[Freesurfer] preproc-sess

Dear Freesurfers, I am still struggling with the retinotopy analysis. Whenever I try to run preproc-sess, I get this message: Session: /home/fsl/structural/LD08 Tue Apr 5 07:22:28 BST 2011 is not in SUBJECTS_DIR SUBJECTS_DIR is /home/fsl/structural I put the retinotopic

Re: [Freesurfer] help with CT scaling

Looks like we can't read the dicom fully. Is this a standard ct produced by the scanner? I guess I would try some other conversion utility like mricro to convert to nifti On Apr 4, 2011, at 5:16 PM, "Andrew R. Dykstra" wrote: > Hi Bruce, > > Here is the output from mri_info on both the mgz

Re: [Freesurfer] resampling vol to surface

Hi Greg, mri_vol2surf will take a --regheader option which tells it to assume that the movable is in the anatomical space. doug On 4/1/11 4:11 PM, GREGORY R KIRK wrote: > Hi guys, > > i am using the freesurfer-fsl integration to use labels from the freesurfer > cortical surface as seeds for pro

Re: [Freesurfer] Visualizing SPM Results on Template FreeSurfer Brain

He Lena, here's a paper that uses this method ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tom.2007.science.LossAversion.pdf doug On 4/3/11 7:52 AM, Lena Palaniyappan wrote: Doug Do you have any citations where people have done this before -- it is relevant for a VBM + SBM an

Re: [Freesurfer] Converting an FSL label to Freesurfer space

Hi Massih, Try looking at http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat doug On 4/4/11 2:38 PM, mmoayedi wrote: > Hi, > > I'm trying to convert the individual FS parcelations to individual > space in FSL. I'm not sure how to proceed. I've made a label from the > indi

[Freesurfer] {Disarmed} Re: Questions about GLM, Random and Fixed Effects Analysis in FsFast

Thank you, your reply was very helpful. I have one more specific question. How is the variance of the "group-level contrast map" estimated in the RFX and WRFX cases (to be used for a t-test or F-test)? Is it simply the sample variance of the lower level contrast maps stored in "ces.nii" files?

Re: [Freesurfer] mri_ca_register error

Hi Thomas, usually that means the partition you are trying to write to is full, cheers Bruce On Mon, 4 Apr 2011, T. Hagen wrote: Hello all, I got this error message while running one of my subjects (freesurfer version 5.0.0): gcamFindOptimalTimeStep: Complete in 23335.062 ms 0388: dt=0.000

Re: [Freesurfer] help with CT scaling

Hi Bruce, Here is the output from mri_info on both the mgz volume and dicom series. Cheers, Andy On Mon, Apr 4, 2011 at 11:08 AM, Bruce Fischl wrote: > Hi Andy > > can you run mri_info on the volume and see what it thinks the voxel > dimensions are? Then also run it on the dicom series? > > c

Re: [Freesurfer] Pial surface correction failure after adding control points

Hi Min, It's difficult to tell what may be going wrong based on that one slice. Could you upload the subject and send it to Khoa so she can investigate? She's an expert in exactly these kinds of problems. Allison On Mon, 4 Apr 2011, Min Liu wrote: > Dear Freesurfer users, > > Thank you Dr.Steve

[Freesurfer] Converting an FSL label to Freesurfer space

Hi, I'm trying to convert the individual FS parcelations to individual space in FSL. I'm not sure how to proceed. I've made a label from the individual subject's parcelation, and have saved it. How would I then convert the label to use it as a mask in the subject's structural space in

Re: [Freesurfer] LGI error in make_outer_surface at 31

Hi Lisa Are you able to see the paths traced from the 'intermediate' files - you can find them in a tmp folder within the subject's surf directory Lena On 04/04/2011 16:24, "Lisa Ronan" wrote: Dear List I have recently come up agains the same problem as described below, namely the error w

Re: [Freesurfer] LGI error in make_outer_surface at 31

Dear List I have recently come up agains the same problem as described below, namely the error when I compute lGI reads >>reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fsp

[Freesurfer] mri_ca_register error

Hello all, I got this error message while running one of my subjects (freesurfer version 5.0.0): gcamFindOptimalTimeStep: Complete in 23335.062 ms 0388: dt=0.00, rms=0.657 (0.000%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation

Re: [Freesurfer] help with CT scaling

Hi Andy can you run mri_info on the volume and see what it thinks the voxel dimensions are? Then also run it on the dicom series? cheers Bruce On Fri, 1 Apr 2011, Andrew R. Dykstra wrote: > Hi all, > > I'm having problems either or converting a series of dicoms from a CT scan > obtained at MG

Re: [Freesurfer] recommende pc and cuda

On Mon, 2011-04-04 at 13:13 +0200, Knut J Bjuland wrote: > I am in the process of acquiring a new computer to run freesurfer on. > I am currently think about buying a PC with a geforce 4X0 and a Tesla > card along with a two screen setup running either Ubuntu or Redhat > Linux enterprise 6.0. I t

Re: [Freesurfer] recommende pc and cuda

Maybe a NVidia GTX590 (it's a dual GPU) On Mon, Apr 4, 2011 at 08:13, Knut J Bjuland wrote: > Hi > > I am in the process of acquiring a new computer to run freesurfer on.  I am > currently think about buying a PC with a geforce 4X0 and a Tesla card along > with a two screen setup running either

[Freesurfer] recommende pc and cuda

Hi I am in the process of acquiring a new computer to run freesurfer on. I am currently think about buying a PC with a geforce 4X0 and a Tesla card along with a two screen setup running either Ubuntu or Redhat Linux enterprise 6.0. I think the PC should be a core i7 with 6 core and above 12 g