Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

FW: talairach and scullstrip, order and control points, questions
by L.Hoekstra＠psy.umcn.nl 08 Dec '10

08 Dec '10

________________________________ From: Hoekstra, Liesbeth Sent: Wed 12/8/2010 11:11 To: freesurfer(a)nmr.mgh.harvard.edu Subject: talairach and scullstrip, order and control points, questions L.S., Let me start by saying that you've got a wonderful webpage! I'm a beginner in the Freesurfer field. I worked my way into the method (incl. tutorial and talks), but I've still got a couple of questions about the cortical thickness measurement. 1) when starting after autorecon1 with the talairach transformation and the scullstrp, is it enough to just save the transformations (save reg)? (in the tutorial it said, that you have to rerun autorecon-all, but if you just start the procedure, it seems unlikely to me) 2) small parts of the dura in scullstrip procedure, can they be left in place in the new version of Freesurfer (I read something on the qeustions-page, that allmost everything is automatically transformed, but that still manually must be checked if BIG differences remain (id est: big parts of skull remaining, brain is removed) 3) It is a little confusing, in the order of the Freesurfer workflow the control points are set between autorecon 1 and autorecon 2, but if you set them you have to run autorecon-cp (again). Can I set the control points just after the autorecon 2? 4) Can I do autorecon 2 than do the white matter edits , pial edits and final surfex and than rerun autorecon 2 before going to autorecon3 , or do I have to rerun after each individual step? thanks a lot for your answers, I'm looking forward to it to continue my analysis, L.Hoekstra Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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mri_head
by Lisa F. Akiyama 07 Dec '10

07 Dec '10

Hello, I am trying to read the header information of some .ima files. Is there a function similar to mri_head that will also display more detailed information such as the subject's date of birth? Below is the output I got from the mri_head command on a particular ima file. Thank you. Best, Lisa Akiyama todd:~$ mri_head -read $SUBJECTS_DIR/k_h/mri/slices/393-2-123.ima rows = 256 cols = 256 succeed fname = /usr/local/freesurfer/subjects/k_h/mri/slices/393-2-123.ima height = 256 width = 256 depth = 120 nframe = 1 imnr0 = 1 imnr1 = 120 xnum = 256 ynum = 256 fov = 256.000000 thick = 1.500000 xstart = -128.000000 xend = 128.000000 ystart = -128.000000 yend = 128.000000 zstart = -90.000000 zend = 90.000000 type = 4 xsize = 1.000000 ysize = 1.000000 zsize = 1.500000 x ras = -0.000000 -1.000000 -0.000000 y ras = -0.000000 0.000000 -1.000000 z ras = -1.000000 0.000000 0.000000 c ras = -4.403150 -14.970646 -10.273973 det(xyz_ras) = -1.000000 ras_good_flag = 1 brightness = 1 subject_name = path_to_t1 = fname_format = ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington E-mail: lrisa87(a)uw.edu P Please consider the environment before printing this e-mail.

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binaries not executable?
by Nathan Dankner 07 Dec '10

07 Dec '10

Hi All, I've just installed freesurfer onto a linux node, and immediately encountered a problem when trying to run my first scan. After executing the recon-all command, the terminal spits out a string of errors saying: [freesurfer home path]/mri_convert: Exec format error. Binary file not executable It does this for every binary which is called upon executing recon-all and exits with errors. Any idea what's wrong? Thanks, Nathan

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Re: [Freesurfer] analysis in v5 vs v4.5
by Douglas N Greve 07 Dec '10

07 Dec '10

selxavg3-sess checks to see whether preproc has been run and runs it if it is needed, so all that stuff can go on in the background. It does look like the differences you are seeing come from the whitening. This attempts to account for temporal correlation in the noise. Whether you need it or not depends on what you actually report. If you report the volume of activation for each subject, then you'll probably want some sort of whitening. In general, people don't report this. If you are going to just hand the 1st level results up to the next higher level (eg, group analysis), then I don't think it makes a difference. A reviewer may balk if there has not been whitening performed at the first level, but this is usually just a misunderstanding on their part. doug Katie Bettencourt wrote: > When I registered the 4.5 version, I did it fully manually, using > tkregister2, but with the version5 one I initially didn't do anything > outside of the commands I listed below (though the register.dat was > present from the 4.5 version), but then to check that I went through > and ran register-sess on the version 5, and then double checked it in > tkregister2 (as the output to register-sess suggested I do) and at > least at a coarse look it looked fairly well aligned, and rerunning > selxavg3-sess after running register-sess didn't change the output (in > fact, the picture I attached before was from the register-sess > version). Does selxavg3-sess automatically run this registration in > version 5 or do you need to do the registration separately everytime? > Similarly, I didn't run preproc-sess separately for version5, did I > need to? > > rerunning it with the -no-whiten flag seems to have pushed it in the > other direction. I now get more activation in v5 than v4.5 (see > attached pictures) which honestly I guess I like better... Do I need > to run it with the -no-whiten flag each time? Exactly what is this > flag doing? > > Katie > > On Tue, Dec 7, 2010 at 2:20 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hmmm, not sure what's going on with that. Can you verify that the > registration is correct in the v5 results? The only other thing > that I can think of is that the whitening may be a bit different > between 4.5 and 5.0. Try turning off the whitening in v5 > (-no-whiten when running mkanalysis-sess). > > doug > > Katie Bettencourt wrote: > > I was attempting to run an analysis that was previously done > in freesurfer 4.5 in version 5 to see if I cuold switch over > to the new version. However, I am getting very different > results for the two versions. Below are the commands I ran in > both and attached are pictures of the differences. I get much > much less activation (and much less than expected) when using > version 5. I assume this is because I've done something wrong > with the way I set up my version 5 analysis, but I don't knwo > what it is. Any help would be appreciated. > > version 5: > mkanalysis-sess -analysis supIPS-gamma-5rh -TR 1.5 -paradigm > supIPS.dat -event-related -runlistfile supIPSruns.txt -nskip 2 > -nconditions 6 -gammafit 2.25 1.25 -surface self rh -fwhm 0 > -refeventdur 6 > mkcontrast-sess -analysis supIPS-gamma-5rh -contrast > act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 > selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis > supIPS-gamma-5rh > tksurfer-sess -s 101103TM_supIPS -a supIPS-gamma-5rh-c > act_vs_fix -df supIPS.dir > > version 4.5 > mkanalysis-sess -analysis supIPS-gamma -TR 1.5 -paradigm > supIPS.dat -designtype event-related -funcstem fmc -motioncor > -runlistfile supIPSruns.txt -inorm -tpexclude tpexclude.dat > -nconditions 6 -gammafit 2.25 1.25 -noautostimdur > mkcontrast-sess -analysis supIPS-gamma -contrast act_vs_fix -a > 1 -a 2 -a 3 -a 4 -a 5 -c 0 > tksurfer-sess -s 101103TM_supIPS -df supIPS.dir -a > supIPS-gamma -c act_vs_fix -hemi rh > > > Katie > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] aligning functionals to anatomicals
by Douglas N Greve 07 Dec '10

07 Dec '10

And how did you reorient to run FS on the anats? Krishna Srihasam wrote: > Hi, > > Yes. We took the anatomicals with the monkey in sphinx position in a > stereotax. > > Rgds, > krsihna > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Tuesday, December 07, 2010 2:32 PM > To: Krishna Srihasam > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] aligning functionals to anatomicals > > How did you re-orient your anatomicals? Was the monkey in the sphinx > position? > > doug > > Krishna Srihasam wrote: > >> Hi, >> >> >> >> I have a question regarding overlay of functional activations on a >> freesurfer map. After much work, I flattened my monkey brain. But, I >> just realized that the input volume , which I used to generate the >> flat maps, had orientation set to LIA. I want to over lay my >> functional activations, which are in RAS orientation on them. One >> way would be to realign all functional data into LIA orientation and >> then analyze the data and then simply use spmregister-see or >> fslregister-sess to register. Is there any simpler way? >> >> >> >> My functionals are 65x85x56 for each slice. I tried using flirt to get >> the alignment matrix. But, it is failing badly.. Any ideas would be >> welcome.. >> >> >> >> Regards, >> >> krishna >> >> >> >> ---------------------------------------------------------------------- >> -- >> >> _______________________________________________ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Freesurfer installation on RHEL 5.4: failed to create OpenGL rendering context
by dahlia＠nmr.mgh.harvard.edu 07 Dec '10

07 Dec '10

Hi, Would really appreciate help with this insallation problem! I'm installing freesurfer on a new system, and at an initial test running "tkmedit bert.mgz" produces GLUT: Fatal Error in tkmedit.bin: failed to create OpenGL rendering context. I thought maybe updating the NVidia card would help, but when I go to their website and try to download NVidia Quadro NVS, there are only Windows options to select as OS. This is a Dell Precision T7500 preinstalled with RHEL 5.4. About a year ago I installed freesurfer on virtually identical hardware (the OS there was CentOS as a virtual machine under the Windows host), and did not run into such a problem Can you help me figure out why it's running into this problem and how to fix it? Thanks! Dahlia.

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aligning functionals to anatomicals
by Krishna Srihasam 07 Dec '10

07 Dec '10

Hi, I have a question regarding overlay of functional activations on a freesurfer map. After much work, I flattened my monkey brain. But, I just realized that the input volume , which I used to generate the flat maps, had orientation set to LIA. I want to over lay my functional activations, which are in RAS orientation on them. One way would be to realign all functional data into LIA orientation and then analyze the data and then simply use spmregister-see or fslregister-sess to register. Is there any simpler way? My functionals are 65x85x56 for each slice. I tried using flirt to get the alignment matrix. But, it is failing badly.. Any ideas would be welcome.. Regards, krishna

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analysis in v5 vs v4.5
by Katie Bettencourt 07 Dec '10

07 Dec '10

I was attempting to run an analysis that was previously done in freesurfer 4.5 in version 5 to see if I cuold switch over to the new version. However, I am getting very different results for the two versions. Below are the commands I ran in both and attached are pictures of the differences. I get much much less activation (and much less than expected) when using version 5. I assume this is because I've done something wrong with the way I set up my version 5 analysis, but I don't knwo what it is. Any help would be appreciated. version 5: mkanalysis-sess -analysis supIPS-gamma-5rh -TR 1.5 -paradigm supIPS.dat -event-related -runlistfile supIPSruns.txt -nskip 2 -nconditions 6 -gammafit 2.25 1.25 -surface self rh -fwhm 0 -refeventdur 6 mkcontrast-sess -analysis supIPS-gamma-5rh -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis supIPS-gamma-5rh tksurfer-sess -s 101103TM_supIPS -a supIPS-gamma-5rh-c act_vs_fix -df supIPS.dir version 4.5 mkanalysis-sess -analysis supIPS-gamma -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -tpexclude tpexclude.dat -nconditions 6 -gammafit 2.25 1.25 -noautostimdur mkcontrast-sess -analysis supIPS-gamma -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 tksurfer-sess -s 101103TM_supIPS -df supIPS.dir -a supIPS-gamma -c act_vs_fix -hemi rh Katie

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---regheader option in mri_label2vol
by Navid Shiee 07 Dec '10

07 Dec '10

Hi, I am trying to transform the volumetric labels from aseg.auto to the original space. As suggested on the wiki I use the command mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz However, I got ERROR: Option --regheader unknown If I don't use that option at all, the image is still in coronal orientation although the header is changed to axial. Would you please help me on this? Thanks, -- Navid

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recon-all
by Yang Liu 07 Dec '10

07 Dec '10

Hi, I am processing the anatomical monkey brain now. When recon-all runs, it stops at the step of "mris_fix_topology" I inserted the last part of my recon-all.log below: It stops at "CORRECTING DEFECT 0 (vertices=65691, convex hull=4296)" for more than 12 hours. Does this step take that long? Or are there some problems in the data that make freesurfer idling? Thanks, Yang #-------------------------------------------- #@# Fix Topology lh Sat Dec 4 17:01:16 EST 2010 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /home/yang/091017Castor/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 091017Castor lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ before topology correction, eno=-810 (nv=213660, nf=428940, ne=643410, g=406) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 156279 ambiguous faces found in tessellation segmenting defects... 64 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 0 -merging segment 11 into 10 -merging segment 23 into 18 -merging segment 33 into 22 -merging segment 40 into 22 -merging segment 62 into 25 -merging segment 39 into 34 -merging segment 35 into 46 56 defects to be corrected 0 vertices coincident reading input surface /home/yang/091017Castor/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8048 (-4.4024) -vertex loglikelihood: -5.5855 (-2.7928) -normal dot loglikelihood: -3.4654 (-3.4654) -quad curv loglikelihood: -5.6070 (-2.8035) Total Loglikelihood : -23.4627 CORRECTING DEFECT 0 (vertices=65691, convex hull=4296)

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