Re: [Freesurfer] amygdala segmentation atlas influence

2018-10-02 Thread Iglesias Gonzalez, Eugenio
External Email - Use Caution Thanks, Raj. I’d argue that, if the volumes of the nuclei were completely driven by the global volume of the amygdala, e.g., in an extreme case, V_nuc = alpha x V_whole, then the effect size of the nucleus at hand would be the same as for the whole

Re: [Freesurfer] Mac OS free surfer instalation

2018-10-02 Thread Hoopes, Andrew
Hi Eduard, we’ll need some more information. What kind of errors are you running into? Are you trying to download v6.0 or the dev version? best Andrew From: on behalf of "Vasile, Eduard" Reply-To: FS Help Date: Tuesday, October 2, 2018 at 4:31 PM To: FS Help Subject: [Freesurfer] Mac OS fr

[Freesurfer] Mac OS free surfer instalation

2018-10-02 Thread Vasile, Eduard
Dear Free Surfer Developers, I have installed freesurfer on my laptop and followed all steps you suggested online for a mac computer but freesurfer is still not working. Could you please assist me in installing it? Kind regards Eduard ___ Freesurfer

Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

2018-10-02 Thread Greve, Douglas N.,Ph.D.
The command is being run from inside of a C-file using the system command, so there is no way for them to change it On 10/02/2018 01:43 PM, Dicamillo, Robert wrote: > It may be complaining about >& for redirection.  Try using 2>&1 instead. > >> On Oct 2, 2018, at 4:56 AM, k3...@free.fr

Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

2018-10-02 Thread Dicamillo, Robert
It may be complaining about >& for redirection. Try using 2>&1 instead. On Oct 2, 2018, at 4:56 AM, k3...@free.fr wrote: sh: 1: Syntax error: Bad fd number ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n

Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

2018-10-02 Thread Greve, Douglas N.,Ph.D.
Sorry, I meant to change your default shell. That command is being run using the system() command from inside of a c-program, which undoubtedly starts your default shell. Just see if it works. On 10/02/2018 10:36 AM, k3...@free.fr wrote: > External Email - Use Caution > > I am using bas

Re: [Freesurfer] Overlay electric field distribution on pial surface

2018-10-02 Thread Meusen - Klooster, D.C.W.
External Email - Use Caution Yes, I made a (pretty stupid) mistake in the coregistration. The overlay is working perfectly now. Only for the visualization, is it possible to set my colorbar from 1 (blue) to approx 200 (red)? Can I get rid of the 'double' color bars for positive

Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

2018-10-02 Thread k3ops
External Email - Use Caution I am using bash shell but I tried with many others as mentioned in my first post (zsh, tcsh, csh, sh) and nothing worked so far... - Mail original - De: "Douglas N. Greve,Ph.D." À: freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 2 Octobre 2018

[Freesurfer] Moving VOI to FreeSurfer Space

2018-10-02 Thread Sarosh, Cyrus
External Email - Use Caution Hello FreeSurfer Experts, I'm trying to find the best method and command to move a hand drawn VOI in original MRI space to FreeSurfer space. These scans have already been ran through the entire FreeSurfer process and the hand drawn VOIs have already

Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

2018-10-02 Thread Greve, Douglas N.,Ph.D.
What shell are you using? Try using cshell or tcshell to see if it works. On 10/2/18 4:56 AM, k3...@free.fr wrote: > External Email - Use Caution > > Hi FS team, > > I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and everything > runs well for most of the subjects that I

Re: [Freesurfer] analyzing and reporting parcellation results

2018-10-02 Thread Greve, Douglas N.,Ph.D.
Unless you have an a priori hypothesis about an effect in a particular ROI, then you need to correct for multiple ROIs On 10/2/18 7:25 AM, Tamir Eisenstein wrote: External Email - Use Caution Hi FS experts, When I'm analyzing regional volumes/thickness using one of the atlases ROI's pa

Re: [Freesurfer] Convert sig.cluster.mgh file to a binary mask in .nii format

2018-10-02 Thread Greve, Douglas N.,Ph.D.
assuming this is a surface-based analysis, then you'll need to run mri_surf2vol to convert it into a volume using fsaverage as the subject. Run it with --help to get more info On 10/2/18 5:14 AM, Carme Uribe Codesal wrote: External Email - Use Caution Dear FreeSurfer users, I am tryin

[Freesurfer] analyzing and reporting parcellation results

2018-10-02 Thread Tamir Eisenstein
External Email - Use Caution Hi FS experts, When I'm analyzing regional volumes/thickness using one of the atlases ROI's parcellation, and for example want to compare all the ROI's between two groups, should I correct for multiple comparisons (for the entire number of the atlas ROI

[Freesurfer] Convert sig.cluster.mgh file to a binary mask in .nii format

2018-10-02 Thread Carme Uribe Codesal
External Email - Use Caution Dear FreeSurfer users, I am trying to extract a binary mask from the file cache.th13.abs.sig.cluster.mgh (I want a ROI from the clusters p<0.05) and convert this mask into a .nii file. I have found a previous message in the forum that reccomends using

[Freesurfer] Error during decompression of DICOM JPEG compressed series

2018-10-02 Thread k3ops
External Email - Use Caution Hi FS team, I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and everything runs well for most of the subjects that I process so first thanks for this great tool. I am facing an issue with a JPEG compressed DICOM series that I am not ab