Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

implementation on Neurodebian
by Cartik Sharma 17 Oct '11

17 Oct '11

Dear Freesurfer developer(s), Is there a way to get Freesurfer run faster on Neurodebian. While the package produces some truly out of the world segmentations and labels for the cortical surface, it seems to take time. For eg: Defect correction and retesellation takes an hour, other steps take longer..I'm not sure if it's the original dataset, the OS platform (i.e Virtual Machine, Neurodebian) or original computational engine itself. Would be happy in efforts and hints to make this run faster. Best regards, Cartik Sharma

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First-level analysis with continuous covariate
by Emily Ward 17 Oct '11

17 Oct '11

How does one execute a first-level (subject-level) analysis with a continuous covariate? For example, in an event-related experiment presenting pictures of scenes, I have two conditions: environment (indoors/outdoors) and openness (a continuous rating obtained independently). I am interested in the environment x openness interaction, so I need to model them together. The parametric modulation paradigm file seems close to what I need, but in the example, there is no discrete variable to consider. Is there a way to model both discrete and continuous variables together? If so, can this method also be used to model out nuisance regressors, like trial performance? Thank you, Emily

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saving adjustments under different names
by Maria Felber 17 Oct '11

17 Oct '11

Dear all, I have run the recon-all process on my subject im01. Now I am checking for errors and found some. I also found the solution steps. However, as far as I understand it, every time I make a change, this will be permanently done. Is there a way to keep the steps I have done so far and to same further changes to a new subject file, e.g. im01_skullcorrected. I would just like to backup the steps I have done in case I worsen the solution so far and in case I want to compare them. Also, is there a way that the results from recon-all are saved under a different name? Thanks, Maria -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522

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mris_convert exporting parcellation per vertex
by Pedro Paulo de Magalhães Oliveira Junior 15 Oct '11

15 Oct '11

I need to create a file where I have the parcellation value (structure name) per vertex. I've tried mris_convert --annot /Applications/freesurfer/subjects/bert/label/lh.aparc.annot /Applications/freesurfer/subjects/bert/surf/lh.pial parc.asc But I get the error: ERROR: unknown file annot file type specified for output: saida.asc Has someone done this before? Thanks --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

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CVS or MNI registration
by Antonella Kis 14 Oct '11

14 Oct '11

Hi Bruce, I will be very grateful if you can give me an advise regarding registration. In TBSS there is recommended if the subjects are young children (the adult-derived FMRIB58_FA target is inappropriate), to identify the "most representative" one, and use this as the target image. This target image is then affine-aligned into MNI152 standard space, and every image is transformed into 1x1x1mm MNI152 space by combining the nonlinear transform to the target FA image with the affine transform from that target to MNI152 space .II wonder if in Freesurfer I can ahve this option or what space/template/transform I should use if my subjects are young children? Also, can you please explain a little what exactly CVS means? Is this specific to Freesurfer only and is there a template for this space? Should I use CVR or MNI in my study having young children? Many thanks, Antonella

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Suggested longitudinal processing stream for already skull stripped images
by Andreas Schuh 14 Oct '11

14 Oct '11

Hi, We are attempting to use FreeSurfer in order to process a longitudinal T1 series. Our input data is partly simulated and already skull stripped. When running $ recon-all -autorecon1 on one of these images, the check of the Talairach transformation fails. Using the option -notal-check results in a successful execution of the program, but we get a bad Talairach transformation which cannot be manually fixed using tkregister2. I suppose the problem is that our images are already skull stripped while the pre-processing of FreeSurfer would perform this step after the computation of the Talairach transformation and hence this computation expects non-skull stripped images as input. What are the suggested processing steps in such case, i.e., having already skull stripped images as input? Thanks, Andreas

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hippo-subfields not creating some files
by Inge Knudson 14 Oct '11

14 Oct '11

Hi Bruce et al., I have a problem with the -hippo-subfields segmentation not creating some files for the left side when I run it on our Linux box located at the Martinos Center, with Freesurfer sourced to /usr/local/freesurfer/nmr-stable51-env. Specifically, it runs to apparent completion and exits without error, but it does not create these three .mgz files: posterior_Left-Cerebral-Cortex.mgz posterior_Left-Cerebral-White-Matter.mgz posterior_Left-Hippocampus.mgz All the other posterior_*.mgz files are created, however. It is only these same 3 that are missing every time. The hippo-subfields.log file also does not get created. This happens whether I run -hippo-subfields as part of the recon-all -all process, or as a stand-alone: recon-all -s mysubject -hippo-subfields The Freesurfer build stamp is freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514 If I copy the subject's directory over to my iMac (OS 10.6.8) which has its own standalone copy of Freesurfer 5.1 installed, and run the same command line there, it runs fine. All the files are created, including the hippo-subfields.log. The build stamp on the iMac is freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Thank you, Inge

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Automatic corrections log/diary and questions about Tkmedit color options
by Vy Dinh 14 Oct '11

14 Oct '11

Dear Experts, Does Freesurfer print an automatic log or diary of the manual corrections (to a brainmask) made in Tkmedit? Also, is there any way that I can change the color of the edited voxels? It would be great to view the edited voxels as anything but black and white (eg dark blue and a bright yellow respectively) when reviewing the corrections. Is it possible to change the color of the crosshair or the surface boundaries? Because the crosshair and the pial surface boundary are both red, it is quite difficult to locate the crosshair when changing the views. I am also concerned that the red/green lines may be an issue for colorblind users. Best, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh(a)rush.edu<mailto:Vy_dinh@rush.edu>

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Image Filtering
by MCLAREN, Donald 14 Oct '11

14 Oct '11

Bruce and others, Are there any spatial filters applied during the segmentation process other than a bias field correction? For example, a spatially adaptive non-linear means filter (e.g VBM8)? If not, do you think denoising filters will improve the accuracy and/or reduce manual editting? Thanks. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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mkcontrasts & retinotopy cannot find eccen error
by Jodie Davies-Thompson 14 Oct '11

14 Oct '11

Dear FreeSurfers, I am new to Freesurfer and attempting to run a very basic analysis, but am finally stuck after trying 3 alternative ways of displaying the data. Any help would be greatly appreciated! I have 4 wedges/quadrants (no expanding rings), and want to show areas responding to each ofthe 4 *on an inflated brain*. tksurfer doesn't allow multiple zstats to be presented simultaneously so overlaying the zstats from FSL isn't an option. My next plan was to use a basic block-related design and run contrasts, but mkcontrast-sess produced an error which I have copied below. (Note: I also tried -ncond 4 -a 4 -c 1 -c 2 -c 3) -------------------------------------------------------- [Main@Brain1]$ mkcontrast-sess -contrast upperright -analysis er.self.lh -ncond 4 -wcond -1 -1 -1 3 INFO: Found 4 Non-Null Conditions INFO: Found 1 Delays Runtime error (func=(main), adr=3): Divide by zero Runtime error (func=(main), adr=4): Divide by zero Condition Weights: -1 -1 -1 3 mkcontrast -anadir er.self.lh -wcond -1 -1 -1 3 -sumconds -o er.self.lh/upperright.mat -wdelay 1 -nocnorm -setwcond -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile er.self.lh/upperright.mat nconds 4, wcond -1 -1 -1 3 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir er.self.lh -wcond -1 -1 -1 3 -sumconds -o er.self.lh/upperright.mat -wdelay 1 -nocnorm -setwcond -no-octave ------------------------------------------------------------------------------ RETINOTOPY ERROR: After the above didn't work, I then started a retinotopic analysis using the steps on the wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis) but as I only have wedges and no rings, in my case I only have 1 run and one rtopy.par file - both under bold/001. However, when I try to view the output using the commard 'tksurfer-sess -a rtopy.self.lh -s L_quads' I get the below error. ------------------------------------------------------------------------------ [Main@Brain1]$ tksurfer-sess -a rtopy.self.lh -s L_V123quads Surface self lh Map Surface self lh $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ Linux Brain1 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux Wed Oct 12 18:02:29 PDT 2011 /usr/local/freesurfer/bin/tksurfer list eccen polar ERROR: cannot find /usr/local/freesurfer/sessions/Subj001/L_V123quads/bold/rtopy.self.lh/eccen ------------------------------------------------------------------------------ I saw the suggestions on a previous thread about fooling the analysis by copying the polar data into the eccen directory, but I'm still confused - should be creating identical directories (ie. 002, 003, 004) containing the identical dataset but different rtopy.par files? All I have under rtopy.self.lh is an 'analysis.info' file. Any ideas? At the moment I have no way of displaying my data, and I'm going round in circles, so any suggestions would be great! Thanks in advance, Jodie -- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology& Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC Canada V5Z 3N9 Tel: 604-875-411 ext 69003

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