Freesurfer August 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
152 discussions

installation on mac
by Babb, Casey 05 Aug '10

05 Aug '10

I am trying to install freesurfer on Mac OS X 10.6. I get an error message that there is no license file. Does anyone know how to get this license? I have joined the mail group and registered (I thought). Please help! Casey -- Casey Babb Data Analyst Department of Psychiatry Washington University School of Medicine 314-747-3962 The materials in this email are private and may contain protected healthcare information. 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.

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[freesurfer] installation failure
by Glen Lee 05 Aug '10

05 Aug '10

Dear freesurfer experts, I'm running into installation failure and can't quite figure this out (I'm a novice Linux user too). It complains there is no such file or directory when I simply followed the instruction by typing the command below in the /usr/local directory. tar xzvf freesurfer-Linux-centos4-stable-pub-v4.5.0-full.tar.gz Would anybody help me how to resolve this issue? Below is the error message and platform info. Many thanks! -GL ------------------------------------------------------------------------------- glen@ubuntu:/usr/local$ uname -a Linux ubuntu 2.6.32-24-generic-pae #39-Ubuntu SMP Wed Jul 28 07:39:26 UTC 2010 i686 GNU/Linux. tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.ifh: Cannot open: No such file or directory freesurfer/average/surf/ tar: freesurfer/average/surf: Cannot mkdir: No such file or directory freesurfer/average/surf/lh.sphere.reg tar: freesurfer/average/surf/lh.sphere.reg: Cannot open: No such file or directory freesurfer/average/surf/rh.sphere.reg tar: freesurfer/average/surf/rh.sphere.reg: Cannot open: No such file or directory freesurfer/average/lh.atlas2002_simple.gcs tar: freesurfer/average/lh.atlas2002_simple.gcs: Cannot open: No such file or directory freesurfer/average/rigidly_aligned_brain_template.tif tar: freesurfer/average/rigidly_aligned_brain_template.tif: Cannot open: No such file or directory freesurfer/average/3T18yoSchwartzReactN32_as_orig.lst tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.lst: Cannot open: No such file or directory freesurfer/average/711-2B_as_mni_average_305.4dfp.hdr tar: freesurfer/average/711-2B_as_mni_average_305.4dfp.hdr: Cannot open: No such file or directory freesurfer/average/mni305.cor.subfov1.reg tar: freesurfer/average/mni305.cor.subfov1.reg: Cannot open: No such file or directory freesurfer/average/rh.average.CURVATURE.tif tar: freesurfer/average/rh.average.CURVATURE.tif: Cannot open: No such file or directory freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs tar: freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs: Cannot open: No such file or directory freesurfer/average/mni_average_305.4dfp.img.rec tar: freesurfer/average/mni_average_305.4dfp.img.rec: Cannot open: No such file or directory freesurfer/average/rh.average.curvature.filled.buckner40.tif tar: freesurfer/average/rh.average.curvature.filled.buckner40.tif: Cannot open: No such file or directory freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.hdr tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.hdr: Cannot open: No such file or directory freesurfer/average/711-2C_as_mni_average_305.4dfp.img.rec tar: freesurfer/average/711-2C_as_mni_average_305.4dfp.img.rec: Cannot open: No such file or directory freesurfer/average/711-2C_as_mni_average_305.4dfp.mat tar: freesurfer/average/711-2C_as_mni_average_305.4dfp.mat: Cannot open: No such file or directory freesurfer/average/mni_average_305.4dfp.ifh tar: freesurfer/average/mni_average_305.4dfp.ifh: Cannot open: No such file or directory freesurfer/average/mni305.cor.subfov2.reg tar: freesurfer/average/mni305.cor.subfov2.reg: Cannot open: No such file or directory freesurfer/average/mni_average_305.4dfp.img tar: freesurfer/average/mni_average_305.4dfp.img: Cannot open: No such file or directory freesurfer/average/711-2B_as_mni_average_305.4dfp.ifh tar: freesurfer/average/711-2B_as_mni_average_305.4dfp.ifh: Cannot open: No such file or directory freesurfer/average/face.gca tar: freesurfer/average/face.gca: Cannot open: No such file or directory freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs tar: freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs: Cannot open: No such file or directory freesurfer/average/711-2B_as_mni_average_305.4dfp.img.rec tar: freesurfer/average/711-2B_as_mni_average_305.4dfp.img.rec: Cannot open: No such file or directory freesurfer/average/rh.average.tif tar: freesurfer/average/rh.average.tif: Cannot open: No such file or directory freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs tar: freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs: Cannot open: No such file or directory freesurfer/average/711-2C_as_mni_average_305.4dfp.img tar: freesurfer/average/711-2C_as_mni_average_305.4dfp.img: Cannot open: No such file or directory freesurfer/average/mni152.register.dat tar: freesurfer/average/mni152.register.dat: Cannot open: No such file or directory freesurfer/average/RB_all_2007-08-08.gca tar: freesurfer/average/RB_all_2007-08-08.gca: Cannot open: No such file or directory freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img tar: freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img: Cannot open: No such file or directory freesurfer/average/mni305.cor.readme tar: freesurfer/average/mni305.cor.readme: Cannot open: No such file or directory freesurfer/average/lh.atlas2005_simple.gcs tar: freesurfer/average/lh.atlas2005_simple.gcs: Cannot open: No such file or directory freesurfer/average/711-2C_as_mni_average_305.4dfp.ifh tar: freesurfer/average/711-2C_as_mni_average_305.4dfp.ifh: Cannot open: No such file or directory freesurfer/average/colortable_desikan_killiany.txt tar: freesurfer/average/colortable_desikan_killiany.txt: Cannot open: No such file or directory freesurfer/average/rh_trans_toSulc.gcs tar: freesurfer/average/rh_trans_toSulc.gcs: Cannot open: No such file or directory freesurfer/average/lh.average.curvature.filled.buckner40.tif tar: freesurfer/average/lh.average.curvature.filled.buckner40.tif: Cannot open: No such file or directory freesurfer/ASegStatsLUT.txt tar: freesurfer/ASegStatsLUT.txt: Cannot open: No such file or directory freesurfer/fsafd/ tar: freesurfer/fsafd: Cannot mkdir: No such file or directory freesurfer/fsafd/lh.SurfRegistrationResidualVar.adf tar: freesurfer/fsafd/lh.SurfRegistrationResidualVar.adf: Cannot open: No such file or directory freesurfer/fsafd/lh.ThicknessMatrix.mgh tar: freesurfer/fsafd/lh.ThicknessMatrix.mgh: Cannot open: No such file or directory freesurfer/fsafd/rh.CorticalLabelingPercentArea_txt.adf tar: freesurfer/fsafd/rh.CorticalLabelingPercentArea_txt.adf: Cannot open: No such file or directory freesurfer/fsafd/TalairachingProbas.adf tar: freesurfer/fsafd/TalairachingProbas.adf: Cannot open: No such file or directory freesurfer/fsafd/lh.CorpusCallosumCutDice.adf tar: freesurfer/fsafd/lh.CorpusCallosumCutDice.adf: Cannot open: No such file or directory freesurfer/fsafd/PonsCutDice.adf tar: freesurfer/fsafd/PonsCutDice.adf: Cannot open: No such file or directory freesurfer/fsafd/lh.CorticalLabelingPercentArea_txt.adf tar: freesurfer/fsafd/lh.CorticalLabelingPercentArea_txt.adf: Cannot open: No such file or directory freesurfer/fsafd/rh.CorpusCallosumCutDice.adf tar: freesurfer/fsafd/rh.CorpusCallosumCutDice.adf: Cannot open: No such file or directory freesurfer/fsafd/WMsegmentationDice.adf tar: freesurfer/fsafd/WMsegmentationDice.adf: Cannot open: No such file or directory freesurfer/fsafd/TalairachingMean.adf tar: freesurfer/fsafd/TalairachingMean.adf: Cannot open: No such file or directory freesurfer/fsafd/RibbonPlacementDice.adf tar: freesurfer/fsafd/RibbonPlacementDice.adf: Cannot open: No such file or directory freesurfer/fsafd/SubcorticalLabelingPercentVol.adf tar: freesurfer/fsafd/SubcorticalLabelingPercentVol.adf: Cannot open: No such file or directory freesurfer/fsafd/lh.EV90.mgh tar: freesurfer/fsafd/lh.EV90.mgh: Cannot open: No such file or directory freesurfer/fsafd/TalairachingCovariance.adf tar: freesurfer/fsafd/TalairachingCovariance.adf: Cannot open: No such file or directory freesurfer/matlab/ tar: freesurfer/matlab: Cannot mkdir: No such file or directory freesurfer/matlab/subcortical_labeling_table.m tar: freesurfer/matlab/subcortical_labeling_table.m: Cannot open: No such file or directory freesurfer/matlab/save_mgh.m tar: freesurfer/matlab/save_mgh.m: Cannot open: No such file or directory freesurfer/matlab/barsegstats.m tar: freesurfer/matlab/barsegstats.m: Cannot open: No such file or directory freesurfer/matlab/cc_cut_dir_afd.m tar: freesurfer/matlab/cc_cut_dir_afd.m: Cannot open: No such file or directory freesurfer/matlab/stringunique.m tar: freesurfer/matlab/stringunique.m: Cannot open: No such file or directory freesurfer/matlab/wm_seg_afd.m tar: freesurfer/matlab/wm_seg_afd.m: Cannot open: No such file or directory freesurfer/matlab/read_curv.m tar: freesurfer/matlab/read_curv.m: Cannot open: No such file or directory freesurfer/matlab/surf_registration_stats.m tar: freesurfer/matlab/surf_registration_stats.m: Cannot open: No such file or directory freesurfer/matlab/fread3.m tar: freesurfer/matlab/fread3.m: Cannot open: No such file or directory freesurfer/matlab/surf_registration_table.m tar: freesurfer/matlab/surf_registration_table.m: Cannot open: No such file or directory freesurfer/matlab/MRIisBHDR.m tar: freesurfer/matlab/MRIisBHDR.m: Cannot open: No such file or directory freesurfer/matlab/pons_cut_afd.m tar: freesurfer/matlab/pons_cut_afd.m: Cannot open: No such file or directory freesurfer/matlab/ssbloch.m tar: freesurfer/matlab/ssbloch.m: Cannot open: No such file or directory freesurfer/matlab/vox2ras_ksolve.m tar: freesurfer/matlab/vox2ras_ksolve.m: Cannot open: No such file or directory freesurfer/matlab/SearchProjectionOnPial.m tar: freesurfer/matlab/SearchProjectionOnPial.m: Cannot open: No such file or directory freesurfer/matlab/read_csf_patch.m tar: freesurfer/matlab/read_csf_patch.m: Cannot open: No such file or directory freesurfer/matlab/MRIextractImage.m tar: freesurfer/matlab/MRIextractImage.m: Cannot open: No such file or directory freesurfer/matlab/read_surf.m tar: freesurfer/matlab/read_surf.m: Cannot open: No such file or directory freesurfer/matlab/fwrite3.m tar: freesurfer/matlab/fwrite3.m: Cannot open: No such file or directory freesurfer/matlab/mesh_adjacency.m tar: freesurfer/matlab/mesh_adjacency.m: Cannot open: No such file or directory freesurfer/matlab/save_cor.m tar: freesurfer/matlab/save_cor.m: Cannot open: No such file or directory freesurfer/matlab/bmm_mcvhist.m tar: freesurfer/matlab/bmm_mcvhist.m: Cannot open: No such file or directory freesurfer/matlab/talairaching_dir_afd.m tar: freesurfer/matlab/talairaching_dir_afd.m: Cannot open: No such file or directory freesurfer/matlab/read_genesis_image.m tar: freesurfer/matlab/read_genesis_image.m: Cannot open: No such file or directory freesurfer/matlab/load_csd.m tar: freesurfer/matlab/load_csd.m: Cannot open: No such file or directory freesurfer/matlab/make_outer_surface.m tar: freesurfer/matlab/make_outer_surface.m: Cannot open: No such file or directory freesurfer/matlab/load_nifti.m tar: freesurfer/matlab/load_nifti.m: Cannot open: No such file or directory freesurfer/matlab/read_label.m tar: freesurfer/matlab/read_label.m: Cannot open: No such file or directory freesurfer/matlab/cc_cut_table.m tar: freesurfer/matlab/cc_cut_table.m: Cannot open: No such file or directory freesurfer/matlab/freesurfer_fread3.m tar: freesurfer/matlab/freesurfer_fread3.m: Cannot open: No such file or directory freesurfer/matlab/vox2ras_rsolveAA.m tar: freesurfer/matlab/vox2ras_rsolveAA.m: Cannot open: No such file or directory freesurfer/matlab/MRIisMGH.m tar: freesurfer/matlab/MRIisMGH.m: Cannot open: No such file or directory freesurfer/matlab/angles2rotmat.m tar: freesurfer/matlab/angles2rotmat.m: Cannot open: No such file or directory freesurfer/matlab/talairaching_stats.m tar: freesurfer/matlab/talairaching_stats.m: Cannot open: No such file or directory freesurfer/matlab/wm_seg_table.m tar: freesurfer/matlab/wm_seg_table.m: Cannot open: No such file or directory freesurfer/matlab/write_curv.m tar: freesurfer/matlab/write_curv.m: Cannot open: No such file or directory freesurfer/matlab/getFaceArea.m tar: freesurfer/matlab/getFaceArea.m: Cannot open: No such file or directory freesurfer/matlab/bmmcost.m tar: freesurfer/matlab/bmmcost.m: Cannot open: No such file or directory freesurfer/matlab/MakeGeodesicOuterROI.m tar: freesurfer/matlab/MakeGeodesicOuterROI.m: Cannot open: No such file or directory freesurfer/matlab/ssblochgrad.m tar: freesurfer/matlab/ssblochgrad.m: Cannot open: No such file or directory freesurfer/matlab/MRIwrite.m tar: freesurfer/matlab/MRIwrite.m: Cannot open: No such file or directory freesurfer/matlab/mri_zcdf.m tar: freesurfer/matlab/mri_zcdf.m: Cannot open: No such file or directory freesurfer/matlab/strlen.m tar: freesurfer/matlab/strlen.m: Cannot open: No such file or directory freesurfer/matlab/mksubfov.m tar: freesurfer/matlab/mksubfov.m: Cannot open: No such file or directory freesurfer/matlab/find_corresponding_center_FSformat.m tar: freesurfer/matlab/find_corresponding_center_FSformat.m: Cannot open: No such file or directory freesurfer/matlab/mri_kurtosis.m tar: freesurfer/matlab/mri_kurtosis.m: Cannot open: No such file or directory freesurfer/matlab/write_path.m tar: freesurfer/matlab/write_path.m: Cannot open: No such file or directory freesurfer/matlab/cc_cut_afd.m tar: freesurfer/matlab/cc_cut_afd.m: Cannot open: No such file or directory freesurfer/matlab/read_asc.m tar: freesurfer/matlab/read_asc.m: Cannot open: No such file or directory freesurfer/matlab/convert_unwarp_resample.m tar: freesurfer/matlab/convert_unwarp_resample.m: Cannot open: No such file or directory freesurfer/matlab/dijk.m tar: freesurfer/matlab/dijk.m: Cannot open: No such file or directory freesurfer/matlab/write_analyze_hdr.m tar: freesurfer/matlab/write_analyze_hdr.m: Cannot open: No such file or directory freesurfer/matlab/load_mgh2.m tar: freesurfer/matlab/load_mgh2.m: Cannot open: No such file or directory freesurfer/matlab/cortical_labeling_dir_afd_txt.m tar: freesurfer/matlab/cortical_labeling_dir_afd_txt.m: Cannot open: No such file or directory freesurfer/matlab/load_mgh.m tar: freesurfer/matlab/load_mgh.m: Cannot open: No such file or directory freesurfer/matlab/ribbon_table.m tar: freesurfer/matlab/ribbon_table.m: Cannot open: No such file or directory freesurfer/matlab/redo_lgi.m tar: freesurfer/matlab/redo_lgi.m: Cannot open: No such file or directory freesurfer/matlab/compute_lgi.m tar: freesurfer/matlab/compute_lgi.m: Cannot open: No such file or directory freesurfer/matlab/subcortical_labeling_dir_afd.m tar: freesurfer/matlab/subcortical_labeling_dir_afd.m: Cannot open: No such file or directory freesurfer/matlab/read_all.m tar: freesurfer/matlab/read_all.m: Cannot open: No such file or directory freesurfer/matlab/vox2ras_tkreg.m tar: freesurfer/matlab/vox2ras_tkreg.m: Cannot open: No such file or directory freesurfer/matlab/MRIseg2labelxyz.m tar: freesurfer/matlab/MRIseg2labelxyz.m: Cannot open: No such file or directory freesurfer/matlab/read_wfile.m tar: freesurfer/matlab/read_wfile.m: Cannot open: No such file or directory freesurfer/matlab/getMeshArea.m tar: freesurfer/matlab/getMeshArea.m: Cannot open: No such file or directory freesurfer/matlab/dtimatrix.m tar: freesurfer/matlab/dtimatrix.m: Cannot open: No such file or directory freesurfer/matlab/talairaching_afd.m tar: freesurfer/matlab/talairaching_afd.m: Cannot open: No such file or directory freesurfer/matlab/isVertexInRadius.m tar: freesurfer/matlab/isVertexInRadius.m: Cannot open: No such file or directory freesurfer/matlab/cortical_labeling_table.m tar: freesurfer/matlab/cortical_labeling_table.m: Cannot open: No such file or directory freesurfer/matlab/read_ascii_curv.m tar: freesurfer/matlab/read_ascii_curv.m: Cannot open: No such file or directory freesurfer/matlab/read_patch.m tar: freesurfer/matlab/read_patch.m: Cannot open: No such file or directory freesurfer/matlab/pons_cut_table.m tar: freesurfer/matlab/pons_cut_table.m: Cannot open: No such file or directory freesurfer/matlab/read_siemens_image.m tar: freesurfer/matlab/read_siemens_image.m: Cannot open: No such file or directory freesurfer/matlab/MRIread.m tar: freesurfer/matlab/MRIread.m: Cannot open: No such file or directory freesurfer/matlab/mesh_vertex_nearest.m tar: freesurfer/matlab/mesh_vertex_nearest.m: Cannot open: No such file or directory freesurfer/matlab/sampleSize.m tar: freesurfer/matlab/sampleSize.m: Cannot open: No such file or directory freesurfer/matlab/mri_cdf2p.m tar: freesurfer/matlab/mri_cdf2p.m: Cannot open: No such file or directory freesurfer/matlab/unwarp_scanners_table.m tar: freesurfer/matlab/unwarp_scanners_table.m: Cannot open: No such file or directory freesurfer/matlab/read_cor.m tar: freesurfer/matlab/read_cor.m: Cannot open: No such file or directory freesurfer/matlab/read_smooth_eccen.m tar: freesurfer/matlab/read_smooth_eccen.m: Cannot open: No such file or directory freesurfer/matlab/llbmm.m tar: freesurfer/matlab/llbmm.m: Cannot open: No such file or directory freesurfer/matlab/MRIsegReg.m tar: freesurfer/matlab/MRIsegReg.m: Cannot open: No such file or directory freesurfer/matlab/load_dicom_fl.m tar: freesurfer/matlab/load_dicom_fl.m: Cannot open: No such file or directory freesurfer/matlab/isdicomfile.m tar: freesurfer/matlab/isdicomfile.m: Cannot open: No such file or directory freesurfer/matlab/load_gca.m tar: freesurfer/matlab/load_gca.m: Cannot open: No such file or directory freesurfer/matlab/load_segstats.m tar: freesurfer/matlab/load_segstats.m: Cannot open: No such file or directory freesurfer/matlab/vox2ras_1to0.m tar: freesurfer/matlab/vox2ras_1to0.m: Cannot open: No such file or directory freesurfer/matlab/labelic.m tar: freesurfer/matlab/labelic.m: Cannot open: No such file or directory freesurfer/matlab/ribbon_afd.m tar: freesurfer/matlab/ribbon_afd.m: Cannot open: No such file or directory freesurfer/matlab/vox2ras_rsolve.m tar: freesurfer/matlab/vox2ras_rsolve.m: Cannot open: No such file or directory freesurfer/matlab/unwarp_init_globals.m tar: freesurfer/matlab/unwarp_init_globals.m: Cannot open: No such file or directory freesurfer/matlab/convert_fieldsign.m tar: freesurfer/matlab/convert_fieldsign.m: Cannot open: No such file or directory freesurfer/matlab/PropagateGeodesic.m tar: freesurfer/matlab/PropagateGeodesic.m: Cannot open: No such file or directory freesurfer/matlab/load_cor.m tar: freesurfer/matlab/load_cor.m: Cannot open: No such file or directory freesurfer/matlab/cortical_labeling_afd_txt.m tar: freesurfer/matlab/cortical_labeling_afd_txt.m: Cannot open: No such file or directory freesurfer/matlab/wm_seg_dir_afd.m tar: freesurfer/matlab/wm_seg_dir_afd.m: Cannot open: No such file or directory freesurfer/matlab/read_type.m tar: freesurfer/matlab/read_type.m: Cannot open: No such file or directory freesurfer/matlab/ComputeGeodesicProjection.m tar: freesurfer/matlab/ComputeGeodesicProjection.m: Cannot open: No such file or directory freesurfer/matlab/getFacesArea.m tar: freesurfer/matlab/getFacesArea.m: Cannot open: No such file or directory freesurfer/matlab/save_mgh2.m tar: freesurfer/matlab/save_mgh2.m: Cannot open: No such file or directory freesurfer/matlab/read_normals.m tar: freesurfer/matlab/read_normals.m: Cannot open: No such file or directory freesurfer/matlab/MRIeuler2Mdc.m tar: freesurfer/matlab/MRIeuler2Mdc.m: Cannot open: No such file or directory freesurfer/matlab/juelichmat2mat.m tar: freesurfer/matlab/juelichmat2mat.m: Cannot open: No such file or directory freesurfer/matlab/surf_registration_afd.m tar: freesurfer/matlab/surf_registration_afd.m: Cannot open: No such file or directory freesurfer/matlab/read_eccen_patch.m tar: freesurfer/matlab/read_eccen_patch.m: Cannot open: No such file or directory freesurfer/matlab/dtifa.m tar: freesurfer/matlab/dtifa.m: Cannot open: No such file or directory freesurfer/matlab/pred2path.m tar: freesurfer/matlab/pred2path.m: Cannot open: No such file or directory freesurfer/matlab/unwarp_resample.m tar: freesurfer/matlab/unwarp_resample.m: Cannot open: No such file or directory freesurfer/matlab/load_ima.m tar: freesurfer/matlab/load_ima.m: Cannot open: No such file or directory freesurfer/matlab/read_ROIlabel.m tar: freesurfer/matlab/read_ROIlabel.m: Cannot open: No such file or directory freesurfer/matlab/getVerticesAndFacesInSphere.m tar: freesurfer/matlab/getVerticesAndFacesInSphere.m: Cannot open: No such file or directory freesurfer/matlab/write_label.m tar: freesurfer/matlab/write_label.m: Cannot open: No such file or directory freesurfer/matlab/randb.m tar: freesurfer/matlab/randb.m: Cannot open: No such file or directory freesurfer/matlab/bmmroc.m tar: freesurfer/matlab/bmmroc.m: Cannot open: No such file or directory freesurfer/matlab/peakfinder.m tar: freesurfer/matlab/peakfinder.m: Cannot open: No such file or directory freesurfer/matlab/write_ascii_curv.m tar: freesurfer/matlab/write_ascii_curv.m: Cannot open: No such file or directory freesurfer/matlab/read_siemens_header.m tar: freesurfer/matlab/read_siemens_header.m: Cannot open: No such file or directory freesurfer/matlab/write_lgi.m tar: freesurfer/matlab/write_lgi.m: Cannot open: No such file or directory freesurfer/matlab/talairaching_table.m tar: freesurfer/matlab/talairaching_table.m: Cannot open: No such file or directory freesurfer/matlab/load_dicom_series.m tar: freesurfer/matlab/load_dicom_series.m: Cannot open: No such file or directory freesurfer/matlab/read_annotation.m tar: freesurfer/matlab/read_annotation.m: Cannot open: No such file or directory freesurfer/matlab/rotmat2angles.m tar: freesurfer/matlab/rotmat2angles.m: Cannot open: No such file or directory freesurfer/matlab/pons_cut_dir_afd.m tar: freesurfer/matlab/pons_cut_dir_afd.m: Cannot open: No such file or directory freesurfer/matlab/MRIvol2vol.m tar: freesurfer/matlab/MRIvol2vol.m: Cannot open: No such file or directory freesurfer/matlab/make_roi_paths.m tar: freesurfer/matlab/make_roi_paths.m: Cannot open: No such file or directory freesurfer/matlab/MRIfspec.m tar: freesurfer/matlab/MRIfspec.m: Cannot open: No such file or directory freesurfer/matlab/load_analyze_hdr.m tar: freesurfer/matlab/load_analyze_hdr.m: Cannot open: No such file or directory freesurfer/matlab/vox2rasToQform.m tar: freesurfer/matlab/vox2rasToQform.m: Cannot open: No such file or directory freesurfer/matlab/read_freq_patch.m tar: freesurfer/matlab/read_freq_patch.m: Cannot open: No such file or directory freesurfer/matlab/xfm_read.m tar: freesurfer/matlab/xfm_read.m: Cannot open: No such file or directory freesurfer/matlab/save_nifti.m tar: freesurfer/matlab/save_nifti.m: Cannot open: No such file or directory freesurfer/matlab/ribbon_dir_afd.m tar: freesurfer/matlab/ribbon_dir_afd.m: Cannot open: No such file or directory freesurfer/matlab/freesurfer_read_surf.m tar: freesurfer/matlab/freesurfer_read_surf.m: Cannot open: No such file or directory freesurfer/matlab/read_moviebyu.m tar: freesurfer/matlab/read_moviebyu.m: Cannot open: No such file or directory freesurfer/matlab/write_wfile.m tar: freesurfer/matlab/write_wfile.m: Cannot open: No such file or directory freesurfer/matlab/load_nifti_hdr.m tar: freesurfer/matlab/load_nifti_hdr.m: Cannot open: No such file or directory freesurfer/matlab/lta_read.m tar: freesurfer/matlab/lta_read.m: Cannot open: No such file or directory freesurfer/matlab/fisher_twoclass.m tar: freesurfer/matlab/fisher_twoclass.m: Cannot open: No such file or directory freesurfer/matlab/remove_spaces.m tar: freesurfer/matlab/remove_spaces.m: Cannot open: No such file or directory freesurfer/matlab/transVertexToNormalAxisBase.m tar: freesurfer/matlab/transVertexToNormalAxisBase.m: Cannot open: No such file or directory freesurfer/matlab/getOrthogonalVector.m tar: freesurfer/matlab/getOrthogonalVector.m: Cannot open: No such file or directory freesurfer/matlab/MRImdc2euler.m tar: freesurfer/matlab/MRImdc2euler.m: Cannot open: No such file or directory freesurfer/matlab/createMeshFacesOfVertex.m tar: freesurfer/matlab/createMeshFacesOfVertex.m: Cannot open: No such file or directory freesurfer/matlab/readrec.m tar: freesurfer/matlab/readrec.m: Cannot open: No such file or directory freesurfer/matlab/reorganize_verticeslist.m tar: freesurfer/matlab/reorganize_verticeslist.m: Cannot open: No such file or directory freesurfer/matlab/isInGeodesicROI.m tar: freesurfer/matlab/isInGeodesicROI.m: Cannot open: No such file or directory freesurfer/matlab/vox2ras_0to1.m tar: freesurfer/matlab/vox2ras_0to1.m: Cannot open: No such file or directory freesurfer/matlab/read_fscolorlut.m tar: freesurfer/matlab/read_fscolorlut.m: Cannot open: No such file or directory freesurfer/matlab/subcortical_labeling_afd.m tar: freesurfer/matlab/subcortical_labeling_afd.m: Cannot open: No such file or directory freesurfer/matlab/read_label_old.m tar: freesurfer/matlab/read_label_old.m: Cannot open: No such file or directory freesurfer/matlab/load_analyze.m tar: freesurfer/matlab/load_analyze.m: Cannot open: No such file or directory freesurfer/matlab/vox2ras_dfmeas.m tar: freesurfer/matlab/vox2ras_dfmeas.m: Cannot open: No such file or directory freesurfer/matlab/read_vf.m tar: freesurfer/matlab/read_vf.m: Cannot open: No such file or directory freesurfer/matlab/MRIvote.m tar: freesurfer/matlab/MRIvote.m: Cannot open: No such file or directory freesurfer/matlab/bmm_mcvect.m tar: freesurfer/matlab/bmm_mcvect.m: Cannot open: No such file or directory freesurfer/build-stamp.txt tar: freesurfer/build-stamp.txt: Cannot open: No such file or directory freesurfer/FreeSurferEnv.csh tar: freesurfer/FreeSurferEnv.csh: Cannot open: No such file or directory tar: Exiting with failure status due to previous errors ysl@ubuntu:/usr/local$ ls bin

1 0

change overlay color
by Michael Scheel 05 Aug '10

05 Aug '10

Hi FS experts, I want to change the visualization of some overlay data in tkmedit. Instead of the Heat (Red-Yellow) Color-Scale I'd like to use a Green-Red or Rainbow Color Scale. Is there a way to achieve this? Do I need to create a respective LUT and where do I have to put it. thanks, michael

2 1

averaging subject error
by rsachdev＠nmr.mgh.harvard.edu 05 Aug '10

05 Aug '10

I am trying to average subjects and I don't know why I am getting this error. Is it because limitations on user account or is it something else. output subject: average mri_add_xform_to_header -c auto /space/huygens/1/users/dgow/subjects//average/mri/mni305.cor.mgz /space/huygens/1/users/dgow/subjects//average/mri/mni305.cor.mgz sh: /space/huygens/1/users/dgow/subjects//average/mri/mni305.cor.mgz: Permission denied ERROR: make_average_surface

2 1

creation of special image...
by Gonzalo Rojas Costa 05 Aug '10

05 Aug '10

Hi: How can I create an image such as the "Be happy" one that appeared in the last slide of "Surface-based Analysis: Intersubject Registration and Smoothing" PPT?... Sincerely, Gonzalo Rojas Costa

6 7

label 28 error
by Ilana Hairston 05 Aug '10

05 Aug '10

Hi there, We've been getting this label 28 error more often recently, and found that by adding '-no-ca-align' to the end of recon-all command, the error went away and visually the brain looks OK (at least first pass). Does this make sense? thanks ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Sentimental Insomnia and Nostalgia Disorders Sciences ********************

2 1

qdec GLMDesign Problem
by Bruehl, Hannah 05 Aug '10

05 Aug '10

Hi there, I am having a problem with qdec when trying to rerun analyses (meaning this worked before), I get the following error message: Data table loading completed successfully. SUBJECTS_DIR is '/Users/bruehh01/Borderline_2' ERROR: QdecGlmDesign::Create: could not create directory /Users/bruehh01/Borderline_2/qdec/Untitled Since I haven't changed anything since I last ran analyses, I don't understand what the problem is. Any suggestions? Thanks and regards, Hannah ...................................................................................................................................... Dr. Hannah Brühl Freie Universität Berlin Institut für Psychologie Arbeitsbereich Emotionspsychologie und affektive Neurowissenschaft Habelschwerdter Allee 45 — Raum JK 25/222h 14195 Berlin Tel.: +49 (0)30 838 564 72 ......................................................................................................................................

2 1

keyboard problem in freesurfer
by Katie Bettencourt 05 Aug '10

05 Aug '10

I am having a problem others have had before, but that I can't seem to see any resolution to in the archives. When I open tksurfer I can't use my keyboard to input anything. I don't get any errors, it just doesn't let me type or delete anything, making it next to impossible to use. I'm running Freesurfer4.5.0 on linux - Red Hat 4.1.2-48 (Centos 5.5) I checked my .cshrc file and couldn't find any issues there. Any other help please? Katie

4 11

converting analyse roi to fs
by Prapti Gautam 05 Aug '10

05 Aug '10

Dear FreeSurfers, I am trying to convert an Analyze object map (saved as a set of .img /.hdr files) where I've traced ROIs so that I can load them as labels or overlays in FreeSurfer. Has anybody done this before? What would be the best way to proceed? Thanks, Prapti

2 1

Re: [Freesurfer] Which version should I download?
by Matt Glasser 04 Aug '10

04 Aug '10

The CentOS 4 download works with Ubuntu. Just make sure to get the correct 32 or 64 bit version that matches your operating system. Use uname -m to tell. Peace, Matt. _____ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Glen Lee Sent: Wednesday, August 04, 2010 3:07 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Which version should I download? Hello, I just installed a recent version of Ubuntu to run the freesurfer and I know nothing about Linux yet. But I'm seeing that the download link only specifies CenOS 4. Does it mean that Ubuntu is not compatible with Freesurfer? Any help would be appreciated. Thanks,

1 0

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Freesurfer August 2010