[Freesurfer] re-calculating stats based on an updated ?h.pial surface

Hi all, We're using a tool which allows direct alteration of the pial surface (http://sites.google.com/site/vxxsoftware/) resulting in another ?h.pial file being created. We've found that it is a good way to both decrease and increase the pial boundary where there are errors. The current proce

Re: [Freesurfer] Cannot allocate memory

How was fsgd_input.mgh created? What do you get when you run: mri_info fsgd_input.mgh On 10/14/10 7:53 PM, Pradeep wrote: Hello All, I get the following error while running mri_glmfit. I am using freesurfer V5.0. But qdce seem to run well with the similar settings. -log--- [pth

[Freesurfer] Cannot allocate memory

Hello All, I get the following error while running mri_glmfit. I am using freesurfer V5.0. But qdce seem to run well with the similar settings. -log--- [pthiyyagura@ fsgd]$ mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd g2v0.fsgd --C group.diff.mtx gdfReadHeader: reading g2v0.fsg

[Freesurfer] ERROR: mpr2mni305 failed

Hi! I get this error running recon_all Applications/freesurfer/bin/talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log parameter 1 1.219086 -> -0.50 qaram1.5209 imgrege: no voxels in register ERROR: 'imgreg_4dfp /data

Re: [Freesurfer] MNI152

Here are some instructions. I have not tested them myself, so make sure you check the registrations along the way. doug 1. Register functional (template.nii) to anatomical matrix (may already be done in fsfast) bbregister --s $subject --bold --init-fsl \ --mov template.nii --reg

Re: [Freesurfer] Problem with intensity normalization

Jing, why are you running these commands by hand instead of just running recon-all? These are very complicated steps and don't lend themselves to running by hand. doug Huo, Jing wrote: > Hi, > > I have a problem with using mri_normalize for intensity normalization for > T1w+contrast 3D volumes

[Freesurfer] Problem with intensity normalization

Hi, I have a problem with using mri_normalize for intensity normalization for T1w+contrast 3D volumes. What I ran: mri_convert t1.hdr t1.mgz mri_normalize -g 1 t1.mgz t1_norm.mgz mri_convert t1_norm.mgz t1_norm.hdr (1) The first problem is that all volumes are 256*256*256 as output. Why are th

Re: [Freesurfer] FDR in gray matter

There is currently not a way to mask for anything but the brain. I just found out that that did not work (and never had). That has been fixed. I also added the ability to specify an FDR mask using an environment variable, like setenv TKM_FDR_MASK yourfdrmask.mgz This will look in the $SUBJECTS

Re: [Freesurfer] Retinotopic mapping of only polar data]

Hi Frank, sfa-sess does not exist in version 5 of FreeSurfer because its functions have been incorporated into selxavg3-sess. It will be a lot easier to support you if you move to version 5. Unfortunately, I have been slow in getting it documented. Having said that, I think the new version is

[Freesurfer] postdoctoral fellow position for dementia research

Postdoctoral Fellow Position on Dementia NeuroImaging Job description: National University of Singapore (NUS) is a leading global university centred in Asia. It offers a global approach to education and research, with a focus on Asian perspectives and expertise. Computation functional anatomy labor

[Freesurfer] postdoctoral fellow position for dementia research

Postdoctoral Fellow Position on Dementia NeuroImaging Job description: National University of Singapore (NUS) is a leading global university centred in Asia. It offers a global approach to education and research, with a focus on Asian perspectives and expertise. Computation functional anatomy labor

[Freesurfer] FDR in gray matter

Hi, Is it possible to restrict FDR correction to gray matter in tkmedit? Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for

Re: [Freesurfer] Fwd: Mapping labels to the RH on Macs

a new qdec, which fixes the rh hemi problem found by Tessa and Derin described below, is available for download from here: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/ for the mac, goto the macos-leopard-intel/ dir, for 64b linux, goto linux-centos4_x86_64/ copy the file qdec.bi

Re: [Freesurfer] converting IMA files

Lisa, does the output directory exist and do you have write permissions? Can you convert it to some other format (eg, mgz)? doug Lisa F. Akiyama wrote: > Any suggestions? > > > Best, > Lisa > __ > > > > On Fri, Oct 8, 2010 at 11:14 AM, Lisa F. Akiyama

Re: [Freesurfer] converting IMA files

Any suggestions? Best, Lisa __ On Fri, Oct 8, 2010 at 11:14 AM, Lisa F. Akiyama wrote: > Hi Doug, > > I have plenty of disk space available. > I am currently running freesurfer-Darwin-leopard-ppc-stable-pub-v5.0.0. > > > Best, > Lisa > > > > > > On Fri, Oct 8, 20

Re: [Freesurfer] Retinotopic mapping of only polar data]

Hi everyone, The e-mail included below I sent some time ago, maybe it slipped through. In the mean time I did find out I can plot the results with tksurfer-sess like tksurfer-sess -s S2_FS -h rh -analysis rtopy -c polar -map h But then two big questions remain: - How to interpret these color co