Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

Any binaries while Martinos disks being repaired / FTP server is down?
by DT 17 Sep '16

17 Sep '16

I tried to download the current freesurfer release from the FTP site, and got a 550 error. After searching, I found the mailing list discussion of the disk problems / server outage with no ETA for its return. (here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-June/046338.html and here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-September/04766… ) Unfortunately, the source code repo, library repo seem unreachable as well. I found an unofficial copy of the source code on github ( https://github.com/neurodebian/freesurfer) but can't compile with the standard ubuntu 14.04 minc library (getting "cannot find miopen: No such file or directory" right now) and my skills at troubleshooting the compilation are... not great. Any chance that - someone can provide the linux distribution file? (i know it's huge) - someone can give me pointers with the library dependencies? - someone knows when the ftp server might be back up? If the packages exist somewhere and the server will be down for a bit, I would be happy to host the FTP site. Please let me know if I can help. Dave

1 0

area and smoothing
by Seung Gul Kang 17 Sep '16

17 Sep '16

Dear Freesurfer experts, 1. I want to compare the area and/or areapial between two groups in qdec menu. I think that the eTIV or total surface area should be used as a covariate. Which is more appropriate between eTIV and total surface area? 2. Is there any guideline or rule for the smoothing in the thickness, area, and volume comparison? How about the smoothing=5? Thank you. Best, Seung-Gul --- *Seung Gul Kang, M.D., Ph.D. * *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical Center, Gachon University, School of Medicine, 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea *Research scholar*; Sleep Disorders Clinical Research Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1 Bowdoin Square, 9th floor, Boston, MA 02114, USA *Collaboration researcher*; Division of Sleep & Circadian Disorders, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston MA 02115 ᐧ

2 2

Paired analysis - mismatch between matrix and contrast
by Nick Corriveau Lecavalier 16 Sep '16

16 Sep '16

Hi Freesurfer team, I'm trying to run a longitudinal group analysis (2 groups, 2 time points) using the paired analysis procedure: https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis. I have followed all the instructions but when it comes to the mri_glmfit, it says that my contrast files has 2 columns, while the matrix has 44. What did I go wrong? I join with this message the log, fsgd and contrasts files. Thank you! Nick Corriveau-Lecavalier, B.Sc. (Hons.) Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819

1 0

longitudinal spc over an ROI
by Rachel Romeo 16 Sep '16

16 Sep '16

Hi, I have 3 participant groups in my data set, all with 2 longitudinal time points approximately evenly spaced. I've run everyone through the longitudinal pipeline, and used the Monte Carlo simulation to find a cluster that differs in SPC between groups 1 and 2. Now I want to calculate the average SPC in that cluster for group 3, simply for qualitative reference. I've extracted the cluster to a label using mri_surfcluster, mapped that label to each of the participants' surfaces using mri_label2label, and used mris_anatomical_stats to extract the average thickness in the ROI, and then I manually calculated SPC per subject. But, no matter whether I use participants' CROSS or LONG surfaces, I can't replicate the average SPC values in the "y.ocn.dat" file generated by the simulation. My guess is that the difference arises because of the averaging -- I'm averaging over thickness, and then calculating SPC, whereas I'm guessing that the GLM calculates SPC per voxel, and then averages over the cluster. Is there a way I can extract the average SPC for group 3 over this ROI? Thanks, Rachel

2 1

Dev builds not found
by Leila Reddy 16 Sep '16

16 Sep '16

Hi,I get an error with mri_nu_correct.mni. I've seen on the FS wiki that this is because I have a new version of perl and that I should download the development version. However, I cannot access this page ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ (nothing happens on a linux machine, and I get a 550 Failed to change directory error on a Mac). Is there another place I can download the fixed version from? Thanks,Leila

2 1

Z-stat - z.mgh
by Robby De Pauw 16 Sep '16

16 Sep '16

Dear FreeSurfer users I am not able to extract the Z-values as they are not present in my output: z.mgh -- z-stat that corresponds to the significance Are these Z-values always produced (or only in case of two group comparison)? Is there a way to produce this map myself? This is my output after fitting the model (mri_glmfit) and after clusterwise correction for MC: C.dat cache.th13.abs.sig.voxel.mgh F.asc cache.th13.abs.y.ocn.dat F.csv cnr.mgh F.mgh gamma.mgh cache.th13.abs.pdf.dat gammavar.mgh cache.th13.abs.sig.cluster.mgh maxvox.dat cache.th13.abs.sig.cluster.summary sig.asc cache.th13.abs.sig.masked.mgh sig.csv cache.th13.abs.sig.ocn.annot sig.mgh cache.th13.abs.sig.ocn.mgh I am currently working on the latest version of FreeSurfer: freesurfer-Darwin-lion-stable-pub-v5.3.0 Thank you for your response, Greetings Robby Robby De Pauw, PT, MT, drs. T +32 09 332 12 19 | Email Robby.DePauw(a)Ugent.be<mailto:Robby.DePauw@ugent.be> Ghent University | Rehabilitation Sciences and Physiotherapy Campus Heymans 3B3 (022) De Pintelaan 185 BE-9000 Ghent Route to my office<https://soleway.ugent.be/routes/1090>

2 2

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

2 1

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

2 3

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/>*

1 0

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

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