Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

trackvis, and a separate question about surface transforms
by Colin Reveley 08 Dec '11

08 Dec '11

Hello; first, regarding the information here: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms This looks to me very much like snippets of code to help people write their own code to read and transform files, byte by byte, with the help of the trackvis .trk header/file spec. That's great. Thanks. But has anyone written a script or some C or something to actually do that. If not, and if I do that in the form probably of C source, does anyone want the code? second: I'm using freeesurfer for ex-vivo macaque data. It's been a struggle but I've got there. There is something I would like to do: as well as keeping what I have, I would like to tilt the volume's nose up a few degrees (I'd probably use the afni "nudge" plugin for that, or something) and then apply the same transform to my white and pial surfaces. The idea there being to use the surfaces as diagrams in the same cut plane as diagrams in an atlas (the pandya white matter atlas, the paxinos atlas), mark areas and then transform those areas off else where (into diffusion data as masks in fact). I hope that's clear. I just want to apply an arbitrary (actually, a rigid body) linear transform to the surfaces and volumes so that when viewed coronally in sequence in freeview they are in the same plane as diagrams in an atlas, and I can compare the two by eye. the pial and white surfaces together look line like diagrams, and this is very helpful actually. especially if they are in the same cut plane as the atlas diagrams. thanks, Colin

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Re: [Freesurfer] tracula ERROR: must specify brain mask volume for output subject
by Priti Srinivasan 08 Dec '11

08 Dec '11

Hi Paula, The * at the end of dtifit_FA.nii.gz may have been a problem (since it gives an unkown extension error? Extension: 146 (Uknown extension)) tcsh source /software/Freesurfer/5.1.0/SetUpFreeSurfer.csh freeview -v /mindhive/gablab/users/cpdla/Documents/s1001/dmri/dtifit_FA.nii.gz can you try running the above commands in that order and tell us if you get the same error? Thanks, Priti > hi, > i am trying to visualize the output of my trac-all results. > here is what i did: > cpdla@ba3:/$ tcsh > ba3:/> source /software/Freesurfer/5.1.0/Set > SetUpFreeSurfer.csh* SetUpFreeSurfer.sh* > ba3:/> source /software/Freesurfer/5.1.0/SetUpFreeSurfer.csh > -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /software/Freesurfer/5.1.0/ > FSFAST_HOME /software/Freesurfer/5.1.0/fsfast > FSF_OUTPUT_FORMAT nii > SUBJECTS_DIR /software/Freesurfer/5.1.0/subjects > MNI_DIR /software/Freesurfer/5.1.0//mni > /usr/share/fsl/4.1/etc/fslconf/fslmachtype.sh: Command not found. > FSL_DIR /usr/share/fsl/4.1 > *ba3:/> freeview -v > /mindhive/gablab/users/cpdla/Documents/s1001/dmri/dtifit_FA.nii.gz* > X Error: BadValue (integer parameter out of range for operation) 2 > Extension: 146 (Uknown extension) > Minor opcode: 3 (Unknown request) > Resource id: 0x24 > Abort > *ba3:/> freeview -tv > /mindhive/gablab/users/cpdla/Documents/s1001/dmri/dtifit_FA.nii.gz* > X Error: BadValue (integer parameter out of range for operation) 2 > Extension: 146 (Uknown extension) > Minor opcode: 3 (Unknown request) > Resource id: 0x24 > Abort > ba3:/> > > > On Thu, Dec 8, 2011 at 10:54 AM, Priti Srinivasan < > rspriti(a)nmr.mgh.harvard.edu> wrote: > >> Hi Paula, >> >> which image are you trying to open? If you're trying to open the merged >> files in freeview, you should use the -tv flag for opening it. Did you >> source the freesurfer environment before opening freeview? Can you give >> us >> the exact commandline you used? >> >> Priti >> >> > hi, >> > i am trying to visualize my results with freeview, and i am running >> into >> > this error. i am using freesurfer 5.1.0. do you know what the problem >> is? >> > : >> > >> > cpdla@ba3:~/Documents/s1001/dmri$ freeview >> > X Error: BadValue (integer parameter out of range for operation) 2 >> > Extension: 146 (Uknown extension) >> > Minor opcode: 3 (Unknown request) >> > Resource id: 0x24 >> > Abort >> > >> > >> > On Wed, Dec 7, 2011 at 12:52 PM, Priti Srinivasan < >> > rspriti(a)nmr.mgh.harvard.edu> wrote: >> > >> >> Hi Paula, >> >> >> >> Tracula uses anatomical labels/files from freesurfer cortical >> >> reconstruction to build the posterior distribution of the tracts. It >> >> looks >> >> like you may not have run freesurfer recon for your subject. >> >> >> >> To run freesurfer recon for your subject please refer to the >> following >> >> page: >> >> >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide >> >> >> >> Especially, >> >> >> >> recon-all \ >> >> -i <one slice in the anatomical dicom series> \ >> >> -s <subject id that you make up> \ >> >> -sd <directory to put the subject folder in> \ >> >> -all >> >> >> >> Once this finishes processing you can re-run tracula to see if that >> >> solves >> >> the issue. >> >> >> >> Hope that is helpful, >> >> Priti >> >> >> >> >> >> >> >> > Hi. >> >> > >> >> > I am running into the following error: >> >> > ERROR: fio_pushd: >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni >> >> > ERROR: must specify brain mask volume for output subject . >> >> > >> >> > I googled this error and it seems like you suggested this to >> someone >> >> else >> >> > : >> >> > "As for your error, it looks like maybe the freesurfer recon wasn't >> >> found, >> >> > so >> >> > it skipped some steps (diffusion-to-anatomical registration and >> mask >> >> > creation). >> >> > Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist? >> >> > >> >> > >> >> > a.y" >> >> > >> >> > What is the freesurfer recon dir supposed to look like? Any >> >> > suggestions on how to fix this error? Below is my output. >> >> > >> >> > Thanks, >> >> > C. Paula >> >> > >> >> > >> >> > >> >> > >> >> > ba3:~/Documents> trac-all -prep -c dmrirc_single_subject >> >> > set: Variable name must begin with a letter. >> >> > INFO: SUBJECTS_DIR is >> >> > /mindhive/gablab/users/cpdla/Documents/diffusion_recons >> >> > INFO: Diffusion root is /mindhive/gablab/users/cpdla/Documents/ >> >> > Actual FREESURFER_HOME /software/Freesurfer/5.1.0 >> >> > trac-preproc -c >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/dmrirc.local >> >> -log >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.log >> >> -cmd >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.cmd >> >> > #------------------------------------- >> >> > /software/Freesurfer/5.1.0//bin/trac-preproc >> >> > #------------------------------------- >> >> > #@# Image corrections Tue Dec 6 22:02:37 EST 2011 >> >> > mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> >> > mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >> >> > reading from /data/memory/sourcemem//s1001/156000-20-1.dcm... >> >> > Getting Series No >> >> > INFO: Found 3207 files in /data/memory/sourcemem//s1001 >> >> > INFO: Scanning for Series Number 20 >> >> > Scanning Directory >> >> > INFO: found 35 files in series >> >> > INFO: loading series header info. >> >> > >> >> > RunNo = 19 >> >> > WARNING: Run 1 appears to be truncated >> >> > Files Found: 35, Files Expected (lRep+1): 60 >> >> > FileName /data/memory/sourcemem//s1001/156000-20-1.dcm >> >> > Identification >> >> > NumarisVer syngo MR B15 >> >> > ScannerModel TrioTim >> >> > PatientName Gab_source_s1001 >> >> > Date and time >> >> > StudyDate 20091119 >> >> > StudyTime 170216.156000 >> >> > SeriesTime 180621.328000 >> >> > AcqTime 180331.855000 >> >> > Acquisition parameters >> >> > PulseSeq ep_b0#1 >> >> > Protocol DIFFUSION_HighRes_Short >> >> > PhEncDir COL >> >> > EchoNo 1 >> >> > FlipAngle 90 >> >> > EchoTime 84 >> >> > InversionTime -1 >> >> > RepetitionTime 7980 >> >> > PhEncFOV 256 >> >> > ReadoutFOV 256 >> >> > Image information >> >> > RunNo 19 >> >> > SeriesNo 20 >> >> > ImageNo 1 >> >> > NImageRows 1024 >> >> > NImageCols 1024 >> >> > NFrames 35 >> >> > SliceArraylSize 64 >> >> > IsMosaic 1 >> >> > ImgPos 863.3041 1153.2142 -113.6526 >> >> > VolRes 2.0000 2.0000 2.0000 >> >> > VolDim 128 128 64 >> >> > Vc -0.9895 -0.1445 0.0066 >> >> > Vr 0.1446 -0.9873 0.0662 >> >> > Vs -0.0031 0.0664 0.9978 >> >> > VolCenter 0.0000 0.0000 0.0000 >> >> > TransferSyntaxUID unknown >> >> > INFO: sorting. >> >> > INFO: (128 128 64), nframes = 35, ismosaic=1 >> >> > Could not parse NUMARIS version string syngo MR B15 >> >> > found in dicom tag 18,1020 (len = 3 != 6) >> >> > Repetition Time = 7980, TR = 7980 ms >> >> > PE Dir COL COL >> >> > AutoAlign matrix detected >> >> > AutoAlign Matrix --------------------- >> >> > 0.989 -0.141 0.034 4.549; >> >> > 0.145 0.949 -0.279 4.841; >> >> > 0.007 0.281 0.960 24.557; >> >> > 0.000 0.000 0.000 1.000; >> >> > >> >> > This looks like an MGH DTI volume >> >> > MGH DTI SeqPack Info >> >> > 0 ep_b0#1 0.000000 1 >> >> > 1 ep_b0#2 0.000000 2 >> >> > 2 ep_b0#3 0.000000 3 >> >> > 3 ep_b0#4 0.000000 4 >> >> > 4 ep_b0#5 0.000000 5 >> >> > 5 ep_b700#1 700.000000 1 >> >> > 6 ep_b700#2 700.000000 2 >> >> > 7 ep_b700#3 700.000000 3 >> >> > 8 ep_b700#4 700.000000 4 >> >> > 9 ep_b700#5 700.000000 5 >> >> > 10 ep_b700#6 700.000000 6 >> >> > 11 ep_b700#7 700.000000 7 >> >> > 12 ep_b700#8 700.000000 8 >> >> > 13 ep_b700#9 700.000000 9 >> >> > 14 ep_b700#10 700.000000 10 >> >> > 15 ep_b700#11 700.000000 11 >> >> > 16 ep_b700#12 700.000000 12 >> >> > 17 ep_b700#13 700.000000 13 >> >> > 18 ep_b700#14 700.000000 14 >> >> > 19 ep_b700#15 700.000000 15 >> >> > 20 ep_b700#16 700.000000 16 >> >> > 21 ep_b700#17 700.000000 17 >> >> > 22 ep_b700#18 700.000000 18 >> >> > 23 ep_b700#19 700.000000 19 >> >> > 24 ep_b700#20 700.000000 20 >> >> > 25 ep_b700#21 700.000000 21 >> >> > 26 ep_b700#22 700.000000 22 >> >> > 27 ep_b700#23 700.000000 23 >> >> > 28 ep_b700#24 700.000000 24 >> >> > 29 ep_b700#25 700.000000 25 >> >> > 30 ep_b700#26 700.000000 26 >> >> > 31 ep_b700#27 700.000000 27 >> >> > 32 ep_b700#28 700.000000 28 >> >> > 33 ep_b700#29 700.000000 29 >> >> > 34 ep_b700#30 700.000000 30 >> >> > bValue = 700 >> >> > nB0 = 5 >> >> > nDir = 30 >> >> > GradFile >> >> > >> >> >> /software/Freesurfer/5.1.0//diffusion/mgh-dti-seqpack/gradient_mgh_dti30.gdt >> >> > FileName /data/memory/sourcemem//s1001/156000-20-35.dcm >> >> > Identification >> >> > NumarisVer syngo MR B15 >> >> > ScannerModel TrioTim >> >> > PatientName Gab_source_s1001 >> >> > Date and time >> >> > StudyDate 20091119 >> >> > StudyTime 170216.156000 >> >> > SeriesTime 180621.328000 >> >> > AcqTime 180804.265000 >> >> > Acquisition parameters >> >> > PulseSeq ep_b700#30 >> >> > Protocol DIFFUSION_HighRes_Short >> >> > PhEncDir COL >> >> > EchoNo 1 >> >> > FlipAngle 90 >> >> > EchoTime 84 >> >> > InversionTime -1 >> >> > RepetitionTime 7980 >> >> > PhEncFOV 256 >> >> > ReadoutFOV 256 >> >> > Image information >> >> > RunNo 19 >> >> > SeriesNo 20 >> >> > ImageNo 35 >> >> > NImageRows 1024 >> >> > NImageCols 1024 >> >> > NFrames 35 >> >> > SliceArraylSize 64 >> >> > IsMosaic 1 >> >> > ImgPos 863.3041 1153.2142 -113.6526 >> >> > VolRes 2.0000 2.0000 2.0000 >> >> > VolDim 128 128 64 >> >> > Vc -0.9895 -0.1445 0.0066 >> >> > Vr 0.1446 -0.9873 0.0662 >> >> > Vs -0.0031 0.0664 0.9978 >> >> > VolCenter 0.0000 0.0000 0.0000 >> >> > TransferSyntaxUID unknown >> >> > sagrev = 0, correv =0, trarev = 0 >> >> > Vs = -0.00309869 0.0664423 0.997786 >> >> > INFO: no Siemens slice order reversal detected (good!). >> >> > TR=7980.00, TE=84.00, TI=-1.00, flip angle=90.00 >> >> > i_ras = (-0.989479, -0.144529, 0.00655128) >> >> > j_ras = (0.144644, -0.987267, 0.0661911) >> >> > k_ras = (-0.00309869, 0.0664423, 0.997786) >> >> > writing to >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz... >> >> > Saving bvals and bvecs >> >> > mri_probedicom --i /data/memory/sourcemem//s1001/156000-20-1.dcm > >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dcminfo.dat >> >> > flip4fsl >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> >> > INFO: input image orientation is LPS >> >> > INFO: input image determinant is 8 >> >> > fslswapdim >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> x >> >> -y z >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> >> > INFO: left-right orientation was flipped by fslswapdim >> >> > fslorient -forceradiological >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> >> > INFO: found >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.mghdti.bvals, >> >> > converting to FSL format >> >> > INFO: found >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.mghdti.bvecs, >> >> > converting to FSL format >> >> > mv -f >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.mghdti.bvecs >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> >> > mv -f >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.mghdti.bvals >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvals >> >> > eddy_correct >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz 0 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0000 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0001 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0002 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0003 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0004 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0005 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0006 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0007 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0008 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0009 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0010 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0011 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0012 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0013 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0014 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0015 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0016 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0017 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0018 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0019 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0020 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0021 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0022 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0023 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0024 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0025 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0026 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0027 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0028 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0029 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0030 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0031 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0032 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0033 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0034 >> >> > mv -f /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs.norot >> >> > xfmrot >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.ecclog >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs.norot >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> >> > fslroi >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz 0 5 >> >> > fslmaths >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> >> > -Tmean >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> >> > bet /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain.nii.gz >> >> -m >> >> -f >> >> > 0.3 >> >> > mv -f >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain_mask.nii.gz >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/diff >> >> > #------------------------------------- >> >> > #@# Inter-subject registration Tue Dec 6 22:15:05 EST 2011 >> >> > flirt -in >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain.nii.gz >> >> -ref >> >> > /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain_mni.nii.gz >> >> > -omat >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/diff2mni.mat >> >> > -cost mutualinfo >> >> > convert_xfm -omat >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/mni2diff.mat >> >> > -inverse >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/diff2mni.mat >> >> > #------------------------------------- >> >> > #@# Masks Tue Dec 6 22:15:47 EST 2011 >> >> > #------------------------------------- >> >> > #@# Tensor fit Tue Dec 6 22:15:47 EST 2011 >> >> > dtifit -k >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz >> >> -m >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/diff/lowb_brain_mask.nii.gz >> >> > -r /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs -b >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvals -o >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dtifit >> >> > 0 128 0 128 0 64 >> >> > 0 slices processed >> >> > 1 slices processed >> >> > 2 slices processed >> >> > 3 slices processed >> >> > 4 slices processed >> >> > 5 slices processed >> >> > 6 slices processed >> >> > 7 slices processed >> >> > 8 slices processed >> >> > 9 slices processed >> >> > 10 slices processed >> >> > 11 slices processed >> >> > 12 slices processed >> >> > 13 slices processed >> >> > 14 slices processed >> >> > 15 slices processed >> >> > 16 slices processed >> >> > 17 slices processed >> >> > 18 slices processed >> >> > 19 slices processed >> >> > 20 slices processed >> >> > 21 slices processed >> >> > 22 slices processed >> >> > 23 slices processed >> >> > 24 slices processed >> >> > 25 slices processed >> >> > 26 slices processed >> >> > 27 slices processed >> >> > 28 slices processed >> >> > 29 slices processed >> >> > 30 slices processed >> >> > 31 slices processed >> >> > 32 slices processed >> >> > 33 slices processed >> >> > 34 slices processed >> >> > 35 slices processed >> >> > 36 slices processed >> >> > 37 slices processed >> >> > 38 slices processed >> >> > 39 slices processed >> >> > 40 slices processed >> >> > 41 slices processed >> >> > 42 slices processed >> >> > 43 slices processed >> >> > 44 slices processed >> >> > 45 slices processed >> >> > 46 slices processed >> >> > 47 slices processed >> >> > 48 slices processed >> >> > 49 slices processed >> >> > 50 slices processed >> >> > 51 slices processed >> >> > 52 slices processed >> >> > 53 slices processed >> >> > 54 slices processed >> >> > 55 slices processed >> >> > 56 slices processed >> >> > 57 slices processed >> >> > 58 slices processed >> >> > 59 slices processed >> >> > 60 slices processed >> >> > 61 slices processed >> >> > 62 slices processed >> >> > 63 slices processed >> >> > #------------------------------------- >> >> > #@# Priors Tue Dec 6 22:15:54 EST 2011 >> >> > /software/Freesurfer/5.1.0//bin/dmri_train --outdir >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni --out >> >> > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt >> >> lh.ilf_AS_avg33_mni_flt >> >> > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt >> >> rh.unc_AS_avg33_mni_flt >> >> > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt >> >> lh.atr_PP_avg33_mni_flt >> >> > rh.atr_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt >> >> rh.ccg_PP_avg33_mni_flt >> >> > lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt >> >> lh.slfp_PP_avg33_mni_flt >> >> > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt >> >> rh.slft_PP_avg33_mni_flt >> >> > --slist /tmp/subj33.s1001.8627.txt --trk >> dlabel/mni/lh.cst_AS.flt.trk >> >> > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk >> >> > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk >> >> > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk >> >> > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk >> >> > dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk >> >> > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk >> >> > dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk >> >> > dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk >> >> > dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz >> >> --cmask >> >> > dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 >> 0 0 >> >> 0 >> >> 0 >> >> > 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz >> >> > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz >> >> dlabel/mni/rh.cst_AS_roi1.flt.nii.gz >> >> > dlabel/mni/rh.cst_AS_roi2.flt.nii.gz >> >> dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz >> >> > dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz >> >> dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz >> >> > dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz >> >> dlabel/mni/lh.unc_AS_roi1.flt.nii.gz >> >> > dlabel/mni/lh.unc_AS_roi2.flt.nii.gz >> >> dlabel/mni/rh.unc_AS_roi1.flt.nii.gz >> >> > dlabel/mni/rh.unc_AS_roi2.flt.nii.gz >> >> dlabel/mni/fmajor_PP_roi1.flt.nii.gz >> >> > dlabel/mni/fmajor_PP_roi2.flt.nii.gz >> >> dlabel/mni/fminor_PP_roi1.flt.nii.gz >> >> > dlabel/mni/fminor_PP_roi2.flt.nii.gz >> >> dlabel/mni/lh.atr_PP_roi1.flt.nii.gz >> >> > dlabel/mni/lh.atr_PP_roi2.flt.nii.gz >> >> dlabel/mni/rh.atr_PP_roi1.flt.nii.gz >> >> > dlabel/mni/rh.atr_PP_roi2.flt.nii.gz >> >> dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz >> >> > dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz >> >> dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz >> >> > dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz >> >> dlabel/mni/lh.cab_PP_roi1.flt.nii.gz >> >> > dlabel/mni/lh.cab_PP_roi2.flt.nii.gz >> >> dlabel/mni/rh.cab_PP_roi1.flt.nii.gz >> >> > dlabel/mni/rh.cab_PP_roi2.flt.nii.gz >> >> dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz >> >> > dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz >> >> > dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz >> >> > dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz >> >> > dlabel/mni/lh.slft_PP_roi1.flt.nii.gz >> >> > dlabel/mni/lh.slft_PP_roi2.flt.nii.gz >> >> > dlabel/mni/rh.slft_PP_roi1.flt.nii.gz >> >> > dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni/lowb_brain_mask.flt.nii.gz >> >> > --fa >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/mni/dtifit_FA.flt.nii.gz >> >> > --ncpts 5 --debug >> >> > ERROR: fio_pushd: >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni >> >> > ERROR: must specify brain mask volume for output subject >> >> > _______________________________________________ >> >> > 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. >> >> >> >> >> > >> >> >

2 1

Re: [Freesurfer] tracula ERROR: must specify brain mask volume for output subject
by Priti Srinivasan 08 Dec '11

08 Dec '11

Hi Paula, which image are you trying to open? If you're trying to open the merged files in freeview, you should use the -tv flag for opening it. Did you source the freesurfer environment before opening freeview? Can you give us the exact commandline you used? Priti > hi, > i am trying to visualize my results with freeview, and i am running into > this error. i am using freesurfer 5.1.0. do you know what the problem is? > : > > cpdla@ba3:~/Documents/s1001/dmri$ freeview > X Error: BadValue (integer parameter out of range for operation) 2 > Extension: 146 (Uknown extension) > Minor opcode: 3 (Unknown request) > Resource id: 0x24 > Abort > > > On Wed, Dec 7, 2011 at 12:52 PM, Priti Srinivasan < > rspriti(a)nmr.mgh.harvard.edu> wrote: > >> Hi Paula, >> >> Tracula uses anatomical labels/files from freesurfer cortical >> reconstruction to build the posterior distribution of the tracts. It >> looks >> like you may not have run freesurfer recon for your subject. >> >> To run freesurfer recon for your subject please refer to the following >> page: >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide >> >> Especially, >> >> recon-all \ >> -i <one slice in the anatomical dicom series> \ >> -s <subject id that you make up> \ >> -sd <directory to put the subject folder in> \ >> -all >> >> Once this finishes processing you can re-run tracula to see if that >> solves >> the issue. >> >> Hope that is helpful, >> Priti >> >> >> >> > Hi. >> > >> > I am running into the following error: >> > ERROR: fio_pushd: >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni >> > ERROR: must specify brain mask volume for output subject . >> > >> > I googled this error and it seems like you suggested this to someone >> else >> > : >> > "As for your error, it looks like maybe the freesurfer recon wasn't >> found, >> > so >> > it skipped some steps (diffusion-to-anatomical registration and mask >> > creation). >> > Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist? >> > >> > >> > a.y" >> > >> > What is the freesurfer recon dir supposed to look like? Any >> > suggestions on how to fix this error? Below is my output. >> > >> > Thanks, >> > C. Paula >> > >> > >> > >> > >> > ba3:~/Documents> trac-all -prep -c dmrirc_single_subject >> > set: Variable name must begin with a letter. >> > INFO: SUBJECTS_DIR is >> > /mindhive/gablab/users/cpdla/Documents/diffusion_recons >> > INFO: Diffusion root is /mindhive/gablab/users/cpdla/Documents/ >> > Actual FREESURFER_HOME /software/Freesurfer/5.1.0 >> > trac-preproc -c >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/dmrirc.local >> -log >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.log >> -cmd >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.cmd >> > #------------------------------------- >> > /software/Freesurfer/5.1.0//bin/trac-preproc >> > #------------------------------------- >> > #@# Image corrections Tue Dec 6 22:02:37 EST 2011 >> > mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> > mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >> > reading from /data/memory/sourcemem//s1001/156000-20-1.dcm... >> > Getting Series No >> > INFO: Found 3207 files in /data/memory/sourcemem//s1001 >> > INFO: Scanning for Series Number 20 >> > Scanning Directory >> > INFO: found 35 files in series >> > INFO: loading series header info. >> > >> > RunNo = 19 >> > WARNING: Run 1 appears to be truncated >> > Files Found: 35, Files Expected (lRep+1): 60 >> > FileName /data/memory/sourcemem//s1001/156000-20-1.dcm >> > Identification >> > NumarisVer syngo MR B15 >> > ScannerModel TrioTim >> > PatientName Gab_source_s1001 >> > Date and time >> > StudyDate 20091119 >> > StudyTime 170216.156000 >> > SeriesTime 180621.328000 >> > AcqTime 180331.855000 >> > Acquisition parameters >> > PulseSeq ep_b0#1 >> > Protocol DIFFUSION_HighRes_Short >> > PhEncDir COL >> > EchoNo 1 >> > FlipAngle 90 >> > EchoTime 84 >> > InversionTime -1 >> > RepetitionTime 7980 >> > PhEncFOV 256 >> > ReadoutFOV 256 >> > Image information >> > RunNo 19 >> > SeriesNo 20 >> > ImageNo 1 >> > NImageRows 1024 >> > NImageCols 1024 >> > NFrames 35 >> > SliceArraylSize 64 >> > IsMosaic 1 >> > ImgPos 863.3041 1153.2142 -113.6526 >> > VolRes 2.0000 2.0000 2.0000 >> > VolDim 128 128 64 >> > Vc -0.9895 -0.1445 0.0066 >> > Vr 0.1446 -0.9873 0.0662 >> > Vs -0.0031 0.0664 0.9978 >> > VolCenter 0.0000 0.0000 0.0000 >> > TransferSyntaxUID unknown >> > INFO: sorting. >> > INFO: (128 128 64), nframes = 35, ismosaic=1 >> > Could not parse NUMARIS version string syngo MR B15 >> > found in dicom tag 18,1020 (len = 3 != 6) >> > Repetition Time = 7980, TR = 7980 ms >> > PE Dir COL COL >> > AutoAlign matrix detected >> > AutoAlign Matrix --------------------- >> > 0.989 -0.141 0.034 4.549; >> > 0.145 0.949 -0.279 4.841; >> > 0.007 0.281 0.960 24.557; >> > 0.000 0.000 0.000 1.000; >> > >> > This looks like an MGH DTI volume >> > MGH DTI SeqPack Info >> > 0 ep_b0#1 0.000000 1 >> > 1 ep_b0#2 0.000000 2 >> > 2 ep_b0#3 0.000000 3 >> > 3 ep_b0#4 0.000000 4 >> > 4 ep_b0#5 0.000000 5 >> > 5 ep_b700#1 700.000000 1 >> > 6 ep_b700#2 700.000000 2 >> > 7 ep_b700#3 700.000000 3 >> > 8 ep_b700#4 700.000000 4 >> > 9 ep_b700#5 700.000000 5 >> > 10 ep_b700#6 700.000000 6 >> > 11 ep_b700#7 700.000000 7 >> > 12 ep_b700#8 700.000000 8 >> > 13 ep_b700#9 700.000000 9 >> > 14 ep_b700#10 700.000000 10 >> > 15 ep_b700#11 700.000000 11 >> > 16 ep_b700#12 700.000000 12 >> > 17 ep_b700#13 700.000000 13 >> > 18 ep_b700#14 700.000000 14 >> > 19 ep_b700#15 700.000000 15 >> > 20 ep_b700#16 700.000000 16 >> > 21 ep_b700#17 700.000000 17 >> > 22 ep_b700#18 700.000000 18 >> > 23 ep_b700#19 700.000000 19 >> > 24 ep_b700#20 700.000000 20 >> > 25 ep_b700#21 700.000000 21 >> > 26 ep_b700#22 700.000000 22 >> > 27 ep_b700#23 700.000000 23 >> > 28 ep_b700#24 700.000000 24 >> > 29 ep_b700#25 700.000000 25 >> > 30 ep_b700#26 700.000000 26 >> > 31 ep_b700#27 700.000000 27 >> > 32 ep_b700#28 700.000000 28 >> > 33 ep_b700#29 700.000000 29 >> > 34 ep_b700#30 700.000000 30 >> > bValue = 700 >> > nB0 = 5 >> > nDir = 30 >> > GradFile >> > >> /software/Freesurfer/5.1.0//diffusion/mgh-dti-seqpack/gradient_mgh_dti30.gdt >> > FileName /data/memory/sourcemem//s1001/156000-20-35.dcm >> > Identification >> > NumarisVer syngo MR B15 >> > ScannerModel TrioTim >> > PatientName Gab_source_s1001 >> > Date and time >> > StudyDate 20091119 >> > StudyTime 170216.156000 >> > SeriesTime 180621.328000 >> > AcqTime 180804.265000 >> > Acquisition parameters >> > PulseSeq ep_b700#30 >> > Protocol DIFFUSION_HighRes_Short >> > PhEncDir COL >> > EchoNo 1 >> > FlipAngle 90 >> > EchoTime 84 >> > InversionTime -1 >> > RepetitionTime 7980 >> > PhEncFOV 256 >> > ReadoutFOV 256 >> > Image information >> > RunNo 19 >> > SeriesNo 20 >> > ImageNo 35 >> > NImageRows 1024 >> > NImageCols 1024 >> > NFrames 35 >> > SliceArraylSize 64 >> > IsMosaic 1 >> > ImgPos 863.3041 1153.2142 -113.6526 >> > VolRes 2.0000 2.0000 2.0000 >> > VolDim 128 128 64 >> > Vc -0.9895 -0.1445 0.0066 >> > Vr 0.1446 -0.9873 0.0662 >> > Vs -0.0031 0.0664 0.9978 >> > VolCenter 0.0000 0.0000 0.0000 >> > TransferSyntaxUID unknown >> > sagrev = 0, correv =0, trarev = 0 >> > Vs = -0.00309869 0.0664423 0.997786 >> > INFO: no Siemens slice order reversal detected (good!). >> > TR=7980.00, TE=84.00, TI=-1.00, flip angle=90.00 >> > i_ras = (-0.989479, -0.144529, 0.00655128) >> > j_ras = (0.144644, -0.987267, 0.0661911) >> > k_ras = (-0.00309869, 0.0664423, 0.997786) >> > writing to >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz... >> > Saving bvals and bvecs >> > mri_probedicom --i /data/memory/sourcemem//s1001/156000-20-1.dcm > >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dcminfo.dat >> > flip4fsl >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> > INFO: input image orientation is LPS >> > INFO: input image determinant is 8 >> > fslswapdim >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz x >> -y z >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> > INFO: left-right orientation was flipped by fslswapdim >> > fslorient -forceradiological >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> > INFO: found >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.mghdti.bvals, >> > converting to FSL format >> > INFO: found >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.mghdti.bvecs, >> > converting to FSL format >> > mv -f >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.mghdti.bvecs >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> > mv -f >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.mghdti.bvals >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvals >> > eddy_correct >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz 0 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0000 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0001 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0002 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0003 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0004 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0005 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0006 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0007 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0008 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0009 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0010 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0011 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0012 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0013 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0014 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0015 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0016 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0017 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0018 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0019 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0020 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0021 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0022 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0023 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0024 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0025 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0026 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0027 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0028 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0029 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0030 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0031 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0032 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0033 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0034 >> > mv -f /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs.norot >> > xfmrot /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.ecclog >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs.norot >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> > fslroi /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz 0 5 >> > fslmaths >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> > -Tmean /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> > bet /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain.nii.gz >> -m >> -f >> > 0.3 >> > mv -f >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain_mask.nii.gz >> > /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/diff >> > #------------------------------------- >> > #@# Inter-subject registration Tue Dec 6 22:15:05 EST 2011 >> > flirt -in >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain.nii.gz >> -ref >> > /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain_mni.nii.gz >> > -omat >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/diff2mni.mat >> > -cost mutualinfo >> > convert_xfm -omat >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/mni2diff.mat >> > -inverse >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/diff2mni.mat >> > #------------------------------------- >> > #@# Masks Tue Dec 6 22:15:47 EST 2011 >> > #------------------------------------- >> > #@# Tensor fit Tue Dec 6 22:15:47 EST 2011 >> > dtifit -k >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz >> -m >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/diff/lowb_brain_mask.nii.gz >> > -r /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs -b >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvals -o >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dtifit >> > 0 128 0 128 0 64 >> > 0 slices processed >> > 1 slices processed >> > 2 slices processed >> > 3 slices processed >> > 4 slices processed >> > 5 slices processed >> > 6 slices processed >> > 7 slices processed >> > 8 slices processed >> > 9 slices processed >> > 10 slices processed >> > 11 slices processed >> > 12 slices processed >> > 13 slices processed >> > 14 slices processed >> > 15 slices processed >> > 16 slices processed >> > 17 slices processed >> > 18 slices processed >> > 19 slices processed >> > 20 slices processed >> > 21 slices processed >> > 22 slices processed >> > 23 slices processed >> > 24 slices processed >> > 25 slices processed >> > 26 slices processed >> > 27 slices processed >> > 28 slices processed >> > 29 slices processed >> > 30 slices processed >> > 31 slices processed >> > 32 slices processed >> > 33 slices processed >> > 34 slices processed >> > 35 slices processed >> > 36 slices processed >> > 37 slices processed >> > 38 slices processed >> > 39 slices processed >> > 40 slices processed >> > 41 slices processed >> > 42 slices processed >> > 43 slices processed >> > 44 slices processed >> > 45 slices processed >> > 46 slices processed >> > 47 slices processed >> > 48 slices processed >> > 49 slices processed >> > 50 slices processed >> > 51 slices processed >> > 52 slices processed >> > 53 slices processed >> > 54 slices processed >> > 55 slices processed >> > 56 slices processed >> > 57 slices processed >> > 58 slices processed >> > 59 slices processed >> > 60 slices processed >> > 61 slices processed >> > 62 slices processed >> > 63 slices processed >> > #------------------------------------- >> > #@# Priors Tue Dec 6 22:15:54 EST 2011 >> > /software/Freesurfer/5.1.0//bin/dmri_train --outdir >> > /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni --out >> > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt >> lh.ilf_AS_avg33_mni_flt >> > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt >> rh.unc_AS_avg33_mni_flt >> > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt >> lh.atr_PP_avg33_mni_flt >> > rh.atr_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt >> rh.ccg_PP_avg33_mni_flt >> > lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt >> lh.slfp_PP_avg33_mni_flt >> > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt >> rh.slft_PP_avg33_mni_flt >> > --slist /tmp/subj33.s1001.8627.txt --trk dlabel/mni/lh.cst_AS.flt.trk >> > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk >> > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk >> > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk >> > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk >> > dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk >> > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk >> > dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk >> > dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk >> > dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz >> --cmask >> > dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 >> 0 >> 0 >> > 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz >> > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz >> dlabel/mni/rh.cst_AS_roi1.flt.nii.gz >> > dlabel/mni/rh.cst_AS_roi2.flt.nii.gz >> dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz >> > dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz >> dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz >> > dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz >> dlabel/mni/lh.unc_AS_roi1.flt.nii.gz >> > dlabel/mni/lh.unc_AS_roi2.flt.nii.gz >> dlabel/mni/rh.unc_AS_roi1.flt.nii.gz >> > dlabel/mni/rh.unc_AS_roi2.flt.nii.gz >> dlabel/mni/fmajor_PP_roi1.flt.nii.gz >> > dlabel/mni/fmajor_PP_roi2.flt.nii.gz >> dlabel/mni/fminor_PP_roi1.flt.nii.gz >> > dlabel/mni/fminor_PP_roi2.flt.nii.gz >> dlabel/mni/lh.atr_PP_roi1.flt.nii.gz >> > dlabel/mni/lh.atr_PP_roi2.flt.nii.gz >> dlabel/mni/rh.atr_PP_roi1.flt.nii.gz >> > dlabel/mni/rh.atr_PP_roi2.flt.nii.gz >> dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz >> > dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz >> dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz >> > dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz >> dlabel/mni/lh.cab_PP_roi1.flt.nii.gz >> > dlabel/mni/lh.cab_PP_roi2.flt.nii.gz >> dlabel/mni/rh.cab_PP_roi1.flt.nii.gz >> > dlabel/mni/rh.cab_PP_roi2.flt.nii.gz >> dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz >> > dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz >> > dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz >> > dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz >> > dlabel/mni/lh.slft_PP_roi1.flt.nii.gz >> > dlabel/mni/lh.slft_PP_roi2.flt.nii.gz >> > dlabel/mni/rh.slft_PP_roi1.flt.nii.gz >> > dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni/lowb_brain_mask.flt.nii.gz >> > --fa >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/mni/dtifit_FA.flt.nii.gz >> > --ncpts 5 --debug >> > ERROR: fio_pushd: >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni >> > ERROR: must specify brain mask volume for output subject >> > _______________________________________________ >> > 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

overlapping of the surfaces from one hemisphere to another
by Eunjin Yoon 08 Dec '11

08 Dec '11

Dear, Freesurfer users I am processing 1.5T MR images, and found some overlapping of the surfaces from one hemisphere to another. I attached captured images of that subject. you can find the error center of the brain image. How can I fix that?? Thank you in advance. Best Regards, Eunjin

3 3

Commands not installed w/ PPC Tiger distribution
by Iain DeWitt 07 Dec '11

07 Dec '11

Following up on Ashley's post from 06 Jun 2011 (see below), I also find certain commands (see below) are not installed with the current (v5.1) PPC OS X Tiger distribution. I had to go back to v4.3 to get a complete set of commands. cheers Iain talairach_avi: Command not found. mri_watershed: Command not found. mri_segment: Command not found. mri_tessellate: Command not found. mri_concatenate_lta: Command not found. mri_normalize_tp2: Command not found. mris_smooth: Command not found. mris_inflate: Command not found. mris_curvature: Command not found. mris_sphere: Command not found. mris_fix_topology: Command not found. mris_topo_fixer: Command not found. mris_ca_label: Command not found. mris_euler_number: Command not found. mris_make_surfaces: Command not found. mris_register: Command not found. mris_volmask: Command not found. mris_anatomical_stats: Command not found. mrisp_paint: Command not found. mris_curvature_stats: Command not found. mris_calc: Command not found. mri_robust_register: Command not found. mri_robust_template: Command not found. mri_segstats: Command not found. Commands missing in freesurfer directory ANN40 Mon, 06 Jun 2011 06:22:06 -0700 Hi all, I recently downloaded and installed freesurfer for a Mac PowerPC. I tried running recon-all on my data and an error message came up saying command not found for talairach_avi and many other commands. I looked in my /Applications/freesurfer/bin directory and that file wasn't there. All the commands that had worked such as mri_convert were. Does anyone know what could be causing this problem? Thanks, Ashley

2 1

Registration issues
by Antonella Kis 07 Dec '11

07 Dec '11

Dear All: I would like to know if to check my DTI's data registration on the anatomical data having the registration encoded in the registration.dat by tkmedit as below: tkregister2 --mov /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51_dti.nii.gz --s /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51 \ --regheader --reg /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51_dti/register.dat --surf I will see my DTI volume as a fuzzy MOVEABLE volume and the target will be my anatomical volume? What will represent the green line? What is the difference is I run without --s and without --regheader so if I run just: tkregister2 --mov /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51_dti.nii.gz --reg /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51_dti/register.dat --surf Thank you very much. Antonella

1 0

entorhinal cortex volume
by Cat Chong 07 Dec '11

07 Dec '11

Another basic question: Could you tell me what is the best way of putting the ?h.entorhinal_exvivo.stats into a spreadsheet for all subjects? Is there a way to achieve a textfile output for all subjects similar in concept to kvlQuantifyHippocampalSubfieldSegmentations.sh ? catherine

1 0

color map in Freeview
by Antonella Kis 07 Dec '11

07 Dec '11

Dear All, I was trying to find an explanation of the color map: min, Mid, MAx and Offset values in Freeview. Can someone please explain me if I have the color map set it up as HEAT what is the meaning of this values if for example I am viewing the existing clusters after multiple comparison for the DTI data.Also can I load my FA group data registered on TAL: group-fa-tal.nii with tkmedit? Many thanks. Antonella

3 4

tracula ERROR: must specify brain mask volume for output subject
by C. Paula de los Angeles 07 Dec '11

07 Dec '11

Hi. I am running into the following error: ERROR: fio_pushd: /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni ERROR: must specify brain mask volume for output subject . I googled this error and it seems like you suggested this to someone else : "As for your error, it looks like maybe the freesurfer recon wasn't found, so it skipped some steps (diffusion-to-anatomical registration and mask creation). Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist? a.y" What is the freesurfer recon dir supposed to look like? Any suggestions on how to fix this error? Below is my output. Thanks, C. Paula ba3:~/Documents> trac-all -prep -c dmrirc_single_subject set: Variable name must begin with a letter. INFO: SUBJECTS_DIR is /mindhive/gablab/users/cpdla/Documents/diffusion_recons INFO: Diffusion root is /mindhive/gablab/users/cpdla/Documents/ Actual FREESURFER_HOME /software/Freesurfer/5.1.0 trac-preproc -c /mindhive/gablab/users/cpdla/Documents//s1001/scripts/dmrirc.local -log /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.log -cmd /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.cmd #------------------------------------- /software/Freesurfer/5.1.0//bin/trac-preproc #------------------------------------- #@# Image corrections Tue Dec 6 22:02:37 EST 2011 mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /data/memory/sourcemem//s1001/156000-20-1.dcm... Getting Series No INFO: Found 3207 files in /data/memory/sourcemem//s1001 INFO: Scanning for Series Number 20 Scanning Directory INFO: found 35 files in series INFO: loading series header info. RunNo = 19 WARNING: Run 1 appears to be truncated Files Found: 35, Files Expected (lRep+1): 60 FileName /data/memory/sourcemem//s1001/156000-20-1.dcm Identification NumarisVer syngo MR B15 ScannerModel TrioTim PatientName Gab_source_s1001 Date and time StudyDate 20091119 StudyTime 170216.156000 SeriesTime 180621.328000 AcqTime 180331.855000 Acquisition parameters PulseSeq ep_b0#1 Protocol DIFFUSION_HighRes_Short PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 84 InversionTime -1 RepetitionTime 7980 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 19 SeriesNo 20 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 35 SliceArraylSize 64 IsMosaic 1 ImgPos 863.3041 1153.2142 -113.6526 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 64 Vc -0.9895 -0.1445 0.0066 Vr 0.1446 -0.9873 0.0662 Vs -0.0031 0.0664 0.9978 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID unknown INFO: sorting. INFO: (128 128 64), nframes = 35, ismosaic=1 Could not parse NUMARIS version string syngo MR B15 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 7980, TR = 7980 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 0.989 -0.141 0.034 4.549; 0.145 0.949 -0.279 4.841; 0.007 0.281 0.960 24.557; 0.000 0.000 0.000 1.000; This looks like an MGH DTI volume MGH DTI SeqPack Info 0 ep_b0#1 0.000000 1 1 ep_b0#2 0.000000 2 2 ep_b0#3 0.000000 3 3 ep_b0#4 0.000000 4 4 ep_b0#5 0.000000 5 5 ep_b700#1 700.000000 1 6 ep_b700#2 700.000000 2 7 ep_b700#3 700.000000 3 8 ep_b700#4 700.000000 4 9 ep_b700#5 700.000000 5 10 ep_b700#6 700.000000 6 11 ep_b700#7 700.000000 7 12 ep_b700#8 700.000000 8 13 ep_b700#9 700.000000 9 14 ep_b700#10 700.000000 10 15 ep_b700#11 700.000000 11 16 ep_b700#12 700.000000 12 17 ep_b700#13 700.000000 13 18 ep_b700#14 700.000000 14 19 ep_b700#15 700.000000 15 20 ep_b700#16 700.000000 16 21 ep_b700#17 700.000000 17 22 ep_b700#18 700.000000 18 23 ep_b700#19 700.000000 19 24 ep_b700#20 700.000000 20 25 ep_b700#21 700.000000 21 26 ep_b700#22 700.000000 22 27 ep_b700#23 700.000000 23 28 ep_b700#24 700.000000 24 29 ep_b700#25 700.000000 25 30 ep_b700#26 700.000000 26 31 ep_b700#27 700.000000 27 32 ep_b700#28 700.000000 28 33 ep_b700#29 700.000000 29 34 ep_b700#30 700.000000 30 bValue = 700 nB0 = 5 nDir = 30 GradFile /software/Freesurfer/5.1.0//diffusion/mgh-dti-seqpack/gradient_mgh_dti30.gdt FileName /data/memory/sourcemem//s1001/156000-20-35.dcm Identification NumarisVer syngo MR B15 ScannerModel TrioTim PatientName Gab_source_s1001 Date and time StudyDate 20091119 StudyTime 170216.156000 SeriesTime 180621.328000 AcqTime 180804.265000 Acquisition parameters PulseSeq ep_b700#30 Protocol DIFFUSION_HighRes_Short PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 84 InversionTime -1 RepetitionTime 7980 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 19 SeriesNo 20 ImageNo 35 NImageRows 1024 NImageCols 1024 NFrames 35 SliceArraylSize 64 IsMosaic 1 ImgPos 863.3041 1153.2142 -113.6526 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 64 Vc -0.9895 -0.1445 0.0066 Vr 0.1446 -0.9873 0.0662 Vs -0.0031 0.0664 0.9978 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID unknown sagrev = 0, correv =0, trarev = 0 Vs = -0.00309869 0.0664423 0.997786 INFO: no Siemens slice order reversal detected (good!). TR=7980.00, TE=84.00, TI=-1.00, flip angle=90.00 i_ras = (-0.989479, -0.144529, 0.00655128) j_ras = (0.144644, -0.987267, 0.0661911) k_ras = (-0.00309869, 0.0664423, 0.997786) writing to /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz... Saving bvals and bvecs mri_probedicom --i /data/memory/sourcemem//s1001/156000-20-1.dcm > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dcminfo.dat flip4fsl /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 fslswapdim /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz x -y z /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz INFO: found /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.mghdti.bvecs /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs mv -f /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.mghdti.bvals /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvals eddy_correct /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz 0 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0000 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0001 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0002 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0003 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0004 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0005 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0006 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0007 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0008 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0009 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0010 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0011 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0012 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0013 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0014 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0015 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0016 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0017 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0018 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0019 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0020 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0021 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0022 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0023 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0024 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0025 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0026 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0027 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0028 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0029 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0030 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0031 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0032 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0033 processing /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0034 mv -f /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs.norot xfmrot /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.ecclog /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs.norot /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs fslroi /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz 0 5 fslmaths /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz -Tmean /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz bet /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain_mask.nii.gz /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/diff #------------------------------------- #@# Inter-subject registration Tue Dec 6 22:15:05 EST 2011 flirt -in /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain_mni.nii.gz -omat /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/diff2mni.mat -cost mutualinfo convert_xfm -omat /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/mni2diff.mat -inverse /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/diff2mni.mat #------------------------------------- #@# Masks Tue Dec 6 22:15:47 EST 2011 #------------------------------------- #@# Tensor fit Tue Dec 6 22:15:47 EST 2011 dtifit -k /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz -m /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/diff/lowb_brain_mask.nii.gz -r /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs -b /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvals -o /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dtifit 0 128 0 128 0 64 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed 44 slices processed 45 slices processed 46 slices processed 47 slices processed 48 slices processed 49 slices processed 50 slices processed 51 slices processed 52 slices processed 53 slices processed 54 slices processed 55 slices processed 56 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed 62 slices processed 63 slices processed #------------------------------------- #@# Priors Tue Dec 6 22:15:54 EST 2011 /software/Freesurfer/5.1.0//bin/dmri_train --outdir /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.s1001.8627.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni/lowb_brain_mask.flt.nii.gz --fa /mindhive/gablab/users/cpdla/Documents//s1001/dmri/mni/dtifit_FA.flt.nii.gz --ncpts 5 --debug ERROR: fio_pushd: /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni ERROR: must specify brain mask volume for output subject

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atlas used for subcortical segmentation
by Wenger, Elisabeth 07 Dec '11

07 Dec '11

Dear Freesurfer specialists, we are currently working on a comparison paper between manual segmentations and freesurfer segmentations of the hippocampus. In the paper by Jovicich and colleagues (2009) they mention that they generated their own segmentation atlas for the full brain freesurfer segmentation that consisted of different people of different age groups. We found this really interesting and wondered which segmentation atlas is used in the default stream of Freesurfer for subcortical segmentation? How many people were in that sample that created this atlas and which age were they? As we are specifically working with the hippocampus segmentations, it would also be very interesting to know what the mean size of their hippocampi was? Or is there maybe a paper that specifically describes in detail the descriptives of the used subjects for the standard atlas you could recommend us? Thank you very much for all your help and your time! Cheers, Johan and Elisabeth

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