Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

Registering ASL-CBF maps to fsaverage
by neuroimage analyst 21 Dec '16

21 Dec '16

Hi, all. I want to register CBF maps derived using pCASL to freesurfer's surface and derive CBF values in the same regions where I report my cortical thickness, and volumes. Hence, I did the following: 1) bbregister --s T1_data --mov asldata_mc_even_brain.nii.gz --reg mean_asl_to_fs_T1 --bold --init-fsl asldata_mc_even_brain is the mean of the control images 2) mri_vol2vol --mov perfusion_calib.nii.gz --targ T1_data/mri/T1.mgz --interp nearest --o perfusion_CBF_to_T1.nii.gz --reg register.dat --no-save-reg where perfusion_calib is the CBF map in the same space asldata_mc_even_brain. 3) mri_vol2surf --mov perfusion_CBF_to_T1.nii.gz --ref orig.mgz --regheader T1_data/ --hemi lh --projfrac 0.5 --interp trilinear --o perfusion_CBF_to_T1_surf_gray.mgh --reg register.dat --noreshape --cortex --surfreg sphere.reg Step (3) takes the CBF map to cortical ribbon and hopefully now I can run mri_segstats and extract CBF values and thickness + do a group comparison using mri_glmfit. In order to do the latter, I have to map the perfusion maps to fsaverage. Can I then simply set --ref to fsaverage in step 3 or what is the correct call to take CBF maps to fsaverage in (3) ? Second, Do i have to pass --surf argument pial or white in step 3? What is the correct way to do this? Third, The statistical comparisons on thickness were done using 10 mm smoothing using -qcache argument in recon-all.I want to generate several smoothing of CBF maps (5-25 in steps of 5 mm) In the call to mri_vol2surf I can set --surf-fwhm 5 and my understanding is it will smooth the output surface 5 mm. Is that right? or should I call mri_fwhm on the output returned from step 3. Thank you for your suggestions. I will really appreciate your thoughts. Regards -VM

3 5

Tutorial data problems for dt_recon
by Hao wen 21 Dec '16

21 Dec '16

Hello, Freesurfer experts: I followed the tutorial for FStutorial/diffusion: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion FsTutorial/Diffusion - Free Surfer Wiki<https://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

1 0

(no subject)
by simone coscetti 21 Dec '16

21 Dec '16

Hello FreeSurfer Developers, I’m attempting to make some performances evaluation on recon-all using GPUs on a node with 4 nVidia K80. Submitting different instances of recon-all on 8 different subjects, every instance run on the same device (#0), compromising the efficiency of the test. Is there a way to address different instances on different devices? Thank you in advance. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz cudawn9:~ # cat /etc/SuSE-release SUSE Linux Enterprise Server 11 (x86_64) VERSION = 11 PATCHLEVEL = 4 cudawn9:~ # uname -a Linux cudawn9 3.0.101-63-default #1 SMP Tue Jun 23 16:02:31 UTC 2015 (4b89d0c) x86_64 x86_64 x86_64 GNU/Linux Simone

2 2

Missing values in fsgd file
by Jennifer Szeto 20 Dec '16

20 Dec '16

Hi freesurfer experts, I am trying to run some mri_glmfit analyses on freesurfer5.3. However there are some missing values in some of my fsgd files due to missing data in my dataset. Is there anyway we can run mri_glmfit analyses with missing values in fsgd files? Thank you very much, Jennifer

2 1

pial surface errors - V6beta
by Antonin Skoch 20 Dec '16

20 Dec '16

Dear experts, in my data I quite often encounter errors in pial surface which is probably induced by errors of white surface, in some cases caused by juxtacortical lesions (even in healthy subjects). See screenshots for examples. I have tested this on freesurfer V6 beta but it is commonly also found in older versions. I have uploaded the subject pial_errors.tar.gz to your server. The error showed pial_error1.png in probably caused by small error in white surface shape in 18,-18,63 (RAS). Another similar problem is in 15,10,53 (RAS). This is probably caused by juxtacortical lesion. Another problematic spot with juxtacortical lesion is on -7,18,47 (RAS). I have observed such kind of errors in quite a large number of subjects, these are either healthy controls or subjects with psychiatric ilnesses, therefore no particular apparent macroscopic pathology should be present in these subjects. Do you think that there could be some improvement in the mris_make_surfaces code to prevent this kind of behaviour (i.e. very small error in white has gross effect on pial), or it is necessary in all these cases to manually intervene ? Especially, I do not see any particular problem in image in case of pial_error1.png. And, in case of editing of problems errors by juxtacortical lesions I find fastest way to edit wm (due to the fact that I can constrain the brush not to draw to existing wm) in contrast to editing aseg (i.e. label the spot as a lesion). Do you think that aseg editing in contrast to wm editing has some benefit in this case? Regards, Antonin Skoch

1 0

Help on ringing artifacts
by Wayne Su 20 Dec '16

20 Dec '16

Hello Experts: I encountered one big issue with cortical segmentation by using Freesurfer. See the image I attached. There are some hyper-intense thin white surface strip at the edge of cortex. Sometimes Freesurfer misclassified them as white matter. Even not, I am not sure whether those are gray matter or not. Anyone knows what are they, and what caused this ³artifacts²? Is there a way to get rid of them on the scanner? I appreciate anyone points me to the right direction. Regards, Wayne

1 0

trac-all error with .nii.gz images, mri_probedicom
by Hao wen 20 Dec '16

20 Dec '16

Hello, FreeSurfer experts: I know that we are going to have a new version of FS 6.0.0, but with the curent newest version of TRACULA(trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp ) for FS5.3.0, I am working on UBUNTU14.0. To run tracula in parallel on my machine, here is my config file( for test, I have two subjects, and all are recon-alled, I stored all the image into .nii.gz(dwi.nii.gz, fmap_magnitude.nii.gz, fmap_phasediff.nii.gz),I use the magnitude and phase image to do the correction for the B0-inhomogeneity, the gradient table format are .bvec and .bval , Here is one of my config file: ### This is to define the CAPS version subjects_dir and subject_id for FreeSurfer setenv SUBJECTS_DIR /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/Freesurfer/Reconall/reconall_GENFI/clinica_reconall_result/prevdemals_67subjs/analysis-series-default/subjects set dtroot = /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/tracula_result set subjlist = ( sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0 ) ### This is to point to the dwi original data set dcmroot = /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test set dcmlist = ( sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.nii.gz) ### This is to define the dwi gradient table(bvel and bvec) set bvecfile = /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.bvec set bvalfile = /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.bval ### This is to define the registration-based B0-inhomogeneity compensation with the magnitude and phase map images set dob0 = 1 set b0mlist = (sub-PREVDEMALS0010001BE/ses-M0/fmap/sub-PREVDEMALS0010001BE_ses-M0_magnitude1.nii.gz) set b0plist = (sub-PREVDEMALS0010001BE/ses-M0/fmap/sub-PREVDEMALS0010001BE_ses-M0_phasediff.nii.gz) # This is to define Echo spacing for field mapping sequence (from sequence printout), only used when doing registration-based B0-inhomogeneity compensation. set echospacing = 0.7 Here is the command to run the preprocessing: trac-all -path -c /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txt But it gave me some errro from mri_probedicom: mri_probedicom --i /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010002VH/ses-M0/fmap/sub-PREVDEMALS0010002VH_ses-M0_phasediff.nii.gz > /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/tracula_result/sub-PREVDEMALS0010002VH/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010002VH_ses-M0/dmri/b0info.dat Linux DELLEED1 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Dec 20 18:22:04 CET 2016 The error is obvious, because the image here is not a dicom file, but I suppose tracula can deal with any format for mri_convert? In case you need the trac-all.log, I atttached one of them here. Really need your help, thanks in advance Hao

2 3

Talairach error in monkey brain
by Qi Ting 19 Dec '16

19 Dec '16

Dear Freesurfer experts, I'm using freesurfer to process my monkey brain data. It reported errors during Talairach registration step. So I added no-tal-check tag to run recon-all autorecon1 and used tkregister2 to manually edit registration. However, I couldn't let them perfectly fitted, especially deformation in sagittal view. But when I checked the final parcellation, I found it worked well. So I was wondering whether the Talairach registration step matters a lot for the final results? And whether I did correctly? Thanks in advance! with best regards, Ting Qi

1 0

Poorly Designed Matrix Two Stage Longitudinal Model
by Timothy Hendrickson 19 Dec '16

19 Dec '16

FreeSurfer experts, I am attempting to use the two stage model for longitudinal analysis, however I keep receiving an error message that my design matrix is poorly scaled. I'm curious, I've used the same format of design matrix on cross sectional without problem. Anyway here is the command line input: mri_glmfit --glmdir rh.AllSite.gender.group.Age.thickness.fwhm10.twoStage.glmdir \ --X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat \ --y rh.testretest.thickness-spc.stack.fwhm10.mgh \ --C DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_pairedAnalysis.DOSSDS.mtx \ --label rh.testretest.fsaverage.cortex.label \ --surf fsaverage rh The error message is attached within file error_designMtx_12_19_16.txt Additionally I've included my analysis script, all timepoint qdec file, temporal average qdec file, fsgd file, and design matrix. Any help would be extremely beneficial. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay)

1 0

TRACULA to define multiple bvals
by Hao wen 19 Dec '16

19 Dec '16

Hello, Freesurfer experts: I want to ask you in TRACULA, we can define multiple bvecs with the variable 'bveclist' in configuration file, so my question is if we have the same option for bval, or it is mandatory to have the same bvals for all the subjects??? I dont see any information about this... Thanks in advance Hao

2 3

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer