Freesurfer

freesurfer@nmr.mgh.harvard.edu

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dt_recon error
by Daniel Davidson Callow 15 Feb '19

15 Feb '19

External Email - Use Caution Hello, When I run dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon/${subj}.${cond}. It does produce a -dwi.bvals -dwi.voxel_space.bvecs file and I get this output in the error log (also attached). For reference the bvals and bvecs files were correct. MatrixReadTxT: could not scan value [1][1] could not allocate 1684305759 x 1144402954 matrix could not allocate 1684305759 x 1144402954 matrix unsupported matlab format 540094003 (unknown) And this is what I get in the command line while it is running. It does create a NIFTI file and it seems like it is trying to eddy current correct. setenv FSLOUTPUTTYPE NIFTI setenv FSLOUTPUTTYPE NIFTI echo "#@#-------------------------------" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo #@#------------------------------- #@#------------------------------- echo "Converting input" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo Converting input Converting input date | tee -a $LF date tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log Fri Feb 15 13:24:19 EST 2019 set f = $OutDir/dwi.nii set f = /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii set cmd = ( mri_convert $InputVol $f ) ; set cmd = ( mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii ) echo "cd `pwd`" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo cd `pwd` pwd cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex echo $cmd | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii $cmd | & tee -a $LF mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log mri_convert.bin /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm... Getting Series No INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex INFO: Scanning for Series Number 171 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 170 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName AES101 Date and time StudyDate 20170409 StudyTime 105710.343000 SeriesTime 120657.984000 AcqTime 120650.230000 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_mddw_D64 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 106 InversionTime -1 RepetitionTime 6300 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 170 SeriesNo 171 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 35 IsMosaic 1 ImgPos 630.8714 646.6747 -31.8394 VolRes 1.6406 1.6406 3.6000 VolDim 128 128 35 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (128 128 35), nframes = 65, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 6300, TR = 6300 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName AES101 Date and time StudyDate 20170409 StudyTime 105710.343000 SeriesTime 120657.984000 AcqTime 120650.230000 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_mddw_D64 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 106 InversionTime -1 RepetitionTime 6300 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 170 SeriesNo 171 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 35 IsMosaic 1 ImgPos 105.8714 121.6747 -31.8394 VolRes 1.6406 1.6406 3.6000 VolDim 128 128 35 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.8714 16.6747 31.1606 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii... Saving bvals and bvecs if ( $status ) exit 1 ; if ( 0 ) exit 1 echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo if ( $#bvals == 0 ) then if ( 0 == 0 ) then if ( $#infodump == 0 ) then if ( 0 == 0 ) then set infodump = $OutDir/dwi-infodump.dat set infodump = /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat set cmd = ( mri_probedicom --i $InputVol ) ; set cmd = ( mri_probedicom --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm ) echo "cd `pwd`" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo cd `pwd` pwd cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex echo $cmd | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo mri_probedicom --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm mri_probedicom --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm $cmd | & tee -a $LF > $infodump mri_probedicom --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log if ( $status ) exit 1 ; if ( 0 ) exit 1 echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo endif endif endif endif set fec = $OutDir/dwi-ec.nii set fec = /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii if ( $DoEddyCorrect ) then if ( 1 ) then echo "#@#-------------------------------" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo #@#------------------------------- #@#------------------------------- echo "Eddy/Motion Correct" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo Eddy/Motion Correct Eddy/Motion Correct date | tee -a $LF date tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log Fri Feb 15 13:24:31 EST 2019 set ectmp = $OutDir/ectmp set ectmp = /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp mkdir -p $ectmp mkdir -p /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp pushd $ectmp > /dev/null pushd /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp set cmd = ( eddy_correct $f $fec $ECRefTP ) set cmd = ( eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0 ) echo "cd `pwd`" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo cd `pwd` pwd cd /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp echo $cmd | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0 eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0 $cmd | & tee -a $LF eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0 tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0000 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0001 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0002 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0003 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0004 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0005 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0006 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0007 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0008 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0009 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0010 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0011 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0012 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0013 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0014 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0015 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0016 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0017 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0018 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0019 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0020 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0021 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0022 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0023 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0024 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0025 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0026 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0027 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0028 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0029 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0030 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0031 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0032 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0033 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0034 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0035 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0036 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0037 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0038 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0039 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0040 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0041 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0042 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0043 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0044 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0045 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0046 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0047 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0048 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0049 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0050 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0051 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0052 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0053 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0054 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0055 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0056 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0057 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0058 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0059 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0060 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0061 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0062 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0063 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0064 if ( $status ) exit 1 ; if ( 0 ) exit 1 if ( ! -e $fec ) then if ( ! -e /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii ) then popd > /dev/null popd rm -r $ectmp rm -r /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo else else echo "#@#-------------------------------" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo #@#------------------------------- #@#------------------------------- echo "Fitting Tensors" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo Fitting Tensors Fitting Tensors date | tee -a $LF date tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log Fri Feb 15 13:33:13 EST 2019 set cmd = ( gzip $f ) set cmd = ( gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii ) echo $cmd | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii $cmd | & tee -a $LF gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log if ( $status ) exit 1 ; if ( 0 ) exit 1 echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo set cmd = ( gzip $fec ) set cmd = ( gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii ) echo $cmd | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii $cmd | & tee -a $LF gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log if ( $status ) exit 1 ; if ( 0 ) exit 1 echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo set cmd = ( mri_glmfit --y $fec.gz --glmdir $OutDir ) ; set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. ) if ( $#bvals == 0 ) then if ( 0 == 0 ) then set cmd = ( $cmd --dti $infodump ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat ) else else if ( $SaveERes ) set cmd = ( $cmd --eres-save ) if ( 0 ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat --eres-save ) if ( $EResPCA ) set cmd = ( $cmd --pca ) if ( 0 ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat --pca ) if ( $#PruneThr ) set cmd = ( $cmd --prune_thr $PruneThr ) if ( 0 ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat --prune_thr ) if ( $#mask ) set cmd = ( $cmd --mask $mask ) ; if ( 0 ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat --mask ) echo "cd `pwd`" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo cd `pwd` pwd cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex echo $cmd | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat $cmd | & tee -a $LF mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex cmdline mri_glmfit.bin --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat sysname Darwin hostname hlhp-105.umd.edu machine x86_64 user administrator FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz logyflag 1 X /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat usedti 2 glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. Loading y from /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz ... done reading. MatrixReadTxT: could not scan value [1][1] When creating the NIFTI file with mri_convert I still get a similar error because the code seems to ignore the NIFTI file input and just looks at the DICOMS I have attached the script I use below. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow(a)umd.edu <dcallow(a)gmail.com> 443-254-6298

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by Daniel Davidson Callow 15 Feb '19

15 Feb '19

External Email - Use Caution Hello, When I run dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon/${subj}.${cond}. It does produce a -dwi.bvals -dwi.voxel_space.bvecs file and I get this output in the error log (also attached). For reference the bvals and bvecs files were correct. MatrixReadTxT: could not scan value [1][1] could not allocate 1684305759 x 1144402954 matrix could not allocate 1684305759 x 1144402954 matrix unsupported matlab format 540094003 (unknown) And this is what I get in the command line while it is running. It does create a NIFTI file and it seems like it is trying to eddy current correct. setenv FSLOUTPUTTYPE NIFTI setenv FSLOUTPUTTYPE NIFTI echo "#@#-------------------------------" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo #@#------------------------------- #@#------------------------------- echo "Converting input" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo Converting input Converting input date | tee -a $LF date tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log Fri Feb 15 13:24:19 EST 2019 set f = $OutDir/dwi.nii set f = /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii set cmd = ( mri_convert $InputVol $f ) ; set cmd = ( mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii ) echo "cd `pwd`" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo cd `pwd` pwd cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex echo $cmd | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii $cmd | & tee -a $LF mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log mri_convert.bin /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm... Getting Series No INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex INFO: Scanning for Series Number 171 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 170 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName AES101 Date and time StudyDate 20170409 StudyTime 105710.343000 SeriesTime 120657.984000 AcqTime 120650.230000 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_mddw_D64 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 106 InversionTime -1 RepetitionTime 6300 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 170 SeriesNo 171 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 35 IsMosaic 1 ImgPos 630.8714 646.6747 -31.8394 VolRes 1.6406 1.6406 3.6000 VolDim 128 128 35 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (128 128 35), nframes = 65, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 6300, TR = 6300 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName AES101 Date and time StudyDate 20170409 StudyTime 105710.343000 SeriesTime 120657.984000 AcqTime 120650.230000 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_mddw_D64 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 106 InversionTime -1 RepetitionTime 6300 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 170 SeriesNo 171 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 35 IsMosaic 1 ImgPos 105.8714 121.6747 -31.8394 VolRes 1.6406 1.6406 3.6000 VolDim 128 128 35 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.8714 16.6747 31.1606 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii... Saving bvals and bvecs if ( $status ) exit 1 ; if ( 0 ) exit 1 echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo if ( $#bvals == 0 ) then if ( 0 == 0 ) then if ( $#infodump == 0 ) then if ( 0 == 0 ) then set infodump = $OutDir/dwi-infodump.dat set infodump = /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat set cmd = ( mri_probedicom --i $InputVol ) ; set cmd = ( mri_probedicom --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm ) echo "cd `pwd`" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo cd `pwd` pwd cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex echo $cmd | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo mri_probedicom --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm mri_probedicom --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm $cmd | & tee -a $LF > $infodump mri_probedicom --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log if ( $status ) exit 1 ; if ( 0 ) exit 1 echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo endif endif endif endif set fec = $OutDir/dwi-ec.nii set fec = /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii if ( $DoEddyCorrect ) then if ( 1 ) then echo "#@#-------------------------------" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo #@#------------------------------- #@#------------------------------- echo "Eddy/Motion Correct" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo Eddy/Motion Correct Eddy/Motion Correct date | tee -a $LF date tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log Fri Feb 15 13:24:31 EST 2019 set ectmp = $OutDir/ectmp set ectmp = /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp mkdir -p $ectmp mkdir -p /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp pushd $ectmp > /dev/null pushd /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp set cmd = ( eddy_correct $f $fec $ECRefTP ) set cmd = ( eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0 ) echo "cd `pwd`" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo cd `pwd` pwd cd /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp echo $cmd | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0 eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0 $cmd | & tee -a $LF eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0 tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0000 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0001 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0002 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0003 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0004 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0005 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0006 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0007 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0008 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0009 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0010 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0011 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0012 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0013 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0014 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0015 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0016 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0017 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0018 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0019 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0020 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0021 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0022 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0023 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0024 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0025 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0026 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0027 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0028 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0029 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0030 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0031 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0032 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0033 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0034 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0035 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0036 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0037 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0038 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0039 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0040 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0041 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0042 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0043 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0044 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0045 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0046 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0047 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0048 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0049 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0050 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0051 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0052 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0053 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0054 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0055 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0056 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0057 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0058 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0059 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0060 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0061 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0062 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0063 processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0064 if ( $status ) exit 1 ; if ( 0 ) exit 1 if ( ! -e $fec ) then if ( ! -e /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii ) then popd > /dev/null popd rm -r $ectmp rm -r /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo else else echo "#@#-------------------------------" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo #@#------------------------------- #@#------------------------------- echo "Fitting Tensors" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo Fitting Tensors Fitting Tensors date | tee -a $LF date tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log Fri Feb 15 13:33:13 EST 2019 set cmd = ( gzip $f ) set cmd = ( gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii ) echo $cmd | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii $cmd | & tee -a $LF gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log if ( $status ) exit 1 ; if ( 0 ) exit 1 echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo set cmd = ( gzip $fec ) set cmd = ( gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii ) echo $cmd | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii $cmd | & tee -a $LF gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log if ( $status ) exit 1 ; if ( 0 ) exit 1 echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo echo "" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo set cmd = ( mri_glmfit --y $fec.gz --glmdir $OutDir ) ; set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. ) if ( $#bvals == 0 ) then if ( 0 == 0 ) then set cmd = ( $cmd --dti $infodump ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat ) else else if ( $SaveERes ) set cmd = ( $cmd --eres-save ) if ( 0 ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat --eres-save ) if ( $EResPCA ) set cmd = ( $cmd --pca ) if ( 0 ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat --pca ) if ( $#PruneThr ) set cmd = ( $cmd --prune_thr $PruneThr ) if ( 0 ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat --prune_thr ) if ( $#mask ) set cmd = ( $cmd --mask $mask ) ; if ( 0 ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat --mask ) echo "cd `pwd`" | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo cd `pwd` pwd cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex echo $cmd | tee -a $LF tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log echo mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat $cmd | & tee -a $LF mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex cmdline mri_glmfit.bin --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat sysname Darwin hostname hlhp-105.umd.edu machine x86_64 user administrator FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz logyflag 1 X /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat usedti 2 glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. Loading y from /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz ... done reading. MatrixReadTxT: could not scan value [1][1] When creating the NIFTI file with mri_convert I still get a similar error because the code seems to ignore the NIFTI file input and just looks at the DICOMS I have attached the script I use below. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298 On Fri, Feb 15, 2019 at 11:18 AM Greve, Douglas N.,Ph.D. < DGREVE(a)mgh.harvard.edu> wrote: > Can you do this in two steps? First, convert the dicom to a volume format > (eg, mgz or nii.gz) with > mri_convert image0000001.dcm dwi.nii.gz > This may or may not create bvals and bvecs. If not, then you will have to > supply them. If they are created, look at them and make sure they are right. > Next run dt_recon specifying the input and the bvals/bvecs > > On 2/15/19 9:22 AM, Daniel Davidson Callow wrote: > > External Email - Use Caution > Hello, > > I tried to run dt_recon, however, I received the following error message. > Attached is the error log. > > dt_recon --debug --i > /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image000001.dcm > --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon/ > > MatrixReadTxT: could not scan value [1][1] > > > No such file or directory > > WARNING: matlab elment type is 1852050003, which is not a matrix. > > mri_glmfit.bin(51624,0x7fffaff913c0) malloc: *** > mach_vm_map(size=9155227648) failed (error code=3) > > *** error: can't allocate region > > *** set a breakpoint in malloc_error_break to debug > > could not allocate 1684305759 x 1144402954 matrix > > > Cannot allocate memory > > mri_glmfit.bin(51624,0x7fffaff913c0) malloc: *** > mach_vm_map(size=13474447360) failed (error code=3) > > *** error: can't allocate region > > *** set a breakpoint in malloc_error_break to debug > > could not allocate 1684305759 x 1144402954 matrix > > > Cannot allocate memory > > unsupported matlab format 540094003 (unknown) > > > Cannot allocate memory > > It also seems when dt_Recon is trying to process different subjects in > parallel they are being processed in the same folder? does this create an > issue? > > Any help you can provide in debugging the issue would be greatly > appreciated! > > *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow(a)umd.edu <dcallow(a)gmail.com> 443-254-6298

1 0

surface cortical lesions mask --> annotation file ???
by Barletta, Valeria 15 Feb '19

15 Feb '19

Dear Freesurfers, I need to extract annotation files from my cortical lesion masks projected to the surface. Do you know whether this is possible? Thank you, Valeria

2 7

lh.PDDvsHC.thinckness.00.mris_preproc
by 妮 15 Feb '19

15 Feb '19

External Email - Use Caution Hello FreeSurfer Developers, I didn't cache the data during recon-all, so I ran the > following: > > mris_preproc –fsgd PDDvsHC.fsgd --target fsaverage > --hemi lh > --meas thickness --out lh.MMSE-AD.thickness.00.mgh > > It seemed to run smoothly (I've attached the log below) > so I > ran the next step: > > mri_surf2surf --hemi lh --s fsaverage --sval > lh.PDDvsHC.thickness.00.mgh --fwhm 10 --cortex --tval > lh.PDDvsHC.thickness.10.mgh > > I got the following error: > > Reading source surface reg > > freesurfer/subjects/fsaverage/surf/lh.sphere.reg > Loading source data > > mghRead(/Users/cengzhou/Desktop/volumetric_FS/FS/lh.PDDvsHC.thickness.00.mgh, -1): could not open file recon-all.log: see attached Platform: mac os 10

2 3

dt_recon error MatrixReadTxT: could not scan value [1][1]
by Daniel Davidson Callow 15 Feb '19

15 Feb '19

External Email - Use Caution Hello, I tried to run dt_recon, however, I received the following error message. Attached is the error log. dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon/ MatrixReadTxT: could not scan value [1][1] No such file or directory WARNING: matlab elment type is 1852050003, which is not a matrix. mri_glmfit.bin(51624,0x7fffaff913c0) malloc: *** mach_vm_map(size=9155227648) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug could not allocate 1684305759 x 1144402954 matrix Cannot allocate memory mri_glmfit.bin(51624,0x7fffaff913c0) malloc: *** mach_vm_map(size=13474447360) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug could not allocate 1684305759 x 1144402954 matrix Cannot allocate memory unsupported matlab format 540094003 (unknown) Cannot allocate memory It also seems when dt_Recon is trying to process different subjects in parallel they are being processed in the same folder? does this create an issue? Any help you can provide in debugging the issue would be greatly appreciated! Thanks, D*aniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow(a)umd.edu <dcallow(a)gmail.com> 443-254-6298

3 3

Re: [Freesurfer] Unexpected termination of freeviewer
by Hoopes, Andrew 15 Feb '19

15 Feb '19

Hi, you were able to use freeview before without it crashing – have you made any changes to the distribution since then? Are you sure that you’ve set FREESURFER_HOME and sourced the FS environment before calling freeview? Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Lykke Silfwerbrand <lykke.silfwerbrand(a)neuro.uu.se> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, February 14, 2019 at 10:59 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Unexpected termination of freeviewer External Email - Use Caution Hi, I used freeviewer a few weeks ago without any problems, but now that I want to continue my analysis it terminates as a try to load a volume or a surface. (same computer, same setting) I have tried the “sudo -E fs_update” and to disable SIP, freeviewer still terminates the same way with the same error message, see below. Any help is much appreciated! Lykke PhD candidate Neuro Science Uppsala University Process: Freeview [1713] Path: /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview Identifier: com.yourcompany.Freeview Version: ??? Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: Freeview [1713] User ID: 271794372 Date/Time: 2019-02-14 16:48:18.395 +0100 OS Version: Mac OS X 10.14.3 (18D109) Report Version: 12 Bridge OS Version: 3.0 (14Y674) Anonymous UUID: A7073C18-5895-3A14-4551-409200FFED72 Time Awake Since Boot: 2500 seconds System Integrity Protection: disabled Crashed Thread: 9 Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY Termination Reason: DYLD, [0x4] Symbol missing Dyld Error Message: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Thread 0:: Dispatch queue: com.apple.main-thread 0 libobjc.A.dylib 0x00007fff6605e681 search_method_list(method_list_t const*, objc_selector*) + 78 1 libobjc.A.dylib 0x00007fff6605e614 getMethodNoSuper_nolock(objc_class*, objc_selector*) + 98 2 libobjc.A.dylib 0x00007fff66060a73 lookUpImpOrForward + 328 3 libobjc.A.dylib 0x00007fff66060494 _objc_msgSend_uncached + 68 4 com.apple.AppKit 0x00007fff3747e426 -[NSView(NSInternal) _allocAuxiliary] + 227 5 com.apple.AppKit 0x00007fff374b241c -[NSView initWithFrame:] + 36 6 com.apple.AppKit 0x00007fff374bd14f -[NSNextStepFrame initWithFrame:styleMask:owner:] + 74 7 com.apple.AppKit 0x00007fff374bb709 -[NSWindow _commonInitFrame:styleMask:backing:defer:] + 610 8 com.apple.AppKit 0x00007fff374baf5e -[NSWindow _initContent:styleMask:backing:defer:contentView:] + 1202 9 com.apple.AppKit 0x00007fff374baaa6 -[NSWindow initWithContentRect:styleMask:backing:defer:] + 45 10 QtGui 0x0000000120ba003f QMacInputContext::reset() + 30319 11 QtGui 0x0000000120b9fedc QMacInputContext::reset() + 29964 12 QtGui 0x0000000120b9289a QWidgetPrivate::setWindowLevel() + 810 13 QtGui 0x0000000120b8ffb1 QWidgetPrivate::createWindow_sys() + 145 14 QtGui 0x0000000120b900bf qt_mac_window_for(QWidget const*) + 159 15 QtGui 0x0000000120b923b1 QWidgetPrivate::setModal_sys() + 145 16 QtGui 0x0000000120c4b698 QWidget::create(long, bool, bool) + 360 17 QtGui 0x0000000120c4c909 QWidget::setVisible(bool) + 121 18 com.yourcompany.Freeview 0x000000010fe7241c FloatingStatusBar::ShowProgress() + 60 19 com.yourcompany.Freeview 0x000000010fe26aab FloatingStatusBar::qt_metacall(QMetaObject::Call, int, void**) + 251 20 QtCore 0x00000001208ede99 QObject::event(QEvent*) + 1081 21 QtGui 0x0000000120c4d83e QWidget::event(QEvent*) + 78 22 QtGui 0x0000000120bf315d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 189 23 QtGui 0x0000000120bf918d QApplication::notify(QObject*, QEvent*) + 349 24 QtCore 0x00000001207f34dc QCoreApplication::notifyInternal(QObject*, QEvent*) + 124 25 QtCore 0x00000001208e10cb QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 731 26 com.apple.CoreFoundation 0x00007fff39f08395 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 27 com.apple.CoreFoundation 0x00007fff39f0833b __CFRunLoopDoSource0 + 108 28 com.apple.CoreFoundation 0x00007fff39eebdd1 __CFRunLoopDoSources0 + 195 29 com.apple.CoreFoundation 0x00007fff39eeb37a __CFRunLoopRun + 1219 30 com.apple.CoreFoundation 0x00007fff39eeac64 CFRunLoopRunSpecific + 463 31 com.apple.HIToolbox 0x00007fff39181ab5 RunCurrentEventLoopInMode + 293 32 com.apple.HIToolbox 0x00007fff391817eb ReceiveNextEventCommon + 618 33 com.apple.HIToolbox 0x00007fff39181568 _BlockUntilNextEventMatchingListInModeWithFilter + 64 34 com.apple.AppKit 0x00007fff3743c363 _DPSNextEvent + 997 35 com.apple.AppKit 0x00007fff3743b102 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1362 36 com.apple.AppKit 0x00007fff37435165 -[NSApplication run] + 699 37 QtGui 0x0000000120bae174 QDesktopWidget::resizeEvent(QResizeEvent*) + 12724 38 QtCore 0x00000001208dfa34 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 68 39 QtCore 0x00000001208dfd54 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 180 40 QtCore 0x00000001208e137c QCoreApplication::exec() + 188 41 com.yourcompany.Freeview 0x000000010ff03f58 main + 6232 42 com.yourcompany.Freeview 0x000000010fe24974 start + 52 Thread 1: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 2: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 3: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 4: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 5:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff6727617a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff672766d0 mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff39eebfde __CFRunLoopServiceMachPort + 337 3 com.apple.CoreFoundation 0x00007fff39eeb52d __CFRunLoopRun + 1654 4 com.apple.CoreFoundation 0x00007fff39eeac64 CFRunLoopRunSpecific + 463 5 com.apple.AppKit 0x00007fff37444f89 _NSEventThread + 160 6 libsystem_pthread.dylib 0x00007fff67330305 _pthread_body + 126 7 libsystem_pthread.dylib 0x00007fff6733326f _pthread_start + 70 8 libsystem_pthread.dylib 0x00007fff6732f415 thread_start + 13 Thread 6: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 7: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 8:: CVDisplayLink 0 libsystem_kernel.dylib 0x00007fff672797de __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff67333593 _pthread_cond_wait + 724 2 com.apple.CoreVideo 0x00007fff3bd2be90 CVDisplayLink::runIOThread() + 722 3 libsystem_pthread.dylib 0x00007fff67330305 _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff6733326f _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff6732f415 thread_start + 13 Thread 9 Crashed: 0 dyld 0x0000000128c4e456 __abort_with_payload + 10 1 dyld 0x0000000128c4dc4d abort_with_payload_wrapper_internal + 82 2 dyld 0x0000000128c4dc7f abort_with_payload + 9 3 dyld 0x0000000128c0baea dyld::halt(char const*) + 343 4 dyld 0x0000000128c0bc17 dyld::fastBindLazySymbol(ImageLoader**, unsigned long) + 170 5 libdyld.dylib 0x00007fff67128c1a dyld_stub_binder + 282 6 ??? 0x00000001204dd018 0 + 4836937752 7 com.yourcompany.Freeview 0x000000010fead0df LayerMRI::LoadVolumeFromFile() + 399 8 com.yourcompany.Freeview 0x000000010ff79ea1 ThreadIOWorker::run() + 1361 9 QtCore 0x00000001208275b5 QThread::setPriority(QThread::Priority) + 469 10 libsystem_pthread.dylib 0x00007fff67330305 _pthread_body + 126 11 libsystem_pthread.dylib 0x00007fff6733326f _pthread_start + 70 12 libsystem_pthread.dylib 0x00007fff6732f415 thread_start + 13 Thread 9 crashed with X86 Thread State (64-bit): rax: 0x0000000002000209 rbx: 0x0000000000000000 rcx: 0x000070000787ea48 rdx: 0x000070000787eeb0 rdi: 0x0000000000000006 rsi: 0x0000000000000004 rbp: 0x000070000787ea90 rsp: 0x000070000787ea48 r8: 0x000070000787eab0 r9: 0x0000000000000000 r10: 0x0000000000000098 r11: 0x0000000000000246 r12: 0x0000000000000098 r13: 0x000070000787eeb0 r14: 0x0000000000000004 r15: 0x0000000000000006 rip: 0x0000000128c4e456 rfl: 0x0000000000000246 cr2: 0x000000012519c000 Logical CPU: 0 Error Code: 0x02000209 Trap Number: 133 ----- När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

2 5

extracting mesh file of layers in ascii format
by Atena Rezaei 15 Feb '19

15 Feb '19

External Email - Use Caution Hi, How can I extract the mesh file of gray matter, white matter, Cerebellum and Thalamus from freesurfer in Ascii format? Thanks in advance! BR, Atena

2 1

dt_recon error log
by Daniel Callow 15 Feb '19

15 Feb '19

External Email - Use Caution Hello, running the following command line script for dt_recon dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon MatrixReadTxT: could not scan value [1][1] could not allocate 1684305759 x 1144402954 matrix could not allocate 1684305759 x 1144402954 matrix unsupported matlab format 540094003 (unknown) Any idea what might be causing this error? *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

1 0

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output
by Matthieu Vanhoutte 14 Feb '19

14 Feb '19

External Email - Use Caution Hi Douglas, Could you help me concerning my previous questions ? Thanks, Matthieu > Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE <matthieuvanhoutte(a)gmail.com> a écrit : > > Hi Douglas, > > Thanks for clarification. Why use "nearest neighbor" instead of classical "trilinear" interpolation ? > > Should it be done as well when projecting from volume to surface with mri_vol2surf ? > > Best, > > Matthieu > > On 11/02/2019 17:32, Greve, Douglas N.,Ph.D. wrote: >> It will not used trilinear interp. Try it with nearest neighbor >> >> On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote: >>> External Email - Use Caution >>> >>> Dear Douglas, >>> >>> Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according your advice to obtain voxel-wise output rescaled without PVC correction, I have done sequentially the different steps to obtain this output. However, when comparing voxel-wise rescaled output (rbv.nii.gz) between the two methods, final values at each voxel are not the same… >>> >>> To obtain first rescaled voxel-wise output I have used sequentially these steps: >>> 1. Concatenate transforms from PET space to gtmseg.mgz >>> 2. Register native PET into gtmseg space (trilin. interpolation) >>> 3. Compute mean PET inside reference regions (with regions masks from gtmseg.mgz) >>> 4. Compute intensity normalized PET images in gtmseg space >>> >>> Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command use these same steps ? >>> >>> Best, >>> Matthieu >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 9

Missing files after recon-all
by Zhi Li 14 Feb '19

14 Feb '19

External Email - Use Caution Hello FreeSurfer experts, I am trying recon-all in a SGE cluster. However, the size of of the results was smaller than that executed in a local CentOs system. I did not found error in the recon-all log file which ended with "recon-all -s sub001 finished without error". But when I used QAtools, it reported: Checking if all files exist...FAILED (read ../a003/scripts/recon_checker.log) ERROR: Subject a003 missing output file ../mri/transforms/talairach.m3z.inv.x.mgz ERROR: Subject a003 missing output file ../mri/transforms/talairach.m3z.inv.y.mgz ERROR: Subject a003 missing output file ../mri/transforms/talairach.m3z.inv.z.mgz ERROR: Subject a003 missing output file ../mri/nu_noneck.mgz ERROR: Subject a003 missing output file ../label/lh.BA1.label ERROR: Subject a003 missing output file ../label/lh.BA2.label ERROR: Subject a003 missing output file ../label/lh.BA3a.label ERROR: Subject a003 missing output file ../label/lh.BA3b.label ERROR: Subject a003 missing output file ../label/lh.BA4a.label ERROR: Subject a003 missing output file ../label/lh.BA4p.label ERROR: Subject a003 missing output file ../label/lh.BA6.label ERROR: Subject a003 missing output file ../label/lh.BA44.label ERROR: Subject a003 missing output file ../label/lh.BA45.label ERROR: Subject a003 missing output file ../label/lh.V1.label ERROR: Subject a003 missing output file ../label/lh.V2.label ERROR: Subject a003 missing output file ../label/lh.MT.label ERROR: Subject a003 missing output file ../label/lh.BA.annot ERROR: Subject a003 missing output file ../stats/lh.BA.stats ERROR: Subject a003 missing output file ../label/rh.BA1.label ERROR: Subject a003 missing output file ../label/rh.BA2.label ERROR: Subject a003 missing output file ../label/rh.BA3a.label ERROR: Subject a003 missing output file ../label/rh.BA3b.label ERROR: Subject a003 missing output file ../label/rh.BA4a.label ERROR: Subject a003 missing output file ../label/rh.BA4p.label ERROR: Subject a003 missing output file ../label/rh.BA6.label ERROR: Subject a003 missing output file ../label/rh.BA44.label ERROR: Subject a003 missing output file ../label/rh.BA45.label ERROR: Subject a003 missing output file ../label/rh.V1.label ERROR: Subject a003 missing output file ../label/rh.V2.label ERROR: Subject a003 missing output file ../label/rh.MT.label ERROR: Subject a003 missing output file ../label/rh.BA.annot ERROR: Subject a003 missing output file ../label/BA.ctab ERROR: Subject a003 missing output file ../stats/rh.BA.stats ERROR: Subject a003 missing output file ../stats/lh.entorhinal_exvivo.stats ERROR: Subject a003 missing output file ../stats/rh.entorhinal_exvivo.stats In addition, the QA results were black. But if I apply QATools on these results in a local CentOs system, the results seemed normal. Should this QA problem be caused by X11? I did not install FSL in the SGE cluster, would this be the problem of missing files after recon-all? Any suggestions would be appreciated. Thanks and best wishes, Lizhi

2 6

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