[Freesurfer] STC - Multiband

2023-01-06 Thread Asa Borzabadi Farahani
External Email - Use Caution Hi, I am using multiband = 4 and according to the dicom files, my slice timing is as below.\ My question is if it is correct to do “-stc –odd “ & “-ngroups 4” in the preproc-sess command? Thank you so much "SliceTiming": [ 0,

Re: [Freesurfer] recon-all terminates with error

2023-01-06 Thread MANSON ERIC NAAB
External Email - Use Caution Thank you for your quick response. Please, can you kindly assist me with freesurfer input image template for sT1-weighted? How do I solve this orientation problem? Thank you. On Fri, 6 Jan 2023, 14:34 Huang, Yujing, wrote: > It looks like there is

Re: [Freesurfer] recon-all terminates with error

2023-01-06 Thread Huang, Yujing
It looks like there is a problem with your input dicom file - image orientation tag is missing. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of MANSON ERIC NAAB Sent: Thursday, January 5, 2023 11:15 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all terminates with

Re: [Freesurfer] How to convert surface-based atlas to annotation?

2023-01-06 Thread Huang, Yujing
Hi Andy, Thanks for the information. The error message that you are getting is actually from GIFTI library. I'm wondering if any other programs using the same library can parse the .gii correctly. I downloaded these files from the site: shen_2mm_268_parcellation.nii.gz 395091.R.func.gii 395091