Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

mri_normalize control in FS 5.2
by Michael Harms 08 Apr '13

08 Apr '13

Hi guys, I see that the recon-all for FS 5.2 now has flags for setting the -b and -n arguments to mri_normalize separately for the two different Normalization stages. Was that just for increased control/flexibility, or did you find that it was actually detrimental to use say "-b 20 -n 5" in the first Normalization stage, if for example using an expert options file for mri_normalize? thanks, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu

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Fwd: [FSL] Neuro Bureau Announces the BRAIN-ART COMPETITION 2013
by MCLAREN, Donald 08 Apr '13

08 Apr '13

In order to recognize the beauty and creativity of artistic renderings emerging from the neuroimaging community, we are launching the third annual Brain-Art Competition. Countless hours are devoted to the creation of informative visualizations for communicating neuroscientific findings. The Brain-Art Competition aims to recognize this often unappreciated aspect of the publication process, and highlight the artistic creativity of our community. We are inviting researchers to submit their favorite unpublished works for entry. Both team and single-person entries are welcomed. The competition will have five award categories: – Best Representation of the Human Connectome – Best Abstract Brain Illustration – Best Humorous Brain Illustration – Best Video Illustration of the Brain – Special Topic: Best Visualization of Probabilistic Connectivity The 'Special Topic' is a new addition to this year’s competition that highlights an important challenge in current connectomics research: visualizing the uncertainty of 3D connections in tractography and functional connectivity data. Submission Deadline: 11:59PM CDT, Wednesday, June 5th, 2013 Award Notification: June 17th during the Neuro Bureau gala event, held at the OHBM Annual Meeting in Seattle. For more information, check out the competition details and submission form at: www.neurobureau.org

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R: Re: cortical thickness normalization
by stdp82＠virgilio.it 08 Apr '13

08 Apr '13

Hi list and Michael, is there a paper that you advise me to cite for mean thickness? Thanks, Stefano ----Messaggio originale---- Da: mharms(a)conte.wustl.edu Data: 4-apr-2013 15.45 A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] cortical thickness normalization If you're studying thickness, I'm a fan of using mean cortical thickness as the covariate (since thickness is what you're studying). I've posted on this in the past. cheers,-MH -- Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <stdp82(a)virgilio.it> Reply-To: <stdp82(a)virgilio.it> Date: Thursday, April 4, 2013 7:21 AM To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] cortical thickness normalization Hi list, I'm reading a lot of post on this list about cortical thickness normalization. I' m noting very different results on my data when I use mean thickness or ICV as nuisance factor than no factor. I'm confuse on this topic, could you advise the best way, please? Thanks, Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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Hacks needed to build freesurfer
by Chris Roat 08 Apr '13

08 Apr '13

I thought I'd share the changes I needed in order to build from the current stable5 source in the repo. I have a Raring Ubuntu distribution, and I tried to install all the necessary libraries. (Independent of building, I still see https://bugzilla.redhat.com/show_bug.cgi?id=905638 in chklc.c of stable5, but I've also commented that out in order to proceed.) Needed updates (diffs below): - Pulled missing unwarpGradientNonlinearity.{h,c} files from somewhere in Google's cache - Updates to configure.in: Bypass gcc 4.4 decision so that libtool is used correctly (Raring has uses 4.7) Correct the MNI libraries link order Change GL include directory Do not create glut Makfile/library (use glut from system) - Update several Makefile.am files to use glut from system - Configure options that I used: --disable-Werror --with-mni-dir=/usr --with-vxl-dir=/usr --with-tcl-include=/usr --with-gl-dir=/usr --x-libraries=/usr/lib/X11 --x-includes=/usr/include/X11 ? include/unwarpGradientNonlinearity.h ? utils/unwarpGradientNonlinearity.c Index: configure.in =================================================================== RCS file: /usr/fscvsroot/dev/configure.in,v retrieving revision 1.519.2.39 diff -b -r1.519.2.39 configure.in 203,210c203,210 < ac_have_gcc_44="no" < if test "${CC}" = "gcc"; then < gcc --version | head -n 1 | awk '{print $2 $3}' | grep "(GCC)4.4." >& /dev/null < if test "$?" = "0"; then < AC_MSG_NOTICE(Have gcc 4.4) < ac_have_gcc_44="yes" < fi < fi --- > ac_have_gcc_44="yes" > # if test "${CC}" = "gcc"; then > # gcc --version | head -n 1 | awk '{print $2 $3}' | grep "(GCC)4.4." >& /dev/null > # if test "$?" = "0"; then > # AC_MSG_NOTICE(Have gcc 4.4) > # ac_have_gcc_44="yes" > # fi > #fi 1229c1229 < LIBS_MNI="-lnetcdf -lhdf5 -lvolume_io2 -lminc2" --- > LIBS_MNI="-lvolume_io2 -lminc2 -lnetcdf -lhdf5" 2748c2748 < [ ac_gl_includes="$withval"/include --- > [ ac_gl_includes="$withval"/include/GL 3472d3471 < glut/Makefile Index: fsgdf/fsgdf_wrap.c =================================================================== RCS file: /usr/fscvsroot/dev/fsgdf/fsgdf_wrap.c,v retrieving revision 1.18 diff -b -r1.18 fsgdf_wrap.c 110c110 < #include <tcl.h> --- > #include <tcl8.5/tcl.h> Index: Makefile.am =================================================================== RCS file: /usr/fscvsroot/dev/Makefile.am,v retrieving revision 1.224.2.13 diff -b -r1.224.2.13 Makefile.am 13d12 < glut \ Index: mri_probedicom/Makefile.am =================================================================== RCS file: /usr/fscvsroot/dev/mri_probedicom/Makefile.am,v retrieving revision 1.7 diff -b -r1.7 Makefile.am 5c5 < AM_CFLAGS=-I$(top_srcdir)/glut $(GL_CFLAGS) \ --- > AM_CFLAGS=$(GL_CFLAGS) \ 14c14 < $(X_LIBS) $(LIBS_OPENGL) $(top_builddir)/glut/libglut.a --- > $(X_LIBS) $(LIBS_OPENGL) -lglut Index: mris2rgb/Makefile.am =================================================================== RCS file: /usr/fscvsroot/dev/mris2rgb/Makefile.am,v retrieving revision 1.8 diff -b -r1.8 Makefile.am 14d13 < -I$(top_srcdir)/glut \ 26,27c25 < $(LIBS_OPENGL) -lGL $(LIBTIFF) \ < $(top_builddir)/glut/libglut.a --- > $(LIBS_OPENGL) -lGL -lX11 $(LIBTIFF) -lglut Index: mris_show/Makefile.am =================================================================== RCS file: /usr/fscvsroot/dev/mris_show/Makefile.am,v retrieving revision 1.7 diff -b -r1.7 Makefile.am 6d5 < -I$(top_srcdir)/glut \ 15c14 < $(LIBS_OPENGL) $(top_builddir)/glut/libglut.a --- > $(LIBS_OPENGL) -lglut Index: nmovie/Makefile.am =================================================================== RCS file: /usr/fscvsroot/dev/nmovie/Makefile.am,v retrieving revision 1.11.4.3 diff -b -r1.11.4.3 Makefile.am 10,11c10 < -I$(top_srcdir)/unix \ < -I$(top_srcdir)/glut --- > -I$(top_srcdir)/unix 16,17c15 < -I$(top_srcdir)/unix \ < -I$(top_srcdir)/glut --- > -I$(top_srcdir)/unix 27c25 < $(top_builddir)/glut/libglut.a --- > -lglut 31c29 < $(top_builddir)/glut/libglut.a --- > -lglut Index: stim_polar/Makefile.am =================================================================== RCS file: /usr/fscvsroot/dev/stim_polar/Makefile.am,v retrieving revision 1.9 diff -b -r1.9 Makefile.am 7c7 < -I$(top_srcdir)/glut $(GL_CFLAGS) --- > $(GL_CFLAGS) 14c14 < $(X_LIBS) $(LIBS_OPENGL) $(top_builddir)/glut/libglut.a --- > $(X_LIBS) $(LIBS_OPENGL) -lglut

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Re: [Freesurfer] Fwd: Error with experimental design using FSGD
by Douglas N Greve 08 Apr '13

08 Apr '13

Hi Joshua, you do not have samples for all of your groups (eg, group0bp2-2-1). doug On 04/04/2013 11:59 PM, Joshua deSouza wrote: > Hello Douglas, > > I have done as you have suggested and have created 16 classes with 2 > different groups, and 3 discreet variables. However, I seem to be > getting the same error but with a a different condo. The error is : > matrix is ill-conditioned or bad scaled, condo = 1e+08. The only 2 > continous variables are age and TIV. There is no strong correlation > between either continous variable. I also used another group instead > because the sample size was larger and I thought it might help. > > The FSGD file = thomas6.txt > The design matrix = Xg.dat > The contrast matrix = t6.txt > > Please let me know on what should be done or if I have overlooked > anything. I have done the necessary processing according to the steps > in the tutorial. Please let me know if you require any morer files > such as the .mgh files. > > Thank you for your time in this matter. > Joshua > > > On Thu, Apr 4, 2013 at 11:47 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Joshua, you should start by not coding gender and handedness as > continuous variables. In doing this, you are saying that you expect > right handers to have 2x the thickness as left handers (or females to > have 2x the thickness as males). You need 8 classes. If your "voxel" > variable is discrete, then you will need 16 classes. > doug > > > > > On 04/04/2013 05:22 AM, Joshua deSouza wrote: > > > > Hello Sir/Madam, > > > > I am currently running a statistical test using the FSGD method. > I am > > encountering a problem in relation to the creation of the glmdir > > folder when I run the mri_glmfit function. I recieve an ERROR > message > > that tells me that the design matrix (automatically generated) > is ill > > conditioned or badly scaled, condo = 10565.7. All the steps before > > creating the glmdir folder have been done in accordance with the > FSGD > > group analysis tutorial on the freesurfer wiki. > > > > The command line is : mri_glmfit --y lh.thomas4.10.mgh --fsgd > > thomas4.txt dods --C t4.txt --surf fsaverage lh --cortex --glmdir > > lh.thomas4.glmdir > > > > The FSGD file = thomas4.txt ( contains 2 groups and 5 variables) > > The data matrix = Xg.dat > > The contrast matrix = t4.txt > > > > There are 3 columns of variables that have discreet values of > either 1 > > or 2. However I have tried this with another FSGD file (thomas3.txt) > > that contained 4 variables of which 2 were continous and the > other 2 > > were in 1s' and 2s'. > > > > The contrast matrix of thomas3.txt = C.dat > > The design matrix of thomas3.txt = Xg1.dat > > > > I was able to generate a glmdir using mri_glmfit with > thomas3.txt and > > generate a surface for tksurfer to use. The file created was the > > sig.mgh file which was then compared with the fsaverage files. > However > > once I added another variable titled "voxel" in thomas4.txt, I > > received the error message. > > > > I did a correlation of the columns containing 1s and 2s in the FSGD > > file thomas4.txt using Matlab and have not found any significant > > correlation with each other. > > > > Please do advise on how to solve this issue and also from where the > > problem could stem from as I am unsure as to the nature of the > problem. > > > > Thank You for your patience and assistance > > > > Joshua > > > > > > > > _______________________________________________ > > 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: 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> > 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. > > -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Permutation doubts
by Douglas N Greve 08 Apr '13

08 Apr '13

On 04/04/2013 03:56 PM, Gabriel Gonzalez Escamilla wrote: > Dear Doug, > > > Thank you so much as always for your answer. > > When you said that the permutation test is done normally, do you mean > that does not take account of the nuisance variables, and only test > for the groups comparison? It creates the full matrix including nuisance, then it permutes the rows of the matrix. > > Now I'm wondering if you have something implemented on matlab or > anything that could do a correction for multiple comparisons? > different than the cluster-wise correction (of mri_surfcluster), and > without having to wait the long time that the mc-z simulations (of > mri_glmfit-sim) take. If you're doing whole hemisphere, then you can used the cached mc-z with mri_glmfit-sim. Run mri_glmfit-sim with --help to get more info. There's also stuff on the wiki. doug > > > Regards, > Gabriel. > > > > El 04/04/13, *Douglas N Greve * <greve(a)nmr.mgh.harvard.edu> escribió: >> Correct, you cannot do a permutation test with continuous variables (or >> with any non-orthogonal design matrix). If you use the --perm-force, it >> will do the permutation test as normal (by randomly swapping the rows), >> but technically the test is not legal. Having said that, I suspect that >> LOTS of people do exactly that. >> doug >> >> >> >> On 04/04/2013 10:03 AM, Gabriel Gonzalez Escamilla wrote: >> > >> > Dear Freesurfer experts, >> > >> > >> > I'm having troubles when setting a permutation test, I'm making group >> > comparisons, but I'm introducing the Age, and cortical thickness as >> > niusance variables (as previously recommended). >> > >> > It seems that permutations only work for orthogonal matrices, does >> > this means that I cannot set any niusance variable? >> > >> > >> > If so, this is telling me that I can run the command with the flag >> > "--perm-force", and I'm wondering, which would be the implications of >> > force to run the permutations with niusance variables? >> > >> > >> > Many thanks in advance, >> > Gabriel >> > >> > >> > _______________________________________________ >> > 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 >> 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 >> >> >> 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. >> > > -- > -------------------------- > PhD. student Gabriel González-Escamilla > Laboratory of Functional Neuroscience > Department of Physiology, Anatomy, and Cell Biology > University Pablo de Olavide > Ctra. de Utrera, Km.1 > 41013 - Seville > - Spain - > > Email: ggonesc(a)upo.es > http://www.upo.es/neuroaging/es/ -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Confused with Coordinate System in FS
by ZhiLiangLong 07 Apr '13

07 Apr '13

Hi all: I am confused with coordinate systems in FS. I have several questions bellow. 1. when we run recon-all -s subjid -all, Is the individual native space transformed to talairach coordinate system?. when run recon-all -s subjid -qcache, does the talairach system go into MNI system (fsaverage space)? 2. what is the tranformation matrix within the file of <subjid>/mri/transforms/talairach.xfm?, what is it used for? 3. Does the coordinates within .label files under <subjid>/label/ belong to the MNI coordinate system? 4. In TkSurfer Tool, does the coordinate of "Vertex RAS" belong to MNI coordinate? Hope someone gives me suggestions. best

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Making mid-gray surfaces without mris_expand?
by Keith Jamison 06 Apr '13

06 Apr '13

I have seen that the official recommendation for making a mid-gray surface is to use mris_expand. This seems to be a very slow procedure on my machine. I have also tried just loading the ?h.white and ?h.pial surfaces into matlab, averaging their vertices, and exporting the result. This seems to result in a nearly identical surface as mris_expand. On a test subject, only 48 out of 127,998 (0.0375%) vertices differed by more than 0.1mm, and these were almost entirely around the edges of the corpus callosum. Is there a reason this alternative is a bad idea? I imagine mris_expand does additional topology checks along the way, but if the vertices vary so little, can that be a major problem? I'm inclined to go with the faster solution, but since I'm relatively new to this procedure, I wanted to see what the community's experience might be. Thanks! Keith _______________________________ Keith Jamison Graduate Research Assistant Department of Biomedical Engineering University of Minnesota 7-105 NHH, 312 Church St. SE Minneapolis, MN 55455 Office: 6-112 Nils Hasselmo Hall Mobile: 607-227-0696 kjamison(a)umn.edu

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Intensity Normalization
by Dan LaFreniere 06 Apr '13

06 Apr '13

Dear Experts, I've been working on cleaning up some 4T nifti images for cortical thickness analysis. Initially our images were quite dark inferiorly due to the nature of the RF coil used (it doesn't extend much further than the temples resulting in signal drop-off). I've managed to find what appears to be a decent fix for the problem by running a higher number of -nuiterations during -autorecon1; usually 20-50 does the trick. Because I'm quite new to this, I was wondering if this is an acceptable fix? Just wanted to double-check with the experts before moving forward. I've attached a screenshot contrasting image quality of default iterations, 10, 20, and 50 iterations. It's also worth mentioning that -surfs appear to be quite accurate especially after I lay down some control points after an initial autorecon2 run. Thank you very much for your help and patience, Dan

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fsaverage mappings
by Satrajit Ghosh 06 Apr '13

06 Apr '13

hi folks, are there predefined mappings between the fsaverage surfaces? for example, i have an array of numbers for all the vertices in fsaverage4. is there an easy way to map those to vertices on to fsaverage/fsaverage5/... without going through surf2surf? something perhaps implemented in matlab or python. e.g., 1->1, 2->1, 3->1, ... 10->2, 11->2, ... i believe fsaverage 6/5/4/3 are icosahedral subsampling of fsaverage -- can i find this mapping somewhere or create it somehow? cheers, satra

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