Re: [Freesurfer] external WM and GM masks as input to recon-all?

Hi Shadia, How did you make the externally-derived ribbons? Can you please send us your recon-all.log and your subject directory so we can take a look? https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange Thanks, Bram From:

Re: [Freesurfer] recon-all exited with error

Hi there I uploaded these last week to the file drop and used Bruce's email as it said it requires a ".nmr.mgh.harvard.edu" email type. Please let me know if you received icbm-202 and icbm-205 as tar.gz files. As I mentioned, I was able to get surfaces for both of these but they seemed to end

Re: [Freesurfer] [CVS_register] Warp field reading through Matlab

Hi Stefano Lilla is going to be out of touch for a while I expect. Have you downloaded the FreeSurfer source code? That might be a good place to start. I think you can also load a .m3z warp into freeview and it will display it as a 3-frame volume. I think the representation is that we keep

Re: [Freesurfer] Loading talairach-space images into FSL

I've never used FSLeyes so I can't say On 01/23/2018 01:05 PM, Helen Beaumont wrote: > Hi > > I have a series of T1 images that I have transformed in Freesurfer to > .nii.gz images in talairach space with mri_convert -at > transforms/talairach.xfm. I am using the skull-stripped image brain.mgz >

Re: [Freesurfer] Value of ROIs different between FreeSurfer versions?

Hi Kaley no, it is inevitable that there will be differences as we are always trying to improve the algorithms. cheers Bruce On Tue, 23 Jan 2018, KALEY E ELLIS wrote: Hello FreeSurfer Developers, I am extracting ROIs of cross-sectional data using FreeSurfer v6.0.  We looked at this data

[Freesurfer] [error] no installation candidates for curl

Dear FreeSurfer experts, I am trying to perform hippocampal subfield segmentation with FreeSurfer 6. I followed the instructions found on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields which said that I first need to download Matlab Runtime. Which brought me to this

[Freesurfer] Loading talairach-space images into FSL

Hi I have a series of T1 images that I have transformed in Freesurfer to .nii.gz images in talairach space with mri_convert -at transforms/talairach.xfm. I am using the skull-stripped image brain.mgz produced by recon-all. When I view them in freeview they look well-registered, and similarly

Re: [Freesurfer] recon-all error

Try setting the FS_LOAD_DWI env var to 0, eg, setenv FS_LOAD_DWI 0 or export FS_LOAD_DWI=0 On 01/23/2018 10:43 AM, Bruce Fischl wrote: > > > > we don't have much experience with it. Can you cc the FS list so that > others can answer? I'll do so on this email. Maybe try some other tool > for

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Yes, it solves medial_wall label problem but not mri_aparc2aseg error.log. I attached you in a previous message: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56610.html Many thanks, M del Mar ___ Freesurfer mailing list

[Freesurfer] Value of ROIs different between FreeSurfer versions?

Hello FreeSurfer Developers, I am extracting ROIs of cross-sectional data using FreeSurfer v6.0. We looked at this data preliminarily about 2 years ago using FreeSurfer v5.3. It looks like there are slight differences in the values of the same subject (see below). Do you know the reason for

Re: [Freesurfer] recon-all error

we don't have much experience with it. Can you cc the FS list so that others can answer? I'll do so on this email. Maybe try some other tool for conversion? If recon-all fails it is not surprising that mri_convert also fails since they use the same DICOM code cheers Bruce On Tue, 23 Jan

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Dear Bruce, Thank you very much for your kind help! Best regards - Mail original - De: "Bruce Fischl" À: "Freesurfer support list" Envoyé: Lundi 22 Janvier 2018 16:12:10 Objet: Re: [Freesurfer] freesurfer segmentation:

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

I’ve never tried. Koen/Oula, what do you think? -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Gabor Perlaki