Freesurfer July 2007

freesurfer@nmr.mgh.harvard.edu

61 participants
99 discussions

Matlab and Freesurfer
by Robert Baldwin 09 Mar '08

09 Mar '08

Hello- I am new to Freesurfer and Matlab. I have Matlab 7.4.0 installed on an Intel Mac. I just installed Freesurfer. Now when I start Matlab I get the following warnings: Warning: Name is nonexistent or not a directory: /matlab. In path at 110 In startup at 4 In matlabrc at 255 Warning: Name is non existent or not a directory: /toolbox. In path at 110 In startup at 11 In Matlabrc at 255 I have tried adding the freesurfer folder to these files to the path for matlab, but the error still occurs. Any suggestions on how to get this error to quit? Thanks! -Robert

2 4

Thickness standard deviation map
by Burmicz, Ryszarda 06 Aug '07

06 Aug '07

Hi Freesurfers, I have tried looking this up on the list, but I don't understand exactly what to do in this scenario: I have a group of subjects (all controls). I want to create a surface map of the standard deviations of the thickness values (i.e. to show how the thicknesses vary across subjects). I am not sure what is the easiest way to go about this - can I: 1) simply convert the ?h.thickness files to .asc and calculate the deviations at each vertex (I am under the impression that this is not correct as they need to be registered to a common surface first), then convert back to .thickness and load into tksurfer 2) use mris_preproc then mris_glmfit? I don't necessarily want to calculate any stats, but I wouldn't mind a pretty picture :) If I have 4 groups of 10 subjects each, so if I churn these all through glm_fit will I be able to access separate thickness files for each group? And how can I map standard deviations for each group in this scenario? Many thanks, Rysia

2 1

measurement of cortical thickness
by T. Song 01 Aug '07

01 Aug '07

Hi All: I am trying to measure the cortical thickness of specific ROI. I got a ROI, and are able to save it to a label file. Should I use mris_thickness to measure the thickness? If so, how do I get the thickness file, using mri_label2vol? Thanks in advance! Tao

2 3

negative value for CWP low
by Robert Levy 31 Jul '07

31 Jul '07

Hello, I tried a between group comparison using mri_glmfit, correcting for multiple comparisons using the z-based monte carlo method. This differed from previous similar analyses I had run in that I did not constrain the analysis with a ROI (not in the glmfit, but I did in surfcluster when outputting corrected results). It seems like something is buggy about this output, but it may actually be correct but I just don't know how to interpret it correctly. The negative CWPLow probability values for certain clusters are what seems puzzling. I don't know what a negative p value could possibly mean [ it is beyond impossible for the cluster to be unreal? : ) ], though I'm sure it's not a real p value. These are not significant clusters regardless, but these are impossible statistics and so I was concerned that something was breaking down in the process that would invalidate the other results. The second part of what I tried possibly shows that there is something going wrong in the code, just because it is drastically different when I would only expect a minor difference (and probably in the opposite direction actually). I ran surfcluster with no ROI, and the same cluster became much more significant than it was reported as being before. This seems strange, so I don't know whether the other results in the same unconstrained analysis are correct. I have included some of the surfcluster output (and attached both of the example files), and the environment and commands. Thanks, Rob before correcting for multiple comparisons rh ASvfix 8s BwGroupError5 ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs 1 -3.474 14231 1786.39 6.3 30.8 20.9 2551 2 -1.476 42121 13.60 3.2 -6.6 21.6 27 3 -1.354 106598 3.66 10.3 -9.8 32.2 8 after correcting for multiple comparisons rh ASvfix 8s BwGroupError5 ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs 1 -3.474 14231 1190.92 6.3 30.8 20.9 0.07400 0.07070 0.07740 2551 2 -1.476 42121 9.07 3.2 -6.6 21.6 1.00000 -0.00010 1.00000 27 3 -1.354 106598 2.44 10.3 -9.8 32.2 1.00000 -0.00010 1.00000 8 some of the output when running surfcluster without using an ROI # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs 1 -3.474 14231 2007.09 6.3 30.8 20.9 0.00160 0.00110 0.00210 3998 2 -3.362 125672 356.48 4.5 -25.9 21.3 0.99010 0.98880 0.99140 907 3 -2.749 95384 360.56 8.3 -38.6 -12.7 0.98830 0.98690 0.98970 993 4 -2.572 132812 143.54 26.1 37.5 27.5 1.00000 -0.00010 1.00000 415 5 -2.531 48150 242.73 20.1 -10.2 -24.3 1.00000 -0.00010 1.00000 563 6 -2.373 80761 156.38 2.6 -32.6 29.3 1.00000 -0.00010 1.00000 421 ... -------- freesurfer-Linux-centos4_x86_64-dev-20070729 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/dev FSFAST_HOME /usr/local/freesurfer/dev/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR MNI_DIR /usr/local/freesurfer/dev/mni FSL_DIR /usr/local/freesurfer/dev/fsl hostname: vantz pwd: $SUBJECTS_DIR * # rh: perform analysis* /space/greve/1/users/greve/freesurfer/bin/mri_glmfit \ --really-use-average7 \ --y rh.ASvfix_8s_BwGroupError5.fsfast.mgh \ --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd \ --glmdir BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir \ --surf average7 rh \ --pca \ --C fsgd_and_contrast_files/BwGroupError5.mat \ --fwhm 4.6 *# rh: report clusters found in analysis before threshold* mri_surfcluster \ --really-use-average7 \ --src BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh \ --sum BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.rh.ASvfix_8s_BwGroupError5.fsfast.sum \ --ocp BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.rh.ASvfix_8s_BwGroupError5.fsfast.mgh \ --clabel average7/label/dACC_rACC_final-rh.label \ --hemi rh \ --srcsubj average7 \ --thmin 1.3 \ --thmax infinity * # rh: apply simulation data to get cluster size threshold* mri_surfcluster \ --src BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM01-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM02-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM03-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM04-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM05-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM06-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM07-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM08-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM09-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM10-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM11-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM12-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM13-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM14-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM15-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM16-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM17-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM18-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM19-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM20-BwGroupError5.csd \ --clabel average7/label/dACC_rACC_final-rh.label \ --sum BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_rh.sum \ --ocp BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_rh.mgh \ --thmax infinity *# rh: apply simulation data to get cluster size threshold (no ROI) * mri_surfcluster \ --src BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM01-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM02-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM03-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM04-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM05-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM06-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM07-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM08-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM09-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM10-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM11-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM12-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM13-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM14-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM15-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM16-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM17-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM18-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM19-BwGroupError5.csd \ --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM20-BwGroupError5.csd \ --sum BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_rh_noroi.sum \ --thmax infinity -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2656 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.37 2007/04/20 20:46:05 greve Exp $ # $Id: mrisurf.c,v 1.551 2007/07/24 19:34:25 kteich Exp $ # CreationTime 2007/07/30-02:48:57-GMT # cmdline mri_surfcluster --src BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM01-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM02-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM03-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM04-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM05-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM06-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM07-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM08-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM09-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM10-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM11-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM12-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM13-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM14-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM15-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM16-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM17-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM18-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM19-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM20-BwGroupError5.csd --clabel average7/label/dACC_rACC_final-rh.label --sum BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_rh.sum --ocp BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_rh.mgh --thmax infinity # cwd /autofs/space/ventzl_001/users/SUBJECTS_DIR # sysname Linux # hostname vantz # machine x86_64 # FixVertexAreaFlag = 1 # # Input BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh # Frame Number 0 # srcsubj average7 # hemi rh # surface white # SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR # Minimum Threshold 1.3 # Maximum Threshold inf # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # clabelfile average7/label/dACC_rACC_final-rh.label # clabelinv 0 # CSD thresh 1.300000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast BwGroupError5 # CSD confint 90.000000 # Overall max 0 at vertex 0 # Overall min -3.47414 at vertex 14231 # NClusters 3 # Total Cortical Surface Area 65350.2 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs 1 -3.474 14231 1190.92 6.3 30.8 20.9 0.07400 0.07070 0.07740 2551 2 -1.476 42121 9.07 3.2 -6.6 21.6 1.00000 -0.00010 1.00000 27 3 -1.354 106598 2.44 10.3 -9.8 32.2 1.00000 -0.00010 1.00000 8 # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.37 2007/04/20 20:46:05 greve Exp $ # $Id: mrisurf.c,v 1.551 2007/07/24 19:34:25 kteich Exp $ # CreationTime 2007/07/31-01:27:21-GMT # cmdline mri_surfcluster --src BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM01-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM02-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM03-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM04-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM05-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM06-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM07-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM08-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM09-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM10-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM11-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM12-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM13-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM14-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM15-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM16-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM17-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM18-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM19-BwGroupError5.csd --csd BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM20-BwGroupError5.csd --sum BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_rh_noroi.sum --thmax infinity # cwd /autofs/space/ventzl_001/users/SUBJECTS_DIR # sysname Linux # hostname vantz # machine x86_64 # FixVertexAreaFlag = 1 # # Input BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh # Frame Number 0 # srcsubj average7 # hemi rh # surface white # SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR # Minimum Threshold 1.3 # Maximum Threshold inf # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 1.300000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast BwGroupError5 # CSD confint 90.000000 # Overall max 2.04638 at vertex 151209 # Overall min -3.47414 at vertex 14231 # NClusters 42 # Total Cortical Surface Area 65350.2 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs 1 -3.474 14231 2007.09 6.3 30.8 20.9 0.00160 0.00110 0.00210 3998 2 -3.362 125672 356.48 4.5 -25.9 21.3 0.99010 0.98880 0.99140 907 3 -2.749 95384 360.56 8.3 -38.6 -12.7 0.98830 0.98690 0.98970 993 4 -2.572 132812 143.54 26.1 37.5 27.5 1.00000 -0.00010 1.00000 415 5 -2.531 48150 242.73 20.1 -10.2 -24.3 1.00000 -0.00010 1.00000 563 6 -2.373 80761 156.38 2.6 -32.6 29.3 1.00000 -0.00010 1.00000 421 7 -2.311 122659 135.90 15.2 -14.1 -21.2 1.00000 -0.00010 1.00000 231 8 -2.269 109398 87.32 48.1 24.5 17.9 1.00000 -0.00010 1.00000 194 9 -2.184 2154 66.84 45.7 -5.2 -10.2 1.00000 -0.00010 1.00000 167 10 -2.110 114979 330.99 57.3 -15.5 -16.2 0.99600 0.99520 0.99680 651 11 2.046 151209 59.59 13.4 -69.9 32.6 1.00000 -0.00010 1.00000 258 12 2.013 39130 44.30 36.5 -85.0 1.2 1.00000 -0.00010 1.00000 100 13 -1.920 29514 53.60 7.3 -24.9 -5.4 1.00000 -0.00010 1.00000 118 14 -1.906 64313 65.04 23.9 56.5 4.4 1.00000 -0.00010 1.00000 95 15 -1.896 67841 69.34 27.5 24.1 -1.7 1.00000 -0.00010 1.00000 152 16 -1.850 151774 113.33 35.6 -30.5 20.6 1.00000 -0.00010 1.00000 312 17 -1.842 45709 71.17 18.0 64.5 14.5 1.00000 -0.00010 1.00000 110 18 -1.795 67367 45.74 46.8 9.9 20.1 1.00000 -0.00010 1.00000 134 19 -1.795 124903 51.58 35.2 2.2 -8.0 1.00000 -0.00010 1.00000 142 20 -1.780 44424 148.33 29.8 11.1 6.7 1.00000 -0.00010 1.00000 383 21 -1.769 68495 34.75 4.6 -22.8 8.2 1.00000 -0.00010 1.00000 87 22 -1.700 115699 19.10 7.8 -20.5 34.4 1.00000 -0.00010 1.00000 74 23 -1.655 155650 96.64 0.1 -9.7 -15.1 1.00000 -0.00010 1.00000 156 24 -1.650 32879 51.99 8.6 0.1 48.4 1.00000 -0.00010 1.00000 142 25 -1.644 76413 66.97 25.4 -41.1 30.3 1.00000 -0.00010 1.00000 178 26 -1.621 128318 20.26 37.4 -44.7 -30.8 1.00000 -0.00010 1.00000 37 27 -1.549 116042 31.69 23.6 -8.3 35.9 1.00000 -0.00010 1.00000 118 28 -1.542 141754 31.22 3.0 -9.1 20.3 1.00000 -0.00010 1.00000 83 29 -1.519 103341 24.62 18.7 -45.2 39.3 1.00000 -0.00010 1.00000 53 30 -1.469 92147 37.18 37.9 -25.6 -28.1 1.00000 -0.00010 1.00000 107 31 -1.411 137447 7.46 39.3 -48.3 -30.3 1.00000 -0.00010 1.00000 20 32 -1.407 35200 15.63 9.6 -11.3 31.9 1.00000 -0.00010 1.00000 60 33 -1.397 108543 9.91 6.0 -6.5 40.5 1.00000 -0.00010 1.00000 33 34 -1.387 71979 10.28 17.9 26.9 38.3 1.00000 -0.00010 1.00000 26 35 -1.368 3990 2.61 18.2 -24.8 39.3 1.00000 -0.00010 1.00000 10 36 -1.354 97916 0.71 38.3 -27.5 -29.4 1.00000 -0.00010 1.00000 2 37 -1.353 134902 6.18 11.8 18.7 -0.0 1.00000 -0.00010 1.00000 10 38 -1.330 117096 2.94 54.4 0.0 19.5 1.00000 -0.00010 1.00000 7 39 -1.325 17909 5.02 30.4 -42.2 25.7 1.00000 -0.00010 1.00000 16 40 -1.312 98368 1.37 53.6 -13.0 25.0 1.00000 -0.00010 1.00000 4 41 -1.310 151969 0.90 38.8 -38.7 19.0 1.00000 -0.00010 1.00000 3 42 -1.303 29812 0.23 50.5 21.8 11.4 1.00000 -0.00010 1.00000 1

2 2

Using Par/Rec Data
by Andrew Ellison 31 Jul '07

31 Jul '07

Hi im asking if anyone has experience analyzing data from Par/Rec, whether it be convert them to analyze or run analysis on them as is. I am using par/rec and have gotten stuck, and am simply wondering if others have been able to sucesfully take Par./ Rec. data and use it in freesurfer, and if so how exactly it was done because i am having problems that may stem back to the Par/Rec format. Thanks! -Andy

1 0

Fake thickness map 2
by Inês Souta 31 Jul '07

31 Jul '07

Hello, I was trying to create a cortical thickness map with constant values in order to perform some tests. At first I tried using mris_convert. I converted my thickness file into ascii: mris_convert lh.thickness lh.thickess.asc then I used matlab to change all the values in the last column to 2,0. I tried to convert the ascii file back to surface file by doing mris_convert lh.thicness.asc lh.thickness but I got "Segmentation fault". How can I convert may ascii file into a surface one? After failling to acomplish this, I tried using the save_mgh and load_mgh file, nevertheless I'm not quite sure which input values are needed. Where can I put my fake values in the save_mgh file? And what is "vol"? Thanks, Ines

4 3

Re: Freesurfer Digest, Vol 41, Issue 48
by Sebastian Moeller 31 Jul '07

31 Jul '07

Hi List, On Jul 31, 2007, at 3:58 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 1 > Date: Mon, 30 Jul 2007 12:06:45 -0400 > From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] keyboard issues > To: Troy Mcan <falcon9202(a)hotmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <1185811605.28784.0.camel(a)fishie.nmr.mgh.harvard.edu> > Content-Type: text/plain > > That's a Tcl shell that you can use to issue commands to tkmedit or > tksurfer. If you don't need to do that, you can pretty much ignore it. > It just means you can't launch the app with & to put it in the > background. Since you must be running under X11 anyway the following is a dirty work around (in csh): xterm -e tkmedit -f /full/path/to/your/data/example.mgz & this will run the tcl shell in another window, that gets "dispatched" from your main window without blocking control there. But it feels somewhat hackish... BTW the tcl shell should end once you quit tkmedit/tksurfer hope that helps Sebastian > > On Thu, 2007-07-26 at 11:33 -0600, Troy Mcan wrote: >> Hi, >> >> When I type freesurfer in my terminal, a new shell opens up (with >> full >> keyboard functionality), in which I type tksurfer (with its >> parameters) or tkmedit (with its parameters). When I enter >> tksurfer or >> tkmedit, a new shell opens WITHIN the existing shell (along with the >> GUI interface). I can only use the alphanumeric keys on my keyboard >> whenever this new shell (for tksurfer or tkmedit) opens within the >> existing freesurfer shell. This is particularly irksome because the >> backspace key does not function (and I am forced to cntrl-c to kill >> the entire session). Are there any solutions for this? Thanks! > > -- > Kevin Teich -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

1 0

Ubuntu, Xeon 64bit multi-core, and freesurfer
by Nicolas Cherbuin 30 Jul '07

30 Jul '07

Hi, I am about to order new hardware that will be used to process scans with freesurfer but also for processing with other packages. Has anyone had experience with the combination of Xeon quad-core processors, Ubuntu, and Freesurfer? And if yes are there any issues I should be aware of? To my knowledge one Freesurfer process cannot run in parallel on multiple processors but I intend to process multiple scans simultaneously, hence the selection of a multi-core architecture. If somebody has some experience of the difference between 2.33 GHZ, 2.66 GHZ, and core-duo 3.00 GHZ I would also be interested to hear about it. Thanks Nic ***************************************** Nicolas Cherbuin Centre for Mental Health Research Australian National University Canberra ACT 0200

2 1

left-right comparsion
by Wang, Xin 30 Jul '07

30 Jul '07

Hello, Group Could anyone kindly share the method to compare the thickness between left and right hemispheres (vertex-by-vertex)? Did David C. Van Essen use Freesurfer in his article (NeuroImage 28 (2005) 635 - 662) to do the left-right comparison? Thank you in advance, Xin Wang

2 1

keyboard issues
by Troy Mcan 30 Jul '07

30 Jul '07

Hi,When I type freesurfer in my terminal, a new shell opens up (with full keyboard functionality), in which I type tksurfer (with its parameters) or tkmedit (with its parameters). When I enter tksurfer or tkmedit, a new shell opens WITHIN the existing shell (along with the GUI interface). I can only use the alphanumeric keys on my keyboard whenever this new shell (for tksurfer or tkmedit) opens within the existing freesurfer shell. This is particularly irksome because the backspace key does not function (and I am forced to cntrl-c to kill the entire session). Are there any solutions for this? Thanks! _________________________________________________________________ PC Magazine’s 2007 editors’ choice for best web mail—award-winning Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migrati…

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Freesurfer July 2007