Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

R: Re: mris resample: Command not found. This error is permanent after new patch download
by stdp82＠virgilio.it 07 Jun '13

07 Jun '13

[iMac-di-Stefano:/Applications/freesurfer/bin] Stefano% ls -ltotal 4780656-rwxr-xr-x 1 root wheel 60776 Jan 29 00:20 #trac-all#-rwxr-xr-x 1 root wheel 27224 May 14 17:07 4dfptoanalyze-rwxr-xr-x 1 root wheel 12925 May 14 17:07 LongQdecTable.py-rwxr-xr-x@ 1 Stefano wheel 7581520 Jun 6 23:24 Unknown-rwxr-xr-x 1 root wheel 936 May 14 17:07 UpdateNeeded-rwxr-xr-x 1 root wheel 22628 May 14 17:07 analyzeto4dfp-rwxr-xr-x 1 root wheel 7660 May 14 17:07 aparc2feat-rwxr-xr-x 1 root wheel 15795 May 14 17:07 aparcstats2table-rwxr-xr-x 1 root wheel 4657 May 14 17:07 aparcstatsdiff-rwxr-xr-x 1 root wheel 7075840 May 14 17:07 applyMorph-rwxr-xr-x 1 root wheel 8927 May 14 17:07 aseg2feat-rwxr-xr-x 1 root wheel 23702 May 14 17:07 asegstats2table-rwxr-xr-x 1 root wheel 3450 May 14 17:07 asegstatsdiff-rwxr-xr-x 1 root wheel 2087 May 14 17:07 avi2talxfm-rwxr-xr-x 1 root wheel 2209 May 14 17:07 batchjobs-rwxr-xr-x 1 root wheel 5756 May 14 17:07 bblabel-rwxr-xr-x 1 root wheel 24890 May 14 17:07 bbregister-rwxr-xr-x 1 root wheel 14696 May 14 17:07 bedpostx_mgh-rwxr-xr-x 1 root wheel 13268 May 14 17:07 bet.fsl-rwxr-xr-x 1 root wheel 7144 May 14 17:07 beta2sxa-rwxr-xr-x 1 root wheel 7710 May 14 17:07 biasfield-rwxr-xr-x 1 root wheel 417 May 14 17:07 brec-rwxr-xr-x 1 root wheel 973 May 14 17:07 brec.awk-rwxr-xr-x 1 root wheel 10814 May 14 17:07 browse-minc-header.tcl-rwxr-xr-x 1 root wheel 2201 May 14 17:07 bugr-rwxr-xr-x 1 root wheel 1245 May 14 17:07 build_desikan_killiany_gcs.csh-rwxr-xr-x 1 root wheel 75584 May 14 17:07 check_siemens_dir-rwxr-xr-x 1 root wheel 2496 May 14 17:07 check_subject-rwxr-xr-x 1 root wheel 1113 May 14 17:07 clear_fs_env.csh-rwxr-xr-x 1 root wheel 4458 May 14 17:07 compute_interrater_variability.csh-rwxr-xr-x 1 root wheel 4490 May 14 17:07 compute_label_volumes.csh-rwxr-xr-x 1 root wheel 214788 May 14 17:07 compute_vox2vox-rwxr-xr-x 1 root wheel 6389728 May 14 17:07 connectgraph-rwxr-xr-x 1 root wheel 6776500 May 14 17:07 conv1d_test-rwxr-xr-x 1 root wheel 7133948 May 14 17:07 conv1d_test_cuda-rwxr-xr-x 1 root wheel 6794716 May 14 17:07 convgaussian_test-rwxr-xr-x 1 root wheel 7119796 May 14 17:07 convgaussian_test_cuda-rwxr-xr-x 1 root wheel 1010 May 14 17:07 cor_to_minc-rwxr-xr-x 1 root wheel 4378 May 14 17:07 cp-dicom-rwxr-xr-x 1 root wheel 6893596 May 14 17:07 createMorph-rwxr-xr-x 1 root wheel 1851 May 14 17:07 cuda_setup-rwxr-xr-x 1 root wheel 76 May 14 17:07 cudadetect-rwxr-xr-x 1 root wheel 13308 May 14 17:07 cudadetect.bin-rwxr-xr-x 1 root wheel 12100 May 14 17:07 datastruct_utils.py-rwxr-xr-x 1 root wheel 6122 May 14 17:07 dcmdir-info-mgh-rwxr-xr-x 1 root wheel 23416 May 14 17:07 dcmunpack-rwxr-xr-x 1 root wheel 938 May 14 17:07 deface_subject-rwxr-xr-x 1 root wheel 8865 May 14 17:07 defect-seg-rwxr-xr-x 1 root wheel 4616 May 14 17:07 dicom-rename-rwxr-xr-x 1 root wheel 6452672 May 14 17:07 dmri_mergepaths-rwxr-xr-x 1 root wheel 6651560 May 14 17:07 dmri_paths-rwxr-xr-x 1 root wheel 6545252 May 14 17:07 dmri_pathstats-rwxr-xr-x 1 root wheel 6460264 May 14 17:07 dmri_spline-rwxr-xr-x 1 root wheel 6525716 May 14 17:07 dmri_tensoreig-rwxr-xr-x 1 root wheel 6660692 May 14 17:07 dmri_train-rwxr-xr-x 1 root wheel 6519924 May 14 17:07 dmri_trk2trk-rwxr-xr-x 1 root wheel 6501728 May 14 17:07 dmri_vox2vox-rwxr-xr-x 1 root wheel 6265 May 14 17:07 dmrirc.example-rwxr-xr-x 1 root wheel 7361 May 14 17:07 dmrirc.long.example-rwxr-xr-x 1 root wheel 20888 May 14 17:07 dsh-rwxr-xr-x 1 root wheel 14691 May 14 17:07 dt_recon-rwxr-xr-x 1 root wheel 31462 May 14 17:07 epidewarp.fsl-rwxr-xr-x 1 root wheel 6944772 May 14 17:07 exportGcam-rwxr-xr-x 1 root wheel 313 May 14 17:07 extract_talairach_avi_QA.awk-rwxr-xr-x 1 root wheel 8070 May 14 17:07 feat2segstats-rwxr-xr-x 1 root wheel 12563 May 14 17:07 feat2surf-rwxr-xr-x 1 root wheel 581 May 14 17:07 findsession-rwxr-xr-x 1 root wheel 756 May 14 17:07 fix_subject-rwxr-xr-x 1 root wheel 1114 May 14 17:07 fix_subject-lh-rwxr-xr-x 1 root wheel 1114 May 14 17:07 fix_subject-rh-rwxr-xr-x 1 root wheel 731 May 14 17:07 fix_subject_corrected-rwxr-xr-x 1 root wheel 1447 May 14 17:07 fix_subject_corrected-lh-rwxr-xr-x 1 root wheel 1358 May 14 17:07 fix_subject_corrected-rh-rwxr-xr-x 1 root wheel 952 May 14 17:07 fix_subject_on_seychelles-rwxr-xr-x 1 root wheel 3369 May 14 17:07 fixup_mni_paths-rwxr-xr-x 1 root wheel 5781 May 14 17:07 flip4fsl-rwxr-xr-x 1 root wheel 23072 May 14 17:07 flip_4dfp-rwxr-xr-x 1 root wheel 9859960 May 14 17:07 flirt.fsl-rw-r--r-- 1 root wheel 2919 May 14 17:07 flirt.newdefault.20080811.sch-rwxr-xr-x 1 root wheel 1408 May 14 17:07 fname2ext-rwxr-xr-x 1 root wheel 1438 May 14 17:07 fname2stem-rwxr-xr-x 1 root wheel 855 May 14 17:07 freesurfer-rwxr-xr-x 1 root wheel 184 May 14 17:07 freeview-rwxr-xr-x 1 root wheel 445424 May 14 17:07 fsPrintHelp-rwxr-xr-x 1 root wheel 4352 May 14 17:07 fs_lib_check-rwxr-xr-x 1 root wheel 635 May 14 17:07 fs_time-rwxr-xr-x 1 root wheel 7691 May 14 17:07 fscalc-rwxr-xr-x 1 root wheel 5794 May 14 17:07 fscalc.fsl-rwxr-xr-x 1 root wheel 138 May 14 17:07 fsfget-rwxr-xr-x 1 root wheel 4391 May 14 17:07 fsfget.tcl-rwxr-xr-x 1 root wheel 2815 May 14 17:07 fsgd_parser.py-rwxr-xr-x 1 root wheel 445424 May 14 17:07 fshelp-rwxr-xr-x 1 root wheel 6368760 May 14 17:08 fsl_label2voxel-rwxr-xr-x 1 root wheel 15462 May 14 17:08 fsl_rigid_register-rwxr-xr-x 1 root wheel 16491 May 14 17:08 fsl_sub_mgh-rwxr-xr-x 1 root wheel 11157384 May 14 17:08 fslmaths.fsl-rwxr-xr-x 1 root wheel 8657972 May 14 17:08 fslorient.fsl-rwxr-xr-x 1 root wheel 20703 May 14 17:08 fslregister-rwxr-xr-x 1 root wheel 5964 May 14 17:08 fslswapdim.fsl-rwxr-xr-x 1 root wheel 445424 May 14 17:08 fsman-rwxr-xr-x 1 root wheel 1340 May 14 17:08 fsr-checkxopts-rwxr-xr-x 1 root wheel 1479 May 14 17:08 fsr-getxopts-rwxr-xr-x 1 root wheel 14608 May 14 17:08 fsutils.py-rwxr-xr-x 1 root wheel 236204 May 14 17:08 gauss_4dfp-rwxr-xr-x 1 root wheel 1069708 May 14 17:08 gca_read_test-rwxr-xr-x 1 root wheel 449800 May 14 17:08 gcamCompare-rwxr-xr-x 1 root wheel 1133256 May 14 17:08 gcam_addstatus_test-rwxr-xr-x 1 root wheel 818320 May 14 17:08 gcam_addstatus_test_cuda-rwxr-xr-x 1 root wheel 1167736 May 14 17:08 gcam_applygradient_test-rwxr-xr-x 1 root wheel 1266424 May 14 17:08 gcam_applygradient_test_cuda-rwxr-xr-x 1 root wheel 1092372 May 14 17:08 gcam_clear_test-rwxr-xr-x 1 root wheel 1217244 May 14 17:08 gcam_clear_test_cuda-rwxr-xr-x 1 root wheel 1101124 May 14 17:08 gcam_cmp_test-rwxr-xr-x 1 root wheel 818320 May 14 17:08 gcam_cmp_test_cuda-rwxr-xr-x 1 root wheel 6710676 May 14 17:08 gcam_jacobenergy_test-rwxr-xr-x 1 root wheel 818352 May 14 17:08 gcam_jacobenergy_test_cuda-rwxr-xr-x 1 root wheel 1146064 May 14 17:08 gcam_jacobterm_test-rwxr-xr-x 1 root wheel 818320 May 14 17:08 gcam_jacobterm_test_cuda-rwxr-xr-x 1 root wheel 1064196 May 14 17:08 gcam_labelenergy_test-rwxr-xr-x 1 root wheel 818328 May 14 17:08 gcam_labelenergy_test_cuda-rwxr-xr-x 1 root wheel 6784284 May 14 17:08 gcam_labelterm_copydeltas_test-rwxr-xr-x 1 root wheel 822472 May 14 17:08 gcam_labelterm_copydeltas_test_cuda-rwxr-xr-x 1 root wheel 6784284 May 14 17:08 gcam_labelterm_final_test-rwxr-xr-x 1 root wheel 822472 May 14 17:08 gcam_labelterm_final_test_cuda-rwxr-xr-x 1 root wheel 6897540 May 14 17:08 gcam_labelterm_mainloop_test-rwxr-xr-x 1 root wheel 822528 May 14 17:08 gcam_labelterm_mainloop_test_cuda-rwxr-xr-x 1 root wheel 6802372 May 14 17:08 gcam_labelterm_postantconsist_test-rwxr-xr-x 1 root wheel 822496 May 14 17:08 gcam_labelterm_postantconsist_test_cuda-rwxr-xr-x 1 root wheel 6869460 May 14 17:08 gcam_labelterm_removeoutliers_test-rwxr-xr-x 1 root wheel 822296 May 14 17:08 gcam_labelterm_removeoutliers_test_cuda-rwxr-xr-x 1 root wheel 6910236 May 14 17:08 gcam_labelterm_test-rwxr-xr-x 1 root wheel 822504 May 14 17:08 gcam_labelterm_test_cuda-rwxr-xr-x 1 root wheel 6735988 May 14 17:08 gcam_lle_test-rwxr-xr-x 1 root wheel 818352 May 14 17:08 gcam_lle_test_cuda-rwxr-xr-x 1 root wheel 6792924 May 14 17:08 gcam_llterm_test-rwxr-xr-x 1 root wheel 822504 May 14 17:08 gcam_llterm_test_cuda-rwxr-xr-x 1 root wheel 6871988 May 14 17:08 gcam_removesingularities_test-rwxr-xr-x 1 root wheel 1266080 May 14 17:08 gcam_removesingularities_test_cuda-rwxr-xr-x 1 root wheel 1133256 May 14 17:08 gcam_removestatus_test-rwxr-xr-x 1 root wheel 818320 May 14 17:08 gcam_removestatus_test_cuda-rwxr-xr-x 1 root wheel 6867788 May 14 17:08 gcam_smoothgradient_test-rwxr-xr-x 1 root wheel 818320 May 14 17:08 gcam_smoothgradient_test_cuda-rwxr-xr-x 1 root wheel 1064212 May 14 17:08 gcam_smoothnessenergy_test-rwxr-xr-x 1 root wheel 818328 May 14 17:08 gcam_smoothnessenergy_test_cuda-rwxr-xr-x 1 root wheel 1137616 May 14 17:08 gcam_smoothnessterm_test-rwxr-xr-x 1 root wheel 818320 May 14 17:08 gcam_smoothnessterm_test_cuda-rwxr-xr-x 1 root wheel 1092340 May 14 17:08 gcam_undogradient_test-rwxr-xr-x 1 root wheel 1217244 May 14 17:08 gcam_undogradient_test_cuda-rwxr-xr-x 1 root wheel 1092260 May 14 17:08 gcam_write_test-rwxr-xr-x 1 root wheel 1403736 May 14 17:08 gcam_write_test_cuda-rwxr-xr-x 1 root wheel 783 May 14 17:08 get_label_thickness-rwxr-xr-x 1 root wheel 968 May 14 17:08 getfullpath-rwxr-xr-x 1 root wheel 205384 May 14 17:08 gifti_test-rwxr-xr-x 1 root wheel 280720 May 14 17:08 gifti_tool-rwxr-xr-x 1 root wheel 16812 May 14 17:08 grad_unwarp-rwxr-xr-x 1 root wheel 228 May 14 17:08 help_xml_validate-rwxr-xr-x 1 root wheel 6668372 May 14 17:08 hiam_make_surfaces-rwxr-xr-x 1 root wheel 6723212 May 14 17:08 hiam_make_template-rwxr-xr-x 1 root wheel 6839244 May 14 17:08 hiam_register-rwxr-xr-x 1 root wheel 6470716 May 14 17:08 histo_compute_joint_density-rwxr-xr-x 1 root wheel 6449756 May 14 17:08 histo_fix_topology-rwxr-xr-x 1 root wheel 6557828 May 14 17:08 histo_register_block-rwxr-xr-x 1 root wheel 6449748 May 14 17:08 histo_segment-rwxr-xr-x 1 root wheel 6462572 May 14 17:08 histo_synthesize-rwxr-xr-x 1 root wheel 13344 May 14 17:08 ico_supersample-rw-r--r-- 1 root wheel 128 May 14 17:08 id.xfm-rwxr-xr-x 1 root wheel 18444 May 14 17:08 ifh2hdr-rwxr-xr-x 1 root wheel 260684 May 14 17:08 imgreg_4dfp-rwxr-xr-x 1 root wheel 993 May 14 17:08 inflate_subject-rwxr-xr-x 1 root wheel 979 May 14 17:08 inflate_subject-lh-rwxr-xr-x 1 root wheel 978 May 14 17:08 inflate_subject-rh-rwxr-xr-x 1 root wheel 1080 May 14 17:08 inflate_subject3-rwxr-xr-x 1 root wheel 1050 May 14 17:08 inflate_subject_new-rwxr-xr-x 1 root wheel 992 May 14 17:08 inflate_subject_new-lh-rwxr-xr-x 1 root wheel 995 May 14 17:08 inflate_subject_new-rh-rwxr-xr-x 1 root wheel 1060 May 14 17:08 inflate_subject_sc-rwxr-xr-x 1 root wheel 1857 May 14 17:08 is-surface-rwxr-xr-x 1 root wheel 1133 May 14 17:08 isanalyze-rwxr-xr-x 1 root wheel 1377 May 14 17:08 isnifti-rw-------@ 1 Stefano wheel 46574724 Mar 22 20:48 kvl.zip-rwxr-xr-x 1 root wheel 5059016 May 14 17:08 kvlAddBorder-rwxr-xr-x 1 root wheel 386448 May 14 17:08 kvlAddMeshToMeshCollection-rwxr-xr-x 1 root wheel 5123480 May 14 17:08 kvlAddProbabilityImages-rwxr-xr-x 1 root wheel 5776276 May 14 17:08 kvlApplyTransform-rwxr-xr-x 1 root wheel 5054592 May 14 17:08 kvlAugmentManualSegmentationWithAutomatedSegmentation-rwxr-xr-x 1 root wheel 5269008 May 14 17:08 kvlAutoCrop-rwxr-xr-x 1 root wheel 5233008 May 14 17:09 kvlBinaryThresholdImage-rwxr-xr-x 1 root wheel 5458048 May 14 17:09 kvlCalculateAtlasMeshCollectionTotalCost-rwxr-xr-x 1 root wheel 5410272 May 14 17:09 kvlCalculatePositionCost-rwxr-xr-x 1 root wheel 386576 May 14 17:09 kvlChangeKOfMeshCollection-rwxr-xr-x 1 root wheel 386576 May 14 17:09 kvlChangePointParametersOfMeshCollection-rwxr-xr-x 1 root wheel 5141260 May 14 17:09 kvlColorCodeProbabilityImages-rwxr-xr-x 1 root wheel 5054592 May 14 17:09 kvlCombineManualSegmentationProtocols-rwxr-xr-x 1 root wheel 5147652 May 14 17:09 kvlCompressImage-rwxr-xr-x 1 root wheel 5099284 May 14 17:09 kvlConvert-rwxr-xr-x 1 root wheel 5054592 May 14 17:09 kvlCorrectLeftSideLabelsToRightSideLabels-rwxr-xr-x 1 root wheel 5064152 May 14 17:09 kvlCrop-rwxr-xr-x 1 root wheel 5331608 May 14 17:09 kvlCropImage-rwxr-xr-x 1 root wheel 6325772 May 14 17:09 kvlEMSegment-rwxr-xr-x 1 root wheel 5041884 May 14 17:09 kvlEvaluateQuantitatively-rwxr-xr-x 1 root wheel 5540468 May 14 17:09 kvlEvaluateQuantitativelyWithHausdorffDistance-rwxr-xr-x 1 root wheel 659156 May 14 17:09 kvlMapDeformationField-rwxr-xr-x 1 root wheel 409828 May 14 17:09 kvlMapLabelsOfAtlasMesh-rwxr-xr-x 1 root wheel 5185832 May 14 17:09 kvlMaskImage-rwxr-xr-x 1 root wheel 5567716 May 14 17:09 kvlMathematicalMorphology-rwxr-xr-x 1 root wheel 386400 May 14 17:09 kvlMergeMeshCollections-rwxr-xr-x 1 root wheel 5469044 May 14 17:09 kvlOptimizePositionsWithICM-rwxr-xr-x 1 root wheel 5058872 May 14 17:09 kvlOverwriteEmptySlices-rwxr-xr-x 1 root wheel 7925 May 14 17:09 kvlQuantifyHippocampalSubfieldSegmentations.sh-rwxr-xr-x 1 root wheel 5068640 May 14 17:09 kvlQuantifyPosteriorProbabilityImages-rwxr-xr-x 1 root wheel 5474896 May 14 17:09 kvlRasterizeAtlasMesh-rwxr-xr-x 1 root wheel 5189624 May 14 17:09 kvlReduceNumberOfIntensityLevels-rwxr-xr-x 1 root wheel 6419628 May 14 17:09 kvlRegister-rwxr-xr-x 1 root wheel 5447184 May 14 17:09 kvlResample-rwxr-xr-x 1 root wheel 5779196 May 14 17:09 kvlSamplePositionsFromMeshCollection-rwxr-xr-x 1 root wheel 386576 May 14 17:09 kvlScaleMeshCollection-rwxr-xr-x 1 root wheel 13393 May 14 17:09 kvlSegmentHippocampalSubfields.sh-rwxr-xr-x 1 root wheel 6576776 May 14 17:09 kvlSegmentWithoutGUI-rwxr-xr-x 1 root wheel 87 May 14 17:09 kvlSetHardCodedLocations.sh-rwxr-xr-x 1 root wheel 386944 May 14 17:09 kvlSetReferencePosition-rwxr-xr-x 1 root wheel 398500 May 14 17:09 kvlSmoothMesh-rwxr-xr-x 1 root wheel 3772 May 14 17:09 kvlTestHippocampalSubfields.sh-rwxr-xr-x 1 root wheel 5252204 May 14 17:09 kvlUpsample-rwxr-xr-x 1 root wheel 707040 May 14 17:09 kvlUpsampleMesh-rwxr-xr-x 1 root wheel 1685 May 14 17:09 kww_setup-rwxr-xr-x 1 root wheel 6568164 May 14 17:09 label2flat-rwxr-xr-x 1 root wheel 6471076 May 14 17:09 label2patch-rwxr-xr-x 1 root wheel 6454060 May 14 17:09 label_area-rwxr-xr-x 1 root wheel 6458356 May 14 17:09 label_border-rwxr-xr-x 1 root wheel 988 May 14 17:09 label_child-rwxr-xr-x 1 root wheel 932 May 14 17:09 label_elderly_subject-rwxr-xr-x 1 root wheel 1795 May 14 17:09 label_subject-rwxr-xr-x 1 root wheel 934 May 14 17:09 label_subject_flash-rwxr-xr-x 1 root wheel 876 May 14 17:09 label_subject_mixed-rwxr-xr-x 1 root wheel 1736 May 14 17:09 labels_disjoint-rwxr-xr-x 1 root wheel 1619 May 14 17:09 labels_intersect-rwxr-xr-x 1 root wheel 1566 May 14 17:09 labels_union-rwxr-xr-x 1 root wheel 58322 May 14 17:09 long_mris_slopes-rwxr-xr-x 1 root wheel 5415 May 14 17:09 long_qdec_table-rwxr-xr-x 1 root wheel 10017 May 14 17:09 long_stats_combine-rwxr-xr-x 1 root wheel 27990 May 14 17:09 long_stats_slopes-rwxr-xr-x 1 root wheel 10048 May 14 17:09 long_stats_tps-rwxr-xr-x 1 root wheel 40308 May 14 17:09 long_submit_jobs-rwxr-xr-x 1 root wheel 11280 May 14 17:09 long_submit_postproc-rwxr-xr-x 1 root wheel 13038 May 14 17:09 lpcregister-rwxr-xr-x 1 root wheel 6416496 May 14 17:09 lta_diff-rwxr-xr-x 1 root wheel 7565 May 14 17:09 make-segvol-table-rwxr-xr-x 1 root wheel 7465 May 14 17:09 make_average_subcort-rwxr-xr-x 1 root wheel 9386 May 14 17:09 make_average_subject-rwxr-xr-x 1 root wheel 19017 May 14 17:09 make_average_surface-rwxr-xr-x 1 root wheel 14641 May 14 17:09 make_average_volume-rwxr-xr-x 1 root wheel 4176 May 14 17:09 make_cortex_label-rwxr-xr-x 1 root wheel 2230 May 14 17:09 make_hemi_mask-rwxr-xr-x 1 root wheel 2088 May 14 17:09 make_symmetric-rwxr-xr-x 1 root wheel 2198 May 14 17:09 make_upright-rwxr-xr-x 1 root wheel 6437328 May 14 17:09 makevol-rwxr-xr-x 1 root wheel 915 May 14 17:09 map_all_labels-rwxr-xr-x 1 root wheel 809 May 14 17:09 map_all_labels-lh-rwxr-xr-x 1 root wheel 849 May 14 17:09 map_central_sulcus-rwxr-xr-x 1 root wheel 2726 May 14 17:09 map_to_base-rwxr-xr-x 1 root wheel 6772308 May 14 17:09 meanfilter_test-rwxr-xr-x 1 root wheel 7137180 May 14 17:09 meanfilter_test_cuda-rwxr-xr-x 1 root wheel 3747 May 14 17:09 meanval-rwxr-xr-x 1 root wheel 20796 May 14 17:09 merge_stats_tables-rwxr-xr-x 1 root wheel 3506 May 14 17:09 minc2seqinfo-rwxr-xr-x 1 root wheel 694 May 14 17:09 misc.py-rwxr-xr-x 1 root wheel 19858 May 14 17:09 mkfsdist-rwxr-xr-x 1 root wheel 9407 May 14 17:09 mkheadsurf-rwxr-xr-x 1 root wheel 555 May 14 17:09 mkima_index.tcl-rwxr-xr-x 1 root wheel 555 May 14 17:09 mkmnc_index.tcl-rwxr-xr-x 1 root wheel 1694 May 14 17:09 mksubjdirs-rwxr-xr-x 1 root wheel 7215 May 14 17:09 mksurfatlas-rwxr-xr-x 1 root wheel 6400044 May 14 17:09 mkxsubjreg-rwxr-xr-x 1 root wheel 6222 May 14 17:09 mni152reg-rwxr-xr-x 1 root wheel 713 May 14 17:09 morph_only_subject-rwxr-xr-x 1 root wheel 989 May 14 17:09 morph_only_subject-lh-rwxr-xr-x 1 root wheel 989 May 14 17:09 morph_only_subject-rh-rwxr-xr-x 1 root wheel 1802 May 14 17:09 morph_rgb-lh-rwxr-xr-x 1 root wheel 1697 May 14 17:09 morph_rgb-rh-rwxr-xr-x 1 root wheel 986 May 14 17:09 morph_subject-rwxr-xr-x 1 root wheel 2740 May 14 17:09 morph_subject-lh-rwxr-xr-x 1 root wheel 2710 May 14 17:09 morph_subject-rh-rwxr-xr-x 1 root wheel 758 May 14 17:09 morph_subject_on_seychelles-rwxr-xr-x 1 root wheel 1166 May 14 17:09 morph_tables-lh-rwxr-xr-x 1 root wheel 1080 May 14 17:09 morph_tables-rh-rwxr-xr-x 1 root wheel 4966 May 14 17:09 mpr2mni305-rwxr-xr-x 1 root wheel 6957 May 14 17:09 mri-func2sph-rwxr-xr-x 1 root wheel 7796 May 14 17:09 mri-funcvits-rwxr-xr-x 1 root wheel 5434 May 14 17:09 mri-sph2surf-rwxr-xr-x 1 root wheel 6716364 May 14 17:09 mri2nc-rwxr-xr-x 1 root wheel 6772596 May 14 17:10 mriMarkLabelBorderVoxelTest-rwxr-xr-x 1 root wheel 7076940 May 14 17:10 mriMarkLabelBorderVoxelTest_cuda-rwxr-xr-x 1 root wheel 6776884 May 14 17:10 mriVoxInLabelPartialVolumeTest-rwxr-xr-x 1 root wheel 7081204 May 14 17:10 mriVoxInLabelPartialVolumeTest_cuda-rwxr-xr-x 1 root wheel 7809 May 14 17:10 mri_add_new_tp-rwxr-xr-x 1 root wheel 6881608 May 14 17:10 mri_add_xform_to_header-rwxr-xr-x 1 root wheel 2560 May 14 17:10 mri_align_long.csh-rwxr-xr-x 1 root wheel 6445660 May 14 17:10 mri_and-rwxr-xr-x 1 root wheel 6542820 May 14 17:10 mri_annotation2label-rwxr-xr-x 1 root wheel 6986576 May 14 17:10 mri_aparc2aseg-rwxr-xr-x 1 root wheel 6530076 May 14 17:10 mri_aparc2wmseg-rwxr-xr-x 1 root wheel 6546244 May 14 17:10 mri_apply_bias-rwxr-xr-x 1 root wheel 6441216 May 14 17:10 mri_apply_inu_correction-rwxr-xr-x 1 root wheel 6508996 May 14 17:10 mri_aseg_edit_reclassify-rwxr-xr-x 1 root wheel 6639060 May 14 17:10 mri_aseg_edit_train-rwxr-xr-x 1 root wheel 6545820 May 14 17:10 mri_auto_fill-rwxr-xr-x 1 root wheel 6658080 May 14 17:10 mri_average-rwxr-xr-x 1 root wheel 6483308 May 14 17:10 mri_bc_sc_bias_correct-rwxr-xr-x 1 root wheel 6467444 May 14 17:10 mri_binarize-rwxr-xr-x 1 root wheel 6581568 May 14 17:10 mri_brain_volume-rwxr-xr-x 1 root wheel 6449940 May 14 17:10 mri_build_priors-rwxr-xr-x 1 root wheel 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May 14 17:15 mris_convert-rwxr-xr-x 1 root wheel 7075312 May 14 17:15 mris_curvature-rwxr-xr-x 1 root wheel 6681628 May 14 17:15 mris_curvature_stats-rwxr-xr-x 1 root wheel 7059836 May 14 17:15 mris_deform-rwxr-xr-x 1 root wheel 6533908 May 14 17:15 mris_density-rwxr-xr-x 1 root wheel 6533604 May 14 17:15 mris_diff-rwxr-xr-x 1 root wheel 6516924 May 14 17:15 mris_distance_map-rwxr-xr-x 1 root wheel 6557252 May 14 17:15 mris_distance_to_label-rwxr-xr-x 1 root wheel 6622540 May 14 17:15 mris_distance_transform-rwxr-xr-x 1 root wheel 6550828 May 14 17:15 mris_divide_parcellation-rwxr-xr-x 1 root wheel 6458332 May 14 17:15 mris_entropy-rwxr-xr-x 1 root wheel 6626300 May 14 17:15 mris_errors-rwxr-xr-x 1 root wheel 6898552 May 14 17:15 mris_euler_number-rwxr-xr-x 1 root wheel 6851748 May 14 17:15 mris_expand-rwxr-xr-x 1 root wheel 6919364 May 14 17:15 mris_extract_main_component-rwxr-xr-x 1 root wheel 6876788 May 14 17:15 mris_exvivo_surfaces-rwxr-xr-x 1 root wheel 80480 May 14 17:15 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mris_parcellate_connectivity-rwxr-xr-x 1 root wheel 7232156 May 14 17:16 mris_pmake-rwxr-xr-x 1 root wheel 39591 May 14 17:16 mris_preproc-rwxr-xr-x 1 root wheel 6893956 May 14 17:16 mris_refine_surfaces-rwxr-xr-x 1 root wheel 7351544 May 14 17:16 mris_register-rwxr-xr-x 1 root wheel 6739604 May 14 17:16 mris_register_to_volume-rwxr-xr-x 1 root wheel 6936400 May 14 17:16 mris_remove_intersection-rwxr-xr-x 1 root wheel 6504668 May 14 17:16 mris_remove_negative_vertices-rwxr-xr-x 1 root wheel 6525444 May 14 17:16 mris_remove_variance-rwxr-xr-x 1 root wheel 6483444 May 14 17:16 mris_rescale-rwxr-xr-x 1 root wheel 6571900 May 14 17:16 mris_reverse-rwxr-xr-x 1 root wheel 7637 May 14 17:16 mris_roiCircle-rwxr-xr-x 1 root wheel 6487692 May 14 17:16 mris_rotate-rwxr-xr-x 1 root wheel 6471124 May 14 17:16 mris_sample_label-rwxr-xr-x 1 root wheel 6580092 May 14 17:16 mris_sample_parc-rwxr-xr-x 1 root wheel 6454884 May 14 17:16 mris_seg2annot-rwxr-xr-x 1 root wheel 6525508 May 14 17:16 mris_segment_vals-rwxr-xr-x 1 root wheel 6732396 May 14 17:16 mris_show-rwxr-xr-x 1 root wheel 6839588 May 14 17:16 mris_shrinkwrap-rwxr-xr-x 1 root wheel 7104880 May 14 17:16 mris_smooth-rwxr-xr-x 1 root wheel 7355672 May 14 17:16 mris_sphere-rwxr-xr-x 1 root wheel 7749348 May 14 17:17 mris_sphere_cuda-rwxr-xr-x 1 root wheel 6597364 May 14 17:17 mris_spherical_average-rwxr-xr-x 1 root wheel 6521204 May 14 17:17 mris_surface_change-rwxr-xr-x 1 root wheel 6542156 May 14 17:17 mris_surface_stats-rwxr-xr-x 1 root wheel 6475332 May 14 17:17 mris_surface_to_vol_distances-rwxr-xr-x 1 root wheel 6487980 May 14 17:17 mris_svm_classify-rwxr-xr-x 1 root wheel 6554788 May 14 17:17 mris_svm_train-rwxr-xr-x 1 root wheel 6483508 May 14 17:17 mris_talairach-rwxr-xr-x 1 root wheel 6868788 May 14 17:17 mris_thickness-rwxr-xr-x 1 root wheel 6462524 May 14 17:17 mris_thickness_comparison-rwxr-xr-x 1 root wheel 6609020 May 14 17:17 mris_thickness_diff-rwxr-xr-x 1 root wheel 6793844 May 14 17:17 mris_topo_fixer-rwxr-xr-x 1 root wheel 6587956 May 14 17:17 mris_transform-rwxr-xr-x 1 root wheel 6458356 May 14 17:17 mris_translate_annotation-rwxr-xr-x 1 root wheel 6571324 May 14 17:17 mris_twoclass-rwxr-xr-x 1 root wheel 7048064 May 14 17:17 mris_volmask-rwxr-xr-x 1 root wheel 7024080 May 14 17:17 mris_volmask_novtk-rwxr-xr-x 1 root wheel 81 May 14 17:17 mris_volmask_vtk-rwxr-xr-x 1 root wheel 7008888 May 14 17:17 mris_volmask_vtk.bin-rwxr-xr-x 1 root wheel 11555 May 14 17:17 mris_volsmooth-rwxr-xr-x 1 root wheel 6454212 May 14 17:17 mris_volume-rwxr-xr-x 1 root wheel 6525444 May 14 17:17 mris_w_to_curv-rwxr-xr-x 1 root wheel 6529676 May 14 17:17 mris_wm_volume-rwxr-xr-x 1 root wheel 7058520 May 14 17:17 mrisp_paint-rwxr-xr-x 1 root wheel 927 May 14 17:17 ms_refine_subject-rwxr-xr-x 1 root wheel 361548 May 14 17:17 nmovie-rwxr-xr-x 1 root wheel 171716 May 14 17:17 optseq2-rwxr-xr-x 1 root wheel 15570 May 14 17:17 parc_atlas_jackknife_test-rwxr-xr-x 1 root wheel 8818 May 14 17:17 pctsurfcon-rwxr-xr-x 1 root wheel 2283 May 14 17:17 petsc_setup-rwxr-xr-x 1 root wheel 22465 May 14 17:17 plot_structure_stats.tcl-rwxr-xr-x 1 root wheel 4323 May 14 17:17 predict_v1.sh-rwxr-xr-x 1 root wheel 26812 May 14 17:17 progressbar.tcl-rwxr-xr-x 1 root wheel 259 May 14 17:17 qdec-rwxr-xr-x 1 root wheel 8733444 May 14 17:17 qdec.bin-rwxr-xr-x 1 root wheel 658640 May 14 17:17 qdec_glmfit-rwxr-xr-x 1 root wheel 1764 May 14 17:17 qt_setup-rwxr-xr-x 1 root wheel 209408 May 14 17:17 rbftest-rwxr-xr-x 1 root wheel 7611 May 14 17:17 rcbf-prep-rwxr-xr-x 1 root wheel 15908 May 14 17:17 rebuild_gca_atlas.csh-rwxr-xr-x 1 root wheel 268538 May 14 17:17 recon-all-rwxr-xr-x 1 root wheel 23095 May 14 17:17 recon-all.makefile-rwxr-xr-x 1 root wheel 22846 May 14 17:17 reg-feat2anat-rwxr-xr-x 1 root wheel 4341 May 14 17:17 reg-mni305.2mm-rwxr-xr-x 1 root wheel 6376400 May 14 17:17 regdat2xfm-rwxr-xr-x 1 root wheel 2503 May 14 17:17 register.csh-rwxr-xr-x 1 root wheel 972 May 14 17:17 register_child-rwxr-xr-x 1 root wheel 1106 May 14 17:17 register_elderly_subject-rwxr-xr-x 1 root wheel 971 May 14 17:17 register_subject-rwxr-xr-x 1 root wheel 967 May 14 17:17 register_subject_flash-rwxr-xr-x 1 root wheel 986 May 14 17:17 register_subject_mixed-rwxr-xr-x 1 root wheel 763 May 14 17:17 reinflate_subject-rwxr-xr-x 1 root wheel 931 May 14 17:17 reinflate_subject-lh-rwxr-xr-x 1 root wheel 931 May 14 17:17 reinflate_subject-rh-rwxr-xr-x 1 root wheel 993 May 14 17:17 remove_talairach-rwxr-xr-x 1 root wheel 763 May 14 17:17 renormalize_T1_subject-rwxr-xr-x 1 root wheel 788 May 14 17:17 renormalize_subject-rwxr-xr-x 1 root wheel 1002 May 14 17:17 renormalize_subject_keep_editting-rwxr-xr-x 1 root wheel 75392 May 14 17:17 repair_siemens_file-rwxr-xr-x 1 root wheel 948 May 14 17:17 reregister_subject_mixed-rwxr-xr-x 1 root wheel 9158 May 14 17:17 rtview-rwxr-xr-x 1 root wheel 6291 May 14 17:17 run-qdec-glm-rwxr-xr-x 1 root wheel 3732 May 14 17:17 run_mris_preproc-rwxr-xr-x 1 root wheel 1676 May 14 17:17 segment_monkey-rwxr-xr-x 1 root wheel 1443 May 14 17:17 segment_subject-rwxr-xr-x 1 root wheel 1732 May 14 17:17 segment_subject_notal-rwxr-xr-x 1 root wheel 1545 May 14 17:17 segment_subject_notal2-rwxr-xr-x 1 root wheel 1516 May 14 17:17 segment_subject_old_skull_strip-rwxr-xr-x 1 root wheel 1585 May 14 17:17 segment_subject_sc-rwxr-xr-x 1 root wheel 1599 May 14 17:17 segment_subject_talmgh-rwxr-xr-x 1 root wheel 3330 May 14 17:17 setlabelstat-rwxr-xr-x 1 root wheel 10224 May 14 17:17 sfa2fieldsign-rwxr-xr-x 1 root wheel 774 May 14 17:17 show_tal-rwxr-xr-x 1 root wheel 220 May 14 17:17 skip_long_make_checks-rwxr-xr-x 1 root wheel 8771600 May 14 17:17 slicetimer.fsl-rwxr-xr-x 1 root wheel 707 May 14 17:17 sphere_subject-rwxr-xr-x 1 root wheel 882 May 14 17:17 sphere_subject-lh-rwxr-xr-x 1 root wheel 881 May 14 17:17 sphere_subject-rh-rwxr-xr-x 1 root wheel 6558884 May 14 17:17 spherical_stats-rwxr-xr-x 1 root wheel 1802 May 14 17:17 spm_t_to_b-rwxr-xr-x 1 root wheel 5922 May 14 17:17 spmmat2register-rwxr-xr-x 1 root wheel 21612 May 14 17:17 spmregister-rwxr-xr-x 1 root wheel 2455 May 14 17:17 sratio-rwxr-xr-x 1 root wheel 6554748 May 14 17:17 stat_normalize-rwxr-xr-x 1 root wheel 1829 May 14 17:17 stem2fname-rwxr-xr-x 1 root wheel 8756 May 14 17:17 stim_polar-rwxr-xr-x 1 root wheel 556 May 14 17:17 subject_info.py-rwxr-xr-x 1 root wheel 10583672 May 14 17:17 surf2vol-rwxr-xr-x 1 root wheel 7698 May 14 17:17 surfreg-rwxr-xr-x 1 root wheel 1494 May 14 17:17 t4img_4dfp-rwxr-xr-x 1 root wheel 265468 May 14 17:17 t4imgs_4dfp-rwxr-xr-x 1 root wheel 1049 May 14 17:17 tal_QC_AZS-rwxr-xr-x 1 root wheel 856 May 14 17:17 tal_compare-rwxr-xr-x 1 root wheel 5185 May 14 17:17 talairach-rwxr-xr-x 1 root wheel 3115 May 14 17:17 talairach2-rwxr-xr-x 1 root wheel 6835816 May 14 17:17 talairach_afd-rwxr-xr-x 1 root wheel 5387 May 14 17:17 talairach_avi-rwxr-xr-x 1 root wheel 1132 May 14 17:17 talairach_mgh-rwxr-xr-x 1 root wheel 14605 May 14 17:17 talsegprob-rwxr-xr-x 1 root wheel 2405 May 14 17:17 tcl_setup-rwxr-xr-x 1 root wheel 10407 May 14 17:17 test_fs_tutorial.csh-rwxr-xr-x 1 root wheel 25884 May 14 17:17 test_recon-all.csh-rwxr-xr-x 1 root wheel 668968 May 14 17:17 tetgen-rwxr-xr-x 1 root wheel 3231 May 14 17:17 thickdiffmap-rwxr-xr-x 1 root wheel 102 May 14 17:17 tkmedit-rwxr-xr-x 1 root wheel 8859 May 14 17:17 tkmeditfv-rwxr-xr-x 1 root wheel 106 May 14 17:17 tkregister2-rwxr-xr-x 1 root wheel 6493700 May 14 17:17 tkregister2_cmdl-rwxr-xr-x 1 root wheel 103 May 14 17:17 tksurfer-rwxr-xr-x 1 root wheel 43553 May 14 17:17 trac-all-rwxr-xr-x 1 root wheel 26633 May 14 17:17 trac-paths-rwxr-xr-x 1 root wheel 58360 May 14 17:17 trac-preproc-rwxr-xr-x 1 root wheel 15106 May 14 17:17 tractstats2table-rwxr-xr-x 1 root wheel 75180 May 14 17:17 tridec-rwxr-xr-x 1 root wheel 110675 May 14 17:17 unpack_ima.tcl-rwxr-xr-x 1 root wheel 45265 May 14 17:17 unpack_ima1.tcl-rwxr-xr-x 1 root wheel 38901 May 14 17:17 unpack_mnc.tcl-rwxr-xr-x 1 root wheel 6596 May 14 17:17 unpackimadir-rwxr-xr-x 1 root wheel 35562 May 14 17:17 unpackimadir2-rwxr-xr-x 1 root wheel 18546 May 14 17:17 unpackmincdir-rwxr-xr-x 1 root wheel 145 May 14 17:17 unpacksdcmdir-rwxr-xr-x 1 root wheel 46836 May 14 17:17 unpacksdcmdir.tcl-rwxr-xr-x 1 root wheel 4690 May 14 17:17 usbtree-rwxr-xr-x 1 root wheel 3743 May 14 17:17 vno_match_check-rwxr-xr-x 1 root wheel 7108540 May 14 17:18 volume_copy_test_cuda-rwxr-xr-x 1 root wheel 4659 May 14 17:18 vsm-smooth-rwxr-xr-x 1 root wheel 3339 May 14 17:18 vtk_setup-rwxr-xr-x 1 root wheel 5376 May 14 17:18 wfilemask-rwxr-xr-x 1 root wheel 7046 May 14 17:18 wm-anat-snr-rwxr-xr-x 1 root wheel 2550 May 14 17:18 xfmrot-rwxr-xr-x 1 root wheel 9128 May 14 17:18 xhemireg-rwxr-xr-x 1 root wheel 445416 May 14 17:18 xmlToHtml-rwxr-xr-x 1 root wheel 5265 May 14 17:18 xsanatreg-rwxr-xr-x 1 root wheel 23032 May 14 17:18 zero_lt_4dfp ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 7-giu-2013 18.02 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] mris resample: Command not found. This error is permanent after new patch download Stefano, step 4 should be: "chmod +x $FREESURFER_HOME/bin/mris_resample" When you do an "ls -l" in the $FREESURFER_HOME/bin directory, you need to see the to see the x's next to mris_resample just like you do with all the other files in that directory. -Zeke On 06/07/2013 11:49 AM, stdp82(a)virgilio.it wrote: > Hi list, > > during trac-all -prep I have this error: > > MRISregister() return, current seed 0 > writing registered surface to > /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... > expanding nbhd size to 1 > mris_resample: Command not found. > Darwin iMac > > I have performed my analysis by the following steps (as recommended by > Zeke and Lilla): > > 1. download "unKnow" file (7.6 MB) at > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample > 2. put file in $FREESURFER/bin/ > 4. chmod +x ~/mris_resample as recommended by Daniel (in the first test > I did not use this command) > 5. start trac-all -prep > 6. ERROR (in inter-reg step) > > What's happen? > > Thank you very much, > > > Stefano > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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mris resample: Command not found. This error is permanent after new patch download
by stdp82＠virgilio.it 07 Jun '13

07 Jun '13

Hi list, during trac-all -prep I have this error: MRISregister() return, current seed 0writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg...expanding nbhd size to 1mris_resample: Command not found.Darwin iMac I have performed my analysis by the following steps (as recommended by Zeke and Lilla): 1. download "unKnow" file (7.6 MB) at ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample2. put file in $FREESURFER/bin/4. chmod +x ~/mris_resample as recommended by Daniel (in the first test I did not use this command)5. start trac-all -prep6. ERROR (in inter-reg step) What's happen? Thank you very much, Stefano

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Yeo_JNeurophysiol11_FreeSurfer.zip
by Peter Savadjiev 07 Jun '13

07 Jun '13

Hello, I'm trying to download ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_FreeSurfer.zip (as linked from http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011) however, the file doesn't seem to be available, or the server is not responsive. Is there another location from where I could download this file? Thank you, Peter

3 2

mris_preproc --qdec-long problem
by Martin Reuter 07 Jun '13

07 Jun '13

Hi Chris, this is a good question for the list (cc'ed), others may or will have the same problem. The problem is with your table file, specifically the new line character. DOS uses \r\n , Mac \r and Linux \n. Your text file uses \r, so it probably was created on a mac. The problem is that the "cat" command (at least in linux) does not work on your file: cat long.qdec.table.dat is empty You can convert the \r to \n (linux format): tr '\r' '\n' < long.qdec.table.dat > long2.qdec.table.dat and then should be able to run the preproc command. People with DOS formats should not run the above "tr' command as they will end up with 2 newlines instead of 1. Maybe DOS txt files work with 'cat' directly (so there is no need)? If anyone on the list knows a good way of cat and awk a file independently of the new line (and working on all OS), let me know. This is the command I use: cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#") printf("%s.long.%s\n", $1, $2)}' to generate the subjects id's from the table's first two columns. Best, Martin On 06/03/2013 03:45 PM, Christopher McCarthy wrote: > Dr. Reuter, > > We corresponded in the past about QDEC, and you gave me great help. > The lab I work for is now moving towards using the Longitudinal Mixed > Effects Model. When I go to run the command: > > mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target > study_average --hemi lh --meas thickness --out lh.thickness.mgh > > I get the error: 'ERROR: no subjects specified.' I am attaching my > long.qdec.table.dat, which works fine when loaded by QDEC. Do you > have any idea of why I am getting this error? > > Thanks, > > Chris McCarthy -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

3 4

Control points: possible bug (only tested in 5.3)
by Garikoitz Lerma-Usabiaga 07 Jun '13

07 Jun '13

Hi list, I've been creating control points and I got the following error: MRIwriteControlPoints(/home/glerma/freesurfer/subjects/TNT/TNT_solosubs/S_11/tmp/control.dat): could not open file No such file or directory I created the /tmp/ folder by hand and then it created the control.dat file properly (going to tkmedit > File > Save Control Points). These are the permission on the S_11 folder: drwxrwxr-x 17 glerma domain users 4096 Jun 7 09:41 S_11 (this is a CentOS 5 machine) thanks! Gari

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R: Re: R: R: Re: R: Re: Tracula
by stdp82＠virgilio.it 06 Jun '13

06 Jun '13

The file that I have downloaded is named "unKnow" and it is of 7.6 MB. I have placed it in $FREESURFER_HOME/bin directory but the error persist. Anastasia, I apologize. Please, have patience with me :-) but .. when I search for "mris_resample" in mail list I did not found any indication. I found my previous mail and first Zeke response. Thanks, Stefano ----Messaggio originale---- Da: lzollei(a)nmr.mgh.harvard.edu Data: 6-giu-2013 23.20 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: R: Re: R: Re: Tracula HI, A patch is now available for the "mris_resample : Command not found" error you encountered. Simply download the file from the following link and place it in your $FREESURFER_HOME/bin directory: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample --Lilla On Thu, 6 Jun 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > > I have resolved the previous problem by writing configuration file with sudo nano in command line. > > Now I'm running trac-all -prep but I have this error: > > > writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... > expanding nbhd size to 1 > mris_resample: Command not found. > > What's happened? > > Thanks, > > > Stefano > > > > ----Messaggio originale---- > Da: stdp82(a)virgilio.it > Data: 6-giu-2013 0.51 > A: <ayendiki(a)nmr.mgh.harvard.edu> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: [Freesurfer] R: Re: R: Re: Tracula > > I obtain /Applications/freesurfer/subjects/subject_prova > my DWI file is in Diff01, Diff02 ... that are in subject_prova folder. > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 6-giu-2013 0.42 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: Tracula > > > What do you get when you run "echo $SUBJECTS_DIR"? > > On Thu, 6 Jun 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > > > yes, I have check the SUBJECTS_DIR. I do not understand why all previous > > configuration file start normally and this no. > > Do you note some line that might be wrong additionally to setenv > > SUBJECTS_DIR line. > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 5-giu-2013 16.09 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: Tracula > > > > > > Is the "setenv SUBJECTS_DIR" line really commented out? You must set > > SUBJECTS_DIR, see the example configuration file on the wiki and under > > $FREESURFER_HOME/bin/dmrirc.example. > > > > On Wed, 5 Jun 2013, stdp82(a)virgilio.it wrote: > > > > > Hi list and Anastasia, > > > I'm performing a set of data with tracula version 3.0. I have change my > > > dmrirc file respect to previous analyses and now I have one problem > > > > > > "set: Variable name must begin with a letter. > > > ERROR: must specify as many DWI dicoms as subjects". > > > > > > I do not find the line that is wrong. I think to have approximately used > > the > > > same lines of previous and correct analysis. > > > > > > I have attached the configuration file. Note that I'm using nii.gz. > > > > > > Thanks and best regards. > > > > > > > > > Stefano > > > > > > > > > > > > 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 mailing list > Freesurfer(a)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 mailing list Freesurfer(a)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.

1 0

field of value too small, wrap-around
by Maria Kharitonova 06 Jun '13

06 Jun '13

Hello, We have a relatively small FOV in our study because we mostly scan kids. Sometimes we scan adults with the same protocol, though, and after looking through the adults' reconned brains, I've noticed wrap-around on some brains. For one subject it's particularly bad; it affects aparc labels, where the very back of the brain gets labeled as orbitofrontal cortex. Is there a way to remedy this (other than increasing the FOV for subsequent subjects)? E.g. manually relabeling the affected regions? I'm pretty new to FreeSurfer, so I apologize in advance if this questions is naive. Thanks! Maria Kharitonova, Ph.D. Postdoctoral Research Fellow Laboratories of Cognitive Neuroscience Boston Children's Hospital

3 2

R: R: Re: R: Re: Tracula
by stdp82＠virgilio.it 06 Jun '13

06 Jun '13

Hi Anastasia, I have resolved the previous problem by writing configuration file with sudo nano in command line. Now I'm running trac-all -prep but I have this error: writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg...expanding nbhd size to 1mris_resample: Command not found. What's happened? Thanks, Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 6-giu-2013 0.51 A: <ayendiki(a)nmr.mgh.harvard.edu> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: R: Re: Tracula I obtain /Applications/freesurfer/subjects/subject_prova my DWI file is in Diff01, Diff02 ... that are in subject_prova folder. Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 6-giu-2013 0.42 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: Tracula What do you get when you run "echo $SUBJECTS_DIR"? On Thu, 6 Jun 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > > yes, I have check the SUBJECTS_DIR. I do not understand why all previous > configuration file start normally and this no. > Do you note some line that might be wrong additionally to setenv > SUBJECTS_DIR line. > > > Stefano > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 5-giu-2013 16.09 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: Tracula > > > Is the "setenv SUBJECTS_DIR" line really commented out? You must set > SUBJECTS_DIR, see the example configuration file on the wiki and under > $FREESURFER_HOME/bin/dmrirc.example. > > On Wed, 5 Jun 2013, stdp82(a)virgilio.it wrote: > > > Hi list and Anastasia, > > I'm performing a set of data with tracula version 3.0. I have change my > > dmrirc file respect to previous analyses and now I have one problem > > > > "set: Variable name must begin with a letter. > > ERROR: must specify as many DWI dicoms as subjects". > > > > I do not find the line that is wrong. I think to have approximately used > the > > same lines of previous and correct analysis. > > > > I have attached the configuration file. Note that I'm using nii.gz. > > > > Thanks and best regards. > > > > > > Stefano > > > > > > > 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 mailing list Freesurfer(a)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.

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Re: [Freesurfer] Still confused by group analysis..
by Tudor Popescu 06 Jun '13

06 Jun '13

Thanks Doug, > So if I want to use the study-specific "average" subject surface with >> mri_surf2surf, rather than the generic "fsaverage" one, how can this be >> done given that the required ls.white file only exists in the latter but >> not in the former? Can I just rename (or duplicate) ls.white into >> ls.white_avg? >> >> You can copy it or create a symbolic link. So it is OK to copy the required lh.white file from the generic average subject "fsaverage" and apply mri_surf2surf upon the study-specific average subject ("average")? It still seems to me that "average" should have its own (different) lh.white... > >> Shouldn't the input to mri_glmfit be the output of mri_surf2surf? In the >> group tutorial, the former is "lh.gender_age.thickness.10.**mgh" while >> the latter is "lh.gender_age.thickness.10B.**mgh". Or should it just be >> the unsmoothed output of mris_preproc? >> >> Yes, I can't remember why I put the "B" there, maybe to keep people from > overwriting lh.gender_age.thickness.10.mgh during the tutorial and having > to wait the 10min or so for it to get recreated. But if all these commands transform the same file (output of mris_preproc becomes input of mri_surf2surf, which then feeds into mri_glmfit), then why is it still necessary to keep intact the original lh.gender_age.thickness.10.mgh, when all you need for the group analysis is the mri_surf2surf'd version? > >> Assuming the label files (corresponding to my ROI, and extracted from the >> Destrieux atlas) are different for each subject, and given mri_glmfit is >> called just once, for all subjects, which label file (corresponding to what >> subject) should I point it to? >> >> You need to create the label in the average subject. There is a > Destrieux atlas there. Again, by "average subject" do you mean here the generic one (fsaverage) or the study-specific one (average)? Should the former be used at any point of a group analysis, if the latter exists?

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Re: [Freesurfer] Freesurfer Digest, Vol 112, Issue 17
by McMains, Stephanie 06 Jun '13

06 Jun '13

Here is the original thread (to at least most of it). Maybe I am just an idiot, but I cant' figure out how to easily reply from the web to an entire thread, and pulling it out of the digests I get is a pain!! They wanted to take an ROI from SPM and put it into free surfer to extract cortical thickness. I thought going through fsaverage was a good way to do this. But as I said, looking at the surface, I have some concerns. I am more confused by when you tell them to run the MNI template through recon-all to get a surface, because I thought fsaverage was a kind of MNI space that has already been run through? Thanks, Stephanie what space is your VBM map in? doug On 06/05/2013 11:06 AM, Ozranov-Palchik, Ola wrote: > Hi Doug, > > Thank you for your response! I am still a bit confused about the vol2surf > command. I have a volumetric mask with voxels of interest based on a VBM > analysis in SPM. I would like to extract the cortical thickness measurements > based on these voxels. I am not clear what specifications I need to include > when using vol2surf. For example, what do I use as my registration matrix? > > Thank you for your help! > Ola > > Ola Ozranov-Palchik M.S. > Research Coordinator, Gaab Lab > Laboratories of Cognitive Neuroscience > Children's Hospital Boston > 1 Autumn Street, Mailbox # 713 > Boston, MA 02115 > olga.ozra...(a)childrens.harvard.edu<http://childrens.harvard.edu> > phone: (617) 334-5046 > main lab: (617) 355-0400 > fax: (617) 730-0518 > http://www.childrenshospital.org/research/gaablab > > > -----Original Message----- > From: freesurfer-boun...(a)nmr.mgh.harvard.edu<http://nmr.mgh.harvard.edu> > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, June 04, 2013 1:48 PM > To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] SPM ROI to Cortical Thickness > > > Make sure that your SPM volume is registered to the anatomical, then use > mri_vol2surf to map the volume to the surface, then mri_segstats to extract > the mean of the thickness > > doug > > > > > On 06/04/2013 01:45 PM, Ozranov-Palchik, Ola wrote: >> main lab: (617) 355-0400 > Dear FreeSurfer Experts, > > I was wondering if anyone can advise on the best way to use an ROI mask > created in SPM (XjView) to extract cortical thickness values in freesurfer. > > Thank you in advance for your help! > > Ola > > Ola Ozranov-Palchik M.S. > Research Coordinator, Gaab Lab > Laboratories of Cognitive Neuroscience > > Children's Hospital Boston > 1 Autumn Street, Mailbox # 713 > Boston, MA 02115 > olga.ozra...(a)childrens.harvard.edu<http://childrens.harvard.edu> > <mailto:olga.ozra...@childrens.harvard.edu> > phone: (617) 334-5046 > main lab: (617) 355-0400 > fax: (617) 730-0518 > http://www.childrenshospital.org/research/gaablab > Then it goes on: Hi Ola, this probably will not work. The tal coordinate is notoriously inaccurate in cortex. You are verylikely to totally miss the area you are looking for. A better way is to run the MNI template through recon-all, map your VBM result to the surface of that, then use mri_surf2surf to map the effect to each individual. doug On 06/05/2013 02:58 PM, Ozranov-Palchik, Ola wrote: > Hi Doug, > > Thank you, again! I decided to try to use the Talairach coordinates from my > analysis for ROI extraction. I created an average subject and preprocessed > the data (mris_preproc). I obtained the vertex index based on the coordinates > from the average subject. Any ideas on how I can now find the corresponding > vertices in all my subjects? > > Thanks very much! > Ola > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu<http://nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422

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Freesurfer June 2013