Re: [Freesurfer] Recon-all Error: _FindFacePath

Hello Khoa, Thank you very much for your suggestion. I checked both brainmask.mgz and wm.mgz and it saw ok for me. I have already sent my two scans to Bruce. Hope something can be done. Cheers! Daniel Ferreira 2011/9/13 Khoa Nguyen Hi Daniel, Usually when I get the FindFace

Re: [Freesurfer] Recon-all Error: _FindFacePath

Hi Daniel, How did you send your scans to Bruce? Thanks, Fatima From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Daniel Ferreira Padilla Sent: 14 September 2011 09:19 To: 'Khoa Nguyen' Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Fre

Re: [Freesurfer] Recon-all Error: _FindFacePath

Hi Fatima, I used the Martinos Center File drop ( https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html). Daniel 2011/9/14 Ahmed, F, Me Hi Daniel, How did you send your scans to Bruce? Thanks,

Re: [Freesurfer] Recon-all Error: _FindFacePath

Thanks Daniel! That's great! From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Daniel Ferreira Padilla Sent: 14 September 2011 10:25 To: Ahmed, F, Me Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all Error: _FindFacePa

[Freesurfer] Segmentation fault during -autorecon1

Hello, I am continuously getting a "Segmentation fault" error during -autorecon1 when it's running mri_binarize. I have been running Freesurfer on a Mac, but now I am trying to implement it using Linux. I am running this version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on Linux 2.6.9-

Re: [Freesurfer] Reference

Hi, On the pages below there are some links to articles describing how the FS cortical and sub-cortical atlases were created. https://surfer.nmr.mgh.harvard.edu/fswiki/SubcorticalSegmentation https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation -Louis On Wed, 14 Sep 2011, Anne Bailey

[Freesurfer] time course within ROI

HI, I am trying to get timecourse from each subject within a ROI with GUI as follows, in tksurfer GUI, Tools > timecourse > Write summary of marked vetices/label, I would like to do it command line, would you tell me what line I can use? I tried to use mri_segstats --i ./filtered_func_data.nii -

[Freesurfer] tksurfer sliver problem

Hi guys, So, the infamous tksurfer "sliver" display problem has reared its ugly head on some of the systems that I'm accessing, but in a manner that I can't make any sense of across the systems. Machine 1: CentOS 5.5, 64 bit, FS versions 4.5.0 and 5.0.0 installed Sliver problem is present for v

Re: [Freesurfer] time course within ROI

You have specified two segmentations (an annotation and a segmentation). Just use one (probably the annot). There will be a column for each label in the annot. Use the --ctab-out to get a color table that indicates which column belongs to which region. doug YUMI MAEDA wrote: > HI, > I am trying

Re: [Freesurfer] tksurfer sliver problem

hi mike, this problem has been a real pain for years, and i've never been able to debug it. it would seem its some interaction with the shared gl libs, and the static glut libs compiled into tksurfer, as indicated by the combinations you list below. fyi, if you havent seen this page already, its

Re: [Freesurfer] mean and stdev group-wise

You can run mris_preproc on each group separately. Then run mri_glmfit with the --osgm flag. The rstd will be the group std, and the osgm/gamma.mgh will be the group mean. You can also call mri_concat on the group files with --mean and again with --std doug Tetiana Dadakova wrote: > Dear list,

Re: [Freesurfer] flipped orientation in tksurfer and tkmedit

When you say on the "right hemi in tkmedit" do you mean on the right side of the image (which is the left side of the brain)? doug Ilana Hairston wrote: > Hi there, > We recently had a problem that tksurfer and tkmedit were flipped > relative to each other. Basically, when saving a point in the

Re: [Freesurfer] .img extension read as analyze even though hdr says nifti1

If it happens with one, it will happen with all of them. We never got around to having our code look in the .img header to see if it is really nifti. Why not use the single-file nifti with nii extension? doug Satrajit Ghosh wrote: > hi all, > > when a .img extension file is passed to freesurfer

Re: [Freesurfer] statical question recon-all -qcache -s (subject) ?

I think that is ok. doug Knut J Bjuland wrote: > Hi > > Can I use a different version of Freesurfer to run recon-all -qcache -s > (subject) than the version used for recon-all -all -s (subject)? > > Knut J > > ___ > Freesurfer mailing list > Freesurfer@n

Re: [Freesurfer] Converting a cluster to a ROI without manually drawing

You can also do it from the command line with mri_surfcluster. doug Nasim Maleki wrote: > Hi all, > > I figured it out. This is easily doable using TkSurfer. > > Thanks, > Nasim > On Sep 13, 2011, at 12:37 PM, Nasim Maleki wrote: > > >> Hi all, >> >> In qdec, is there a way to convert a cluster

Re: [Freesurfer] mri_mcsim and mri_glmfit-sim

mri_mcsim just runs the monte carlo simulation that mri_glmfit runs (but more efficiently). Either way, you still need a FWHM to do a cluster-wise correction. You can probably run mri_glmfit (and mri_glmfit-sim) on the data that you use as input to your GLM software. Alternatively, you can hav

[Freesurfer] TRACULA: how to implement DTI repeat sequence?

Dear Anastasia and Team FreeSurfer, First of all thanks so much for developing TRACULA. I think it has a lot of potential! Here is my question: I'm trying to modify "dmrirc_single_subject" file in order to reflect our local sequence and wondered how you are dealing with DTI repeat sequences for the

[Freesurfer] pial surface file format

I wish to extract the pial and GW surfaces from their surface files to manipulate in Matlab. As far as I can determine, these are the files l&Rh.white and l&rh.pial. Can someone please confirm this, and also confirm that these are in the "triangle surface file" binary format? If this is all true, I

Re: [Freesurfer] pial surface file format

Yes, and we provide m files for reading them Cheers Bruce On Sep 14, 2011, at 9:46 PM, Jeff Eriksen wrote: > I wish to extract the pial and GW surfaces from their surface files to > manipulate in Matlab. As far as I can determine, these are the files > l&Rh.white and l&rh.pial. Can someone ple

Re: [Freesurfer] pial surface file format

Super! Please tell me how to obtain the m-files. -Jeff On 9/14/11 6:49 PM, "Bruce Fischl" wrote: >Yes, and we provide m files for reading them >Cheers >Bruce > > > >On Sep 14, 2011, at 9:46 PM, Jeff Eriksen wrote: > >> I wish to extract the pial and GW surfaces from their surface files to >> ma