Freesurfer December 2016

freesurfer@nmr.mgh.harvard.edu

95 participants
146 discussions

Demeaning in DODS and correlation
by Jennifer Szeto 22 Dec '16

22 Dec '16

Hi Freesurfer experts, I am trying to look at differences in cortical thickness between the following three groups : (1) MCI, (2) AD, and (3) control group using mri_glmfit (DODS), and want to control for age (continuous) and gender (categorical). I have read some other posts on the topic of demeaning age (i.e. subtracting each participant's age from the entire sample's mean age) but I am not sure if I will need it/am on the right track so would like to seek some guidance from you. 1) In order to decide whether I should demean age when including age as a covariate in the fsgd file (i.e. using demeaned age instead of participants' 'real' age) and control for gender, I should include gender as a categorical factor and check if there are any interactions between groups (MCI/AD/Control) x gender x age by running the following: Research question: Are the three groups different in terms of cortical thickness, when controlling for age and gender Groups: FemaleMCI MaleMCI FemaleAD MaleAD FemaleControl MaleControl Contrast: 0 0 0 0 0 0 0.5 -0.5 -0.5 0.5 0 0 for group (i.e. MCI versus AD) x gender x age interaction 0 0 0 0 0 0 0.5 -0.5 0 0 -0.5 0.5 for group (i.e. MCI versus control) x gender x age interaction, and 0 0 0 0 0 0 0 0 0.5 -0.5 -0.5 0.5 for group (i.e. AD versus control) x gender x age interaction If none of these is significant, then re-run the analyses using DODS/fsgd file with contrasts of interest e.g.: 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 for differences between MCI and AD. However, if there's there're any significant interactions, I will have to demean age? Is this correct? Or do i have to check for interactions in the first place at all given my research question? Also, say if there's a gender effect, how should I control for it? 2) On a separate question, if I want to correlate disease groups (MCI/AD) with behavioural data such as depression - i.e. to see if cortical thickness in MCI/AD is correlated with depression, do i just have to create fsgd files with only one group (MCI OR AD) in each file and correlate with depression by running contrast [0 1]? Sorry about this silly question, just wanted to double check as I am new to freesurfer! Thanks for your help in advance! Regards, Jen

2 3

cortical label mask fro mri_glmfit
by neuroimage analyst 22 Dec '16

22 Dec '16

Hi, I am just curious whether the mask.mgh file returned in glmdir folder created from lh.cortex.label? If so, how can I create my own surface mask from the label file? (mri_label2vol and mri_vol2surf ?) Second: How can I compare the subcortical volumes between the 2 groups using glm tools in freesurfer? Specifically, how do I call mris_preproc and mri_glmfit? I appreciate your response. Thank you Regards --VM

2 4

Poorly Designed Matrix Two Stage Longitudinal Model
by Timothy Hendrickson 22 Dec '16

22 Dec '16

Just following up on the message below. I would appreciate a comment on this issue. -Tim 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. 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If you seek help with this problem, make sure to send: 1. Your command line: 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 --X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat --C DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_pairedAnalysis.DOSSDS.mtx --label rh.testretest.fsaverage.cortex.label --surf fsaverage rh 2. The FSGD file (if using one) 3. And the design matrix above Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay)

2 2

pial surface errors - V6beta
by Antonin Skoch 22 Dec '16

22 Dec '16

Dear experts, I noticed that my original mail did not appear in mail archive, therefore I am reposting, to prevent this request left unattended. The reason of omitting the original post from mail archive was probably the attachments (screenshots). Therefore this time I am reposting without attachments. They are included in the original mail. Best regards and merry Christmas, Antonin Skoch From: Antonin Skoch <ansk(a)ikem.cz> To: <freesurfer(a)nmr.mgh.harvard.edu> Sent: 12/21/2016 1:41 AM Subject: pial surface errors - V6beta 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

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

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Freesurfer December 2016