[Freesurfer] FSL to FreeSurfer registration
Hello all, I took the FS course last June at the OHBM in San Francisco, and am now playing with it to get to know it better. One of the slides on the talk about FSL-FS integration mentioned that the input data (from FEAT) for the reg-feat2anat command should have not been smoothed prior to registering to FS. Considering that FEAT 1st level analysis has a default of 5mm spatial smoothing (and that's what I used on my data), it seems counterintuitive to need to run a 1st level analysis again so the output files are not spatially smoothed. So my questions are: 1) having the example_func file spatially smoothed will necessarily hinder a proper registration to the FS anatomical?; 2) if so, should I re-run all my FEAT 1st level analysis without smoothing or is there any other way? I know this is quite a beginners question, but I could not find the answers on the FS FAQ or the mailing list archives. I appreciate any light on this. Regards, Estephan Moana, DDS Graduate Student Oral Biology PhD Program - Neurobiology track School of Dentistry, UNC- Chapel Hill 2140 Old Dental Building, CB# 7455 Chapel Hill, NC 27599 Phone: (919) 966-5680 Fax: (919) 966-5339 Cell: (612) 702-3295 mo...@email.unc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using tksurfer to dispaly the surface
Hi Nick, It cannot display correctly for bert either. I have asked the question of displaying in tksurfer and tkmedit. I cannot fix the image window such as "fsaverage". And I have to input the command "exit" in terminal to colse the window of fsaverage. I cannot close it by right-click the window and choosing the closure option. I don't use vnc to display the surface. Maybe I should have a try. Shoud I update the graphics driver? Thanks. Q.Q. 2009/9/22 Nick Schmansky > QQ, > > Does the sample subject 'bert', found in freesurfer/subjects/bert, > display overlays correctly? ie. does thickness display normally? > > I need to disambiguate whether its a system problem or a data problem. > > If bert doesnt display correctly, then I'd try updating the graphics > driver. Also, are you displaying over vnc, or locally? vnc connections > can be problematic for display. > > Nick > > On Tue, 2009-09-22 at 07:23 -0400, Bruce Fischl wrote: > > Hi QQ, > > > > you should post these to the list so someone else can help. > > > > Nick: any ideas? > > > > Bruce > > On Tue, 22 Sep > > 2009, QQ Liu wrote: > > > > > Hi Bruce, > > > > > >Although I chose the auto-redraw in the menu of view, the picture is > > > still as before. Then I choose all the options, but it's still > discrete, > > > which is attached in this mail. > > > > > > Thanks > > > > > > QQ > > > 2009/9/21 Bruce Fischl > > > > > >> can you try clicking redraw? > > >> > > >> On Mon, 21 Sep 2009, QQ Liu wrote: > > >> > > >> Hi Bruce, > > >>> I did not click the redraw button. tksurfer cannot show the image > > >>> staidly and there isn't the smooth surface. I have to put the mouse > on it > > >>> and click the image then I can capture the picture attached in the > last > > >>> mail. > > >>> Not only tksurfer but also tkmedit cannot give the steady picture > in the > > >>> window. > > >>> > > >>> I only used this command: > > >>> > > >>> tksurfer fsaverage lh inflated -annot > > >>> lh.g1v0.glmdir/onegroup/mc-z.negative.sig.ocn.annot -fthresh 2 -curv > > >>> -gray > > >>> > > >>> Thanks. > > >>> > > >>> QQ > > >>> > > >>> 2009/9/21 Bruce Fischl > > >>> > > >>> it looks cool. I assume you tried clicking the redraw button? > > > > On Mon, 21 Sep 2009, QQ Liu wrote: > > > > Hi all, > > > > > > > > When I use tksurfer to display the results of group analysis, > there is > > > a problem. I have to put the mouse on the image then it can be in > the > > > front. > > > However, there is not the smooth surface as that in the tutorial of > > > group > > > analysis in wiki. The image showed up is just some dots in the > black > > > ground. > > > > > > > > > What's wrong about this? and how to solve this problem? The image > > > captured is attached in this mail. > > > > > > Thanks a lot. > > > > > > QQ > > > > > > > > > > > > > > >>> > > >>> > > >>> > > > > > > > > > > > > > > > -- Best wishes. Q.Q Liu +8613426232824 qqli...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How do Control Points and Pial Surfaces Interact?
Hello - I am trying to compare normalized segmentation stats across groups. We are adding control points to the white matter in an attempt to push out the pial surfaces when it appears grey matter has been clipped or cut short.I am loading the following: tkmedit [SubjectID] brainmask.mgz lh.white -aux wm.mgz -aux-surface rh.white. The CPs are being saved, and after running autorecon-all the CPs are referenced in the recon-all.log file - however the pial surfaces are not redrawn around the control points. Should the white matter CPs force new pial surfaces? Am I missing a step in here? I checked the archive for the last year without luck - so I apologize if this is a repeat question. Thanks much for your help - Sherri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Bvecs and image orientation
This question was asked on the FSL list and I thought it would be pertinent on this list as well in relation to mri_convert. -- Forwarded message -- From: Saad Jbabdi The bvecs are supposed to be relative to the image grid. On 22 Sep 2009, at 13:34, Laura Mancini wrote: Dear all, > > In FSL, do the x, y, z components of the bvecs correspond to the image > axes (i.e. along the directions of the data matrix indices), or to the > patient axes as defined in the nifti header, or something else? > > Many thanks, > Laura > when one converts a dicom data set containing diffusion data with mri_convert it generates bvecs and bvals. the bvecs are unit vectors relative to some coordinate system. is this the coordinate system of the scanner or the coordinate system of the image volume? cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Getting Started
Try this: cd ~ vi .bashrc You wont see the .bashrc unless you use ls -a --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business 2009/9/22 Weisinger, Brian (NIH/OD) [E] > I must be really cpu challenged because I can't even seem to get this > thing started. > I am trying to perform basic set up right now. I have downloaded freesurfer > so far and in the freesurfer setup and configuration section of the wiki I > have been able to > > If using bash or sh, type: > > export FREESURFER_HOME=/freesurfer > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > And I do have this come up in the window. > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer > FSFAST_HOME /usr/local/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii > SUBJECTS_DIR/usr/local/freesurfer/subjects > MNI_DIR /usr/local/freesurfer/mni > > Now this is where my problems start > I would like to do this but I do not see any of these files anywhere. I am > using bash but I do not see the corresponding .bashrc file anywhere to > include the export and source commands. > > > Alternately, the resource file for the shell can be configured to source > the file automatically each time the shell is started. In the home directory > of the user who will be running FreeSurfer binaries, edit the file .cshrc if > C-shell will be used, the .tcshrc for enhanced C-shell, the .bashrc file for > Bash, and .profile for sh, to include the previous two lines (which setenv > FREESURFER_HOME, and then source the SetUpFreeSurfer.csh(or sh) script). > > Also I am having trouble with the license step.I tried making the .license > file and pasting my information in as well as trying the ways suggested in > previous peoples problems (using pico). I guess I am having a problem > understanding where my $FREESURFER_HOME is located to put my .lisence file. > > > I am still fresh to using the unix terminal so I apologize if my problem is > due to my inexperience but if you could help me out I would really > appreciate it. > > Thank you > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Getting Started
I must be really cpu challenged because I can't even seem to get this thing started. I am trying to perform basic set up right now. I have downloaded freesurfer so far and in the freesurfer setup and configuration section of the wiki I have been able to If using bash or sh, type: export FREESURFER_HOME=/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh And I do have this come up in the window. Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR/usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni Now this is where my problems start I would like to do this but I do not see any of these files anywhere. I am using bash but I do not see the corresponding .bashrc file anywhere to include the export and source commands. Alternately, the resource file for the shell can be configured to source the file automatically each time the shell is started. In the home directory of the user who will be running FreeSurfer binaries, edit the file .cshrc if C-shell will be used, the .tcshrc for enhanced C-shell, the .bashrc file for Bash, and .profile for sh, to include the previous two lines (which setenv FREESURFER_HOME, and then source the SetUpFreeSurfer.csh(or sh) script). Also I am having trouble with the license step.I tried making the .license file and pasting my information in as well as trying the ways suggested in previous peoples problems (using pico). I guess I am having a problem understanding where my $FREESURFER_HOME is located to put my .lisence file. I am still fresh to using the unix terminal so I apologize if my problem is due to my inexperience but if you could help me out I would really appreciate it. Thank you ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using tksurfer to dispaly the surface
QQ, Does the sample subject 'bert', found in freesurfer/subjects/bert, display overlays correctly? ie. does thickness display normally? I need to disambiguate whether its a system problem or a data problem. If bert doesnt display correctly, then I'd try updating the graphics driver. Also, are you displaying over vnc, or locally? vnc connections can be problematic for display. Nick On Tue, 2009-09-22 at 07:23 -0400, Bruce Fischl wrote: > Hi QQ, > > you should post these to the list so someone else can help. > > Nick: any ideas? > > Bruce > On Tue, 22 Sep > 2009, QQ Liu wrote: > > > Hi Bruce, > > > >Although I chose the auto-redraw in the menu of view, the picture is > > still as before. Then I choose all the options, but it's still discrete, > > which is attached in this mail. > > > > Thanks > > > > QQ > > 2009/9/21 Bruce Fischl > > > >> can you try clicking redraw? > >> > >> On Mon, 21 Sep 2009, QQ Liu wrote: > >> > >> Hi Bruce, > >>> I did not click the redraw button. tksurfer cannot show the image > >>> staidly and there isn't the smooth surface. I have to put the mouse on it > >>> and click the image then I can capture the picture attached in the last > >>> mail. > >>> Not only tksurfer but also tkmedit cannot give the steady picture in the > >>> window. > >>> > >>> I only used this command: > >>> > >>> tksurfer fsaverage lh inflated -annot > >>> lh.g1v0.glmdir/onegroup/mc-z.negative.sig.ocn.annot -fthresh 2 -curv > >>> -gray > >>> > >>> Thanks. > >>> > >>> QQ > >>> > >>> 2009/9/21 Bruce Fischl > >>> > >>> it looks cool. I assume you tried clicking the redraw button? > > On Mon, 21 Sep 2009, QQ Liu wrote: > > Hi all, > > > > > When I use tksurfer to display the results of group analysis, there is > > a problem. I have to put the mouse on the image then it can be in the > > front. > > However, there is not the smooth surface as that in the tutorial of > > group > > analysis in wiki. The image showed up is just some dots in the black > > ground. > > > > > > What's wrong about this? and how to solve this problem? The image > > captured is attached in this mail. > > > > Thanks a lot. > > > > QQ > > > > > > > > > >>> > >>> > >>> > > > > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
