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