Freesurfer August 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
152 discussions

Re: [Freesurfer] {Spam?} Re: preproc-sess error
by Douglas N Greve 02 Aug '10

02 Aug '10

you can setenv FSLDIR /usr/pubsw/packages/fsl/3.3.7 then re-source the stable3 environment. doug jkuster(a)PARTNERS.ORG wrote: > Hi Doug, > > Thanks for your messages. We have to keep using stable3 for the rest of this study. Does this mean we can just use a command to use the older version of fsl to fix the ispl error? > > Thanks, > Jake > ------Original Message------ > From: Douglas N Greve > To: swoodman(a)nmr.mgh.harvard.edu > Cc: freesurfer(a)nmr.mgh.harvard.edu > Cc: jkuster(a)partners.org > Subject: Re: [Freesurfer] preproc-sess error > Sent: Aug 2, 2010 1:54 PM > > If you're going to continue to use stable3 then you will need to have an > old version of FSL (the ip program is an FSL program from several > versions ago). Can you start using the new version of FSFAST? > > doug > > swoodman(a)nmr.mgh.harvard.edu wrote: > >> Additional info: >> >> FREESURFER_HOME: /usr/local/freesurfer/stable3 >> >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-v3.0.5-20070714 >> >> RedHat release: CentOS release 5.5 (Final) >> >> Kernel info: Linux 2.6.18-194.8.1.el5 x86_64 >> >> NMR Center info (/space/freesurfer exists): >> >> Does this give you the info you're looking for? >> >> Thanks, >> >> Sandra >> >> >> >> >> >> >>> which version are you using? >>> >>> swoodman(a)nmr.mgh.harvard.edu wrote: >>> >>> >>>> Hello everyone, >>>> >>>> I keep encountering the same error when running some preprocessing steps >>>> (spatial smooting part). >>>> >>>> I run the command line: >>>> >>>> preproc-sess -s CD_DMRFASL_pat4 -df sessdirfile -mcout fmc5 -fwhm 5 >>>> -smin >>>> fmc5 -smout fmcsm5 >>>> >>>> And I encounter this error: >>>> >>>> ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip >>>> ERROR: ipfsl failed >>>> ERROR: spatialsmooth-sess failed >>>> >>>> Any help/advice would be much appreciated! >>>> >>>> Thanks, >>>> >>>> Sandra >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> >>> >>> >> >> > > -- 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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preproc-sess error
by swoodman＠nmr.mgh.harvard.edu 02 Aug '10

02 Aug '10

Hello everyone, I keep encountering the same error when running some preprocessing steps (spatial smooting part). I run the command line: preproc-sess -s CD_DMRFASL_pat4 -df sessdirfile -mcout fmc5 -fwhm 5 -smin fmc5 -smout fmcsm5 And I encounter this error: ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip ERROR: ipfsl failed ERROR: spatialsmooth-sess failed Any help/advice would be much appreciated! Thanks, Sandra

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Question re: "Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction"
by Andrea L. Gold 02 Aug '10

02 Aug '10

Hi, My question is in reference to the recommended high res structural scans (T1) for optimal FS reconstruction. Within the "Documentation" section of the FS wiki, the page titled "Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction <http://martinos.org/~andre/>" lists two MPRAGE scans, which I understand has been recommended for 1.5T scanners. Is it still the recommendation to collect two high res structurals on 3T scanners (in our case, Siemens TIM Trio) or is one sufficient? Thanks, Andrea -- Andrea Gold Graduate Student Dept. of Psychology Yale University P.O. Box 208205 New Haven, CT 06520-8205 andrea.gold(a)yale.edu

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Errors with the "Cut Plane" feature in tksurfer
by Salzwedel, Andy 02 Aug '10

02 Aug '10

I've been trying to implement the cut plane feature to get an occipital patch but every time my tksurfer crashes and I get this message: % tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. Abort I can't figure out if I am doing something drastically wrong with selecting my cutting points or whether my system is having the problem. Any advice would be most appreciated, Andy

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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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Freesurfer August 2010