[Freesurfer] Calculating Gray Matter Density

External Email - Use Caution Hello, Does FreeSurfer have an option for calculating gray matter density during recon-all, or does one need to calculate it manually? In that case, what is the formula? The reason I would like to compute density is to replicate the effects show in th

[Freesurfer] Talairach Failure

Hi, I got the following error when trying to run recon-all on an MP-RAGE T1-weighted image: Fri Apr 10 16:25:01 EDT 2009 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n # #...@# Talairach Failure Detection Fri Apr 10 1

[Freesurfer] Multiple Processors

Hi, I am running Freesurfer on a Mac OS X 10.5 computer with a 2x2.8 GHz Quad-Core Intel Xeon processor. My question is, are there any subcommands to run recon-all assigning the processors to different jobs? Or is the speed of recon-all just dependent on pure processing power, no more? Thanks!

[Freesurfer] Unable to Open GUI

Hi, We are operating x86_64 redhat linux on a server, and we recently installed FreeSurfer on the surfer to help with running multiple recon-all's. However, whenever I attempt to run tkmedit or tksurfer, I get the following error: [and...@scan2 Anatomicals]$ tkmedit Focus_reg_009 brainmask.mgz GL

[Freesurfer] RE: GLUT Error

Hi again, I have been encountering an error when attempting to use either tksurfer or tkmedit via VNC on a local server. Here is the output whenever I type tkmedit or tksurfer: GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: 1.0 I looked through the threads rega

[Freesurfer] Finishing WMParc

Hello, I recently ran a batch file on several subjects, but set a time limit which prevented some of them from finishing all the steps of recon-all. In the recon-all-status.log for some of them, the last line is "WMParc". I was unable to find which option of recon-all would do only this step; sh

[Freesurfer] Binary files not executable

Hello, I recently installed FreeSurfer on one of my laptops running Ubuntu and get the following error when I attempt to run tkmedit: Exec format error. Binary file not executable. I thought I remembered something about setting a soft link for one of the libraries in Ubuntu. Am I on the right

[Freesurfer] Rerunning aseg.stats

Hello, I recently ran a batch file which seemed to run fine for nearly all the participants. Yet, when I did an asegstats2table command on all the subjects, I received the following error for three of them: WARNING: cannot find /nfs/01/osu5323/freesurfer/freesurfer/subjects/JUL11_2009E/stats/ase

[Freesurfer] asegstats2table command not found

Hi, I am running FreeSurfer version 4.3, and when I type 'asegstats2table' I get a "command not found" error. I have my path set correctly (virtually all of the other commands in the freesurfer/bin directory work), but for some reason both asegstats2table and aparcstats2table do not. Any ideas?

Re: [Freesurfer] asegstats2table command not found

; > Krish > > > On Oct 26, 2009, at 12:29 PM, Andrew Jahn wrote: > > Hi, >> >> I am running FreeSurfer version 4.3, and when I type 'asegstats2table' I >> get a "command not found" error. I have my path set correctly (virtually >

Re: [Freesurfer] asegstats2table command not found

e time it > is.. if you don't have, change that line to the path of the executable -- > like #!/opt/local/bin/python ) > > The next release will fix this. > > Thanks > Krish > > > On Oct 26, 2009, at 1:46 PM, Andrew Jahn wrote: > > Here is the outpu

[Freesurfer] 2nd Level Analyses in FreeSurfer

Hi all, I am interested in using Freesurfer to project volume data onto the inflated brains run through the FS pipeline. I am using SPM and have been able to project 1st level con and spmT images onto the corresponding subject's inflated anatomical. My question is, if I wanted to look at 2nd lev

[Freesurfer] Parametrics in FreeSurfer

Hi FreeSurfer experts, I was wondering whether you are able to use parametric modulators during FS-FAST. All I can see from the mkanalysis-sess gui is setting up contrasts, but I would also like to see how other parameters affect the size and shape of the bold response. Is there any way to do th

Re: [Freesurfer] Parametrics in FreeSurfer

to change? Eg, delay or dispersion of > the HRF? > > doug > > Andrew Jahn wrote: > >> Hi FreeSurfer experts, >> >> I was wondering whether you are able to use parametric modulators during >> FS-FAST. All I can see from the mkanalysis-sess gui is setting up >&

Re: [Freesurfer] Path Setup of FREESURFER_HOME

Hello, I just downloaded and installed Freesurfer onto a new computer, and after going through all the steps outlined on the download and installation page, I get the following error when trying to run recon-all: sudo recon-all -s bert -all FREESURFER_HOME: Undefined variable. However, I have s

[Freesurfer] Visualizing SPM Results on Template FreeSurfer Brain

Hello, I have second-level results in .img/.hdr format that I have just run through SPM. I was wondering whether there is a way to visualize these results onto a template FreeSurfer surface model in MNI space. Is this possible, or can you only visualize second-levels which have been processed th

[Freesurfer] Registering Two Anatomical Images

External Email - Use Caution Hello, I have a raw anatomical image called raw.mgz, which I have manually annotated using Freeview; the resulting annotations are saved in a file called seg.mgz. I want to compare this to the annotations automatically generated by recon-all, so I ran