Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

using tkmedit
by Robert Levy 14 Sep '07

14 Sep '07

Hi, I am attempting to work with volume data for the first time and trying to figure out how to control what temporal offset is shown in the functional overlay. I checked the options, the wiki, etc, but didn't find anything yet. That is most like because I'm looking at old data that was generated in a way that is incompatible (it seems) with newer versions, so I am sourcing stable2. The command that originally generated the group comparison I am viewing is intergroupavg-sess -analysis EMerror -contrast ASevASc -group1 BwGroupNormalsError5 -group2 BwGroupAspError5 -intergroup BwGroupError5 -space tal -spacedir tal This is the path to the resulting group comparison /space/balagula/8/users/EMexec/fMRI/GROUP_ANALYSIS/BwGroupError5/bold/EMerror/tal-rfx/ASevASc/ To view it I am running: tkmedit-sess -analysis EMerror -contrast ASevASc -space tal -map minsig -s BwGroupError5 -isxavg random -fthresh 1.3 My environment looks like: FREESURFER_HOME /usr/local/freesurfer/stable2 FSFAST_HOME /usr/local/freesurfer/stable2/fsfast SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR FUNCTIONALS_DIR /usr/local/freesurfer/stable2/sessions MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib PERL5LIB /usr/pubsw/packages/mni/current/lib/perl5/5.8.5 GSL_DIR /usr/pubsw/packages/gsl/current QTDIR /usr/pubsw/packages/qt/current TCLLIBPATH /usr/local/freesurfer/stable2/lib/tcltktixblt/lib FSL_DIR /usr/pubsw/packages/fsl/current Thanks for any advice, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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QDEC question
by Narly A Golestani 14 Sep '07

14 Sep '07

Dear all, I have 2 questions regarding doing analyses using QDEC: 1) can I use QDEC to analyse results on data for which I ran recon-all using the last (ie: older, not most recent) version of Freesurfer, or should I rerun recon-all on all the data using the new version of Freesurfer? (I hope not the latter!) 2) I have run the preprocessing required for using QDEC (ie, recon-all -s <subjid> -qcache) on one subject for whom I had run recon-all using the previous version of Freesurfer, and I get the following error messages: WARNING: File rh.volume does not exist skipping creation of smoothed data for rh.volume WARNING: File rh.white.K does not exist skipping creation of smoothed data for rh.white.K WARNING: File rh.white.H does not exist skipping creation of smoothed data for rh.white.H WARNING: File rh.jacobian_white does not exist skipping creation of smoothed data for rh.jacobian_white what might this mean? thanks in advance, best, Narly.

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High Resolution Standard Brain
by Dick, Rachel 14 Sep '07

14 Sep '07

Hello, I have T1 images at 0.8 x 0.8 x 0.8...Is there a high resolution (0.5-0.8) standard brain that I can co-register my images to in place of Freesurfer's? Also, does anyone know of a standard child/adolescent brain that is in use? Thanks in advance, Rachel Rachel Marie Dick Research Assistant/Coordinator Brain Research and Imaging Neurosciences Dept. of Psychiatry & Behavioral Neuroscience WSU Medical School brain.wayne.edu <mailto:rcondon@med.wayne.edu> (313)577-6279 CONFIDENTIALITY NOTICE This message is confidential, intended only for the named recipient(s) and may contain information that is privileged, or exempt from disclosure under applicable law. If you are not the intended recipient(s), you are notified that the dissemination, distribution or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the e-mail address. Delete this e-mail from your computer, and destroy any copies in any form immediately. Thank you.

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RV: Re: [Freesurfer] Spherical ROIs areas in the fsaverage
by jorge luis 14 Sep '07

14 Sep '07

Ok, but my automatic procedure constructed the ROI masks on the lh.sphere (not on lh.sphere.reg)of the fsaverage subject. Is it wrong to compute the area of a ROI in the fsaverage spherical surface by adding the areas of the triangular faces inside this region? (The area of each triangular face being computed using the spherical coordinates of its vertices and the Heron formula for the triangle area) Thank you for your useful help Jorge ____________________________________________________________________________________ Sé un Mejor Amante del Cine ¿Quieres saber cómo? ¡Deja que otras personas te ayuden! http://advision.webevents.yahoo.com/reto/entretenimiento.html

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question re: p-vals and t-vals in FreeSurfer
by d.g.lawyer＠medisin.uio.no 14 Sep '07

14 Sep '07

Hi, I'm seeing some odd behavior in t-values and p-values exported from FreeSurfer. In geeky detail: fit a linear model using FreeSurfer, saving t and p-values convert output files to ascii load ascii files into R convert the FreeSurfer "p-values" into real p-values via lh.pval <- 10^(-1*abs(freesurfer.lh.pvals)) # this is necessary as FreeSurfer writes the -log10 of the pvalue, with the sign # demonstrating direction of effect. convert these pvalues to tvalues lh.convert.t <- qt(lh.pval,XX) # where XX is the degrees freedom # I have several studies, 60 < XX < 200 A histogram of lh.convert.t is roughly OK, could be zero-mean. HOWEVER, the t-values exported by FreeSurfer are not. In one study, the range of the converted t-values was [-3.8, 3], but the range of the raw t-values was [-0.6,3.8]. In a second study, the range of the raw t-values was [0,17]. As you could guess from these ranges, histograms of the two versions of t-values also differ radically. Regarding version numbers and such, I have three experiments I have checked for this phenomenon. Two are old, and were run using version 1.2 (output files in .w format, etc), and the third study is new (version 3.X, outputs are F.mgz and sig.mgz). We run the linux/RHEL versions. My questions: why are the t-values output by FreeSurfer so oddly distributed? and why don't they agree with what i get when I convert the p's to t's? Silly user error on my part? Thanks much for any insights

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Freesurfer error: Load Time Course causes abort
by raij＠nmr.mgh.harvard.edu 14 Sep '07

14 Sep '07

Hi guys, On machine inv (more or less the same error on machine ai) nmr-dev-env (same error on nmr-std-env) cd /space/cuzco/2/users/raij/avml_fmri_mctogether/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJECT fsaverage tksurfer fsaverage lh inflated -overlay avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr -timecourse avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr Output: surfer: current subjects dir: /space/cognito/5/users/raij/subjects_mri/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/cuzco_002/users/raij/avml_fmri_mctogether surfer: Reading header info from /space/cognito/5/users/raij/subjects_mri//fsaverage/mri/T1.mgz reading group avg surface area 822 cm^2 from file surfer: vertices=163842, faces=327680 INFO: bvolumeRead: min = 0, max = 0 *** glibc detected *** corrupted double-linked list: 0x00000000060b7db0 *** Abort Oddly enough, on machine ai, if I leave out the -timecourse part of the command line, the FreeSurfer window opens with the correct overlay and I can scroll through conditions and time points. Further, if I then manually load the timecourse from File/Load Time Course... menu, this works giving the time course display just as it should Even more oddly, on machine inv (which is spanking new and has lots of RAM etc) even the above basic command line with only loading the overlay gives the above glibc error. I have 8 subjects * 66 labels = timecourses of 528 labels to extract, which makes this clearly a script job - the only practical solution would be to find a way to make the command line work. Suggestions? For example, could it be that this has something to do with nvidia drivers? Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Possible to pass 2 identical analyses but with different names to intergroupavg-sess?
by Dan Dillon 13 Sep '07

13 Sep '07

Dear FreeSurfers, I have two groups (patients vs. controls) whose data I'd like to compare using intergroupavg-sess. Here's the problem: I ran identical analyses on the two groups, but they were named differently (e.g., "control_analysis" vs "patient_analysis"). Is there a way to run intergroupavg-sess without having to either re-name or re-run one of these analyses? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: <mailto:dillon@wjh.harvard.edu> dillon(a)wjh.harvard.edu

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New Neuroscience Forum
by Toby Fernsler 12 Sep '07

12 Sep '07

Hello World, Announcing a new neuroimaging-specific forum as well as a data analysis and programming consulting business, at http://neuroimagingnetwork.com/ ABOUT THE FORUM The forum is intended to be an informal central site for neuroimaging researchers and professionals to discuss and troubleshoot the various software and hardware they use, as well as announce and discuss workshops, meetings, jobs, sell used lab equipment, etc. It is a modern, versatile forum running on vbulletin and hosted on a high- bandwidth VPS by HostICan, who have a 99.9% average uptime rating. Forum Organizational Highlights: * Forums for troubleshooting and discussing each software and hardware product, such as FreeSurfer and Net Station. Don't see your software? Let me know and I'll add it. * Forums for upcoming meetings, job postings, grant opportunities, lab equipment resale, etc. Forum Technical Features: * Customizable login allows for creation of an avatar (icon to represent yourself), fields to describe yourself, attach a picture, provide contact information and enter your CV/Resume. * Advanced search capabilities allow you to search by forum, thread, author, etc. * Social features allow you to see who is logged in (and login anonymously), message them, and make buddy and ignore lists. * Subscribe to forums and threads and receive email notification of new posts. * Threads can be moved, moderated, edited, closed etc. * It's pretty. Please check it out at: http://neuroimagingnetwork.com/forums/ I will of course be participating in discussions and answering questions, and as a former developer of EEGLAB, a mathematician and Matlab expert I will provide better-than-average responses on those topics. If you happen to want more detailed assistance I have... ABOUT FERNSLERSERVICESLLC This is my consulting/contracting business for assistance/analysis with EEGLAB as well as other data-mining, mathematical, programming, and neuroscience-related tasks. Troubleshooting and debugging. Order up a program and I'll write it. Send me your data and I'll tell you what's interesting about it in nice graphics and down-to-earth language. You may find details about rates and services here: http://neuroimagingnetwork.com/fernslerservicesllc/index.html Thank you for your attention. Hope to meet you on the forum! Toby Fernsler

1 0

recon-all flags -normalization2 and -maskbfs
by Greg Harris 12 Sep '07

12 Sep '07

Dear FreeSurfers, I am trying to be a user of 'recon-all -make all'. The method stops when it attempts the step 'recon-all -s $(subj) -hemi lh -finalsurfs'. The problem at that point is that the file mri/brain.finalsurfs.mgz does not exist. The command to create this file, the only possible command if we go through rec on-all, is 'recon-all -s $(subj) -maskbfs'. Doing this command by hand after the error permits a repeated 'recon-all -make all' command to continue happily. One plausible place to fix this is in bin/recon-all.makefile, at or about line 83-84: $(BRAIN): $(BRAINMASK) $(NORM) recon-all -s $(subj) -normalization2 recon-all -s $(subj) -maskbfs i.e. add the step for making the brain masked brain.finalsurfs.mgz file after the -normalization2 step. Would this be correct, and should I do this or something like it? Sincerely, Greg

4 5

error.. help?
by Britni Crocker 12 Sep '07

12 Sep '07

after autorecon2, I sometimes get this error: preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM: nan +- nan [100000.0 --> -100000.0] GM: nan +- nan [100000.0 --> -100000.0] mri_segment: class statistics not finite - check input volume! Linux theta.cis.jhu.edu 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 14:30:58 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Sep 5 15:49:00 EDT 2007 how do i fix this? britni _________________________________________________________________ Kick back and relax with hot games and cool activities at the Messenger Café. http://www.cafemessenger.com?ocid=TXT_TAGHM_SeptHMtagline1

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Freesurfer