Freesurfer November 2011

freesurfer@nmr.mgh.harvard.edu

110 participants
165 discussions

T1 mapping, mri_ms_fitparms and flip angle map
by Dr.med. Johannes C. Klein 21 Nov '11

21 Nov '11

Dear all, For a structural study, I would like to determine cortical T1 values. T1 map generation from two FLASH images works like a charm, and I would like to add B1 correction now. I have acquired flip angle maps for my subjects (using the Yarnykh method with interleaved FLASH and two TRs), and would like to correct my T1 maps accordingly. Looking at the online help of mri_ms_fitparms, I think the parameter -afi should do the trick. However, I'm not sure about the properties of the flip angle map that I need to supply to mri_ms_fitparms. Does that programme expect absolute flip angle values? Or can I feed in my two AFI FLASH volumes in some way? If anyone can point me in the right direction, that would be great! Thanks for you help, Johannes

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when to invoke reg-feat2anat in fsl ppi
by Michelle Umali 21 Nov '11

21 Nov '11

Dear Freesurfers, I am using seeds based on Freesurfer masks to run a PPI analysis and am wondering if I am using reg-feat2anat at the right fsl feat registration step. First, I ran an fsl analysis to generate a feat directory. Then I ran reg-feat2anat using that feat directory. Next I ran aseg2feat and fslmaths to generate binary masks Next I extracted the timeseries by using the filtered func of the feat and the binary masks from aseg2feat. So now I want to do another feat analysis, but this time using the extracted timeseries But this timeseries is based on the first feat and associated masks from the reg-feat2anat registration. 1) Is it still valid to use this timeseries in this new feat since FSL will be running another registration? 2) Do I have to run reg-feat2anat again? Thanks. Michelle

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use of --a2009s flag
by LAOUCHEDI MAKHLOUF 21 Nov '11

21 Nov '11

hi everyone i am trying to use the mri_aparc2aseg command with the --a2009s flag to have the aparc.a2009s labels and i have the following message " Option --a2009s unknown" thanks

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mri_nu_correct error
by Baris Demiral 21 Nov '11

21 Nov '11

Hello everybody, I am trying to use mri_nu_correct.mni function in freesurfer on the XUbuntu system installed on the VirtualBox on a Windows 7 machine. I converted Siemens IMA into analyze format .img (with function; mri_convert -i input_file_name.IMA -ot analyze -o output_file_name.img), then when I called the function mri_nu_correect for the inhomogeneity correction, it gave me an error message (see below). What is wrong? Cheers, Baris FreeSurfer:~/Documents/EEGLAB/NFT/MPRAGE/7031> mri_nu_correct.mni --i S1.img --o S1inh.img --n 2/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/home/virtualuser/freesurfer/bin/mri_nu_correct.mni--i S1.img --o S1inh.img --n 2nIters 2$Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/LinuxMon Nov 21 10:53:06 EST 2011Program nu_correct, built from:Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13tmpdir is ./tmp.mri_nu_correct.mni.3086/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031mri_convert S1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt floatmri_convert S1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $reading from S1.img...TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-0.0286335, -0.999213, 0.0274527)j_ras = (-0.00717244, -0.0272578, -0.999603)k_ras = (-0.999564, 0.028819, 0.00638633)changing data type from short to float (noscale = 0)...writing to ./tmp.mri_nu_correct.mni.3086/nu0.mnc... --------------------------------------------------------Iteration 1 Mon Nov 21 10:53:10 EST 2011nu_correct -clobber ./tmp.mri_nu_correct.mni.3086/nu0.mnc ./tmp.mri_nu_correct.mni.3086/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3086/0/[virtualuser@FreeSurfer:/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/] [2011-11-21 10:53:11] running: /home/virtualuser/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.3086/0/ ./tmp.mri_nu_correct.mni.3086/nu0.mnc ./tmp.mri_nu_correct.mni.3086/nu1.imp Assertion failed at line 827 in file templates/CachedArray.ccnu_estimate_np_and_em: crashed while running volume_stats (termination status=256)nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)ERROR: nu_correct -- Ş. Barış Demiral, PhD. Department of Psychiatry Washington University School of Medicine 660 S. Euclid Avenue Box 8134 Saint Louis, MO 63110 Phone: +1 (314) 7477 1603

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gcut memory requirements
by Michael Harms 19 Nov '11

19 Nov '11

Hello, Approximately how much memory does one need when using the -gcut option with FS 5.1? I had submitted 30+ recons to a cluster that alloted a default of 2.5 GB for processes submitted under this particular queue, and all of them aborted with a bad_alloc error at the gcut stage of skull stripping. Should 4 GB be sufficient? thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Errors with recon-all -autorecon2
by Linda Zhang 19 Nov '11

19 Nov '11

Hi, I'd been having trouble with "recon-all -all -subjid [mysubject]", so I broke it down with -autorecon1 and -autorecon2. -autorecon1 worked fine, it seems that the problem is somewhere in -autorecon2. I've included the system information below, as well as the error message I got, and the recon-all log. I've tried this with another subject as well and the same error occurs. It'd be great if someone could tell me what the problem is and how I can fix it. --------------------------------------------------------------------- FREESURFER_HOME: /home/virtualuser/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Debian version: squeeze/sid Kernel info: Linux 2.6.31-23-generic i686 --------------------------------------------------------------------- The command line: FreeSurfer:~/freesurfer/subjects> recon-all -subjid avo0260 -autorecon2 The error message: GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z GCAMwrite:: the popen error code is: 12 mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Fri Nov 18 11:23:25 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s avo0260 exited with ERRORS at Fri Nov 18 11:23:26 EST 2011 The recon-all.log and recon-all.error files are attached. Thanks for your time and help! Regards, Linda Zhang University of Hong Kong

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Corpus Callosum Volume
by Alan Francis 18 Nov '11

18 Nov '11

Hi Bruce et al, Thanks for the stimulating discussion on the Hippocampal subfields. I have a question. How exactly does FS segment and parcellate the Corpus Callosum volume ? thanks again, Alan

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Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
by Nolan Nichols 18 Nov '11

18 Nov '11

Thanks, Pedro! I am glad to see that you posted a public AMI for freesurfer. And thanks to Thomas for producin documentation on how to use it. This thread inspired me share a StarCluster AMI (ami-27f1384e in the us-east-1 region) that I built for batch FS jobs, which includes the initial setup for installing tools from the NeuroDebian repository. I've also been playing around with using s3fs, which allows Amazon's S3 to be mounted as a drive and accessed directly as the "subjects_dir". The AMI can be launched here: https://console.aws.amazon.com/ec2/home?region=us-east-1#launchAmi=ami-27f1… I did not include the .license for FS as I wasn't sure about licensing issues, but I would be happy to publish an AMI with a built-in license if I get the go ahead. For now you will need to start a cluster and your license to each instance. A few details: Ubuntu 10.04 x86 built from StarClusters ami-8cf913e5 us-east-1 region See the StarCluster details at http://web.mit.edu/stardev/cluster/ Customizing StarCluster (http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html) s3fs (http://code.google.com/p/s3fs/) Freesurfer 5.1 32-bit NeuroDebian ready (so you can apt-get install mricron, fsl, nipype, etc.) Thanks again for starting this thread, and let me know if I can help in any way. It would be great to see "cloud" resources be readily accessibly to the community with minimal effort to get a cluster with freesurfer and tools available via neurodebian up and running. Cheers, Nolan

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Cerebellum Edits
by Jordan Pierce 18 Nov '11

18 Nov '11

We've been manually editing brainmask.mgz to remove voxels that are included in the pial surface that shouldn't be, and recently found on the wiki that to remove cerebellum voxels we should be editing brain.finalsurfs.manedit.mgz instead. What is the reason for this difference? Do we need to redo edits that we've done only on brainmask.mgz? We are going to be looking at cortical thickness. Thanks, Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia

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Re: [Freesurfer] Cerebellum Edits
by Allison Player 18 Nov '11

18 Nov '11

You can copy your edited brainmask.mgz to brain.finalsurfs.manedit.mgz then rerun the case from the beginning using: recon-all -all -clean-bm -s subjid This will recreate the brainmask.mgz so no chunks of cerebellum are missing (and therefore cerebellum volume estimates won't be off). If you don't care about cerebellum and the aseg is still accurate everywhere else despite the missing cerebellum, you don't have to do this. Make a backup copy of brain.finalsurfs.manedit.mgz somewhere else just in case it gets written over when you rerun. Allison > Date: Fri, 18 Nov 2011 11:55:49 -0800 (PST) > From: Jordan Pierce <jepierce87(a)yahoo.com> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] Cerebellum Edits > > We've been manually editing brainmask.mgz to remove voxels that are included > in the pial surface that shouldn't be, and recently found on the wiki that > to remove cerebellum voxels we should be editing > brain.finalsurfs.manedit.mgz instead. What is the reason for this > difference? Do we need to redo edits that we've done only on brainmask.mgz? > We are going to be looking at cortical thickness. > > Thanks, > > Jordan Pierce > Graduate Student > Behavioral and Brain Sciences Program > Psychology Department > The University of Georgia _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer November 2011