Freesurfer

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30093 discussions

Mac mountain lion installation problem
by Vieweg, Paula /DZNE 25 Feb '13

25 Feb '13

Hi, I have installed Freesurfer (Leopard version) on Mac Mountain Lion and tried to use it for a full segmentation (recon-all -all). On my own files I get a problem with Talairach, the program aborts and I get the recommendation to try it with -notal–check. I have done this and Freesurfer has since then taken 6 days to run one brain. I have started the example script with Bert and it has run 4 days. I have aborted all the processes now and am asking for help. All other steps in the Testing protocol with Bert seem to work apart from the recon-all -all. I am using 7T data (but with just 1mm isotropic resolution), which is where I thought the problem came from. Since the example script also does not run (that is, does not finish), it seems to be a problem with the installation and possibly my Mac version. Do you have any suggestion how to solve this? Best, Paula Paula Vieweg Aging & Cognition Research Group German Center for Neurodegenerative Diseases (DZNE) Building 15, Room 309a Leipziger Str. 44 39120 Magdeburg GERMANY phone: +49-391-67-24520 email: paula.vieweg(a)dzne.de<mailto:paula.vieweg@dzne.de>

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Re: [Freesurfer] Recon-all with my own template
by Douglas N Greve 25 Feb '13

25 Feb '13

The first cmd (mris_register, or use the surfreg script) will create a new registration file in subject/surf. Make sure you don't overwrite the original one (?h.sphere.reg). mris_preproc will just create a single output file with all of your subjects' thickness data (unless you use --qcache) doug On 02/18/2013 05:58 AM, Sophie Maingault wrote: > > Hello, > > Thank you for your answer. I found this page : > http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates > > So I have to do the point “Creating a registration template > initialized with FreeSurfer template (DG)” : first the command > mris-register –curv and then mris_preproc –surfreg ? But what type of > file it will create ? In the directory surf ? It will change the > parcellation ? > > Cheers > > Sophie > > ------------------------------------------------------------------------ > > *De :*freesurfer-bounces@nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *De la p**art > de*Douglas Greve > *Envoyé :* vendredi 15 février 2013 18:02 > *À :* freesurfer(a)nmr.mgh.harvard.edu > *Objet :* Re: [Freesurfer] Recon-all with my own template > > > You can also register your subjects to the new average subject > (creates a new spherical registragtion). Use the surfreg script (run > with --help for more info). > doug > > On 2/15/13 8:55 AM, Bruce Fischl wrote: > >> Hi Sophie >> >> what template do you mean? You can't rerun the subcortical segs or >> parcellations since they depend on manual labelings. You could >> regenerate our cortical folding patterns atlas, but I don't think >> that buys you much since the atlas you would build is by definition >> in register with our current one (if it wasn't you wouldn't be able >> to use our cortical parcellations) >> >> >> cheers >> Bruce >> >> >> On Fri, 15 Feb 2013, Sophie Maingault wrote: >> >> >> >> Hello Freesurfer experts ! >> >> >> >> I created a new template with make_average_subject called 80tvs and I >> would >> like to re-run some of my subjects with this new template. I can?t >> find the >> command line in FAQ. Is it for example : recon-all ?all ?s t0001 ?target >> 80tvs ?? So I need the repertory of this new template in the >> subject_dir ? >> >> >> >> Thank you for the answer ! >> >> >> >> Sophie >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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extracting hand drawn ROIs to Afni space
by Paul Beach 25 Feb '13

25 Feb '13

Hi there, Through the help of the Freesurfer Q&A staff I've been able to get ROIs drawn in tksurfer into an augmented aparc+aseg file of an averaged subject. I need to be able to get those ROIs, which are not part of the color LUT, into Afni space. For ROIs that are already in the LUT, getting them to Afni is no problem, I simply use a 3dcalc command. However, I have the problem of needing to export newly parcellated and segmented ROIs that aren't in the Freesurfer LUT to Afni space. Is there a way to do this short of creating a new "spot" for them in our LUT? If not, how does one go about adding ROIs to the LUT and/or creating a LUT specific to my needs (since the Wiki suggests not fussing with the original LUT)? Thanks, Paul --

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re qdec
by Linn Mittlestein 25 Feb '13

25 Feb '13

Dear Freesurfer experts, I have a question about qdec...as it is supposed to be doing whole brain cortical analyses, how come one first has to generate statistical tables, and chose thicknesses of different regions from these tables? Is this just an option, rather than being necessary for qdec? Thank you very much, Kind Regards, Linn

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question mris_preproc
by j janssen 25 Feb '13

25 Feb '13

Hi, freesurfer-x86_64-redhat-linux-gnu-stable5-20110522 $Id: mris_preproc,v 1.66 2012/12/06 16:06:17 mreuter Exp $ after recon-all i ran recon-all -s $subject -qcache this generates lh.area.fsaverage.mgh which only contains values 0 and higher while negative values exist for the lh.area of the same subject. is this normal and if so, why? thanks, -joost

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Change of thickness with age with tksurfer
by Sophie Maingault 25 Feb '13

25 Feb '13

Hello, I used qdec to visualize correlation between cortical thickness and age. With tksurfer, when I load the file sig.mgh I can see the p-value for each vertex (log10 pvalue) but I would like to load a file which show the value of the slope, I mean the change of thickness with age. Which file I have to use as overlay or how can I do it? Thanks a lot! Sophie

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obtaining residuals after regressing out nuisance parameters
by Caspar M. Schwiedrzik 25 Feb '13

25 Feb '13

Dear Freesurfer experts, I am running some functional connectivity analyses using FSFAST in Freesurfer 5.1. I would like to compare seed time courses (which I later use as predictors) obtained after regular pre-processing with seed time courses obtained after regressing out several nuisance parameters. I am a little bit unsure how to use the output from selxavg3-sess for the latter. After defining a single subject analysis with mkanalysis-sess with -notask and only the nuisanance regressors (-nuisreg), I currently run selxavg3-sess with -no-con-ok and -run-wise. Can I then take the time courses from the respective beta.nii per run? Or am I completely off here? Thanks! Caspar

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Re: [Freesurfer] mgh conversion
by Douglas N Greve 25 Feb '13

25 Feb '13

Hi Glen, I think there is some confusion here about what this conversion is doing and what you want it to do. This conversion simply changes the way the information is stored, but it is still surface data. SPM/MRIcron cannot display surface data even if it is in nifti format. It sounds like what you want to to transform the surface data into volume data. For that you should use mri_surf2vol. doug On 02/21/2013 05:17 PM, Glen Lee wrote: > Hi Doug, > Just to re-assure your message below as I'm having the same issue, > > I've converted an mgh file with a total of 163,842 vertices into a > nifti file using . And it reshapes the structure > to 3D as shown below. > > fname: 'test_via_mr_conv.nii' > dim: [27307 1 6] > mat: [4x4 double] > pinfo: [3x1 double] > dt: [16 0] > n: [1 1] > descrip: 'FreeSurfer May 25 2011' > private: [1x1 nifti] > > The fact that I'm not able to display the nifti file in SPM or MRIcron > means that the conversion to Nifti doesn't work correct? > > - Glen > > > > On Mon, Jan 28, 2013 at 2:09 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > How many vertices are on the surface? For nifti you have to > reshape the > size of the image so that it fits in the nifti format (requires > each dim > be less than 32k). If the number of vertices has a prime factor > that is > more than 32k, then you cannot convert it to nifti and use it in > another > software package (it still works in FreeSurfer, but then you could > just > use an mgh file then). > doug > > > > On 01/28/2013 01:58 PM, Courtney Haswell wrote: > > Hi, > > > > Was there a resolution to this thread on the FreeSurfer mail > archive? > > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17886.html > > > > I am having the same issue trying to convert a cortical > thickness sig.mgh to > > a NIfTI file. I want to use the statistically significant area > as an ROI in > > another analysis. > > > > Thanks, > > Courtney Haswell > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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mri_vol2vol call problem
by Gregory Kirk 25 Feb '13

25 Feb '13

Greetings lords of freesurfer! I am having a problem getting a combined cvs warp+bbregister to map an FA volume onto a template. mri_vol2vol --targ 816 --m3z combined_to816_elreg_afteraseg-norm.m3z --noDefM3zPath --reg /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff.bbr.dat --mov /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/dtifit_FA.nii.gz --o test --no-save-reg spits out Using the m3z file as it is; no assumed location. movvol /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/dtifit_FA.nii.gz targvol 816 outvol test regfile /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff.bbr.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Morphing InvertMorph 0 Synth 0 SynthSeed 1362252270 corRead(): can't open file /study5/aa-scratch/TEENEMO/twins_freesurfer/816/COR-.info i know i have not seen a file COR-.info in the top level subject directory in the modern age of the universe. i know i saw this before but my notes from the last time i figured this out got lost in a file system cleanup. can one of you tell me where i went astray ? thank you Greg

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Generate mask from surface in diffusion space
by Shani Ben Amitay 25 Feb '13

25 Feb '13

Dear freesurfers I'm using bbregister and mri_surf2surf to transform intermediate cortical surfaces and mid surfaces normals to diffusion space. Next I'm trying to generate volumes from these surfaces (in the same diffusion space), however the generated volumes are much thicker then the generated surfaces. for example to generate surface normals I used the following: mri_surf2surf --s subjectid --hemi lh --sval-nxyz white_surface_in_diffusion --tval lhwhitediffusion_n.mgh mri_surf2vol --surfval lhwhitediffusion_n.mgh --hemi lh --surf white --reg mri/register.dat --outvol lh_white_n.img --template lowb.img Any idea what am I doing wrong? Thanks! Shani

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