[Freesurfer] mask of premotor cortex and primary cortex

External Email - Use Caution Dear Freesurfer Developers, I have analyzed connectivity between striatum and different brain cortex with diffusion weighted MRI. I completed recon-all on all participants. *SHINui-iMac:~ shinsangho$ recon-all -s NOR86_AHJ -i ~/sangho/NOR86_AHJ/NOR86_A

[Freesurfer] Exporting ROI segmentation in T1 DICOM header

External Email - Use Caution Dear Freesurfer developers, Is it possible to export the ROI segmentations that are stored in ?h.aparc.a2009s.annot or ?h.aparc.annot files into the header of the DICOM file? I would like to open those files with corresponding segmentations in RayStati

Re: [Freesurfer] Exporting ROI segmentation in T1 DICOM header

External Email - Use Caution I meant to say "parcellations" instead of "segmentations". Regards, Vânia de Aguiar, PhD Assistant Professor in Neurolinguistics University of Groningen Faculty of Arts Oude Kijk in 't Jatstraat 26 Room 1315.0408 9712 EK, Groningen The Netherlands O

[Freesurfer] FS-FAST: cluster size from 1st level analysis

External Email - Use Caution Hi From the 1st level analysis of an fMRI study I'm trying to extract the size of the clusters of activation from each subject, but don't know how to go about this. I know that for the group analysis you can get the cluster sizes from the output from m

[Freesurfer] Main effect of sex for total surface area, but not for summed vertex-wise surface area

External Email - Use Caution Hello all Freesurfer experts! Through my analysis I found that, if I plot the "white surface total area" found in subjid/stats/?h.aparc.stats by sex, I as expected find that males have overall larger surface area as compared to females. When pl

[Freesurfer] Curvature estimation from Hessian

External Email - Use Caution Hi, I am trying to understand how exactly FreeSurfer estimates the curvature values from the white surface. From the mailing lists I understood that the white surface is modeled by fitting a second-order polynomial function and curvatures are estima

[Freesurfer] FreeSurfer freezing during processing.

External Email - Use Caution Hello FreeSurfer Developers, I have installed the FreeSurfer how described here https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport. I launch an Ubuntu terminal and stat a freesurfer application from an Ubuntu command line. [cid:4348455d-9967-4

Re: [Freesurfer] Exporting ROI segmentation in T1 DICOM header

Hi Vânia you can convert the aparc+aseg.mgz to nifti and find something that goes from there to dicom, but we don't at the moment support writing dicom, although I think Paul (ccd) has worked on it and might have something to add cheers Bruce On Thu, 3 Oct 2019, Correia de Aguiar, V.M. wr

Re: [Freesurfer] Curvature estimation from Hessian

Hi Philipp the Hessian is estimated at each vertex by doing a quadratic fit to the local surface as the height function over the tangent plane of all the vertices in a 2-neighborhood of that vertex. I'm not sure what the gradient vanishing is about, but the curvatures are just the eigenvalues

[Freesurfer] question about aparcstats2table

External Email - Use Caution Hi FreeSurfer experts, I want to converts a cortical stats file into a table by the aparcstats2table command. However, there are totally 500 subjects. And it is really hard to input subject numbers one by one. The Numbers are arranged in a regular wa

Re: [Freesurfer] Exporting ROI segmentation in T1 DICOM header

External Email - Use Caution Hi Vânia, You can use this repository to convert some FreeSurfer outputs to dicom. https://github.com/corticometrics/fs2dicom Unfortunately, the aparc+aseg is not supported at this time, only the aseg.mgz. -Paul On Thu, Oct 3, 2019 at 9:57 AM Bruce

[Freesurfer] Freesurfer's last version installation

Dear Freesurfers, We need to install the last version of Freesurfer, but we need to keep the wm edits that we made with version 5.3 How can this be done? Is there any specific command? Thanks a lot, Vale ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

[Freesurfer] Freesurfer - issue after installation in Linux

External Email - Use Caution Hi, I just installed freesurfer in Linux Ubuntu 14.04, and I got a critical (and strange) problem in the earlier tests of freesurfer (Example 2). Any help would be appreciated. Basically, when trying example 2 in instructions homepage I got the follow

Re: [Freesurfer] Freesurfer - issue after installation in Linux

External Email - Use Caution You need to install the tcsh shell: sudo apt-get install tcsh Best, Tim > On October 3, 2019 at 6:30 PM Tim Schäfer wrote: > > > You need to install the tcsh shell: > > sudo apt-get install tcsh > > Best, > > Tim > > > On October 3, 2019

Re: [Freesurfer] Question about using tkregisterfv to check registration

External Email - Use Caution Hi Doug, Thanks for your respond! I ran the the command with debug flag and figured out the problem. It is because I use a space in the name of the PET data directory. After removing the space character, tkregisterfv works great! But one PET image did

Re: [Freesurfer] Freesurfer's last version installation

Hi Vale I think it should happen by default, but definitely test it on one subject before you launch them all! Bruce On Thu, 3 Oct 2019, Barletta, Valeria wrote: > Dear Freesurfers, > We need to install the last version of Freesurfer, but we need to keep the > wm edits that we made with version

Re: [Freesurfer] Freesurfer - issue after installation in Linux

yes, depending on your hardware it can take >12 hours, particularly if you aren't using -openmp On Thu, 3 Oct 2019, Theotonio Pauliquevis wrote: External Email - Use Caution Hi,  Thanks for the prompt reply.  After I installed tcsh it did run successfully.  Since this fixing