Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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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coregistration - FA to Freesurfer
by Joana Braga Pereira 14 Oct '11

14 Oct '11

Dear FreeSurfers, I'm trying to coregister FA images pre-processed with FSL to Freesurfer, however i'm having a few problems and was wondering if someone could help me out. These are the steps that i carried out: mri_convert subj_01/mri/brain.mgz brain.nii.gz fslswapdim brain.nii.gz x z -y brain_swap.nii.gz flirt -ref brain_swap.nii.gz -in nodif_brain.nii.gz -out XXX.nii.gz -omat XXX.mat -cost corratio -dof 6 -interp trilinear flirt -in myFA.nii.gz -ref XXX.nii.gz -out myFA_coregistered.nii.gz -applyxfm -init XXX.mat Unfortunately myFA_coregistered.nii.gz was not as good as i expected since I want to extract the mean FA values of a subcortical ROI from freesurfer and to do that you need quite good coregistration. Does anyone know a better way to do this? Many thanks, Joana

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Re: [Freesurfer] mri_concat
by Douglas Greve 13 Oct '11

13 Oct '11

Hi Cooper, try using the --f option to mri_concat. This takes a text file in which you can list all the files you want. doug On 10/13/11 5:40 PM, Cooper Roddey wrote: > I think my problem is not with mri_concat after all, but with matlab's > 'unix' function. In any case, reading a list of input files saved in a > single file would be a nice option... > > CR > > On Thu, Oct 13, 2011 at 2:28 PM, Cooper Roddey<cooper.roddey(a)gmail.com> wrote: >> Hi Doug, >> >> I have run into a command line length problem when using mri_concat to >> compile about 1000 .mgh files together. The command line is about 133k >> characters long, and the max length on my Linux box appears to be >> 128k. I have a temporary work-around involving symbolic links but I'm >> looking for a more robust solution. Is it possible for mri_concat to >> read a text file containing the full paths of my 1000 .mgh files, >> instead of including all the files explicitly in the command line? >> Have others run into this problem? >> >> Cheers, >> Cooper >> >

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inhomogeneity causes poor segementation
by Ping-Hong Yeh 13 Oct '11

13 Oct '11

Hello, We have a quite a few 3T data got poor result due to the field inhomogeneity, especially in the occipital region (see attached). We've tried several ways of correcting inhomogeneity beforehand, but still not getting good results. Any suggestions in fixing these without manually editing the pial and wm? Thank you, Ping

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Re: [Freesurfer] question about contrast file during group analysis with command line
by Douglas N Greve 13 Oct '11

13 Oct '11

ZhiLiangLong wrote: > > Hi doug > Thanks for your suggestions. I have another two questions: > 1: I can't clearly understand that why i should firstly run DODS to > find interaction between my group variables and age,then run DOSS to > obtain difference between groups specified in my contrast files if > there are no interactions as you suggested.If the interactions > exist,does it mean that DOSS is not suitable for this situation and > only DODS can be used ? If there is an interaction, then DOSS is not suitable because there is no simple difference between the groups. > 2: If i want to obtain the main effect of factor(difference between > the three groups),how can i setup my contrast file? Do a search on our Wiki for FSGD. There's a page of examples there, including an example of your current design. doug > Hope you can give me some suggestions > > At 2011-10-12 00:21:34,"Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > >Yes, that looks correct. Since you have a covariate as a nuisance > >variable, you should first run your analysis with a DODS model > >(different-offset, different-slope) and look for an interaction between > >your group variables and age (the contrasts are similar, swap the first > >6 numbers with the last 6 zeros). If you do not find an interaction, > >then re-run the analysis with DOSS and use a contrast that has 7 > >numbers: the first 6 as you have given, the last number = 0. > > > >doug > > > >ZhiLiangLong wrote: > >> Hi all : > >> I'm performing general linear model (GLM) analysis in the surface,the > >> attachments above are FSGD file and contrast files(the last three > >> attachments).i wonder if my contrast files are correct. > >> the attachment named diff-C-H-thickness.txt is about difference > >> between C and H and the last two are about difference between C and p > >> and difference between P and H,Here,C H and P represent three groups > >> Any suggestions appreciated > >> > >> > >> ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> 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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