Freesurfer January 2011

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

Error FsFast Tutorial
by Fernanda Palhano 10 Jan '11

10 Jan '11

Hi, I am trying to run the FsFast tutorial, but I am getting the following error: Fernanda-Palhanos-Mac-Pro:fsfast/fsfast-tutorial/fb1-analysis-study] fernandapalhano% tkmedit-sess -s mgh-101.1 -a sm-gamma-fwhm5 -c odd-v-0 -aparc+aseg tmp: Subscript out of range. tmp: Subscript out of range. tmp: Subscript out of range. tmp: Subscript out of range. ERROR: cannot find /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/register.dof6.dat [Fernanda-Palhanos-Mac-Pro:fsfast/fsfast-tutorial/fb1-analysis-study] fernandapalhano% tksurfer-sess -s mgh-101.1 -a sm-gamma-fwhm5 -c odd-v-0 -hemi lh -aparc tmp: Subscript out of range. tmp: Subscript out of range. tmp: Subscript out of range. tmp: Subscript out of range. $Id: tksurfer-sess,v 1.15.2.1 2010/07/14 16:08:04 greve Exp $ Darwin Fernanda-Palhanos-Mac-Pro.local 10.4.0 Darwin Kernel Version 10.4.0: Fri Apr 23 18:28:53 PDT 2010; root:xnu-1504.7.4~1/RELEASE_I386 i386 Mon Jan 10 15:08:15 BRT 2011 /Applications/freesurfer/bin/tksurfer list odd-v-0 con/map odd-v-0 /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii maplist /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii mri_concat /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii --o /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/tksconcat.nii ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/tksconcat.nii ERROR: cannot find /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/register.dof6.dat I checked all the mgh files in fb1-analysis-study and any of them have register.dof6.dat, there is only register.dat. Where can I obtain these file? Thanks in advance, Fernanda Palhano

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Re: [Freesurfer] Freesurfer Digest, Vol 83, Issue 13
by Bevil R. Conway 10 Jan '11

10 Jan '11

I will be out of the country from Jan. 10 - Jan 18, 2011, and will not have access to email. For issues concerning my laboratory, please contact my lab manager, Rosa Lafer-Sousa (rlaferso(a)wellesley.edu) Thank-you and I'll be in touch when I get back. Bevil

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64 bits Mac
by Ed Gronenschild 10 Jan '11

10 Jan '11

Hi, The Mac OSX 10.6 version offers the possibility to run in 64 bits mode (by pressing simultaneously the 6 and 4 keys during startup). I was wondering if Freesurfer can be used in 64 bits mode? In other words: does it use the 64 bits or does it run only in compatibility mode and in fact in 32 bits mode? Ed

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Group analysis, contrasts
by Per Selnes 10 Jan '11

10 Jan '11

I'm trying to set ut a freesurfer group analysis. In my fsgd file there are four groups/classes and 2 variables, like so: GroupDescriptorFile 1 Title Class Class1 Class Class2 Class Class3 Class Class4 SomeTag Variables Variable1 Variable2 Input subj1 Class1 49 1 Input subj2 Class2 50 2 Input subj3 Class3 51 3 Input subj3 Class4 52 4 Input... I'm a bit puzzled as to how I should set up the contrasts. With DODS, there should be a matrix of 12 regressors, and I want to model how thickness varies with Variable2, ignoring the effects of Variable1 and Class. Should my contrast be 0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25 or 0 0 0 0 0 0 0 0 1 1 1 1 or something completely different? I have tried both contrasts, and they yield identical (and plausible) results. Kind Regards, Per Selnes

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"segfault error" after reinstallation of ati videocard driver
by Alexander Lebedev 09 Jan '11

09 Jan '11

Dear Freesurfer users and developers, I sent a message to you yesterday ("unable to download FS"). The matter is that I have got "segfault error" after reinstallation of ati videocard driver. First of all I would like to say that I am a newbie in FS and the last thing i want to do is to disturb you by trifles. But honestly I tried my best to find a solution (as well as ".xdebug_tkmedit") and I keep being stuck at running tkmedit. I am providing a bug report. Would you be so kind to help me in solving this problem? -- Best Regards, Alexander Lebedev. I.P. Pavlov State Medical University, 197022, Lev Tolstoy str. 6/8, Saint Petersburg, Russian Federation. tel.:+7-921-441-79-42 e-mail: awlman(a)rambler.ru Skype ID: alexander.vl.lebedev

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unable to download data from wiki page
by Alexander Lebedev 08 Jan '11

08 Jan '11

Dear Freesurfer users, Sorry for disturbing... I've got some problems with FS after updating my workstation (segfault error). Before reporting a bug I decided to try to reinstall FS. But for some reasons I can't download any data from wiki page: looks like server is closed... I need freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.0.0/freesurfer-Linux…] Would you be so kind to provide me any other links to this archive? Thank you beforehand. -- Best Regards, Alexander Lebedev, I.P. Pavlov State Medical University, 197022, Lev Tolstoy str. 6/8, Saint Petersburg, Russian Federation. tel.:+7-921-441-79-42 e-mail: awlman(a)rambler.ru Skype ID: celtic__frost -- Твой город, улица и дом на http://maps.rambler.ru

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label2label error
by Lena Palaniyappan 07 Jan '11

07 Jan '11

For some of my data, label2label (one of the PALS labels from fsaverage being mapped on to a subject) gives this message Performing mapping from target back to the source label ERROR: srcvtxno = -1 < 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table Is there anything I can do to circumvent this? Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. 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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using mri_glmfit-sim; precached or not
by Chris Hyatt 07 Jan '11

07 Jan '11

Dear Freesurfer users, I am using mri_glmfit-sim to do clusterwise correction for multiple comparisons. I ran the Z Monte Carlo simulation for 5000 iterations for my 43 subjects (vertex wise threshold of 2.0 or p < 0.01), but I received different results than when I ran the correction using the "new" pre-cached simulation (using threshold of 2.0). In general, I get fewer clusters when running the simulation from scratch when compared with the pre-cached simulation. I used the fsaverage subject brain in the original analysis. Here are the commands I ran: initial glmfit (uncorrected): mri_glmfit --y lh.HCvsCD.thickness.10.mgh --fsgd HCvsCD.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.HCvsCD.glmdir Then corrections for multiple comparisons .... from scratch: mri_glmfit-sim --glmdir lh.HCvsCD.glmdir --sim mc-z 5000 2.0 mc-z.pos --sim-sign pos --bg 5 using pre-cached: mri_glmfit-sim --glmdir lh.HCvsCD.glmdir --cache 2.0 pos Which method is most accurate? Also, how does one turn off the polling writes to the console when running MC-Z from scratch? Thanks, Christopher Hyatt Olin Neuropsychiatric Research Center / IOL Hartford, CT

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monkey surface
by Christidis, Patricia P. (NIH/NIMH) [C] 07 Jan '11

07 Jan '11

Hello, I'm trying to make a surface for a monkey volume that is 256 by 296 by 256 voxels in size. I know that if I use recon-all -autorecon, I can add the -cw256 flag to deal with that FOV of 296. But with a monkey volume, my understanding is that I can't use recon-all. Instead, I need to use the older programs like mri_convert, correct? If so, how do I deal with a FOV greater than 296? Thank you Peggy Christidis

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Qdec and 3 groups GLM
by Lena Palaniyappan 07 Jan '11

07 Jan '11

I have a single factor with three levels (diagnosis) and trying to setup qdec, but I get the following message - I have a .levels file with all 3 groups specified - the contrasts are not getting generated automatically. Data table loading completed successfully. SUBJECTS_DIR is '/Volumes/FREECOM/Applications/freesurfer/subjects/conn' ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 87 Checking inputs nframestot = 87 Allocing output Done allocing nframes = 87 Writing to /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled/y.mgh gdfReadHeader: reading /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled/qdec.fsgd INFO: gd2mtx_method is dods Reading source surface /Volumes/FREECOM/Applications/freesurfer/subjects/conn/fsaverage/surf/lh.white ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled/y.mgh --fsgd /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled/qdec.fsgd dods --glmdir /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled --surf fsaverage lh --label /Volumes/FREECOM/Applications/freesurfer/subjects/conn/fsaverage/label/lh.aparc.label Any help? Thanks Lena ________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. 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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Freesurfer January 2011