Re: [Freesurfer] How to edit GM when WM is ok

2021-04-08 Thread Fischl, Bruce
Hi Carolin I think our lab manager Leah Morgan (ccd) is going to find an RA to take a look. Leah: has anyone had a chance yet? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Caroline Chwiesko Sent: Thursday, April 8, 2021 3:52 PM To: Freesurfer support list Subject:

Re: [Freesurfer] How to edit GM when WM is ok

2021-04-08 Thread Caroline Chwiesko
External Email - Use Caution Hello Bruce, I haven't heard back from you so I just wanted to follow up and ask if you had the chance to look at the data that I uploaded. Cheers Carolin On Mon, Mar 29, 2021 at 4:01 PM Caroline Chwiesko wrote: > Because the dataset is already

Re: [Freesurfer] mri_convert problem

2021-04-08 Thread Hoopes, Andrew
Have you made sure that you have read permission to open those files? What is the output of `ls -l asta.mgh`? And asta.nii doesn’t seem to be a file in your working directory. Best, Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Pierpaolo Croce Date: Thursday, April 8,

Re: [Freesurfer] thalamic nuclei segmentation

2021-04-08 Thread Iglesias Gonzalez, Juan E.
Dear Sara, You can download Freesurfer 7, install it side by side with FreeSurfer 6, and run the thalamic module on the already reconned subjects. Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Sara

[Freesurfer] Decompressed problem during reconall

2021-04-08 Thread Banu Femir
External Email - Use Caution Dear FreeSurfer Developers, I've a problem that cannot solve for the last week. I am using virtual box, FS7 on my windows. I run reconall for Bert and checked that it is working.I have an MRI scan of sepstic patients that I got via CD, these are DICOM

[Freesurfer] thalamic nuclei segmentation

2021-04-08 Thread Sara PONTICORVO
External Email - Use Caution Hi Freesurfer experts, I processed ~150 subjects with freesurfer v6 (recon-all) and I was wondering if it is possible to use the script for the segmentation of the thalamic nuclei on these subjects. I know this part of the processing is now integrated