[Freesurfer] Begginer!

Hi there, I am totally a begginer in the Neurodebian "world" so please be patient :( I installed FS but I don't know how to setup freesurfer? I don't know how to locate my FS home Simply, I'm stuck at this step: setenv FREESURFER_HOME /freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh any hel

[Freesurfer] R: Re: R: Re: R: Re: R: Re: incomplete tracts

I have this error: writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff01/surf/rh.cvs.tocvs_avg35.sphere.reg...expanding nbhd size to 11109: 1 negative trianglesmris_resample: Command not found. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harv

[Freesurfer] Visualize a fixed number of voxels using Tksurfer

Hi all, is there a way to visualize a fixed number of voxesl using TKsurfer. I want to display the 200 most active voxels (i.e. highest beta values) on the inflated surface. Is there a possibility within tksurfer or do I have to determine the corresponding threshold beforehand? Thanks Martin

[Freesurfer] How to flip L/R image in the freeview?

Freesurfer users, I'm a newbie for FS and have a rudimentary question for you. I have to overlay the group map for right hemisphere onto the lh.inflated (due to using sym space, where left surface map became symmetrical to the right), but I wonder if there is any way of reverting it back to rh.in

Re: [Freesurfer] setting up FS

Hi Asha, from the screen shot it looks like FS is installed properly. Have you tried running it? You could try: tksurfer fsaverage lh inflated -curv cheers Bruce On Wed, 1 May 2013, Ash Rafea wrote: Hi there, I am totally a begginer in the Neurodebian "world" so please be patient :( I insta

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: incomplete tracts

Hi Stefano you need to tell us what command you were running. cheers Bruce On Wed, 1 May 2013, std...@virgilio.it wrote: I have this error: writing registered surface to/Applications/freesurfer/subjects/subject_prova/Diff01/surf/rh.cvs.tocvs_av g35.sphere.reg... expanding nbhd size to

Re: [Freesurfer] Visualize a fixed number of voxels using Tksurfer

Hi Martin I guess you could do this using the histogram in tksurfer (left and right clicking in it will set the min and max thresholds). Or it would be pretty easy in matlab. cheers Bruce On Wed, 1 May 2013, Martin Bleichner wrote: Hi all,  is there a way to visualize a fixed number of voxe

Re: [Freesurfer] How to flip L/R image in the freeview?

Hi Glen have you done the cross-hemisphere registration? If so, you can do this with mri_surf2surf, although the syntax is a bit tricky. Doug would know the details, but he's probably not going to be able to answer questions until tomorrow cheers Bruce On Wed, 1 May 2013, Glen Lee wrote: Fr

[Freesurfer] Which space is TRACULA statistics in?

Hi FreeSurfing researchers, I am looking at the pathstats.overall.txt, and wanted to see if anybody knew which space these voxels are in - I assume MNI space (given that I used the MNI template) and not individual diffusion space, but would like to confirm. Does anybody know for certain what spac

Re: [Freesurfer] Use our own training subjects?

Hi Susan - Currently the only way to read in the manually labeled streamlines from the training subjects is in .trk format, which is what trackvis writes out. If you prefer to use another program for manual labeling, then its output would have to be converted to .trk format. This format is de

Re: [Freesurfer] Which space is TRACULA statistics in?

Hi Susan - All outputs of tracula are in native diffusion space. Tractography is performed in the native space, without any transformationon the DWIs to another space. a.y On Wed, 1 May 2013, Susan Kuo wrote: Hi FreeSurfing researchers,   I am looking at the pathstats.overall.txt, and wan

Re: [Freesurfer] Which space is TRACULA statistics in?

Thank you, Anastasia! I will keep this in mind when I analyze the group statistics. On Wed, May 1, 2013 at 11:07 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Susan - All outputs of tracula are in native diffusion space. > Tractography is performed in the native space, w

Re: [Freesurfer] Use our own training subjects?

Thank you, Anastasia. I think we can recruit some hard-working neuroanatomists here to help us with the labeling. I believe I will give this a shot for the IFO. Again, thanks for your support on this - I really appreciate it! Susie Kuo On Wed, May 1, 2013 at 11:04 AM, Anastasia Yendiki < ayend..

[Freesurfer] error in longitudinal processing "dimension mismatch"

Dear Freesurfer experts, I have a dataset of 2 time points. I ran into problems when I tried to use the two-stage approach to pull out statistics such as the rate of change in Freesurfer 5.1. I could not even get the first stage working. The error messages I got were “ERROR: MRISar1: Surf/Src dim

[Freesurfer] incomplete tracts

Hi Bruce, trac-all -prep -c $FREESURFER_HOME/dmrirc_single_subject_d11_NEW.I'm also attaching dmrirc files. Thank you very much. Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 1-mag-2013 15.39 A: Cc: , Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: incomplet

Re: [Freesurfer] error in longitudinal processing "dimension mismatch"

Hi Keith what were the recon-all command lines you ran? Bruce On Wed, 1 May 2013, Qi Wu wrote: Dear Freesurfer experts, I have a dataset of 2 time points. I ran into problems when I tried to use the two-stage approach to pull out statistics such as the rate of change in Freesurfer 5.1. I co

Re: [Freesurfer] incomplete tracts

Hi Stefano - You'll have to include the log file, so that we can see the exact command line that was being run when the error happened. Thanks, a.y On Wed, 1 May 2013, std...@virgilio.it wrote: Hi Bruce, trac-all -prep -c $FREESURFER_HOME/dmrirc_single_subject_d11_NEW.I'm also attaching d

Re: [Freesurfer] error in longitudinal processing "dimension mismatch"

Keith On Wed, May 1, 2013 at 12:43 PM, Bruce Fischl wrote: Hi Keith can you cc the list so that others can answer? Like Martin! thanks Bruce On Wed, 1 May 2013, Qi Wu wrote: Hi Bruce, Thank you so much for your quick reply. I used the followi

Re: [Freesurfer] convert labels to volumetric masks

Hi Meng, On 04/30/2013 09:53 PM, limengsecret wrote: > Hi Doug, > Thanks for your reply. > I have downloaded some freesurfer files (.annot, .label, .curv, .w) > about the specific regions. what do you mean you downloaded them? where did they come from exactly? Are they your own data? > And I want

[Freesurfer] (no subject)

Has anyone ever ran a post contrast sequence in FreeSurfer? Thanks, Ashley -- * * ___ 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 f

Re: [Freesurfer] (no subject)

Hi Ashley yes, a bunch of times. The dura can cause some problems, but mostly they run ok Bruce On Wed, 1 May 2013, Ashley Hannah wrote: Has anyone ever ran a post contrast sequence in FreeSurfer? Thanks,  Ashley -- ___ Freesurfer mailing list

[Freesurfer] Using the muscle ROI in the FreeSurferColorLUT

Hello Freesurfers, I would like to use the muscle ROI in the LUT (number 123). Can anyone tell me which muscles (all cranial? cervical too?) are included? I tried making a subject-specific label using the following command: mri_cor2label --c /cluster/ablood/1/${experimental_directory}/$

Re: [Freesurfer] Using the muscle ROI in the FreeSurferColorLUT

Hi Jeff our standard segmentation doesn't include muscle. We did have some prototypes that labeled all cranial muscles but they are not much more than prototypes Bruce On Wed, 1 May 2013, jwa...@nmr.mgh.harvard.edu wrote: > Hello Freesurfers, > I would like to use the muscle ROI in the LUT

[Freesurfer] Freesurfer License issue/bug on Opensuse 12.3

Hi, I've run into a license problem with the latest version of Freesurfer on OpenSuse 12.3. 64 bit. FREESURFER_HOME: /usr/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Kernel info: Linux 3.7.10-1.1-desktop x86_64 When running a test: /usr/freesurfer>echo $shell /bin

Re: [Freesurfer] convert labels to volumetric masks

Hi Doug, The relative freesurfer files were downloaded from http://ltl.tkk.fi/wiki/Atlas about the retinotopic visual areas. And I want to convert the files to volumetric masks to use for my own data. The functional data have been preprocessed with slice-timing, realignment, and normalization.

Re: [Freesurfer] convert labels to volumetric masks

Hi Meng, I don't know anything about that atlas. What space is it in? And how did you process the functional data? On 5/1/13 9:14 PM, limengsecret wrote: > > > Hi Doug, > > > The relative freesurfer files were downloaded from > http://ltl.tkk.fi/wiki/Atlas about the retinotopic visual areas

[Freesurfer] mri_convert Segmentation fault (core dumped) lubuntu 13.04

Dear freesurfer administrators, recently upgraded our system to freesurfer 5.2 on lubuntu 13.04. After the installation I accounted problems when testing freesurfer. tkmedit did not display the subject bert, instead an error message was shown: tkmedit bert orig.mgz