Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30097 discussions

mri_convert WARNING: files are not found to be different and cannot be sorted
by Olivia Walton Stanley 18 Jul '16

18 Jul '16

Hello all, I have run mri_convert on a series of dicoms and received the following error for several of my images. As with the previous bug report for this I have run mri_info on my dicom series and it’s output is below. My main concern is since these dicoms are being jumbled up and I am not sure what that warning means. Is it the dicom header it is comparing? Can you elaborate or put me on track to debug this error? Thanks, Olivia mri_info is below: mri_info 500/Image_SLC0_CON0_PHS0_REP1_SET0_AVE0_2.dcm Getting Series No Scanning Directory INFO: Found 9218 files in 500 INFO: Scanning for Series Number 3076 INFO: found 4608 files in series INFO: loading series header info. INFO: sorting. WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC0_CON0_PHS0_REP13_SET0_AVE0_2.dcm File2: 500/Image_SLC0_CON0_PHS0_REP1_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC0_CON0_PHS0_REP25_SET0_AVE0_2.dcm File2: 500/Image_SLC0_CON0_PHS0_REP2_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC0_CON0_PHS0_REP37_SET0_AVE0_2.dcm File2: 500/Image_SLC0_CON0_PHS0_REP3_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC0_CON0_PHS0_REP49_SET0_AVE0_2.dcm File2: 500/Image_SLC0_CON0_PHS0_REP4_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC0_CON0_PHS0_REP5_SET0_AVE0_2.dcm File2: 500/Image_SLC0_CON0_PHS0_REP61_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC0_CON0_PHS0_REP6_SET0_AVE0_2.dcm File2: 500/Image_SLC0_CON0_PHS0_REP73_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC0_CON0_PHS0_REP7_SET0_AVE0_2.dcm File2: 500/Image_SLC0_CON0_PHS0_REP85_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC10_CON0_PHS0_REP1_SET0_AVE0_2.dcm File2: 500/Image_SLC10_CON0_PHS0_REP20_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC10_CON0_PHS0_REP2_SET0_AVE0_2.dcm File2: 500/Image_SLC10_CON0_PHS0_REP32_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC10_CON0_PHS0_REP4_SET0_AVE0_2.dcm File2: 500/Image_SLC10_CON0_PHS0_REP56_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC10_CON0_PHS0_REP3_SET0_AVE0_2.dcm File2: 500/Image_SLC10_CON0_PHS0_REP44_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC10_CON0_PHS0_REP5_SET0_AVE0_2.dcm File2: 500/Image_SLC10_CON0_PHS0_REP68_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC10_CON0_PHS0_REP6_SET0_AVE0_2.dcm File2: 500/Image_SLC10_CON0_PHS0_REP80_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC11_CON0_PHS0_REP0_SET0_AVE0_2.dcm File2: 500/Image_SLC11_CON0_PHS0_REP10_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC10_CON0_PHS0_REP7_SET0_AVE0_2.dcm File2: 500/Image_SLC10_CON0_PHS0_REP92_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC11_CON0_PHS0_REP1_SET0_AVE0_2.dcm File2: 500/Image_SLC11_CON0_PHS0_REP22_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC11_CON0_PHS0_REP3_SET0_AVE0_2.dcm File2: 500/Image_SLC11_CON0_PHS0_REP46_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC11_CON0_PHS0_REP4_SET0_AVE0_2.dcm File2: 500/Image_SLC11_CON0_PHS0_REP58_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC11_CON0_PHS0_REP6_SET0_AVE0_2.dcm File2: 500/Image_SLC11_CON0_PHS0_REP82_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC11_CON0_PHS0_REP7_SET0_AVE0_2.dcm File2: 500/Image_SLC11_CON0_PHS0_REP94_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC11_CON0_PHS0_REP5_SET0_AVE0_2.dcm File2: 500/Image_SLC11_CON0_PHS0_REP70_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC11_CON0_PHS0_REP2_SET0_AVE0_2.dcm File2: 500/Image_SLC11_CON0_PHS0_REP34_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC11_CON0_PHS0_REP106_SET0_AVE0_2.dcm File2: 500/Image_SLC11_CON0_PHS0_REP8_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC10_CON0_PHS0_REP104_SET0_AVE0_2.dcm File2: 500/Image_SLC10_CON0_PHS0_REP8_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC1_CON0_PHS0_REP15_SET0_AVE0_2.dcm File2: 500/Image_SLC1_CON0_PHS0_REP1_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC1_CON0_PHS0_REP27_SET0_AVE0_2.dcm File2: 500/Image_SLC1_CON0_PHS0_REP2_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC1_CON0_PHS0_REP39_SET0_AVE0_2.dcm File2: 500/Image_SLC1_CON0_PHS0_REP3_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC1_CON0_PHS0_REP4_SET0_AVE0_2.dcm File2: 500/Image_SLC1_CON0_PHS0_REP51_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC1_CON0_PHS0_REP6_SET0_AVE0_2.dcm File2: 500/Image_SLC1_CON0_PHS0_REP75_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC1_CON0_PHS0_REP5_SET0_AVE0_2.dcm File2: 500/Image_SLC1_CON0_PHS0_REP63_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC1_CON0_PHS0_REP7_SET0_AVE0_2.dcm File2: 500/Image_SLC1_CON0_PHS0_REP87_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC2_CON0_PHS0_REP17_SET0_AVE0_2.dcm File2: 500/Image_SLC2_CON0_PHS0_REP1_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC2_CON0_PHS0_REP29_SET0_AVE0_2.dcm File2: 500/Image_SLC2_CON0_PHS0_REP2_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC2_CON0_PHS0_REP4_SET0_AVE0_2.dcm File2: 500/Image_SLC2_CON0_PHS0_REP53_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC2_CON0_PHS0_REP3_SET0_AVE0_2.dcm File2: 500/Image_SLC2_CON0_PHS0_REP41_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC2_CON0_PHS0_REP5_SET0_AVE0_2.dcm File2: 500/Image_SLC2_CON0_PHS0_REP65_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC2_CON0_PHS0_REP7_SET0_AVE0_2.dcm File2: 500/Image_SLC2_CON0_PHS0_REP89_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC2_CON0_PHS0_REP6_SET0_AVE0_2.dcm File2: 500/Image_SLC2_CON0_PHS0_REP77_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC3_CON0_PHS0_REP19_SET0_AVE0_2.dcm File2: 500/Image_SLC3_CON0_PHS0_REP1_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC3_CON0_PHS0_REP3_SET0_AVE0_2.dcm File2: 500/Image_SLC3_CON0_PHS0_REP43_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC3_CON0_PHS0_REP5_SET0_AVE0_2.dcm File2: 500/Image_SLC3_CON0_PHS0_REP67_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC3_CON0_PHS0_REP4_SET0_AVE0_2.dcm File2: 500/Image_SLC3_CON0_PHS0_REP55_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC3_CON0_PHS0_REP6_SET0_AVE0_2.dcm File2: 500/Image_SLC3_CON0_PHS0_REP79_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC3_CON0_PHS0_REP7_SET0_AVE0_2.dcm File2: 500/Image_SLC3_CON0_PHS0_REP91_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC3_CON0_PHS0_REP2_SET0_AVE0_2.dcm File2: 500/Image_SLC3_CON0_PHS0_REP31_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC4_CON0_PHS0_REP1_SET0_AVE0_2.dcm File2: 500/Image_SLC4_CON0_PHS0_REP21_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC4_CON0_PHS0_REP2_SET0_AVE0_2.dcm File2: 500/Image_SLC4_CON0_PHS0_REP33_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC4_CON0_PHS0_REP3_SET0_AVE0_2.dcm File2: 500/Image_SLC4_CON0_PHS0_REP45_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC4_CON0_PHS0_REP4_SET0_AVE0_2.dcm File2: 500/Image_SLC4_CON0_PHS0_REP57_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC4_CON0_PHS0_REP5_SET0_AVE0_2.dcm File2: 500/Image_SLC4_CON0_PHS0_REP69_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC4_CON0_PHS0_REP7_SET0_AVE0_2.dcm File2: 500/Image_SLC4_CON0_PHS0_REP93_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC5_CON0_PHS0_REP0_SET0_AVE0_2.dcm File2: 500/Image_SLC5_CON0_PHS0_REP11_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC4_CON0_PHS0_REP6_SET0_AVE0_2.dcm File2: 500/Image_SLC4_CON0_PHS0_REP81_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC5_CON0_PHS0_REP1_SET0_AVE0_2.dcm File2: 500/Image_SLC5_CON0_PHS0_REP23_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC4_CON0_PHS0_REP0_SET0_AVE0_2.dcm File2: 500/Image_SLC4_CON0_PHS0_REP9_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC5_CON0_PHS0_REP3_SET0_AVE0_2.dcm File2: 500/Image_SLC5_CON0_PHS0_REP47_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC5_CON0_PHS0_REP2_SET0_AVE0_2.dcm File2: 500/Image_SLC5_CON0_PHS0_REP35_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC5_CON0_PHS0_REP5_SET0_AVE0_2.dcm File2: 500/Image_SLC5_CON0_PHS0_REP71_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC5_CON0_PHS0_REP6_SET0_AVE0_2.dcm File2: 500/Image_SLC5_CON0_PHS0_REP83_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC5_CON0_PHS0_REP7_SET0_AVE0_2.dcm File2: 500/Image_SLC5_CON0_PHS0_REP95_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC5_CON0_PHS0_REP4_SET0_AVE0_2.dcm File2: 500/Image_SLC5_CON0_PHS0_REP59_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC6_CON0_PHS0_REP24_SET0_AVE0_2.dcm File2: 500/Image_SLC6_CON0_PHS0_REP2_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC6_CON0_PHS0_REP48_SET0_AVE0_2.dcm File2: 500/Image_SLC6_CON0_PHS0_REP4_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC6_CON0_PHS0_REP5_SET0_AVE0_2.dcm File2: 500/Image_SLC6_CON0_PHS0_REP60_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC6_CON0_PHS0_REP6_SET0_AVE0_2.dcm File2: 500/Image_SLC6_CON0_PHS0_REP72_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC6_CON0_PHS0_REP8_SET0_AVE0_2.dcm File2: 500/Image_SLC6_CON0_PHS0_REP96_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC6_CON0_PHS0_REP7_SET0_AVE0_2.dcm File2: 500/Image_SLC6_CON0_PHS0_REP84_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC6_CON0_PHS0_REP36_SET0_AVE0_2.dcm File2: 500/Image_SLC6_CON0_PHS0_REP3_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC6_CON0_PHS0_REP12_SET0_AVE0_2.dcm File2: 500/Image_SLC6_CON0_PHS0_REP1_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC7_CON0_PHS0_REP14_SET0_AVE0_2.dcm File2: 500/Image_SLC7_CON0_PHS0_REP1_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC7_CON0_PHS0_REP26_SET0_AVE0_2.dcm File2: 500/Image_SLC7_CON0_PHS0_REP2_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC7_CON0_PHS0_REP38_SET0_AVE0_2.dcm File2: 500/Image_SLC7_CON0_PHS0_REP3_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC7_CON0_PHS0_REP4_SET0_AVE0_2.dcm File2: 500/Image_SLC7_CON0_PHS0_REP50_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC7_CON0_PHS0_REP6_SET0_AVE0_2.dcm File2: 500/Image_SLC7_CON0_PHS0_REP74_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC7_CON0_PHS0_REP5_SET0_AVE0_2.dcm File2: 500/Image_SLC7_CON0_PHS0_REP62_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC7_CON0_PHS0_REP7_SET0_AVE0_2.dcm File2: 500/Image_SLC7_CON0_PHS0_REP86_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC7_CON0_PHS0_REP8_SET0_AVE0_2.dcm File2: 500/Image_SLC7_CON0_PHS0_REP98_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC8_CON0_PHS0_REP16_SET0_AVE0_2.dcm File2: 500/Image_SLC8_CON0_PHS0_REP1_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC8_CON0_PHS0_REP28_SET0_AVE0_2.dcm File2: 500/Image_SLC8_CON0_PHS0_REP2_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC8_CON0_PHS0_REP4_SET0_AVE0_2.dcm File2: 500/Image_SLC8_CON0_PHS0_REP52_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC8_CON0_PHS0_REP3_SET0_AVE0_2.dcm File2: 500/Image_SLC8_CON0_PHS0_REP40_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC8_CON0_PHS0_REP5_SET0_AVE0_2.dcm File2: 500/Image_SLC8_CON0_PHS0_REP64_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC8_CON0_PHS0_REP7_SET0_AVE0_2.dcm File2: 500/Image_SLC8_CON0_PHS0_REP88_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC8_CON0_PHS0_REP6_SET0_AVE0_2.dcm File2: 500/Image_SLC8_CON0_PHS0_REP76_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC9_CON0_PHS0_REP18_SET0_AVE0_2.dcm File2: 500/Image_SLC9_CON0_PHS0_REP1_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC9_CON0_PHS0_REP2_SET0_AVE0_2.dcm File2: 500/Image_SLC9_CON0_PHS0_REP30_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC9_CON0_PHS0_REP3_SET0_AVE0_2.dcm File2: 500/Image_SLC9_CON0_PHS0_REP42_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC9_CON0_PHS0_REP5_SET0_AVE0_2.dcm File2: 500/Image_SLC9_CON0_PHS0_REP66_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC9_CON0_PHS0_REP4_SET0_AVE0_2.dcm File2: 500/Image_SLC9_CON0_PHS0_REP54_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC9_CON0_PHS0_REP6_SET0_AVE0_2.dcm File2: 500/Image_SLC9_CON0_PHS0_REP78_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC9_CON0_PHS0_REP7_SET0_AVE0_2.dcm File2: 500/Image_SLC9_CON0_PHS0_REP90_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC9_CON0_PHS0_REP102_SET0_AVE0_2.dcm File2: 500/Image_SLC9_CON0_PHS0_REP8_SET0_AVE0_2.dcm WARNING: files are not found to be different and cannot be sorted File1: 500/Image_SLC8_CON0_PHS0_REP100_SET0_AVE0_2.dcm File2: 500/Image_SLC8_CON0_PHS0_REP8_SET0_AVE0_2.dcm RunNo = 3075 WARNING: file 500/Image_SLC6_CON0_PHS0_REP0_SET0_AVE0_2.dcm does not contain a Siemens ASCII header has this file been anonymized? Proceeding as best as I can ... INFO: (380 380 12), nframes = 384, ismosaic=0 PE Dir ROW ROW Volume information for 500/Image_SLC0_CON0_PHS0_REP1_SET0_AVE0_2.dcm type: siemens_dicom dimensions: 380 x 380 x 12 x 384 voxel sizes: 0.5053, 0.5053, 0.5000 type: SHORT (4) fov: 380.000 dof: 0 xstart: -190.0, xend: 190.0 ystart: -190.0, yend: 190.0 zstart: -6.0, zend: 6.0 TR: 1250.00 msec, TE: 24.60 msec, TI: 2500.00 msec, flip angle: 40.00 degrees nframes: 384 PhEncDir: ROW ras xform present xform info: x_r = 1.0000, y_r = -0.0000, z_r = 0.0000, c_r = -0.0000 : x_a = -0.0000, y_a = -0.7593, z_a = -0.6508, c_a = -41.5207 : x_s = 0.0000, y_s = -0.6508, z_s = 0.7593, c_s = -3.6854 Orientation : RPS Primary Slice Direction: axial voxel to ras transform: 0.5053 -0.0000 0.0000 -96.0000 -0.0000 -0.3836 -0.3254 33.3216 0.0000 -0.3288 0.3796 56.5112 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -0.127645 ras to voxel transform: 1.9792 -0.0000 -0.0000 190.0001 0.0000 -1.5027 -1.2880 122.8593 -0.0000 -1.3015 1.5185 -42.4449 0.0000 0.0000 0.0000 1.0000

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Regarding: Concatenating hippocampal to generate sig.mgh
by Dr Sampada Sinha 18 Jul '16

18 Jul '16

Dear freesurfer experts, Will you please let me know if it's possible to get one average mgz image file by concatenating the hippocampal volumes of different subjects using dev version? Since, I already have the hippocampal subfields mgz volume files, I intend to run the glmfit later on between two groups to get sig.mgh files. Thanks and regards? Sampada -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India

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Re Re: Checking Surfaces vs. aseg outputs
by Tamara Tavares 18 Jul '16

18 Jul '16

Thank you again Bruce. Since I am primarily interested in ventricular volume, do you think it is necessary to check the the brainmask.mgz for bright or dark spots indicating an intensity normalization error? As well, what about a skull strip error such as removal of brain tissue? I have noticed that sometimes skull strip removes parts of the occipital lobe and I was going to adjust the watershed parameters and re-run recon-all. Do you think this is necessary or would affect the ventricular volume results? Thank you in advance for your help, Tamara

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white and pail surface editing
by Ritobrato Datta 18 Jul '16

18 Jul '16

Hi All, We have some subjects who have both wm errors and gm errors. Is the following workflow possible Step 1) control points for the white matter edits. DONT RUN recon-all Step 2) add the pial surface edits. DONT RUN recon-all Step 3) Run recon-all to incorporate control points for wm edits (recon-all -autorecon2-cp -autorecon3 -subjid cp_before) AFTER step 3 is COMPLETE, run Step 4) Run recon-all to create a fixed pial surface (recon-all -autorecon-pial -subjid pial_edits_before) OR Can step 3 and Step 4 be run together as recon-all -autorecon2-cp -autorecon-pial -autorecon3 -subjid cp_before Please let me know. Thanks Ri

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can not find module 'dev'
by Yun Wang 18 Jul '16

18 Jul '16

Dear All, I recently tried to gain access the read-only CVS source-code repository, however, I have this kind of error: cvs server: cannot find module `dev' - ignored cvs [checkout aborted]: cannot expand modules anyone have idea what is going on here? Thank you so much! Best, Yun Wang

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Re: [Freesurfer] Freesurfer Digest, Vol 149, Issue 31
by Tamara Tavares 18 Jul '16

18 Jul '16

Hi Bruce, Thank you for your quick reply. We are primarily interested in ventricular volume but we may look at other areas in the future; this is why I thought it would be a good idea to check the surfaces. Is the reasoning why the surface outputs vs. aseg outputs should be checked is because the surface outputs are used the calculate the structure's volumes? I am fairly new to Freesurfer so I am trying to get a good understanding of it. Thank you in advance, Tamara --- Tamara Tavares, HBSc <http://H.B.Sc> PhD Candidate Brain and Mind Institute, Department of Neuroscience The Schulich School of Medicine and Dentistry The University of Western Ontario 519-661-2111, ext 84623 On Sun, Jul 17, 2016 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Checking Surfaces vs. aseg outputs (Bruce Fischl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 16 Jul 2016 13:35:10 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Checking Surfaces vs. aseg outputs > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1607161334500.21946(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Tamara > > if you are more interested in things like ventricular volume then the > surfaces aren't so important to check. > > cheers > Bruce > > > On Fri, 15 Jul 2016, Tamara Tavares wrote: > > > Hi All, > > > > I was hoping to get some help with understanding the surface and aseg > > volumes. I have some patient's scans and I am interested in examining the > > ventricular volume but may look at other areas later on. I understand > from > > earlier threads that it is important to check the surface volumes (pial > and > > wm) vs. the aseg output. Why is it more important to check the surfaces > vs > > the aseg outputs if I am interested in getting the volumes? > > > > Thank you in advance for your help. > > > > Best, > > Tamara > > > > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 149, Issue 31 > ******************************************* > > > 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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Integrate SPM activation maps to FreeSurfer structural volumes
by Mahtab Farahbakhsh 18 Jul '16

18 Jul '16

Dear FreeSurfer, I am trying to register my SPM activation maps to the structural data of each subjects. Except for the commands I could find for the registration, I could not find a guide on the registration of activation maps from SPM to FreeSurfer. Would you please guide me how I should do that? Best Regards, Mahtab.

2 1

LME contrasts
by Clara Kühn 18 Jul '16

18 Jul '16

Dear FreeSurfer experts, I am following the mass-univariate (spatiotemporal) model in the LME tutorial. My design matrix X has the following columns: intercept, time, time², group1, group1*time, group1*time², group2, group2*time, group2*time², sex, age, mean_thickness I actually have 3 groups but group1 and group2 in X are dummy coded. I would like to check whether there are group differences in the quadratic term but I don't understand what this command expresses and how the contrast was formed: CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)]; Could you please explain it on the example design matrix so I can adapt it to mine? Thank you! Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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can not find module 'dev'
by Yun Wang 17 Jul '16

17 Jul '16

1 0

Checking Surfaces vs. aseg outputs
by Tamara Tavares 16 Jul '16

16 Jul '16

Hi All, I was hoping to get some help with understanding the surface and aseg volumes. I have some patient's scans and I am interested in examining the ventricular volume but may look at other areas later on. I understand from earlier threads that it is important to check the surface volumes (pial and wm) vs. the aseg output. Why is it more important to check the surfaces vs the aseg outputs if I am interested in getting the volumes? Thank you in advance for your help. Best, Tamara

2 1

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