Re: [Freesurfer] Quality control with different pipelines

Hi, You can simply rerun 'recon-all -all’ on top of your already processed/edited subject, and it will respect your previous edits.  Of course, it is a good idea to still review/QC the results afterwards, to make sure that the outcome of those edits is satisfactory under the new FS v

Re: [Freesurfer] Quality control with different pipelines

Thank you Michael! So - just to be super sure I'm on the same page here. If I've run a subject using 5.3 I take that same subject directory (after backing it up somewhere) and then run the dev version of recon-all with the -all flag. After it's completed I (should - contingent on checking again as

Re: [Freesurfer] Quality control with different pipelines

Yes on all fronts. --  Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-7

Re: [Freesurfer] Quality control with different pipelines

Brilliant - many thanks. Kx On 22 June 2016 at 14:57, Harms, Michael wrote: > > Yes on all fronts. > > -- > Michael Harms, Ph.D. > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Dep

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi all, I'll give some feedback about the two methods you've mentioned. I also tried using a 0.5 T1 image and then: *Changing the headers of the T1 and T2 images:* It worked for the 0.7mm T1, however, in the 0.5mm the tailarach aligment failed. In both cases I had the warning "MRIsetRas2VoxFromM

[Freesurfer] doubts

Hi, *After the command: * asegstats2table --subjects AntonioMagnani -- meas volume --tablefile TESTE.txt This message: [image: Imagem inline 1] Thanks. elias. -- Atte. Elias Vergílio Da Cás - Físico UFES/HUCAM/EBSERH ___ Freesurfer mailing li

[Freesurfer] New Post Doctoral Position in Neuroimaging Available at Washington University in St Louis

NEW POST DOCTORAL POSITION IN NEUROIMAGING AVAILABLE POSITION SUMMARY: Applications are invited for a post doctoral position in the Ances Laboratory at Washington University in St. Louis. The primary focus of the lab is to understand how neurodegenerative diseases (especially Alzheimer’s disease)

[Freesurfer] New Research Assistant Position in Neuroimaging Available at Washington University in St Louis

NEW RESEARCH ASSISTANT POSITION IN NEUROIMAGING AVAILABLE POSITION SUMMARY: Applications are invited for a research assistant position in the Ances Laboratory at Washington University in St. Louis. The primary focus of the lab is to understand how neurodegenerative diseases (especially Alzheimer’s

[Freesurfer] X11 / mesa update broke tkmedit snapshots

Hi all, I run the pipelines for the CNDA and various other XNAT installations. We recently updated some of our packages, and our Freesurfer snapshots (generated with tkmedit using a tcl script) have broken. We're on Centos 6.8. The package that seems to cause the breakage is one of the mesa pa

Re: [Freesurfer] X11 / mesa update broke tkmedit snapshots

I should add that we're running tkmedit using xvfb since the process is automated and runs without a physical screen. Flavin > On Jun 22, 2016, at 4:15 PM, Flavin, John wrote: > > Hi all, > > I run the pipelines for the CNDA and various other XNAT installations. We > recently updated some of o

[Freesurfer] Any updates on recon-all GPU support?

Anyone manage to successfully configure recon-all to run with -use-gpu for recent cuda toolkit versions? I realize cuda support has ceased over the past few years for Freesurfer, but have there been any successful builds for CUDA toolkit versions 6 and up? I am currently looking to configure cud

Re: [Freesurfer] Any updates on recon-all GPU support?

On 22 June 2016 at 18:17, Derek Pisner wrote: > Anyone manage to successfully configure recon-all to run with -use-gpu for > recent cuda toolkit versions? I realize cuda support has ceased over the past > few years for Freesurfer, but have there been any successful builds for CUDA > toolkit ver

Re: [Freesurfer] registering to fsaverage

Hi Bruce Is there is a way to set the probability of an overlay between 0 and 1? Would this have to be done when creating the overlay using mri_vol2surf? thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Mon, Jun 20, 2016 at 12:11 PM, Bruce

Re: [Freesurfer] Any updates on recon-all GPU support?

Hi Richards, Thanks for the very quick reply. Good to know that someone has successfully compiled GPU binaries for newer CUDA versions. I took a quick look at the developer's guide for building the cuda binaries from source, but it seems like a very involved process? Do your compiled binaries

Re: [Freesurfer] Any updates on recon-all GPU support?

On 22 June 2016 at 19:32, Derek Pisner wrote: > Thanks for the very quick reply. Good to know that someone has successfully > compiled GPU binaries for newer CUDA versions. I took a quick look at the > developer's guide for building the cuda binaries from source, but it seems > like a very i

Re: [Freesurfer] registering to fsaverage

Hi Trisanna if you are using mri_average you can give it -p as the first argument and it will compute a percent at the end Bruce On Wed, 22 Jun 2016, Trisanna Sprung-Much wrote: Hi Bruce Is there is a way to set the probability of an overlay between 0 and 1? Would this have to be done when

Re: [Freesurfer] registering to fsaverage

thanks Bruce - I had found that option for my fsaverage maps and it worked. What about if I am importing probability maps formed as .mnc and creating overlays from them? The percentages seem to be very odd for min and max threshold. Trisanna -- Ph.D. Candidate McGill University Integrated Progra

[Freesurfer] patch error

Hello all, I'm trying to make a patch and have run into the 'bad vertex' error. It's come up a few times on the listserv, but I never saw a public resolution. One possible source of errors is that I had to do a manual correction in FreeView, including a 'remove intersections' in FreeView. However,

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

Hi Bronwyn, You raise a good point. You can consider creating a cortical mask using aparc+aseg.mgz and use that to mask the networks. However, another approach (which might be more accurate) is to take cortical networks in fsaverage space and transform to your subject's surface and then transform

[Freesurfer] FSGD error: class Input not defined

Dear Freesurfer experts, I am trying to perform the resting state fMRI analysis as in: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough I got stuck with the STEP8, when I tried to use my own fsgd file. I tried to test for two group difference, no covariance as in:

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

Hi Thomas, Thanks for your reply. The fsaverage directory I have for fs v 5.1 does not include the lh and rh Yeo2011_7Networks_N1000.annot files. I only have this in the 5.3 version of fsaverage. Can I still use the 5.3 version annot files or would I need a seperate set processed with version

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

You should be able to use the 5.3 version. Regards, Thomas On Thu, Jun 23, 2016 at 2:16 PM, Bronwyn Overs wrote: > Hi Thomas, > > Thanks for your reply. > > The fsaverage directory I have for fs v 5.1 does not include the lh and rh > Yeo2011_7Networks_N1000.annot files. I only have this in the

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

Thanks very much Thomas. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au Follow