Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

BrainSegVolNotVent
by Eryilmaz, H. Hamdi 18 Jul '16

18 Jul '16

Hello Doug and Freesurfers, I am trying to compute a structural measure called 'BrainSegVolNotVent' as an approximate value of total brain volume. 'BrainSegVolNotVent' is now present in aseg.stats files but the dataset I'm working on was preprocessed using FS 5.0, which did not produce this variable. Per your advice I found in a previous email, I reran mri_segstats adding the flags --brainmask mri/brainmask.mgz --brain-vol-from-seg. The new aseg.stats file contains the following lines that were added after running this command: # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1667093, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1667093.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 232145.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1410666, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1410666.000000, mm^3 The numbers look a bit odd. BrainSegVol and BrainSegVolNotVent should normally be close to each other, right? Also unitless values such as BrainSegNVox and BrainMaskNVox seem to be equal to their corresponding volumetric values. Do you have any idea what might have gone wrong? Here's the command I ran: mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/stable5_0_0/ASegStatsLUT.txt --subject SUBJECT_ID --brainmask mri/brainmask.mgz --brain-vol-from-seg Thanks very much for your help! Best, Hamdi

2 3

mri_glmfit error: Matrix is ill-conditioned or badly scaled
by Jennifer Legault 18 Jul '16

18 Jul '16

Hi Freesurfer Experts, I am trying to run mri_glmfit and while 90% of my files work, some of them display the error below. I have tried demeaning, and then tried multiplying this value by 100, and I still get the same error. Any feedback would be greatly appreciated. mris_preproc done srcsubject = fsaverage srcval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00.mgh srctype = trgsubject = fsaverage trgval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh gdfReadHeader: reading /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 19.5833 1.32025 1 eTIV 1.61645e+06 145343 2 EnglishParityRT 0.00012207 25139.1 Class Means of each Continuous Variable 1 Monolingual_male 19.7143 1678946.5893 -4197.2796 2 Monolingual_female 19.4000 1528966.6750 5876.1917 INFO: gd2mtx_method is dods Reading source surface /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /gpfs/scratch/jtl190/Math_reconstruction cmdline mri_glmfit --y rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd --C /gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt --surf fsaverage rh --cortex --glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir sysname Linux hostname cyberstar129.hpc.rcc.psu.edu machine x86_64 user jtl190 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh logyflag 0 usedti 0 FSGD /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd labelmask /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir Loading y from /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh INFO: gd2mtx_method is dods Saving design matrix to rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir/Xg.dat Normalized matrix condition is 22568.9 Design matrix ------------------ 1.000 0.000 18.000 0.000 1865790.250 0.000 -8952.208 0.000; 0.000 1.000 0.000 19.000 0.000 1520429.625 0.000 -4605.208; 1.000 0.000 19.000 0.000 1749716.750 0.000 -39407.207 0.000; 0.000 1.000 0.000 18.000 0.000 1589109.250 0.000 -17967.209; 1.000 0.000 21.000 0.000 1472295.125 0.000 19531.791 0.000; 1.000 0.000 18.000 0.000 1580381.375 0.000 -17027.209 0.000; 1.000 0.000 20.000 0.000 1813373.500 0.000 16152.792 0.000; 1.000 0.000 21.000 0.000 1638616.500 0.000 -9074.208 0.000; 0.000 1.000 0.000 21.000 0.000 1297920.500 0.000 61860.793; 0.000 1.000 0.000 18.000 0.000 1634762.625 0.000 -22671.209; 0.000 1.000 0.000 21.000 0.000 1602611.375 0.000 12763.792; 1.000 0.000 21.000 0.000 1632452.625 0.000 9395.292 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 22568.9 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd --C /gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt --surf fsaverage rh --cortex --glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir 2. The FSGD file (if using one) 3. And the design matrix above I am also attaching the FSGD file. Best, Jennifer Legault

3 3

registering to fsaverage
by Trisanna Sprung-Much 18 Jul '16

18 Jul '16

Hi there So I have sulcal labels from another software (.mnc format) from which I am trying to generate some probability maps. I was able to convert the .mnc to .mgz surface overlay using mri_vol2surf for my MRIs after running all MRIs in recon-all. So, now I have all my painted voxels as surface overlays, as I was instructed to do a few months ago. I was told that the next step would be to use mri_surf2surf to resample the overlays to fsaverage. I am a bit confused as I would think that the next step would be to take the surface overlays and inflate them before I register them to fsaverage. I see that when recon-all runs, it computes the registration of the MRI surface to fsaverage and saves it as sphere.reg. *Is there a way I can inflate my surface overlays in a similar manner and then apply this same registration to my surface overlays?* Or am I missing something? thanks very much! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

3 35

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

2 1

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

3 5

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

2 1

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

2 1

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

1 0

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. > >

2 1

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.

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