[Freesurfer] how to transfer .label file to .nii file

Hi, Our lab have managed to generate ROIs in T1 images using Freesurfer, which led to .label files. We succesfully measured the cortical thickness in these ROIs for each subject in Freesurfer. Now we are aiming to track white matter fibers from these ROIs in a tractography software Trackvis.

Re: [Freesurfer] Fwd: LGI path problem

Dear Marie, Thank you, I use bash and changed my .bashrc and this worked, I previously had used wrong syntax. Thank you very much for your help. However, I now recieve another error and do not know what it means at all. I copy in the error ! Thank you. Improper assignment with rectangular empty

[Freesurfer] Power analysis for Qdec

Hi Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec? That would be great if I can get an answer in more detail since I have seen the post in FAQ, just

Re: [Freesurfer] CVS registration questions

Hi Tommi, I am preparing to CVS register 30+ subjects to improve FSL probabilistic tractography alignment across subjects. First, thanks for a really cool tool! Then, I have some questions: 1. mri_cvs_register step1 is spherical registration. However, I have already run FS5.3 recon-all

Re: [Freesurfer] freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz doesnot have mri_strip_skull codes

Rujing, mri_strp_skull is not a FreeSurfer binary. -Zeke On 10/28/2013 01:31 AM, Rujing Zha wrote: Dear FreeSurfer Users, I downloaded FreeSurfer latest version in this

Re: [Freesurfer] Issue with 5.3.0 nu_correction?

Hello Natalie, 'nu_correct' should be found in your '$FREESURFER_HOME/mni/bin' directory. That directory should be added to your PATH when your source the SetUpFreeSurfer.sh file. You can probably get around this issue by adding $FREESURFER_HOME/mni/bin to your PATH environment variable. But

Re: [Freesurfer] CVS registration questions

Thanks Lilla! Which MNI152 version was used as template when doing nonlinear CVS-registering from cvs_avg35 into MNI152 space? For example, was this MNI152 ICBM 2009a 1mm Nonlinear Asymmetric? Bests, Tommi Hi Tommi, I am preparing to CVS register 30+ subjects to improve FSL probabilistic

[Freesurfer] Freeview

Hi all, I recently updated to FreeSurfer version 5.3.0, and I am now having problems with freeview that I didn't have on the older versions. When I go to Surfaces and Load Labels, it only shows one label at a time. Previously, I could add several labels and all would appear on the Figure. Does

Re: [Freesurfer] Problem generating volume stats with hippocampal segmentation script

Hi, I haven't received any word so re-sending in the event my email was missed. I am wondering what might be causing the volume stat issue-- is there a problem with permissions in a file or something else entirely? Thanks for any input, Best, Erin -- Erin Walsh, Ph.D. Postdoctoral Research

Re: [Freesurfer] Freeview

Hi Lindsay, I think there was no such option to display multiple surface labels at once even in the old version. However, we will add it in the future. Best, Ruopeng On 10/28/2013 01:48 PM, Lindsay Squeglia wrote: Hi all, I recently updated to FreeSurfer version 5.3.0, and I am now having

Re: [Freesurfer] Issue with 5.3.0 nu_correction?

Hi Zeke, Thanks so much for your prompt response. My PATH variable is /usr/global/freesurfer/5.3.0/freesurfer. I do see nu_correct in the /usr/global/freesurfer/5.3.0/freesurfer/mni/bin, so that seems to be correct as well. Should I export my PATH environment variable to include /mni/bin?

Re: [Freesurfer] LGI path problem

Hi Linn, We have an issue using lGI with matlab 2013 in the current version. It will be updated in the new version, but in the mean time if you want to use it, it's a very small change that you have to do. See the following post:

Re: [Freesurfer] Freeview

Was that from freeview or tksurfer? On 10/28/2013 02:06 PM, Lindsay Squeglia wrote: Hi Ruopeng, Thanks for your response! I used to do it all the time in the previous versions of FreeSurfer (see attached). I am not sure why the new version is different. Thanks! Lindsay On Mon, Oct 28,

Re: [Freesurfer] sim ocn clusters mean effect size

Hi all, I would like to calculate the 95% confidence interval of the slope for a thickness cluster (vs age in years) produced by mri_glmfit-sim. I have obtained values for my clusters from gamma.mgh and gammavar.mgh using these two commands: mri_segstats --i gamma.mgh --seg

Re: [Freesurfer] Freeview

It was definitely from freeview. These are the notes I wrote for creating figures previously, and I didn't have a problem: **Type freeview in command line in file where Freesurfer fsaverage brain is, will open file, go to File-- Load Surface --fsaverage--surf. Choose lh.pial; then do again for

Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

Hi Anastasia, I've attached my configuration file, and below is pasted the contents of the error log. Below that, I've pasted the last few lines of the trac-all log (not the error log), because it says something about a dyld that cannot be loaded...might be related to the problem. Thanks, Mike

Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

Mike, You need to install XQuartz: http://xquartz.macosforge.org/landing/ Also see the following troubleshooting page: http://ftp.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting -Zeke On 10/28/2013 03:17 PM, Michael Datko wrote: Hi Anastasia, I've attached my configuration file,

Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

The XQuartz website you linked makes it sound like it is identical to X11, is it different in some way? I have X11 already and it works flawlessly with other applications such as AFNI and FSL. On Mon, Oct 28, 2013 at 12:36 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Mike, You need to

Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

Hello, I installed XQuartz and the processing gets a little bit farther than it did before. However, I now run into an error about not being able to move the bvecs file. To my knowledge I specified the bvecs file correctly (in the same log file I attached previously), and it is in a format that

Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

Im of the understanding that X11 and XQuartz will not conflict. Many users running Mac OSX Snow Leopard have both applications installed on their systems. But if you are extremely weary of potential issues than I suppose you could create a symbolic link from /opt/X11 to /usr/X11. Additional

Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

Hi Michael - Two things: First, in the dmrirc that you attached previously, the bvecfile and bvalfile lines are commented out. Second, these files need to be in column, not row format, as shown in the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Hope this helps, a.y

Re: [Freesurfer] Issues with rh.white and rh.orig surfaces

Hi Jon The segmentation looks really poor, which probably causes a topological defect resulting in what you see. I would try using expert opts to set the segmentation thresholds better Cheers Bruce On Oct 28, 2013, at 1:10 PM, Jonathan Holt whats...@umich.edu wrote: FS experts, both of

Re: [Freesurfer] Issues with rh.white and rh.orig surfaces

Where can I find more info on expert opts? On Oct 28, 2013, at 6:22 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jon The segmentation looks really poor, which probably causes a topological defect resulting in what you see. I would try using expert opts to set the segmentation