Freesurfer May 2011

freesurfer@nmr.mgh.harvard.edu

120 participants
155 discussions

Freesurfer GLM and measurement of an interaction
by Chris Hyatt 25 May '11

25 May '11

For a two factor GLM analysis with two levels, I'm uncertain as to why the Freesurfer GLM measurement of the interaction effect of say, group and gender, is a t-test and not an F-test. In my case, my factors are group (healthies vs patients) and gender (male vs female). For a 2x2 two-way ANOVA analysis, the measurement of an interaction is always an F-test. For example, on the following Freesurfer FSGD Wiki page (Four Groups (Two Factors/Two Levels), No Covariates) http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G0V under Contrast 7, it claims the gender-x-handedness is a t-test. Is this contrast a t-test or actually an F-test? Thanks, Chris

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new FreeSurfer release, v5.1
by Nick Schmansky 25 May '11

25 May '11

FreeSurfer Users, The long anticipated, much awaited, release v5.1 of FreeSurfer is finally here. It's everything 5.0 should have been, and now much more! The ReleaseNotes page describes the new features and changes: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes and the Download page will take you to the tarballs: https://surfer.nmr.mgh.harvard.edu/fswiki/Download As always, we recommended not mixing results in a group study processed with other versions or across OS platforms. This new version can still be used to view and post-process results, or to re-run recon-all (edits are retained). The FreeSurfer Team

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job opportunity
by Paige Scalf 25 May '11

25 May '11

Beginning August 15th, a two-year position is available for a highly motivated and talented postdoctoral fellow in the Department of Psychology at the University of Arizona. The goal of this research program is to study the neural processes that support vision, perception and attention using functional neuoimaging (including ultra high resolution and time resolved fMRI) and behavioral (including eye-tracking) methods. Candidates will be expected to support the research goals of the PI, but will also be given the opportunity to develop more independent lines of research. The candidate will be encouraged to take advantage of the highly collaborative departmental environment. The Department of Psychology is part of the School of Mind, Brain, and Behavior (MBB), and is a member of the College of Science, in keeping with its strong research-oriented approach and scientifically-derived knowledge base. Its faculty and students interact and collaborate with those of other MBB programs and departments—Neuroscience, Cognitive Science, and Speech, Language and Hearing Science—as well as with other academic units across campus. The fMRI facilities at the University of Arizona includes a GE 3.0T Signa scanner that is fully available for research use 5 days per week. The University of Arizona is a premier (NSF ranking: # 16) public research university located in Tucson, Arizona. The sun shines nearly every day in Tucson, which is surrounded by four mountain ranges that include the southernmost downhill ski resort in the USA. Tucson also supports great opportunities for hiking and cycling, and is one of the most bicycle friendly cities in the US. Candidates must have a PhD in neuroscience or a related field and the capacity to make a substantive intellectual contribution to the research program. Candidates with previous neuroimaging experience and strong programming skills will will be preferred. Of particular interest are those candidates with experience using python-based programs such as the Vision Egg and SciPy. For more information, contact Dr. Paige Scalf (pscalf(a)gmail.com) Applications may be submitted to job #47659 at http://www.uacareertrack.com.

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flattened patch ascii file & matlab
by Cris Lanting 25 May '11

25 May '11

Dear all, I'm trying to read a flattened patch (ascii) using matlab but I'm slightly confused: after performing mris_flatten and mris_convert -p rh.patch.flat rh.patch.flat.asc I get the following file: #!ascii version of patch ./rh.orig. The 1st index is not a vertex number 12755 25052 -46888 vno=46887 -47.306606 -24.583883 0.000000 -46894 vno=46893 -44.649334 -26.691339 0.000000 ... 94637 48206 48190 46887 94661 48221 48205 46896 And based on the read_patch script (freesurfer_dir/matlab) I'm able to extract the vertices and faces. vertices_flatmap: -47.3066 -24.5839 0 -44.6493 -26.6913 0 -45.1151 -25.9817 0 ... & faces_flatmap 48206 48190 46887 48221 48205 46896 46893 48218 48219 ... Yet, if I call Hpa = patch('vertices',vert_flat,'faces',face_flat,... 'EdgeColor',edgecolor,'FaceColor',facecolor); it comes up with an error: Warning: Values in patch Faces must be in [1 : rows(Vertices)] - not rendering. I suppose this relates to the fact that it is a subset of the actual complete surface and that it therefore does not start with index 1 (but 48206 instead). Any suggestions how to proceed from here? In the end, I'd like to visualise an overlay (saved as .w file) onto the flattened patch instead of on the inflated surface. Kind regards and thanks in advance, Cris Lanting

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Error compiling freesurfer
by Jordi Delgado 25 May '11

25 May '11

Hi Freesurfers, I've downloaded FS from CVS, and I have Cent OS 5.5 (32 bits) I've done: ./configure --prefix="/tmp/freesurfer" --with-mni-dir="/tmp/packages/mni/current" --with-tcl-dir="/tmp/packages/tcltktixblt/current" --with-vtk-dir="/tmp/packages/vtk/current" --with-vxl-dir="/tmp/packages/vxl/current" --enable-fermi-gpu make -j 9 Then the process throws this error: make[2]: Leaving directory `/tmp/dev/nmovie' Making all in mris_show make[2]: Entering directory `/tmp/dev/mris_show' /bin/sh ../libtool --tag=CC --mode=link g++ -L/tmp/packages/mni/current/lib -L/tmp/packages/vxl/current/lib -o mris_show -L/usr/X11R6/lib -lX11 mris_show.o ../utils/libutils.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lGLU -lGL -L/usr/X11R6/lib -lX11 -lm ../glut/libglut.a -lz -lm -lcrypt -ldl -lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib libtool: link: warning: library `/tmp/packages/mni/current/lib/ libvolume_io.la' was moved. libtool: link: warning: library `/tmp/packages/mni/current/lib/libminc.la' was moved. libtool: link: warning: library `/tmp/packages/mni/current/lib/ libvolume_io.la' was moved. libtool: link: warning: library `/tmp/packages/mni/current/lib/libminc.la' was moved. g++ -o mris_show mris_show.o -L/tmp/packages/mni/current/lib -L/tmp/packages/vxl/current/lib -L/usr/X11R6/lib ../utils/libutils.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lGLU /usr/lib/libGL.so -lXext -lX11 ../glut/libglut.a -lz -lcrypt -ldl -lpthread /tmp/packages/mni/current/lib/libvolume_io.a -L/usr/pubsw/packages/mni/current/lib /tmp/packages/mni/current/lib/libminc.a -lnetcdf -lm -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils.a(pgmstubs.o)' is incompatible with i386 output ../glut/libglut.a(glut_cmap.o): In function `__glutSetupColormap': /tmp/dev/glut/glut_cmap.c:253: undefined reference to `XmuLookupStandardColormap' collect2: ld returned 1 exit status make[2]: *** [mris_show] Error 1 make[2]: Leaving directory `/tmp/dev/mris_show' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/tmp/dev' make: *** [all] Error 2 Any idea? Thank you!

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Re: [Freesurfer] temporal pole label
by Bruce Fischl 25 May '11

25 May '11

the easiest thing to do is to convert all the annotations to labels, then just use the temporal pole one. I don't think there is an option at the moment to only extract a single label, but Doug will correct me if I'm wrong :) cheers Bruce On Wed, 25 May 2011 kwa1(a)rice.edu wrote: > Dear Bruce, > > Thanks for the prompt response again. With mri_annotation2label how do I > specify just the TP label vertices to export as a .label file? I'm assuming I > would use the hemisphere-specific annotation and label files but I'm not sure > how to do that. > > Best, > Kareem > > Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > >> Hi Kareen, >> >> I'll cc the list as others may be interested. You can use >> mri_annotation2label to extract the label you want. As for which to use, it >> depends what you want to do with it, but I would expect the individual >> labels are what you want since they are adjusted to account for individual >> variations in the anatomy. >> >> cheers >> Bruce >> >> >> On Wed, 25 May 2011 kwa1(a)rice.edu wrote: >> >>> Dear Bruce, >>> >>> How can I access these temporal pole labels within each subject? For each >>> of these TP labels I would like a .label file -- how can I export a file in >>> this format for the R and L TPs? Furthermore, do you recommend the use of >>> this fsaverage subject that you have to apply to all our subjects? >>> >>> Thank you very much for your help, >>> Kareem >>> >>> >>> Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>> >>>> Hi Kareem, >>>> >>>> both the annotations we automatically compute contain temporal pole >>>> labels. Also, the average subject we provide (fsaverage) has both >>>> parcellations, so you could just use one of them >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Wed, 25 May 2011 kwa1(a)rice.edu wrote: >>>> >>>>> Hello, >>>>> >>>>> I have a question about the labeling in tksurfer. My goal is to take >>>>> an average inflated surface of 10 controls and then make a temporal >>>>> pole label out of that average. >>>>> >>>>> Alternatively, if FS provides a label for the TP for each patient I >>>>> could average the labels together. >>>>> >>>>> Do you have any idea how best to do this? >>>>> >>>>> Thanks in advance. >>>>> >>>>> Warm regards, >>>>> Kareem >>>>> >>>>> _______________________________________________ >>>>> 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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Re: [Freesurfer] temporal pole label
by Bruce Fischl 25 May '11

25 May '11

Hi Kareen, I'll cc the list as others may be interested. You can use mri_annotation2label to extract the label you want. As for which to use, it depends what you want to do with it, but I would expect the individual labels are what you want since they are adjusted to account for individual variations in the anatomy. cheers Bruce On Wed, 25 May 2011 kwa1(a)rice.edu wrote: > Dear Bruce, > > How can I access these temporal pole labels within each subject? For each of > these TP labels I would like a .label file -- how can I export a file in this > format for the R and L TPs? Furthermore, do you recommend the use of this > fsaverage subject that you have to apply to all our subjects? > > Thank you very much for your help, > Kareem > > > Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > >> Hi Kareem, >> >> both the annotations we automatically compute contain temporal pole labels. >> Also, the average subject we provide (fsaverage) has both parcellations, so >> you could just use one of them >> >> cheers >> Bruce >> >> >> On Wed, 25 May 2011 kwa1(a)rice.edu wrote: >> >>> Hello, >>> >>> I have a question about the labeling in tksurfer. My goal is to take >>> an average inflated surface of 10 controls and then make a temporal >>> pole label out of that average. >>> >>> Alternatively, if FS provides a label for the TP for each patient I >>> could average the labels together. >>> >>> Do you have any idea how best to do this? >>> >>> Thanks in advance. >>> >>> Warm regards, >>> Kareem >>> >>> _______________________________________________ >>> 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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FS5.1 for CentOS4 works for CentOS5-like OS?
by Xinian Zuo 25 May '11

25 May '11

Dear FS team, Only see new 5.1 version for CentOS4 in the website. Thanks, XN. -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn)

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temporal pole label
by kwa1＠rice.edu 25 May '11

25 May '11

Hello, I have a question about the labeling in tksurfer. My goal is to take an average inflated surface of 10 controls and then make a temporal pole label out of that average. Alternatively, if FS provides a label for the TP for each patient I could average the labels together. Do you have any idea how best to do this? Thanks in advance. Warm regards, Kareem

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Error from cudadetect
by Howison, Mark 25 May '11

25 May '11

Dear Freesurfer developers, We have installed Freesurfer 5.0.0 (CentOS x86_64) on our compute cluster at Brown and are seeing the following error when running 'cudadetect': ERROR: cuda driver does not appear to be installed! Detecting CUDA... There are 2 devices supporting CUDA: Device 0: "Tesla M2050" CUDA Driver Version: 3.20 (etc.) However, the NVIDIA driver is installed and other CUDA programs function correctly: [mhowison@gpu001 ~]$ nvidia-smi ==============NVSMI LOG============== Timestamp : Fri May 13 10:19:48 2011 Driver Version : 260.19.29 You can see our hardware specs here: http://www.brown.edu/Departments/CCV/doc/techspecs And output from bugr is: --------------------------------------------------------------------- FREESURFER_HOME: /gpfs/runtime/opt/freesurfer/5.0.0 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 RedHat release: CentOS release 5.4 (Final) Kernel info: Linux 2.6.18-164.el5 x86_64 --------------------------------------------------------------------- We are using CentOS 5.4 and CUDA 3.2.16. Any ideas why Freesurfer cannot use our GPUs? Thanks, Mark Howison Application Scientist Center for Computation & Visualization Brown University

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Freesurfer May 2011