surfcluster problem
hi, i am having a strange problem with mri_surfcluster. i give it the following command line: mri_surfcluster --in /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh --subject fsaverage --hemi lh --thmin 0.5 --thmax 1.0 --sign pos --minarea 6 --sum /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.clusters/2.ccf.pos.output.sum.txt and i get this result in the summary: # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.26.2.4 2006/07/13 17:50:28 greve Exp $ # $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $ # CreationTime 2007/06/01-19:04:15-GMT # cmdline mri_surfcluster --in /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh --subject fsaverage --hemi lh --thmin 0.5 --thmax 1.0 --sign pos --minarea 6 --sum /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.clusters/2.ccf.pos.output.sum.txt # cwd /disks/gpfs/fmri/emily.permutations/correlation.permutations # sysname Linux # hostname andrew.bsd.uchicago.edu # machine i686 # FixVertexAreaFlag = 1 # # Input /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # SUBJECTS_DIR /home/ecooper/subjects # Minimum Threshold 0.5 # Maximum Threshold 1 # Threshold Signpos # AdjustThreshWhenOneTail 1 # Area Threshold6 mm^2 # Overall max 0.632052 at vertex 5494 # Overall min 0.12689 at vertex 750 # NClusters 2 # Total Cortical Surface Area 70394.7 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZNVtxs 10.6325494 85426.29-50.2 -16.0 -7.2 161181 20.2239300 23.61-31.7 -26.79.968 the problem is that this is just entirely incorrect. when i view the input dataset in tksurfer, it's clear just from scanning over the vertices that 161181 out of 163842 total of them do not have intensity values between .5 and 1 (thmin and thmx), let alone in a giant cluster together. furthermore, when i make a historgram of a text file containing these intensity values, it shows that the majority of them are less than .5, and thus shouldn't be recognized as part of a cluster based on my specifications in the mri_surfcluster command: $breaks [1] -0.10 -0.05 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 [13] 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 $counts [1]10 205 1320 3881 7834 12333 16777 20168 21369 20405 17219 13789 [13] 10453 7479 4897 2988 1599 737 2838114 1 $intensities [1] 0.0012206880 0.0250241086 0.1611308456 0.4737490997 0.9562871547 [6] 1.5054747867 2.0479486334 2.4618840102 2.6084886659 2.4908143211 [11] 2.1019030529 1.6832069921 1.2759854006 0.9129527227 0.5977710233 [16] 0.3647416413 0.1951880470 0.0899647221 0.0345454767 0.0098875746 [21] 0.0017089635 0.0001220688 $density [1] 0.0012206880 0.0250241086 0.1611308456 0.4737490997 0.9562871547 [6] 1.5054747867 2.0479486334 2.4618840102 2.6084886659 2.4908143211 [11] 2.1019030529 1.6832069921 1.2759854006 0.9129527227 0.5977710233 [16] 0.3647416413 0.1951880470 0.0899647221 0.0345454767 0.0098875746 [21] 0.0017089635 0.0001220688 $mids [1] -0.075 -0.025 0.025 0.075 0.125 0.175 0.225 0.275 0.325 0.375 [11] 0.425 0.475 0.525 0.575 0.625 0.675 0.725 0.775 0.825 0.875 [21] 0.925 0.975 any ideas as to what is going wrong here? am i using the thmin and thmax flags wrong? thanks so much, emily ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
