Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images
by Emil H.J. Nijhuis 08 May '14

08 May '14

Hi, I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio scanner with a 32-channel head coil. Unfortunately for half of my subjects I receive an rather odd pial surface artefact, while the 'white' surfaces do not suffer from the same issue. The command line I have used was: recon-all -all -subjid <subjectid> -T2 <subjectdir>/mri/orig/T2.mgz -T2pial -3T Are you familiar with this issue and do you have some advice for me? Thank you very much for your help. Yours sincerely, Emil -- ---------------------------------------------- Emil H.J. Nijhuis, PhD Researcher - Division of Diagnostic and Interventional Neuroradiology University Hospital Basel Petersgraben 4 CH 4031 Basel Switzerland

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2x3 ANOVA question
by sabin khadka 08 May '14

08 May '14

Hi all, I am trying to run 2x3 factorial model correcting for age, sex and intracranial volume. Just to give you insight in my data I have my fsgd file as GroupDescriptorFile 1 Title DOSS analysis 2x3 factorial Class MaleGroup1Low Class MaleGroup1Medium Class MaleGroup1High Class MaleGroup2Low Class MaleGroup2Medium Class MaleGroup2HighClass FemaleGroup1Low Class FemaleGroup1Medium Class FemaleGroup1High Class FemaleGroup2Low Class FemaleGroup2Medium Class FemaleGroup2High Variables Age normVol Input SUB001 MaleGroup1Low 18 0.4 And also my contrast files as Group1Group2.mtx [1 1 1 -1 -1 -1 1 1 1 -1 -1 -1]/3 MainEffectState.mtx 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 HighvLow.mtx -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 HighvMed.mtx 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5 GroupxState-interaction.mtx 0.5 -0.5 0 -0.5 0 0.5 0.5 -0.5 0 -0.5 0 0.5 0.5 0 -0.5 -0.5 0 0.5 0.5 0 -0.5 -0.5 0 0.5 I'd appreciate if anyone could please let me know that my design is correct. Thanks for help. -Sabin

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ADNI freesurfer annotation/labels file
by Tanya 08 May '14

08 May '14

Hi Freesurfers, I'd like to work with ADNI freesurfer data to do analysis on cortical segments, but could not find the annotation files for these studies. Where in the ADNI freesurfer files can I find the annotation/labels files containing the labels for each vertex on the cortical surfaces? Thanks!

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Re: [Freesurfer] LOOK FOR HELP!
by 刘东博 07 May '14

07 May '14

Dear Greve： Thank you for your reply！ I want to use surf2vol to get volume files of gray thickness.And the --volreg Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. So I use bbregister.Why I need not invert the BBR registration matrix with surf2vol?I mean , the BBR registration matrix is functional to anatomial volume,the surf2vol need anatomical to XYZ And I use bbregister --s sub1 --mov /sub1/mri/orig.nii --init-fsl --reg/sub1/register.dat --t1;mri_surf2vol --surfval /sub1/surf/lh.thickness.fwhm0.fsaverage.mgh --hemi lh --surf pialfs --volreg /sub1/register.dat --outvol ./ --template /sub1/mri/orig.nii the resluts are 256 volumes.Why this happen?Should the voulme be 1 file? 2014-05-07 0:00 GMT+08:00 <freesurfer-request(a)nmr.mgh.harvard.edu>: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Coordinate transformation to average surface space > (ISAAC PEDISICH) > 2. Re: using multiple cores (Z K) > 3. Fwd: Fwd: Optseq2: ntp (Conchy PF) > 4. Help with subject's functional overlay (Cesar Echavarria) > 5. Re: Help with subject's functional overlay (Bruce Fischl) > 6. Re: Help with subject's functional overlay (Cesar Echavarria) > 7. Re: problems about extracting specific vertex thickness value > and getting a average thickness for a specific mask (Douglas N Greve) > 8. Re: Fwd: Fwd: Optseq2: ntp (Douglas N Greve) > 9. Re: When/What to edit? (Douglas N Greve) > 10. Re: qdec question (Douglas N Greve) > 11. Re: Help with subject's functional overlay (Douglas N Greve) > 12. Re: Brain Seg Volumes (Douglas N Greve) > 13. Re: using multiple cores (Lukas.Scheef(a)ukb.uni-bonn.de) > 14. Re: comparing two conditions with disproportionate number of > trials (Eryilmaz, Huseyin Hamdi) > 15. Re: Help with subject's functional overlay (Cesar Echavarria) > 16. Re: using multiple cores (Z K) > 17. Re: Help with subject's functional overlay (Douglas N Greve) > 18. Re: using multiple cores (Bruce Fischl) > 19. Registering functional data to inflated brain (Sherryse Corrow) > 20. Viewing functional data on the inflated brain (Sherryse Corrow) > 21. vertex-wise cortical thickness and whole brain labeling (Caka) > 22. Re: Registering functional data to inflated brain (Douglas Greve) > 23. Re: LOOK FOR HELP (???) > 24. LOOK FOR HELP (???) > 25. Re: vertex-wise cortical thickness and whole brain labeling > (Douglas Greve) > 26. Re: Viewing functional data on the inflated brain (Douglas Greve) > 27. Two positions are available @ Queensland Brain Institute > (Yong Liu) > 28. Re: qdec question (Anna Jonsson) > 29. aseg.stats volume mismatch (Gabor Perlaki) > 30. Re: aseg.stats volume mismatch (Bruce Fischl) > 31. -3T and -mprage flags (Jason Tourville) > 32. Re: LOOK FOR HELP (Douglas Greve) > 33. Re: qdec question (Douglas Greve) > 34. Re: -3T and -mprage flags (Bruce Fischl) > 35. freeview fails to open (JacobML(a)nmr.mgh.harvard.edu) > 36. mri_glmfit restricted to a label (Garikoitz Lerma-Usabiaga) > 37. Re: freeview fails to open (Ruopeng Wang) > 38. Re: freeview fails to open (JacobML(a)nmr.mgh.harvard.edu) > 39. Re: freeview fails to open (Ruopeng Wang) > 40. Re: freeview fails to open (JacobML(a)nmr.mgh.harvard.edu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 5 May 2014 12:19:29 -0400 > From: ISAAC PEDISICH <iped(a)sas.upenn.edu> > Subject: Re: [Freesurfer] Coordinate transformation to average surface > space > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > CAPUS5aqNf_zYu185Sf723Ad9wpp59b02hC3e-K0KZ2nLjQJMdQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Any other thoughts as to what might be going wrong with our coordinate > transformations / any other transformations that we might not be taking > into account? > > Thanks, > Isaac > > > On Tue, Apr 29, 2014 at 4:52 PM, ISAAC PEDISICH <iped(a)sas.upenn.edu> > wrote: > > > The purpose of what I'm trying to do is getting specific points from the > > CT onto the average surface. > > These points lie on the surface of the brain. > > > > Originally, we were using flirt to register the CT to the MRI, then > > registering the MRI to the talairach brain, to get the CT into the same > > space as the surface. This method worked okay, but we were hoping to > > improve on it. > > > > The new method, using robust register and tkregsiter2, produces > > coordinates that are on the surface of the brain in freeview, but not in > > matlab (for some subjects). > > > > Here is the info for one problem subject: > > > > mri_info --vox2ras-tkr [subj]_CT_combined.img > > INFO: using NIfTI-1 qform > > -0.47461 0.00000 0.00000 121.50000 > > 0.00000 0.00000 0.62634 -69.83636 > > 0.00000 -0.47461 0.00000 121.50000 > > 0.00000 0.00000 0.00000 1.00000 > > > > > > # transform file reg_avg.lta > > # created by ---- on Thu Mar 27 15:55:39 2014 > > type = 1 > > nxforms = 1 > > mean = 256.0000 228.0000 111.0000 > > sigma = 10000.0000 > > 1 4 4 > > 9.349995851516724e-01 -2.874486744403839e-01 -2.077235281467438e-01 > > -3.043334960937500e+01 > > 3.062604963779449e-01 9.497789144515991e-01 6.422379612922668e-02 > > 1.133301696777344e+02 > > 1.788303703069687e-01 -1.236666887998581e-01 9.760769009590149e-01 > > -1.039845886230469e+02 > > 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 > > 1.000000000000000e+00 > > src volume info > > valid = 1 # volume info valid > > filename = [subj]_CT_combined.img > > volume = 512 512 223 > > voxelsize = 4.746093750000000e-01 4.746093750000000e-01 > > 6.263351440429688e-01 > > xras = -9.999999403953552e-01 0.000000000000000e+00 > 0.000000000000000e+00 > > yras = 0.000000000000000e+00 9.703245759010315e-01 > 2.418061196804047e-01 > > zras = -0.000000000000000e+00 -2.418061196804047e-01 > > 9.703245759010315e-01 > > cras = 7.629394531250000e-06 -1.615307769775391e+02 > 1.476517486572266e+02 > > dst volume info > > valid = 1 # volume info valid > > filename = /data/eeg/freesurfer/subjects/average/mri/orig.mgz > > volume = 256 256 256 > > voxelsize = 1.000000000000000e+00 1.000000000000000e+00 > > 1.000000000000000e+00 > > xras = -1.000000000000000e+00 0.000000000000000e+00 > 0.000000000000000e+00 > > yras = -2.220446049250313e-16 -1.490116119384766e-08 > > -1.000000000000000e+00 > > zras = 4.440892098500626e-16 1.000000000000000e+00 > 8.443226899772703e-18 > > cras = 0.000000000000000e+00 0.000000000000000e+00 > 0.000000000000000e+00 > > > > > > Here are a set of eight coordinates, all of which are on the surface in > > CRS space on the CT: > > 242 267 47 > > 241 283 36 > > 234 298 28 > > 221 313 23 > > 203 321 19 > > 183 323 24 > > 172 312 33 > > 164 297 42 > > > > After applying the transform, these coordinates come out as: > > 5.2486 -168.8798 78.8261 > > 2.2243 -174.6209 70.8729 > > 2.5230 -179.4546 62.9121 > > 6.0596 -183.3221 54.4805 > > 12.6010 -187.6878 48.8390 > > 22.2656 -187.3245 46.1419 > > 29.8070 -184.1168 50.5152 > > 36.3566 -180.7347 57.0374 > > > > Those middle coordinates are all off the brain - the coordinates are far > > too negative. > > > > When run through the first method, they come out to: > > 20.6235 -15.8172 -23.1366 > > 19.041 -5.94338 -28.5567 > > 20.8091 3.8041 -32.346 > > 25.8047 13.9764 -34.4435 > > 34.3347 20.7722 -36.4294 > > 44.7823 23.7184 -33.5718 > > 52.1009 18.1343 -29.1088 > > 58.3186 10.0044 -24.8649 > > > > Which are (approximately) on the surface of the brain. > > > > However, when I load up the average surface in freeview, and apply > > reg_avg.lta to the CT, the two overlay exactly. > > > > I'm mostly trying to figure out why the coordinates that I get in MATLAB > > do not agree with the coordinates that I see in freeview. > > > > Thanks again for your help, > > Isaac > > > > On Tue, Apr 29, 2014 at 1:43 PM, Douglas N Greve < > > greve(a)nmr.mgh.harvard.edu> wrote: > > > >> > >> It sounds like you are doing the right thing with the right equation. > >> Can you elaborate on what is going wrong? > >> > >> > >> On 04/28/2014 05:10 PM, ISAAC PEDISICH wrote: > >> > Sorry - I meant just the matrix. > >> > > >> > I'm trying to map from CRS in the CT to tkrRAS in the anatomical, I > >> > believe. I'm a little unclear as to what exactly anat space means, but > >> > I know that I'm trying to get it from CRS in the CT to the space in > >> > which the surface is plotted in MATLAB, which I believe is tkrRAS, > >> > anatomical. I'm certain it's no longer CRS space, as the x-coordinates > >> > must contain some negative indices. > >> > > >> > > >> > > >> > On Mon, Apr 28, 2014 at 5:02 PM, Douglas N Greve > >> > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > >> > > >> > > >> > When you say the content is the same, do you mean exactly the same > >> or > >> > just the matrix? Also, what coordinate system are you trying to go > >> to? > >> > The equation you have below takes CRS in the CT and maps it to > >> > tkrRAS in > >> > the anatomical. If you want to map the CRS in the anat then use > >> > > >> > inv(Tanat) * inv(Reg_avg) * Tmov * CT_coords > >> > > >> > > >> > On 04/28/2014 03:58 PM, ISAAC PEDISICH wrote: > >> > > Hi Doug, > >> > > Thanks for the response. > >> > > I'm not seeing lta_convert as an executable that I can run. I > have > >> > > freesurfer v5.3.0 installed - is there another version that I > >> should > >> > > be using? > >> > > > >> > > For using tkregister2, I'm a bit confused as to what I should be > >> > > doing. I had assumed (erroneously, it seems) that the .lta and > >> .dat > >> > > files contained the same information. > >> > > I just tried re-running tkregister2 with the command: > >> > > tkregsiter2 --mov [sub_CT].img --reg reg_avg.dat --surf pial --s > >> > > average --lta reg_avg.lta > >> > > Such that I can pass in the reg_avg.lta file created from robust > >> > > register, and have it output a reg_avg.dat file. The contents of > >> > these > >> > > two files, however, seem to be exactly the same. > >> > > > >> > > I also running tkregister2 with the --fslregout and --freeview > >> > flags, > >> > > but neither of those produced a correct transformation either. > >> > > > >> > > Martin: > >> > > We are indeed registering the CT to an average MRI, and for the > >> > moment > >> > > we are correcting inaccuracies manually with tkregister2. > >> > > I just tried bbregister with one of our problem subjects, and it > >> > still > >> > > produced a matrix that had to be significantly adjusted in > >> > > tkregister2. Furthermore, the matrix that it produced still did > >> not > >> > > transform the coordinates correctly in MATLAB. > >> > > > >> > > -Isaac > >> > > > >> > > > >> > > On Mon, Apr 28, 2014 at 2:32 PM, Douglas N Greve > >> > > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >> > <mailto:greve@nmr.mgh.harvard.edu > >> > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > >> > > > >> > > > >> > > The matrix in the lta is probably not the right one. Try > using > >> > > lta_convert or tkregister2 to change it to a register.dat > file > >> > > (which is > >> > > what is expected in your formula) > >> > > doug > >> > > > >> > > On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote: > >> > > > Hi All, > >> > > > > >> > > > I am attempting to transform sets of coordinates from > >> > subject CRS > >> > > > space into the surfaceRAS space of an average subject, > >> > made with > >> > > > make_average_subject. > >> > > > > >> > > > By our current method, we register the individual CT to > >> > the average > >> > > > surface using mri_robust_register with the command: > >> > > > mri_robust_register --mov [subj_CT].img --dst > >> > average_orig.mgz > >> > > --lta > >> > > > reg_avg.lta --iscale --satit > >> > > > and then check and adjust the registration with: > >> > > > tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf > >> pial > >> > > --s average > >> > > > > >> > > > These steps work fine, and when I load the average brain > in > >> > > freeview, > >> > > > then load the subject CT with with the registration file > >> > reg_avg.lta > >> > > > applied, the two overlap just as they should. > >> > > > > >> > > > However, when I attempt to do the same thing in matlab, > >> > some (though > >> > > > not all) of the subjects present a problem. > >> > > > I do the coordinate transformation (as suggested on > >> > > > http://freesurfer.net/fswiki/CoordinateSystems) by > >> applying: > >> > > > > >> > > > inv(Reg_avg) * Tmov * CT_coords > >> > > > > >> > > > with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg > as > >> > > > reg_avg.lta, and CT_coords as the relevant coordinates in > >> > CRS space > >> > > > from the CT (with a vector of ones appended). > >> > > > > >> > > > As I said, some of the scans come out fine, with the > >> > coordinates in > >> > > > the correct place on the average surface, while others are > >> > very far > >> > > > removed from their correct location. How can I fix this? > >> > > > > >> > > > Thanks, > >> > > > Isaac > >> > > > > >> > > > > >> > > > _______________________________________________ > >> > > > Freesurfer mailing list > >> > > > Freesurfer(a)nmr.mgh.harvard.edu > >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > >> > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> > > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > >> > > -- > >> > > Douglas N. Greve, Ph.D. > >> > > MGH-NMR Center > >> > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >> > <mailto:greve@nmr.mgh.harvard.edu <mailto: > greve(a)nmr.mgh.harvard.edu > >> >> > >> > > Phone Number: 617-724-2358 <tel:617-724-2358> > >> > <tel:617-724-2358 <tel:617-724-2358>> > >> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > >> > <tel:617-726-7422>> > >> > > > >> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >> > > < > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >> > > Outgoing: > >> > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> > > > >> > > _______________________________________________ > >> > > Freesurfer mailing list > >> > > Freesurfer(a)nmr.mgh.harvard.edu > >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> > <mailto:Freesurfer@nmr.mgh.harvard.edu > >> > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > >> > > > >> > > The information in this e-mail is intended only for the > >> > person to > >> > > whom it is > >> > > addressed. If you believe this e-mail was sent to you in > >> > error and > >> > > the e-mail > >> > > contains patient information, please contact the Partners > >> > > Compliance HelpLine at > >> > > http://www.partners.org/complianceline . If the e-mail was sent > >> to > >> > > you in error > >> > > but does not contain patient information, please contact the > >> > > sender and properly > >> > > dispose of the e-mail. > >> > > > >> > > > >> > > > >> > > > >> > > _______________________________________________ > >> > > Freesurfer mailing list > >> > > Freesurfer(a)nmr.mgh.harvard.edu > >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > -- > >> > Douglas N. Greve, Ph.D. > >> > MGH-NMR Center > >> > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >> > Phone Number: 617-724-2358 <tel:617-724-2358> > >> > Fax: 617-726-7422 <tel:617-726-7422> > >> > > >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >> > Outgoing: > >> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer(a)nmr.mgh.harvard.edu <mailto: > >> Freesurfer(a)nmr.mgh.harvard.edu> > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > > >> > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer(a)nmr.mgh.harvard.edu > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> greve(a)nmr.mgh.harvard.edu > >> Phone Number: 617-724-2358 > >> Fax: 617-726-7422 > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > > >

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Re: [Freesurfer] vertex-wise cortical thickness and whole brain labeling
by Douglas N Greve 07 May '14

07 May '14

Hi Caka, please remember to post to the list and not to us personally. Thanks! We do not have a procedure to parcellate 1170 regions. Try contacting the authors directly. doug On 05/07/2014 12:01 AM, Caka wrote: > Dear Douglas, > > Thanks for your reply. Indeed, the work in ‘An anatomical substrate for integration among functional networks in human cortex, Martijn P. van den Heuvel and Olaf Sporns, 2013’ used Freesurfer to automatically parcellate the cerebral cortex into 1170 regions. The authors didn’t describe the details. I am wondering if Freesurfer provides an existing template with 1170 parcels of neocortex, or what procedure do I need to take to get the 1170 parcels template? > > Thank you very much! > > Qiongmin Ma > > > On 5/5/14 10:41 PM, Caka wrote: >> Hi Douglas and all, >> >> I have used the ?recon-all? command to segment the gray matter of 140 subjects. I have three questions: >> >> (1) as the segmentation is done in the individual space, how can I register the results into the template brain? The results includes the surface and the vertex. Is it ?mri_surf2surf?? > mri_surf2surf is used when mapping surface data to the surface of an > average subject such as fsaverage. Is that what you want? >> (2) If the gray matter is registered into the template brain, then same number of vertex in every region would be obtained. Then what information does the value of each vertex stands? Is it the cortical thickness changes? > I don't understand what you mean. >> (3) We know that Freesurfer provides two kinds of brain region labeling, 68 regions and 77 regions in the cerebral cortex respectively. I am wondering whether I can use my own labeling, like 1000 regions? How can I do this? > Do you mean you've labeled 1000 regions on a brain? You would have to do > that for a number of subjects (eg, 40), you can then build an atlas. The > problem is that such small regions will not be very reliable > doug >> Thank you very much! >> >> Qiongmin Ma > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Question about Qdec p-values
by Las Blawimo 07 May '14

07 May '14

Dear sir, madam, I am currently using Freesurfers Qdec and I have a question about the statistical output: is it possible to have a peak p-value that is larger (i.e. less significant) than the clusterwise p-value? My peak p-value (after using a - log10 transformation) = 0.0038, while my clusterwise p-value = 0.0029. Could you maybe give an explanation how the clusterwise p-value is computed? Thank you very much! Kind regards, Las Blawimo

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Recon All on a 3 years old subject
by Francesco Baldacchini 07 May '14

07 May '14

Hi, I'm trying to use recon-all on subjects between 3-12 years old, but I'm getting bad results as you can see from the image I attached, these subject in particular is 3 years. It seems like it is unable to distinguish well the borders of grey and white matter also if by looking at the structural images the contrast is quite good. Do you have any idea or suggestion on why I'm having these issues? Can you point out the exact points where I can look to find the error? I guess you'll need the entire recon-all, I can send it off if you wish. Thanks in advance, Francesco Baldacchini

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bbregister and surf2vol
by 刘东博 07 May '14

07 May '14

Dear Freesurfer I want to use surf2vol to get volume files of gray thickness.And the --volreg Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. So I use bbregister.Why I need not invert the BBR registration matrix with surf2vol?I mean , the BBR registration matrix is functional to anatomial volume,the surf2vol need anatomical to XYZ And I use bbregister --s sub1 --mov /sub1/mri/orig.nii --init-fsl --reg /sub1/register.dat --t1; mri_surf2vol --surfval /sub1/surf/lh.thickness.fwhm0.fsaverage.mgh --hemi lh --surf pialfs --volreg /sub1/register.dat --outvol ./ --template /sub1/mri/orig.nii the resluts are 256 volumes.Why this happen?Should the voulme be 1 file?

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surf2vol
by 刘东博 06 May '14

06 May '14

I want to use surf2vol to get volume files of gray thickness.And the --volreg Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. So I use bbregister.Why I need not invert the BBR registration matrix with surf2vol?I mean , the BBR registration matrix is functional to anatomial volume,the surf2vol need anatomical to XYZ

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Help with subject's functional overlay
by Cesar Echavarria 06 May '14

06 May '14

Hello freesurfer experts, The functional overlay for one of our subjects looks like the image attached. You'll notice the "holes" on the overlay that have a value of 0. I'm trying to get ride of these as I expect (as with other subjects) to have values for these vertices that are not 0. Myself and a colleague have tried improving the registration as much as we see possible, but the problem remains. Any tips on how to correct this issue would be greatly appreciated. Thanks in advance for your help! Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012

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