[Freesurfer] problem with labels

2010-12-21 Thread Irene Altarelli
Dear Freesurfers, I have a problem with labels. I select a given Talairach coordinate that interests me, draw an approximately circular label around it in tksurfer, and save it. When I open that same label in tkmedit, the central Talairach coordinate is changed and the whole label is somewhat shif

Re: [Freesurfer] problem with labels

2010-12-21 Thread Bruce Fischl
Hi Irene, the label has to shift somewhat in tksurfer, since it will sample it onto the surface. Unless the entire label you drew was exactly on the surface boundary to begin with. cheers Bruce On Tue, 21 Dec 2010, Irene Altarelli wrote: > Dear Freesurfers, > > I have a problem with labels. I

Re: [Freesurfer] {Spam?} Re: preproc-sess error

2010-12-21 Thread Douglas N Greve
you can setenv FSLDIR /usr/pubsw/packages/fsl/3.3.7 then re-source the stable3 environment. doug jkus...@partners.org wrote: > Hi Doug, > > Thanks for your messages. We have to keep using stable3 for the rest of this > study. Does this mean we can just use a command to use the older version of

[Freesurfer] help

2010-12-21 Thread subramanyam
Dear Colleague, Following is the error we get upon running the mri_annotation2label command r...@ubuntu:~# mri_annotation2label --subject one \ --h rh --labelbase ./label/aparc-rh ERROR: Option --h unknown r...@ubuntu:~# mri_annotation2label --subject one \ --hemi rh --labelbase ./label/apar

Re: [Freesurfer] help

2010-12-21 Thread Bruce Fischl
that works for me: mri_annotation2label --subject bruce --hemi rh --labelbase . subject = bruce annotation = aparc hemi = rh labelbase = . surface = white Reading surface . . can you remove the \ in your command line? Bruce On Tue, 21 Dec 2010 subraman...@nbrc.ac.in wrote: > > Dear Collea

Re: [Freesurfer] ICV differs systematically in repeated measurements

2010-12-21 Thread Martin Reuter
Hi Diederick, the ICV is computed from the linear talairach.xfm transform (including skull). There are all kinds of other talairach transforms produced by recon all, so make sure you are looking at the talairach.xfm (not ...lta or ..._with_skull.lta). You might want to read: http://surfer.nmr.mgh

Re: [Freesurfer] ICV differs systematically in repeated measurements

2010-12-21 Thread Martin Reuter
As I said, there are several talairach transforms. You need to look at the talairach.xfm. The wiki says: To check the quality of the registration file talairach.xfm file: cd $SUBJECTS_DIR/subject/mri/transforms tkregister2 --xfm talairach.xfm \ --targ $FREESURFER_HOME/average/RB_all_withskull

[Freesurfer] Freesurfer longitudinal analysis

2010-12-21 Thread rong chen
Hi, I want to use FreeSurfer to analyze a longitudinal study. For each subject in my study, I already used FreeSurfer 4.2 to perform the cross-sectional analysis. However, FreeSurfer 4.2 did not have a longitudinal pipeline. Therefore, I want to use FreeSurfer 4.5 for this purpose (in the FreeSurfe

[Freesurfer] orig/conform

2010-12-21 Thread Harrington, Gregory S.
Is there a quick way to transform the orig.mgz data back to the 'original" orientation of the orig/001.mgz data set? i.e., undo the conform? Greg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/list

Re: [Freesurfer] orig/conform

2010-12-21 Thread Bruce Fischl
That's what the rawavg.mgz is. You can use mri_convert with -rl rawavg.mgz to realize other conformed volumes back to that space On Dec 21, 2010, at 5:50 PM, "Harrington, Gregory S." wrote: > Is there a quick way to transform the orig.mgz data back to the > 'original" orientation of the orig

[Freesurfer] volume - surface shift in tkmedit

2010-12-21 Thread Micheli, C.
Dear all I would like to write an MRI anatomical volume and a surface in freesurfer format. The surface is correspondent to the white matter tessellation, while the volume represents T1 anatomical slices, both obtained from softwares external to FreeSurfer. Using the two functions save_mgh.m an