Re: [Freesurfer] (no subject)

Forwarding a previous answer from doug. I tried it before (and recently). It does seem to work. >>> >>> Try running mri_annotation2label with --lobes lh.lobes.annot >>> >>> doug >>> >>> >>> On Thu, 20 May 2010, Rudolph Pienaar wrote: >>> Hi all -- Is there a simple way to create a

[Freesurfer] downsampling 4D volume

Hi, I am trying to downsample a 4D volume using mri_convert. However, it seems to be killing the 4 dimension. For example, if I do mri_convert -voxsize 4 4 4 tmp.mgz tmp444.mgz The original volume which is 256 x 256 x 256 x 120 becomes 64 x 64 x 64. Thanks, Thomas

[Freesurfer] showing all slices in freeview

Hi, is it possible to show all slices (or every N slices) of a volume in freeview in a particular orientation (e.g. axial or coronal)? Thanks, Thomas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/l

Re: [Freesurfer] showing all slices in freeview

yes. Thanks! --Thomas On Mar 18, 2010, at 10:37 AM, Ruopeng Wang wrote: > You mean in light box (mosaic) style? No. I will put that on my > features-to-consider list. > > Ruopeng > > On 3/18/10 10:34 AM, ythomas wrote: >> Hi, >> >> is it possible to show

Re: [Freesurfer] tksurfer and tcl scripting: looping over subjects

Hi Carrie, I believe you just need to use the command "exit" at the end of the tcl script to exit from tksurfer. --Thomas On Mar 18, 2010, at 5:43 PM, Carrie Niziolek wrote: > Hello all, > > I've had great success using tcl scripts to loop over surfaces and > overlays for a given subject. Ar

[Freesurfer] recon-all error

but does so in the recon-all.log file. You can find the failed subject here: /autofs/space/terrier_002/users/ythomas/GSP/failed_FS_subjects/ 090620_JG49ZK_FS Thanks, Thomas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] make_average_subject with large cohorts

I am a little out of the loop. Just to clarify, Marie is trying to create an average subject out of 400+ subjects that have been run through the freesurfer pipeline? I don't see a problem with that (except possibly memory issues). If the subjects are from a homogeneous population (whatever

[Freesurfer] error in running fsfast tutorial

Hi, I am trying to run the fsfast tutorial, and I am getting the following matlab error: Undefined function or method 'MRIwrite' for input arguments of type 'struct'. I ran the following commands: nexlin7:ythomas[test_fsfast/fsfast-tutorial/my-study] pwd /autofs/cl

[Freesurfer] bbregister with 4.5.0 fsfast

Hi, I have finished the 4.5.0 fsfast tutorial, and am wondering about the structure-function registration part. Currently, the tutorial recommends: fslregister-sess -s mgh-101.1. I notice that a single register.dat is produced. How are the multiple runs being handled now? Is only the first

[Freesurfer] saving snapshots with white background

Hi, Is there an option to save snapshots in tksurfer with a white background instead of the usual black? Thanks, Thomas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The infor

Re: [Freesurfer] Fwd: Plotting functional data on surface

Is this a preprocessed (whole brain regression, bandpass filter, etc) rest-state volume? If so, I would suggest using the volume before the preprocessing (which works well for me). Thanks, Thomas On Jul 2, 2010, at 9:58 AM, Corey Keller wrote: > Hi Bruce, > > Thanks for the info. I am trying

Re: [Freesurfer] the difinition about VentralDC

I believe the segmentation definitions can be found here: http://www.cma.mgh.harvard.edu/manuals/segmentation/ --Thomas On Aug 9, 2010, at 4:28 AM, leemon albert wrote: > Dear Pedro, Dear Bruce, > Dear all, > > In the previous discussion about VentralDC in the aseg stats file, I > learned tha

[Freesurfer] overlaying surfaces on volumes in freeview

Hi, when we load a mri volume and a surface at the same time, such as: freeview -v mri/norm.mgz -f surf/lh.white should we expect to see the lh.white surface be on top of the norm.mgz volume? I certainly do not see the surface unless I "unhighlight" the volume. Thanks, Thomas __

[Freesurfer] loading surfaces in freeview

Hi, when I try to load my own generated surfaces in freeview (e.g. generated from cerebellum), I am getting the following printed errors even though it did save out the images I want. Seems like freeview is assuming that ?h.inflated, etc has the same dimensions as the surfaces I am loading

Re: [Freesurfer] a question about VirtualBoxFS4.5

Hi Guang, the error message implies you probably do not have access to those files or directory. You should probably ask a sysadmin to do it or if you have admin access, you can probably do something like sudo The sudo command will prompt you type the root password. --Thomas On Aug 22,

[Freesurfer] problem with mri_vol2surf

owing command: mri_vol2surf --regheader 090425_QF86JB_FS --mov /autofs/cluster/ con_003/users/ythomas/test_mri_vol2surf/090425_QF86JB_FS/data/ 090425_QF86JB_vol2vol.nii.gz --hemi lh --projfrac .5 --trgsubject fsaverage --o /autofs/cluster/con_003/users/ythomas/test_mri_vol2surf/ 090425_QF86JB_FS

Re: [Freesurfer] problem with mri_vol2surf

wrong (see details below)? Thanks, Thomas On Sep 9, 2010, at 6:29 PM, ythomas wrote: > Hi, > > I am trying to sample a volume of integers in subject's anatomical > space to fsaverage surf. However, the output does not seem to be > integer valued anymore even though