Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
200 discussions

hide colored slices in 3d view?
by j.oschwald＠psychologie.uzh.ch 16 Sep '16

16 Sep '16

Hi Freesurfer users, I wrote a script to automatize taking screenshots in Freeview. Unfortunately, in the 3d view the colored slices are automatically included in the picture. Is there a way to hide them? I am using the current 5.3 version of Freesurfer. I know that the development build includes this option (-hide-3d-slices), but I cannot access the FTP server right now to download it. Is there probably also a command in the version I am currently using? Best Jessica

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Fwd: Tkregister2 error, moveable not present just white screen
by A Nunes 16 Sep '16

16 Sep '16

Hi Doug I can't see any errors in the log file, and with other datasets I did not have this issue. My register.dat is: 50664 3.000000 4.500000 0.150000 9.996076822280884e-01 -2.117119915783405e-02 -1.833262108266354e-02 3.139470825195312e+02 1.872027479112148e-02 1.825972087681293e-02 9.996579289436340e-01 2.150849456787109e+02 -2.082921005785465e-02 -9.996089935302734e-01 1.864889077842236e-02 4.339286499023438e+02 0 0 0 1 round and my register.dat.log is: setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5 cd /Users/adonay/Desktop/data/prepo_cpac /Applications/freesurfer/bin/bbregister --s 50664 --mov 50664_preprocessed.nii.gz --init-header --reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --bold $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Darwin sc-155014 15.6.0 Darwin Kernel Version 15.6.0: Mon Aug 29 20:21:34 PDT 2016; root:xnu-3248.60.11~1/RELEASE_X86_64 x86_64 FREESURFER_HOME /Applications/freesurfer mri_convert 50664_preprocessed.nii.gz /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii mri_convert 50664_preprocessed.nii.gz /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from 50664_preprocessed.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) writing to /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii... tkregister2_cmdl --s 50664 --mov /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii --regheader --reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat --noedit tkregister_tcl /Applications/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii reg file /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /Users/adonay/Desktop/data/freesurfer/5/50664/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii Tmov: -------------------- -3.000 0.000 0.000 96.000; 0.000 0.000 4.500 -63.000; 0.000 -3.000 0.000 96.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 307.685; 0.000 0.000 1.000 216.216; 0.000 -1.000 0.000 435.341; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 307.685; 0.000 0.000 1.000 216.216; 0.000 -1.000 0.000 435.341; 0.000 0.000 0.000 1.000; Determinant 1 subject = 50664 RegMat --------------------------- 1.000 0.000 0.000 307.685; 0.000 0.000 1.000 216.216; 0.000 -1.000 0.000 435.341; 0.000 0.000 0.000 1.000; mri_segreg --mov /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii --init-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat --out-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5 cd /Users/adonay/Desktop/data/prepo_cpac mri_segreg --mov /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii --init-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat --out-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname sc-155014 machine x86_64 user adonay movvol /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii regfile /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat subject 50664 dof 6 outregfile /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1473407392 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 0.000 0.000 307.685; 0.000 0.000 1.000 216.216; 0.000 -1.000 0.000 435.341; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 10.000000 1 -25.0 -25.0 25.0 10.000000 2 -25.0 25.0 -25.0 10.000000 3 -25.0 25.0 25.0 10.000000 4 25.0 -25.0 -25.0 10.000000 5 25.0 -25.0 25.0 10.000000 6 25.0 25.0 -25.0 10.000000 7 25.0 25.0 25.0 10.000000 REL: 8 10.000000 80.000000 10.000000 rel = 1 Initial costs ---------------- Number of surface hits 0 WM Intensity nan +/- nan Ctx Intensity nan +/- nan Pct Contrast nan +/- nan Cost 10.0000 RelCost 1.0000 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 10.0000 10.0000 0.0 Brute Force -------------------------- Min cost was 10.000000 Number of iterations 729 Search time 0.723000 sec Parameters at best (transmm, rotdeg) -4.000 -4.000 -4.000 -4.000 -4.000 -4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -4 1 -4 2 -4 3 -4 4 -4 5 -4 Powell done niters = 0 Computing relative cost 0 -25.0 -25.0 -25.0 10.000000 1 -25.0 -25.0 25.0 10.000000 2 -25.0 25.0 -25.0 10.000000 3 -25.0 25.0 25.0 10.000000 4 25.0 -25.0 -25.0 10.000000 5 25.0 -25.0 25.0 10.000000 6 25.0 25.0 -25.0 10.000000 7 25.0 25.0 25.0 10.000000 REL: 8 10.000000 80.000000 10.000000 rel = 1 Number of iterations 0 Min cost was 10.000000 Number of FunctionCalls 109 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.105000 sec Parameters at optimum (transmm) -1.38389 -1.38389 -1.38389 Parameters at optimum (rotdeg) -1.38389 -1.38389 -1.38389 Final costs ---------------- Number of surface hits 0 WM Intensity nan +/- nan Ctx Intensity nan +/- nan Pct Contrast nan +/- nan Cost 10.0000 RelCost 1.0000 Reg at min cost was 0.999 0.024 0.025 301.214; -0.024 -0.025 0.999 218.039; 0.024 -0.999 -0.024 435.913; 0.000 0.000 0.000 1.000; Writing optimal reg to /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/bbr.pass1.dat, type = 14 Original Reg 1.000 0.000 0.000 307.685; 0.000 0.000 1.000 216.216; 0.000 -1.000 0.000 435.341; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.001 -0.024 -0.025 6.471; 0.024 0.025 0.001 -1.823; -0.024 -0.001 0.024 -0.573; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 6.969701 Computing change in rh position Surface RMS Diff (mm) 6.712317 9.940387 mri_segreg done mri_segreg --mov /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii --init-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/bbr.pass1.dat --out-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat.mincost --dof 6 --nmax 36 --param /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat.param --surf white --cur-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5 cd /Users/adonay/Desktop/data/prepo_cpac mri_segreg --mov /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii --init-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/bbr.pass1.dat --out-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat.mincost --dof 6 --nmax 36 --param /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat.param --surf white --cur-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname sc-155014 machine x86_64 user adonay movvol /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii regfile /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/bbr.pass1.dat subject 50664 dof 6 outregfile /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1474349903 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.999 0.024 0.025 301.214; -0.024 -0.025 0.999 218.039; 0.024 -0.999 -0.024 435.913; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 10.000000 1 -25.0 -25.0 25.0 10.000000 2 -25.0 25.0 -25.0 10.000000 3 -25.0 25.0 25.0 10.000000 4 25.0 -25.0 -25.0 10.000000 5 25.0 -25.0 25.0 10.000000 6 25.0 25.0 -25.0 10.000000 7 25.0 25.0 25.0 10.000000 REL: 8 10.000000 80.000000 10.000000 rel = 1 Initial costs ---------------- Number of surface hits 0 WM Intensity nan +/- nan Ctx Intensity nan +/- nan Pct Contrast nan +/- nan Cost 10.0000 RelCost 1.0000 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 10.0000 10.0000 0.0 Brute Force -------------------------- Min cost was 10.000000 Number of iterations 729 Search time 0.976000 sec Parameters at best (transmm, rotdeg) -0.100 -0.100 -0.100 -0.100 -0.100 -0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -0.1 1 -0.1 2 -0.1 3 -0.1 4 -0.1 5 -0.1 Powell done niters = 0 Computing relative cost 0 -25.0 -25.0 -25.0 10.000000 1 -25.0 -25.0 25.0 10.000000 2 -25.0 25.0 -25.0 10.000000 3 -25.0 25.0 25.0 10.000000 4 25.0 -25.0 -25.0 10.000000 5 25.0 -25.0 25.0 10.000000 6 25.0 25.0 -25.0 10.000000 7 25.0 25.0 25.0 10.000000 REL: 8 10.000000 80.000000 10.000000 rel = 1 Number of iterations 0 Min cost was 10.000000 Number of FunctionCalls 109 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 3.303000 sec Parameters at optimum (transmm) 2.51611 2.51611 2.51611 Parameters at optimum (rotdeg) 2.51611 2.51611 2.51611 Final costs ---------------- Number of surface hits 0 WM Intensity nan +/- nan Ctx Intensity nan +/- nan Pct Contrast nan +/- nan Cost 10.0000 RelCost 1.0000 Reg at min cost was 1.000 -0.021 -0.018 313.947; 0.019 0.018 1.000 215.085; -0.021 -1.000 0.019 433.929; 0.000 0.000 0.000 1.000; Writing optimal reg to /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat, type = 14 Original Reg 0.999 0.024 0.025 301.214; -0.024 -0.025 0.999 218.039; 0.024 -0.999 -0.024 435.913; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.045 0.043 -12.733; -0.043 -0.043 -0.000 2.954; 0.045 0.000 -0.043 1.985; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 13.402319 Computing change in rh position Surface RMS Diff (mm) 13.076895 18.900088 mri_segreg done Cleaning up Started at Thu Sep 8 19:09:02 PDT 2016 Ended at Thu Sep 8 19:09:28 PDT 2016 BBR-Run-Time-Sec 26 bbregister Done To check results, run: tkregister2 --mov 50664_preprocessed.nii.gz --reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --surf Thanks, Adonay Douglas Greve <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Sun, 11 Sep 2016 19:14:45 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> What is your command line and log file? Sounds like the initial registration failed. ---------- Forwarded message ---------- From: A Nunes <adonay.s.nunes(a)gmail.com> Date: Sun, Sep 11, 2016 at 7:04 PM Subject: Tkregister2 error, moveable not present just white screen To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Hi, After doing a bbregistration I visualized the results with tkregister2. The target is alright, however, the moveable is not present, it is just a white screen. What steps could I take to solve this issue? Thanks Adonay

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Postdoctoral position - Amyloid Imaging - Barcelonabeta Brain Research Center
by Juan Domingo Gispert López 16 Sep '16

16 Sep '16

The Pasqual Maragall Foundation invites applications for a full-time postdoctoral position within the context of the AMYPAD project, as part of a clinical research program of the Barcelonaβeta Brain Research Centre (Barcelona, Spain). AMYPAD is a European project to establish the true value of amyloid PET in a diagnostic and prognostic setting (http://www.amypad.eu/) This 5-year project is a collaboration between industry (GEHC, Piramal, Janssen, Ixico) and academic partners funded by the IMI-2 program (total budget 27 million euro). Throughout Europe we will recruit 900 memory clinic patients and 3100 preclinical or prodromal AD subjects from natural history cohorts. Up to 50% of subjects will undergo dynamic scanning and have repeat imaging, for a total of 6000 amyloid PET scans. Main study goals include 1) diagnostic impact including patient-reported outcomes and healthcare resource utilization, 2) prognostic value and enrichment of treatment trials, and 3) quantitative assessment of treatment effects. In close collaboration with EPAD (www.ep-ad.org) the cohorts will be followed with careful longitudinal monitoring and MRI to determine (surrogate) outcomes of cognitive decline and neurodegeneration. The consortium brings together a word-class team of highly synergistic partners to form a pan-European network including the most active PET sites. This will ensure effective access to patients and also maximise exposure to technical knowledge and disease modelling. In addition, AMYPAD will develop expertise in image data collection, including β-amyloid PET and MRI data from the EPAD project. The Barcelonaβeta Brain Research Center (Barcelonaβeta) is a new research infrastructure, constituted by the Pasqual Maragall Foundation and with the participation of the Pompeu Fabra University, dedicated to research on Alzheimer’s disease. The new building will be completed by summer 2014, and will contain excellent technical facilities including a research-dedicated 3T MR scanner, dedicated to clinical research on neurodegenerative diseases. In collaboration with other AMYPAD partners, the responsibilities for this position includes: · Develop technical procedures to enhance amyloid PET quantification; · Engage in the management of the project; · Modelling of amyloid PET data in disease models; · Participate in analysis and publication of results; · Participate in regular meetings with our partners throughout Europe; Required Qualifications: · PhD in neuroscience or image analysis; · Excellent communication and writing skills; · Experience with PET acquisition and analysis; · Affiliation with (or experience with) project management. · Ability to think independently and work collaboratively. Benefits: · Starting date: Jan 2017. · The postdoctoral position is scheduled initially for two years (open to renewal). · Salary will depend on experience. Additional Information: To apply, please submit a single PDF file containing the following: 1) Cover letter describing research interests and relevant background; 2) CV with list of publications; 3) The names of three individuals who could provide reference letters. All files or inquiries should be submitted electronically to: cminguillon(a)fpmaragall.org. Deadline for submitting applications: November 4th 2016. -- *Juan D Gispert* Head Neuroimaging Research *Barcelona**β**eta **Brain Research Center - Fundació Pasqual Maragall* T. (+34) 93 326 31 90 C/ Wellington, 30 08005 Barcelona *www.fpmaragall.org <http://www.fpmaragall.org/>*

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FTP server error
by Chris Filo Gorgolewski 15 Sep '16

15 Sep '16

FYI - there is something wrong with the FTP server: $ wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/freesurfer-L… --2016-09-15 20:04:51-- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/freesurfer-L… => 'freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP.tar.gz' Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu) 132.183.202.158 Connecting to surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)|132.183.202.158|:21... connected. Error in server response. Closing. Retrying.

2 1

Cortical thickness to AAL template
by neuroimage analyst 15 Sep '16

15 Sep '16

Hello, freesurfer users. Reposting the previous question again here. I would appreciate any response. I tried searching for this question on the mailing list but couldn't get an answer. Hence, I am posting this here again. I ran the freesurfer analysis and got cortical thickness map for my group. I want to build an adjacency matrix by finding the correlation between the cortical thickness of various ROIs on an atlas (Either the default freesurfer atlas or AAL atlas). 1) How can I map the cortical thickness map to freesurfer template volume so that I can average the cortical thickness in the ROI to build the connectivity matrix? 2) Instead of mapping to freesurfer template, if I have to use AAL atlas can I simply map the cortical thickness map to MNI template and use AAL atlas in MNI template to carry out step (1). If yes, how should I go about doing that? I would appreciate any response. Thanks Regards!

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FS V6.0 gtmseg unsegmented WM
by Pradeep 15 Sep '16

15 Sep '16

Dear Freesurfers, I am interested us using centrum semiovale as reference region while calculation SUVR values. Is there a way to save the unsegmented white matter [5001& 5002] during the gtmseg step ? in other words looking for an option like this --keep-unsegmented-WM :do not relabel unsegmented_WM as WM Thanks, Pradeep

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group by age-squared interaction on thickness
by Eryilmaz, H. Hamdi 15 Sep '16

15 Sep '16

Dear Doug/FreeSurfers, We are looking at effects of age-squared on cortical thickness in two different groups. We are interested in age-squared by group interactions on cortical thickness across the surface. Nuisance covariates include age, sex, scanner, and total brain volume. The sig map for the interaction shows numerous highly significant regions. When we extract cortical thickness from individual subjects for these regions, and then plot the relationship between age-squared and cortical thickness (after adjusting for the covariates) in group 1 versus group 2, the interaction is very clear. However, using linear regression in SPSS, we are not able to reproduce these results. I suspect we are not using the same model in SPSS that FreeSurfer is using to do the interaction analysis. This is how our fsgd file looks like: GroupDescriptorFile 1 Title GroupAgesqInteraction Class Group1 Class Group2 Variables Agesq Age Gender Scanner TBV Input 3662291 Group1 0.607 0.654 -1.061 1.041 0.706 Input 3665043 Group1 1.294 1.237 -1.061 1.041 -0.747 . . This is the contrast we used: [0 0 1 -1 0 0 0 0 0 0 0 0] What would be the translation of this contrast to a linear model, where we are interested in the age -squared by group interaction on cortical thickness after controlling for the four nuisance covariates? Thanks very much! Hamdi and Josh

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(no subject)
by Rodriguez-Thompson, Anais 14 Sep '16

14 Sep '16

Hi FreeSurfer experts, I'm running a task-based analysis on mni305 space, running a regression of load-dependent activation on RBC folate values, regressing out the effects of age and gender. The analysis runs fine, but when I visualize the sig.mgh map in tkmedit there is a border of functional values that are ridiculously high (10000000000 and -10000000000). I've attached an image of one of the slices to this email as well as the mri_glmfit log, the fsgd file, and the contrast matrix. My glmfit command is mri_glmfit --y cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/136_GDD_2vFix_RBC_Folate/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/ces.nii.gz --fsgd /cluster/roffman/users/fsgd/GDD/136_GDD_2vFix_Covary_RBC_Folate_linear.fsgd --no-prune --fwhm 6 --C /cluster/roffman/users/fsgd/OneGroupOneCovariateRegressOut2Covariates.mtx --glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/136_GDD_2vFix_RBC_Folate/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/Tal2vFix_Covary_RBCFolate_Nuis_Gender_Age_noprune Do you know why my command is creating these artificially high values and how to fix it? Any guidance would be greatly appreciated. Thanks, Anais Rodriguez-Thompson Clinical Research Coordinator Brain Genomics Laboratory Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617) 643-3215

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"Talairach Transform: transforms/talairach.xfm ***FAILED***"
by Uquillas, Federico D'Oleire 14 Sep '16

14 Sep '16

Dear fellow FreeSurfer users, I can't get a subject to recon-all all the way through without crashing, regardless of the FS version used (deleted and started from scratch several times). It always fails with a Talairach transform fail error. Wondering if anybody else has experienced this issue before and if there's a way to solve it. Thank you very much. All the best, Fred

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Convert 4D volume time-series into surface time-series
by Prokopis Prokopiou 14 Sep '16

14 Sep '16

Hello freesurfer experts, I am trying to register a functional volumetric image (.nii) into a surface (.gii) to produce a functional surface image (.gii), where each node of the image will contain a time-series. My purpose for doing this is to use freeview to visualize the time-series of each node. I've tried to do this using bbregister to obtain a registration matrix of the functional image into a structural image, mri_vol2surf to resample the functional volume, and finally mris_convert to convert the resampled functional volume into a (4d) functional surface. The details of how I used these commands are as follow: bbregister --s AL_subject/AL \ --mov /home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet. feat/filtered_func_data.nii \ --reg /home/osboxes/Desktop/AL_registrations/AL.mat \ --init-fsl --t2 mri_vol2surf --mov /home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet. feat/filtered_func_data.nii --reg /home/osboxes/Desktop/AL_registrations/AL.mat --projfrac 0.5 --hemi lh --o /home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.mgh --projfrac 0.5 --interp nearest mris_convert -f /home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.mgh \ /home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/EEG_fMRI_FreeSurfer _anatomies/AL_subject/AL/surf/lh.white \ /home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.gii Although these commands run without any error, the result (AL_surface_time_series_lh.gii) cannot be opened in freeview, presumably because the produced 4d functional surface does not have the necessary surface information (vertices, faces) needed by freeview in order to open it. More specifically, when I try to open it I get MRISread failed mriseadGIFTIfile: mris is NULL! found when parsing file /home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.gii in the terminal. I am new user of freesurfer and I would appreciate if someone could help me with this. Thanks, Prokopis

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