Re: [Freesurfer] T2 FLAIR Images

2023-09-07 Thread Alan Francis
the new surfaces. For example: > > > > recon-all -s subjectname -T2 /path/to/T2_volume -T2pial -autorecon3 > > “ > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.

Re: [Freesurfer] T2 FLAIR Images

2023-09-01 Thread Huang, Yujing
Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Alan Francis Sent: Friday, September 1, 2023 5:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] T2 FLAIR Images External Email - Use Caution I tried the following command with the --flair flag but it di

Re: [Freesurfer] T2 FLAIR Images

2023-09-01 Thread Alan Francis
External Email - Use Caution I tried the following command with the --flair flag but it did not work: [DMK6P4G6FJ1G:~/SUBJECTS/NCANDA_S00033] alanfrancis% recon-all -s S00033 -i t1.nii.gz -i t2.nii.gz --flair -all ERROR: Flag --flair unrecognized. Could you please tell me where

Re: [Freesurfer] T2 FLAIR Images

2023-08-22 Thread Douglas N. Greve
External Email - Use Caution Sorry, you need to pass it to recon-all with --flair or --T2 On 8/21/2023 1:19 PM, Alan Francis wrote: External Email - Use Caution Hi Doug: Thanks for your reply. I am trying to set the T1.nii.gz as 001.mgz and the T2.nii.gz as 002.mgz. S

Re: [Freesurfer] T2 FLAIR Images

2023-08-21 Thread Alan Francis
External Email - Use Caution Hi Doug: Thanks for your reply. I am trying to set the T1.nii.gz as 001.mgz and the T2.nii.gz as 002.mgz. So will the following command work? mri_convert t2.nii.gz --flair 002.mgz or is it: mri_convert --flair t2.nii,gz 002.mgz Thanks, Alan On Su

Re: [Freesurfer] T2 FLAIR Images

2023-08-20 Thread Douglas N. Greve
External Email - Use Caution How did you set up the T2? Did you set 001.mgz to be the T1 and the 002.mgz to be the T2FLAIR? If so, that will not work. You should pass the FLAIR with the --flair flag. recon-all will register them together. Or do you just want to register them outs

[Freesurfer] T2 FLAIR Images

2023-08-14 Thread Alan Francis
External Email - Use Caution Good evening Doug et all: I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: I opened the T2 image on Freeview. It looks normal. I tried running a second brain. Same probl

[Freesurfer] T2 FLAIR images

2023-08-11 Thread Alan Francis
External Email - Use Caution Good evening all: I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: Thanks, Alan [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid NCANDA_S00042/ fs-check-v

Re: [Freesurfer] T2/FLAIR images longitudinal stream

2013-05-08 Thread Martin Reuter
Hi Donald, the T2/FLAIR should also work for longitudinal processing (just pass -T2pial along in cross and long). Long grabs the image from the cross run and improves it surfaces. Best, Martin On 04/30/2013 06:46 PM, MCLAREN, Donald wrote: > Martin and others, > > As the T2/FLAIR image is only

[Freesurfer] T2/FLAIR images longitudinal stream

2013-04-30 Thread MCLAREN, Donald
Martin and others, As the T2/FLAIR image is only available for cross-sectional processing; if we are doing a longitudinal study, is there any advantage of using the T2/FLAIR image? Will the improved pial surface can transferred to the base and long surfaces? Best Regards, Donald McLaren =