[Freesurfer] How to see the effect of external regressors?

Dear FS and fsfast expert: We want to know the effect of some external regressors such as the reaction time of every trial. We found that external regressor can be integrated into the GLM model with mkanalysis-sess's 'extreg' option, but we did not find the way to do comparison of these external

[Freesurfer] Problem: 'source'

Dear collegues, I had a problem during the installation of Freesurfer on my computer. I have a Mac Intel, and since the shell I'm using is the bash, I've entered those two lines written in the installation instructions: export FREESURFER_HOME=/Applications/freesurfer source

RE: [Freesurfer] Problem: 'source'

Henrique. Are you sure that freesurfer is at /Applications/freesurfer? Execute ls -l /Applications/freesurfer Regards PPJ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Henrique Fernandes Sent: terça-feira, 19 de fevereiro de 2008 08:52 To:

[Freesurfer] CentOS 5.1 and freesurfer and tksurfer

Dear FS experts, I install CentOS 5.1 and latest version of ATI driver and FS4.0.2, when I start tkmedit, it looks fine. In tksurfer, it just appear a sliver of surface without error message. In console, it stock on reading vertex. Is there anyway to correct it ? Thanks replay Kl chen

Re: [Freesurfer] .license file

Henrique You should call the file .license. Then it will work. The file will be invisible to your in unix unless you search for it with ls -a. Avram Avram Holmes Department of Psychology Harvard University 1210 William James Hall

Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer

Does glxgears work? That is an app that comes with Linux that exercises the GLX (OpenGL X extension) code. On Tue, 2008-02-19 at 20:41 +0800, [EMAIL PROTECTED] wrote: Dear FS experts, I install CentOS 5.1 and latest version of ATI driver and FS4.0.2, when I start tkmedit, it looks fine. In

[Freesurfer] .license file

Thanks for the suggestions, I'm now having another problem. I created a .license file with the information about my license. Although, to keep the file stored I must have a name for it other else the system won't allow me to create that file. So, after giving a random name to the file,

Re: [Freesurfer] .license file

Try using pico to create the file, like this: pico $FREESURFER_HOME/.license (paste three lines of license file and press Ctrl-X to save). On Tue, 2008-02-19 at 14:52 +, Henrique Fernandes wrote: Thanks for the suggestions, I'm now having another problem. I created a .license file

[Freesurfer] '.license' file

The installation was successful! I have created the file in 'pico', as Nick Schmansky told me to do, and fortunately the file '.license' was successfully created. Thank you all for your kind attention, Regards, Henrique Fernandes ___ Freesurfer

Re: [Freesurfer] Problem make_average_subject

Sorry to say but, just like for Juergen, the same error pops up for make_average_volume when run by itself or within the new make_average_subject scripts. - Jim Porter Graduate Student Clinical Science Psychopathology Research University of Minnesota James N. Porter wrote:

Re: [Freesurfer] creating a custom overlay

Sorry for the delayed follow-up. Doug, I don't think mri_surfcluster allows me to implement the criteria I want (only include clusters containing a peak vertex above threshold x, but vertices within those clusters can be included if they exceed threshold y (where y x). Bruce, I am

[Freesurfer] checking accuracy of talairach_with_skull.lta transform

Hello, In your experience, is the talairach_with_skull.lta transform always reasonable, or does it sometimes fail (and if the latter, is the failure rate dependent on the FS version, as is the case for talairach.xfm ?) I ask because the ICV (eTIV) value is derived from the determinant of

Re: [Freesurfer] creating a custom overlay

Hi Cate, hmmm, not sure about removing cluster. If you can draw around the ones you want to retain, the significances will be saved in the .label file Bruce On Tue, 19 Feb 2008, Catherine Hartley wrote: Sorry for the delayed follow-up. Doug, I don't think mri_surfcluster allows me to

Re: [Freesurfer] checking accuracy of talairach_with_skull.lta transform

Those are good questions. Bruce, does this use the mni305 template or a different one? On Tue, 19 Feb 2008, Michael Harms wrote: Hello, In your experience, is the talairach_with_skull.lta transform always reasonable, or does it sometimes fail (and if the latter, is the failure rate

Re: [Freesurfer] mri_surf2surf

Try it without the --sval (it will get the sval from the xyz in the surface). doug On Sun, 17 Feb 2008, Daniel Wakeman wrote: Hi Doug, Thanks. I tried this and got the following: [EMAIL PROTECTED] test2bem]$ mri_surf2surf --srcsubject $SUBJECT --sval-xyz smhead.surf --sval

Re: [Freesurfer] checking accuracy of talairach_with_skull.lta transform

Hi Mike, sorry, forgot to respond to this one. Not sure about tkregister2 - I'll leave that for Doug. I think you should be able to use mri_convert with the .gca file to extra the mean image frame (frame 0), then check the aligment to that. cheers, Bruce On Tue, 19 Feb 2008, Michael Harms

Re: [Freesurfer] How to see the effect of external regressors?

I don't have a way to easily test an external regressor. There are a couple of ways to do this type of analysis though. You can use a 4 column paraidgm file and code the weight (4th col) as the reaction time. This will weight the HRF for each presentation by its RT. Alternatively, you can recode

Re: [Freesurfer] mri_label2vol

Yes, you can convert almost any registration file to a register.dat with tkregister2. See the --help. mri_label2vol does not interpolate, per se. You can run into the situation where more than one label maps to a single output voxel. In that case, it uses the label that most frequently falls

Re: [Freesurfer] checking accuracy of talairach_with_skull.lta transform

no, it's our own (.gca) template. It's the same type of linear registration that is used in the aseg, just this time to a template that has a skull in it On Tue, 19 Feb 2008, Doug Greve wrote: Those are good questions. Bruce, does this use the mni305 template or a different one? On Tue,

Re: [Freesurfer] Register Nifti files on Siemens raw data

You can give mri_convert input direction cosines for the cols, rows, and slices (-iid, -ijd, -ikd), then load the volume into tkmedit to see if you got it right. Note: this is a difficult and frustrating process. doug On Sat, 16 Feb 2008, Joerg Magerkurth wrote: Hi, I have siemens mrs

Re: [Freesurfer] creating a custom overlay

There's a slightly convoluted way to do this: 1. Run mri_surfcluster with --thmin y. Save the output cluster number overlay with --ocn. This is a surface overlay where the value is the cluster number. 2. Since the clusters are ordered based on descending peak vertex value, you can create a

Re: [Freesurfer] checking accuracy of talairach_with_skull.lta transform

You can try something like this: mri_convert $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca gca.mgh --frame 0 tkregister2 --targ gca.mgh --mov T1.mgz \ --lta transforms/talairach_with_skull.lta --reg tmp.reg doug On Tue, 19 Feb 2008, Bruce Fischl wrote: no, it's our own (.gca)

[Freesurfer] Extracting brain region with a mask

Hello All, I used mri_binarize to create stg masks (inclusive of gray and white matter). I'm trying to take this a step forward to see if I can extract the actual brain region encompassed by the mask - in other words, is there a way to cut out the portion of the brain that the mask encloses. So

Re: [Freesurfer] Extracting brain region with a mask

Hi Anil, I think mri_mask will do this. Bruce On Tue, 19 Feb 2008, Anil Roy wrote: Hello All, I used mri_binarize to create stg masks (inclusive of gray and white matter). I'm trying to take this a step forward to see if I can extract the actual brain region encompassed by the mask - in

Re: [Freesurfer] checking accuracy of talairach_with_skull.lta transform

p.s. remember if/when you check it that it is supposed to align skull, not necessarily brain. On Tue, 19 Feb 2008, Michael Harms wrote: Hello, In your experience, is the talairach_with_skull.lta transform always reasonable, or does it sometimes fail (and if the latter, is the failure rate