Hello, Freesurfer experts:
I followed the tutorial for FStutorial/diffusion:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion
FsTutorial/Diffusion - Free Surfer Wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion surfer.nmr.mgh.harvard.edu The purpose of this tutorial is to give you experience with the integration of Diffusion Tensor Imaging (DTI) with FreeSurfer. The data were collected at MGH as part ...
And i export the variables and run the command dt_recon both on my MAC and Ubuntu for the tutorial subject which located in:
TUTORIAL_DIR=$TUTORIAL_DATA/diffusion_tutorial/Diff001
Just to be sure, So I run it on both systems, and I got the same errors:
dt_recon --i /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm --s Diff001 --o /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon INFO: SUBJECTS_DIR is /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_recons dt_recon logfile Wed Dec 21 15:13:51 CET 2016 VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $ setenv SUBJECTS_DIR /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_recons cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion /Applications/freesurfer/bin/dt_recon --i /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm --s Diff001 --o /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon UMR-COGIM-MP008 junhao.wen /usr/local/fsl/bin/eddy_correct ECRefTP 0 #@#------------------------------- Converting input Wed Dec 21 15:13:51 CET 2016 cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion mri_convert /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii mri_convert /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm... Getting Series No INFO: Found 3 files in /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig INFO: Scanning for Series Number 6 Scanning Directory INFO: found 1 files in series INFO: loading series header info.
RunNo = 5 WARNING: Run 1 appears to be truncated Files Found: 1, Files Expected (lRep+1): 120 FileName /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm Identification NumarisVer syngo MR 2002B 4VA21A ScannerModel Sonata PatientName anon Date and time StudyDate 00000000 StudyTime 110208.000000 SeriesTime 114533.812000 AcqTime 114020.732488 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes_auto PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 80 InversionTime -1 RepetitionTime 8900 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 5 SeriesNo 6 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 1 SliceArraylSize 64 IsMosaic 1 ImgPos 958.4660 1120.5343 -85.7814 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 64 Vc -0.9981 -0.0596 -0.0171 Vr 0.0588 -0.9972 0.0460 Vs -0.0198 0.0449 0.9988 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2 INFO: sorting. INFO: (128 128 64), nframes = 1, ismosaic=1 Numaris Version: syngo MR 2002B 4VA21A Maj = 4, Min=2, MinMin = 1 Repetition Time = 8900, TR = 8900 ms PE Dir COL COL This looks like an MGH DTI volume MGH DTI SeqPack Info 0 ep_b0#0 0.000000 0 bValue = 700 nB0 = 10 nDir = 60 GradFile /Applications/freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti60.gdt FileName /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm Identification NumarisVer syngo MR 2002B 4VA21A ScannerModel Sonata PatientName anon Date and time StudyDate 00000000 StudyTime 110208.000000 SeriesTime 114533.812000 AcqTime 114020.732488 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes_auto PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 80 InversionTime -1 RepetitionTime 8900 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 5 SeriesNo 6 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 1 SliceArraylSize 64 IsMosaic 1 ImgPos 116.8592 173.6140 -59.8600 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 64 Vc -0.9981 -0.0596 -0.0171 Vr 0.0588 -0.9972 0.0460 Vs -0.0198 0.0449 0.9988 VolCenter -4.6346 41.2132 7.7661 TransferSyntaxUID 1.2.840.10008.1.2 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0.0197543 0.0448988 0.998796 INFO: no Siemens slice order reversal detected (good!). TR=8900.00, TE=80.00, TI=-1.00, flip angle=90.00 i_ras = (-0.998075, -0.0596198, -0.0170599) j_ras = (0.0587821, -0.997211, 0.0459901) k_ras = (-0.0197543, 0.0448988, 0.998796) writing to /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii... Saving bvals and bvecs
cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion mri_probedicom --i /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm
#@#------------------------------- Eddy/Motion Correct Wed Dec 21 15:13:52 CET 2016 cd /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/ectmp eddy_correct /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii 0 processing /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec_tmp0000
#@#------------------------------- Fitting Tensors Wed Dec 21 15:14:05 CET 2016 cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion mri_glmfit --y /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii --glmdir /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon --dti /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-infodump.dat
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion cmdline mri_glmfit --y /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii --glmdir /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon --dti /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-infodump.dat sysname Darwin hostname UMR-COGIM-MP008 machine x86_64 user junhao.wen FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii logyflag 1 X /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-infodump.dat usedti 1 glmdir /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon Loading y from /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii Using DTI bValue = 700 nB0 = 10 nDir = 60 GradFile /Applications/freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti60.gdt Saving design matrix to /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/Xg.dat Normalized matrix condition is 27.8243 Matrix condition is 979968 Pruning voxels by thr: 50.000000 Found 961982 voxels in mask Saving mask to /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/mask.nii search space = 7695856.000000 ERROR: dimension mismatch between y and X. y has 1 inputs, X has 70 rows. ✘ ~/Hao/tutorial/Freesurfer/diffusion export TUTORIAL_DIR=/Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial ~/Hao/tutorial/Freesurfer/diffusion export SUBJECTS_DIR=/Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_recons ~/Hao/tutorial/Freesurfer/diffusion dt_recon --i $TUTORIAL_DIR/$subj/orig/*-1.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon zsh: no matches found: /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial//orig/*-1.dcm ✘ ~/Hao/tutorial/Freesurfer/diffusion subj=Diff001 ~/Hao/tutorial/Freesurfer/diffusion dt_recon --i $TUTORIAL_DIR/$subj/orig/*-1.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon INFO: SUBJECTS_DIR is /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_recons dt_recon logfile Wed Dec 21 15:18:49 CET 2016 VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $ setenv SUBJECTS_DIR /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_recons cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion /Applications/freesurfer/bin/dt_recon --i /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm --s Diff001 --o /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon UMR-COGIM-MP008 junhao.wen /usr/local/fsl/bin/eddy_correct ECRefTP 0 #@#------------------------------- Converting input Wed Dec 21 15:18:49 CET 2016 cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion mri_convert /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii mri_convert /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm... Getting Series No INFO: Found 3 files in /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig INFO: Scanning for Series Number 6 Scanning Directory INFO: found 1 files in series INFO: loading series header info.
RunNo = 5 WARNING: Run 1 appears to be truncated Files Found: 1, Files Expected (lRep+1): 120 FileName /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm Identification NumarisVer syngo MR 2002B 4VA21A ScannerModel Sonata PatientName anon Date and time StudyDate 00000000 StudyTime 110208.000000 SeriesTime 114533.812000 AcqTime 114020.732488 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes_auto PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 80 InversionTime -1 RepetitionTime 8900 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 5 SeriesNo 6 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 1 SliceArraylSize 64 IsMosaic 1 ImgPos 958.4660 1120.5343 -85.7814 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 64 Vc -0.9981 -0.0596 -0.0171 Vr 0.0588 -0.9972 0.0460 Vs -0.0198 0.0449 0.9988 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2 INFO: sorting. INFO: (128 128 64), nframes = 1, ismosaic=1 Numaris Version: syngo MR 2002B 4VA21A Maj = 4, Min=2, MinMin = 1 Repetition Time = 8900, TR = 8900 ms PE Dir COL COL This looks like an MGH DTI volume MGH DTI SeqPack Info 0 ep_b0#0 0.000000 0 bValue = 700 nB0 = 10 nDir = 60 GradFile /Applications/freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti60.gdt FileName /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm Identification NumarisVer syngo MR 2002B 4VA21A ScannerModel Sonata PatientName anon Date and time StudyDate 00000000 StudyTime 110208.000000 SeriesTime 114533.812000 AcqTime 114020.732488 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes_auto PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 80 InversionTime -1 RepetitionTime 8900 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 5 SeriesNo 6 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 1 SliceArraylSize 64 IsMosaic 1 ImgPos 116.8592 173.6140 -59.8600 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 64 Vc -0.9981 -0.0596 -0.0171 Vr 0.0588 -0.9972 0.0460 Vs -0.0198 0.0449 0.9988 VolCenter -4.6346 41.2132 7.7661 TransferSyntaxUID 1.2.840.10008.1.2 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0.0197543 0.0448988 0.998796 INFO: no Siemens slice order reversal detected (good!). TR=8900.00, TE=80.00, TI=-1.00, flip angle=90.00 i_ras = (-0.998075, -0.0596198, -0.0170599) j_ras = (0.0587821, -0.997211, 0.0459901) k_ras = (-0.0197543, 0.0448988, 0.998796) writing to /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii... Saving bvals and bvecs
cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion mri_probedicom --i /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm
#@#------------------------------- Eddy/Motion Correct Wed Dec 21 15:18:50 CET 2016 cd /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/ectmp eddy_correct /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii 0 processing /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec_tmp0000
#@#------------------------------- Fitting Tensors Wed Dec 21 15:19:02 CET 2016 cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion mri_glmfit --y /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii --glmdir /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon --dti /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-infodump.dat
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion cmdline mri_glmfit --y /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii --glmdir /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon --dti /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-infodump.dat sysname Darwin hostname UMR-COGIM-MP008 machine x86_64 user junhao.wen FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii logyflag 1 X /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-infodump.dat usedti 1 glmdir /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon Loading y from /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii Using DTI bValue = 700 nB0 = 10 nDir = 60 GradFile /Applications/freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti60.gdt Saving design matrix to /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/Xg.dat Normalized matrix condition is 27.8243 Matrix condition is 979968 Pruning voxels by thr: 50.000000 Found 961982 voxels in mask Saving mask to /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/mask.nii search space = 7695856.000000 ERROR: dimension mismatch between y and X. y has 1 inputs, X has 70 rows.
I think the problem is from fitting tensor, so do you think it is the problems of you tutorial data, I know you are going to release the new version, but anyway, this should be work, no?
Freesurfer version 5,3,0
Thanks in advance