Freesurfer

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30132 discussions

Freesurfer and AFNI - 3dmaskave problems
by Wu, Paula (NIH/NIMH) [F] 02 Aug '10

02 Aug '10

Hello, I am trying to create white matter, grey matter, and CSF masks (along with some other finer segmentations) using Freesurfer, and then use these to find the average BOLD response for all voxels within each mask using AFNI's 3dmaskave. So far, I have performed the following steps. -Talairach-aligned the T1 using @auto_tlrc in AFNI @auto_tlrc -base TT_N27+tlrc -input mprage_scan_3+orig -ran recon-all -notalairach using this T1 recon-all -s 09_07_23_DM -all -notalairach -created the masks using mri_convert and 3dcalc. For example, mri_convert -it mgz -ot nii -i aseg.mgz -o aseg.nii 3dcalc -a aseg.nii -expr 'equals(a,4) +equals(a,43) +equals(a,14) +equals(a,15) +equals(a,5) +equals(a,44)' -prefix mask_ventricles_all I am now attempting ot use 3dmaskave to pull out the average response from talairach aligned trial averages, but I get the error that the input (trial averages - preprocessing and deconvolution done in AFNI) and mask datasets are not the same dimensions. E.g. 3dmaskave -mask [nameoffile]+orig -quiet s04_trialavg_dt_st_reg_20mmHg20s_10sshifted_al+tlrc > mask_{$roi}_$condition.1D.txt Any suggestions? Paula

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Re: [Freesurfer] Comparing results of independent experiments
by Douglas N Greve 02 Aug '10

02 Aug '10

This is with FSFAST? You can run isxconcat-sess on both analyses. For version4.X, this will create output files like lh.ces.mgh. If you keep the subject order the same for both analyses, then you can use mris_calc to take the difference between them (ie, a paired analysis). You will then have a file with number of frames equal to the number of subjects, each representing the difference between the two experiments. You can then run a one-sample-group-mean (--osgm) with mri_glmfit. You should make sure that all the imaging parameters are the same between the two experiments. doug Shahin Nasr wrote: > Hi Doug and freesurfers, > > My subjects have participated in two independent experiments > within two different sessions (e.g. experiment 1 in day 1 and > experiment 2 in day 2). Now I want to see if the contrast between > conditions of experiment 1 and 2 is significant or not. For instance I > want to compare condition_1 of experiment_1 with condition_2 of > experiment_2. How should I do that? Actually I want to see the > contrast map and then apply ROI-based (fun2roi) analysis. > > Thanks for your help > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > -- 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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Non-linear correlations
by mmoayedi 02 Aug '10

02 Aug '10

Hi Everyone, I was wondering if there's a method to examine non-linear correlations in FreeSurfer. Specifically, I'd like to use a behavioural correlate and see if there are any correlations in the cortex. The linear correlation wasn't as fruitful as I'd hoped, but there is evidence that a non-linear relationship may exist. Is there any way of testing this? Thanks. Regards, Massieh Moayedi PhD Candidate Dr. Karen Davis' Lab Institute of Medical Science University of Toronto MP14-303 Brain, Imaging and Behaviour Toronto Western Research Institute University Health Network 399 Bathurst St. Toronto, ON M5T 2S8 massih.moayedi(a)utoronto.ca mmoayedi(a)uhnres.utoronto.ca t: 416-603-5502 f: 416-603-5745

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Error when doing Talairach transformation
by Xue, Feng 02 Aug '10

02 Aug '10

Dear Freesurfer experts, I'm reconstructing 40 subjects' sMRI data. I succeeded in most of them except one subject. I tried many times and on different computers, however, I always met the same error. Could you please give me some suggestions on reconstruting this data? Many Thanks! In the attached, please find my entire recon-all.log file, and below is where the error is: #@# Talairach Failure Detection Mon Aug 2 19:07:35 CST 2010 /expdata/xfgavin/2010/meng_2010/Raw/MPRAGE/freesurfer/sub213/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0165, pval=0.0000 < threshold=0.0050) Linux dlpfc 2.6.26-2-amd64 #1 SMP Sun Jun 20 20:16:30 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Aug 2 19:07:35 CST 2010 -- Best Regards Xue, Feng Ph.D. Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

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.license file on Mac
by sere f 02 Aug '10

02 Aug '10

Hi All, I am new user of Freesurfer and i am getting trouble to install it. I want to install it on MacBook Pro and I have problem with the license file. I have tried to create it with: pico /Applications/freesurfer/.license and when I save it, I get this message: Error writing /Applications/freesurfer/.license: Permission denied and it is not saved. How can i do? any idea? Thanks. Serena.

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Linux Unix Comparisons
by Tyler Blazey 01 Aug '10

01 Aug '10

Hi, I recently ran several subjects through both a Linux version of FreeSurfer (4.5, 64bit) and a Mac version (4.5, 64 bit processors), and noticed some differences in the results. I know that you advise against comparing across different versions of FreeSurfer, but I wasn't sure about different platforms. Is there any thing I can do to make the results identical, or should I just make sure to process everything on one platform? Or is this something that will be fixed in an upcoming version of FreeSurfer like the Linux 32/64 bit issue? Also I am a bit confused as to the 64 bit status of the Mac version of FreeSurfer. Obviously it runs fine on 64 bit machines, but are the binaries themselves 64 bit? When I run: file /Applications/freesurfer/bin/[freesurfer executable] it returns that the file is a i386 Mach-O executable. Am I correct in thinking that this means that the current Mac version of FreeSurfer does not run in 64 bit mode? And if so, are there any plans to release a Mac version in the future that does have 64 bit binaries? Thanks in advance for for any answers, - Tyler

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Comparing results of independent experiments
by Shahin 01 Aug '10

01 Aug '10

Hi Doug and freesurfers, My subjects have participated in two independent experiments within two different sessions (e.g. experiment 1 in day 1 and experiment 2 in day 2). Now I want to see if the contrast between conditions of experiment 1 and 2 is significant or not. For instance I want to compare condition_1 of experiment_1 with condition_2 of experiment_2. How should I do that? Actually I want to see the contrast map and then apply ROI-based (fun2roi) analysis. Thanks for your helpShahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Cerebellar hurdle
by Lena Palaniyappan 31 Jul '10

31 Jul '10

Is there any way I can recon-all for images that have cerebellum missing? These fail repeatedly at talairach, no-talcheck flag doesn¹t help Cheers thanks _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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tkmedit scripting question
by Sebastian Moeller 30 Jul '10

30 Jul '10

Aloha fellow surfers, I am trying to script a few steps of my freesurfer pipeline. At the moment I am facing the problem that all my brainmasks need some manual intervention. Following advice from the wiki I try to set up tkmedit to clone from the aux to the main volume on the pressing button 3. Now my question how do I configure Button 3 from a tcl script so that my users do not have to do this manually every time? I would expect something like SetBrushInfo that takes more arguments than just brush, low, high, new, but my tcl-foo is very weak. If someone has a pointer how to set Button 3 to clone from aux vol I would be happy to hear it. Thanks in advance. Best Sebastian -- Sebastian Moeller telephone: 626-395-6713 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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spmregister error
by swoodman＠nmr.mgh.harvard.edu 30 Jul '10

30 Jul '10

Hello, When running spmregister-sess (standard environment was sourced) I encountered this error: ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg ERROR: spmregister failed __________________________________________________________ Our information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: purkinje SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons PWD: /cluster/ablood/1/DMRF_ASL ssh purkinje setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons cd /cluster/ablood/1/DMRF_ASL __________________________________________________________________ We appreciate any help you can give us!! Thanks, Sandra Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital 120 6th St. Charlestown, MA 02129 Tel: 617-643-6245 Fax: 617-726-1351 Email: swoodman1(a)partners.org

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