Re: [Freesurfer] FreeSurfer load nifti error

External Email - Use Caution Dear Dr. Greve, This happens on all the MEG inputs I've tried not just one or two (I'm using files/data from the OMEGA dataset). I've put some print statements in the  load_nifti.m file to see the nitemsread and nvoxels variables that (I think) seem

[Freesurfer] Correlating two modalities in group-level surface-based analyses

External Email - Use Caution Hello, Does Freesurfer offer the option for group-level surface-based vertex-wise analyses comparing two imaging modalities? For example, I want to find clusters of vertices where cortical thickness and a PET, DTI, or fMRI measure mapped onto the

Re: [Freesurfer] Problem with quantifyHAsubregions.sh

Please try the command without the -4393 because now the code believes that -4393 is the output text file and testhippo.txt is the subjects directory… Cheers, /E -- Juan Eugenio Iglesias http://www.jeiglesias.com From: Georgina Angelopoulou Date: Thursday, January 26, 2023 at 1:02 PM To:

[Freesurfer] Postdoc Position in Developmental/Educational Neuroscience at Vanderbilt

External Email - Use Caution The Education and Brain Sciences Research Lab

[Freesurfer] Passcode of Ubuntu 7z file for VirtualBox

External Email - Use Caution Hi! I'm installing the VirtualBox version of Freesurfer (Ubuntu 18, the FS_7_2_0_Ubuntu_18_04_06.ova.7z file), and I would like to request the pass code to unzip the .ova file. Thank you, Regards, --

[Freesurfer] MGH35 template in tracula

External Email - Use Caution Quick question - I'm looking for the T1 image that goes along with (i.e. in same space, or at least in same participants) as the MGH35_HCP_FA_template image which is used in TRACULA? Does anyone know where I can find this? Thanks! Mark

Re: [Freesurfer] Problem with quantifyHAsubregions.sh

External Email - Use Caution Dear Eugenio, Thank you for your kindly reply. Actually, I tried both options and neither worked. When I renamed one subject and ran the following command, an error occurred. Please see below: Georginas-MacBook-Pro:ALBION georginaangelopoulou$

[Freesurfer] trac-all error

External Email - Use Caution Hi: I tried to use trac-all using following syntax: trac-all -prep -s name -i SIEMENS_DICOM_256_GRADIENTS_TRACTOGRAPHY_FILES_PATH and I got the following error message: "ERROR: for B0 distortion correction with reverse-polarity DWIs ERROR: or for

Re: [Freesurfer] FreeSurfer load nifti error

Does this happen on every volume or just with this one. If just this one, then it is probably a problem with the volume itself and not the code On 1/25/2023 9:15 PM, Siamak Sorooshyari wrote: External Email - Use Caution Dear FreeSurfer, I am using the FieldTrip software to process

Re: [Freesurfer] FS FAST

Something like set MATLAB=/usr/pubsw/common/matlab/8.4 Now that I think about it, you may be able to use the compiled version of fsfast. There are only two programs that use matlab, mkcontrast-sess and selxavg3-sess. You can try adding -bin on to both of those to use the compiled version

Re: [Freesurfer] Extracting Yeo network volumes for individual subjects

Hi, Here are two related postings from the list: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg60854.html https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64872.html I hope they are helpful. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf