Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

hippocampus volume
by Zhangyuanchao 06 Aug '10

06 Aug '10

Hi, expert, I would like to measure the volume of hippocampus, is there any way i can obtain the raw volume of hippocampus for each subject? How can I obtain it? In fact, in the folder stats, there is a file named aseg.stat, where I can find a line which contains "ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange", I wonder whether the corresponding volume of the Left-hippocampus is what I want. I mean the volume of the left hippocampus. Thanks a lot ! Yuanchao Zhang

3 6

eTIV and aseg.stats
by Yolanda Vives 06 Aug '10

06 Aug '10

Hi all, I have read about the eTIV and how to obtain it in the paper from Buckner et al. but I have a question related to the implementation of it in Freesurfer, just to be sure that I have correctly understood it. Regarding the volumes of the subcortical structures presented in "aseg.stats", are these volumes measured in atlas space and therefore, it is not necessary to normalize them to the TIV or should we apply a normalization method (i.e. covariance method) using the eTIV (ICV from aseg.stats)? Thank you for your time, Yolanda

2 1

Command line to map volume data to surface data
by Xinian Zuo 06 Aug '10

06 Aug '10

Dear surfers, Hi, I used freeesurfer to visualize my volume from FEAT outputs on the surface in the way: tksurfer fsaverage rh inflated_pre -overlay data.nii.gz -mni152reg , then save surface overlay as a mgh file. My question is, how can I get the identical mgh data by using a command line without launching the tksurfer gui? I found there is a command mri_vol2surf, but not sure about these default settings in tksurfer gui. Really appreciate it if some know and like to give your suggestions. -- Xinian Zuo, Ph.D Associate Research Scientist Institute for Pediatric Neuroscience NYU Child Study Center 215 Lexington Ave., 14th Floor New York, NY 10016 Phone: (212) 263 2485

3 6

Sulci
by Oya, Hiroyuki 05 Aug '10

05 Aug '10

Dear All, Looking at pial surface, sulci looks wider than those of the actual brain. Is there any parameter to be tuned? Does watershed threshold have any effect on the pial surface estimation ? Hiroyuki

2 1

skull strip on raw data
by Zhang, Yuning 05 Aug '10

05 Aug '10

hi,experts, is there a way to use -skullstrip of freesurfer on my raw data (.mgz format) without any correction,i.e , intensity correction , normalization ? thanks a lot yuning

2 1

aparc.anot of average contains 35 ROIs
by wanlin 05 Aug '10

05 Aug '10

HI, I am using freesurfer4.5.0. After processed using recon-all, the ?aparc.annot of each subject contains 36 ROIs (including insula), However the ?aparc.annot of average subject ( make_average_subject) only has 35 ROIs(without insula). Did i do anything wrong or it is a bug? Thanks.

2 2

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.

1 0

[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

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