Re: [Freesurfer] mri_cvs_register quit for mris_resample: Command not found

Hi Z K The contents of build-stamp.txt are freesurfer-Darwin-lion-stable-pub-v5.3.0. Best Wishes Cong Chen > Date: Tue, 18 Oct 2016 11:09:20 -0400 > From: Z K > > > Hello, > > Can you provide me with the contents of your >

Re: [Freesurfer] Optimal combination of MRI-sequences

Hi Erik if you mean what sequences should you acquire, Andre van der Kouwe has a website with recommendations for different platforms. Typicall we like a multi-echo MPRAGE and a T2-SPACE FLAIR scan as well if you have time cheers Bruce On Tue, 18 Oct 2016, Erik Lindberg wrote: Dear

Re: [Freesurfer] Cortical Thickness Zero Values

Hi Taha none that I can think of. The medial wall is pretty substantial region though - I am more concerned about your subject with only 53 vertices in it. You can visualize it by loading the ?h.cortex.label onto the inflated surface. Everything not in the label should be set to 0 cheers

Re: [Freesurfer] Training Tracula to add more pathways

Bump On Thu, Sep 29, 2016 at 4:02 PM, Kristafor Farrant wrote: > Hi there, > > As a complete newbie to the Tracula tool, I have a questions about using > it. Is it possible to train tracula to track additional pathways other than > the 18 thats are already included? I was to

Re: [Freesurfer] Optimal combination of MRI-sequences

What do you mean by ³combining² sequences? Peace, Matt. From: on behalf of Erik Lindberg Reply-To: Freesurfer support list Date: Tuesday, October 18, 2016 at 2:52 PM To:

Re: [Freesurfer] Cortical Thickness Zero Values

I see now, thanks for the answer. If I may, is there any particular reason why such a disparity between two subjects, is this due to anatomical variability between individuals? I was surprised by the 9,000 values that was missing. On Fri, Oct 14, 2016 at 10:40 AM, Douglas Greve

Re: [Freesurfer] Using "for" to run multiple subjects

The * is what makes the script useful as that allows it to process all the subjects without you having to specify every subject. That script only works if you have already set up your subject's folders in the directory structure freesurfer expects. Is this the case? Or are you working from

[Freesurfer] Optimal combination of MRI-sequences

Dear Freesufer experts, We are in the process of starting a large MRI project on normal aging and dementia. There has been a lot of discussions about what sequences to use. We are now thinking about combining several sequences. Is there an optimal combination of MRI sequences for

Re: [Freesurfer] 2 beginner questions

Hi Brad, I don't have any experience with your first issue, but with regards to your second issue: are you running Windows10 as the host OS and Ubuntu as the guest OS? Ubuntu requires root (or admin) access to install packages. If you installed Ubuntu yourself, it should have prompted you to

Re: [Freesurfer] recon-all -s bert exited with errors

Hi Zeke, Thanks for your reply! The issue has been resolved - it was the temp folder on the system running out of space. But thank you very much for your suggestions! Best, Qinggang On Tue, Oct 18, 2016 at 10:07 AM, Z K wrote: > What version of perl are you

Re: [Freesurfer] GLM on cortical and subcortical volume

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI this does not have the mri_glmfit command, but that is the same doing the voxel-wise stats with the change in --y. This does not include correction for ICV On 10/18/16 10:53 AM, miracle ozzoude wrote: hello doug, Thanks for

Re: [Freesurfer] mri_cvs_register quit for mris_resample: Command not found

Hello, Can you provide me with the contents of your /Applications/freesurfer/build-stamp.txt file? On 10/18/2016 10:13 AM, Cong wrote: > Dear freesufer experts > I’m learning DTI image process according to steps in FsTutorial/ > Diffusion_DtiIntegration. In Spatial Normalization I need

Re: [Freesurfer] GLM on cortical and subcortical volume

hello doug, Thanks for the response. Please can you send me the link. Also, does GLM correct for total intracranial volume or do I need to create fsgd file with total intracranial volume as covariate? Thanks On Tue, Oct 18, 2016 at 10:48 AM, Douglas Greve wrote: > do

Re: [Freesurfer] GLM on cortical and subcortical volume

do you mean volumes of ROIs? Yes, there is a tutorial on this in our wiki, but basically you need to run aparcstats2table and/or asegstats2table to create a table of volumes for each subject and ROI. Then use mrI_glmfit with the --table option instead of --y On 10/18/16 10:18 AM, miracle

[Freesurfer] GLM on cortical and subcortical volume

Hello Expert, Is there are way to perform glm analysis on cortical and subcortical volumes. Thanks Best,. Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

Re: [Freesurfer] recon-all -s bert exited with errors

What version of perl are you using? $> perl --version If its perl 5.20 (or maybe 5.22) than the error you are encountering is because because that version of perl is incompatible with the MNI tools shipped with the version of freesurfer you are using. The easiest way to remedy the

[Freesurfer] mri_cvs_register quit for mris_resample: Command not found

Dear freesufer experts    I’m learning DTI image process according to steps in  FsTutorial/ Diffusion_DtiIntegration. In Spatial Normalization I need create a .m3z morph file through mir_cvs_register. I used command mri_cvs_register --mov subjectname --template cvs_avg35. But it always stop for 

Re: [Freesurfer] mri_nu_correct crash

Oops, I meant to write "Ubuntu 16 comes with a version of perl that is *incompatible* with the MNI tools..." On 10/18/2016 10:03 AM, Z K wrote: > Ubuntu 16 comes with a version of perl that is compatible with the MNI > tools shipped with the version of freesurfer you are using. > > The easiest

Re: [Freesurfer] mri_nu_correct crash

Ubuntu 16 comes with a version of perl that is compatible with the MNI tools shipped with the version of freesurfer you are using. The easiest way to remedy the situation is to download and install the development version of freesurfer which fixes this issue and will be included in the