Re: [Freesurfer] mri_compute_volume_fractions

External Email - Use Caution Thanks Antonin, I will probably try with version 6. Thanks, Dhivya From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Antonin Skoch [a...@ikem.cz] Sent: Thursday, Apr

Re: [Freesurfer] Using mprage flag.

if you have an mprage it usually helps a bit cheers Bruce On Thu, 26 Apr 2018, Aaron Tanenbaum wrote: External Email - Use Caution Hello FreeSurfers When should I use the MPRAGE flag for recon-all?  Aaron Tanenbaum ___ Freesurfer

[Freesurfer] Using mprage flag.

External Email - Use Caution Hello FreeSurfers When should I use the MPRAGE flag for recon-all? Aaron Tanenbaum ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

[Freesurfer] Comparison between T1 only recon-all and T1 + FLAIR recon-all

External Email - Use Caution Hello, In the past we have only used the T1 image as input for recon-all. However, we are now also acquiring a FLAIR image and were thinking of using both for new studies. Does anyone have any data on the differences/advantages of using FLAIR images

Re: [Freesurfer] mri_compute_volume_fractions

External Email - Use Caution Dhivya, this syntax works for me with version 6. With version 5.3.0 I am getting the same error mesage. I do not know how the correct syntax is with version 5.3.0. Antonin Skoch Yep , I am using "o" .I am running it on Ubuntu 16.04 and my freesurfe

Re: [Freesurfer] mri_compute_volume_fractions

External Email - Use Caution Yep , I am using "o" . I am running it on Ubuntu 16.04 and my freesurfer version is , freesurfer/5.3.0/bin/freesurfer mri_compute_volume_fractions --o test --regheader 002_S 002_S/mri/norm.mgz still I am getting , unknown option --o Trying to g

Re: [Freesurfer] aparcstats2table for white surface total area

If you just run aparcstats2table it should be in the table. I don't think there is a way to only get that value On 04/26/2018 11:20 AM, Sian Emma Davies wrote: > > External Email - Use Caution > > Hello, > > Forgive me, I’m new to FreeSurfer. I wish to collate values of white > surface

[Freesurfer] aparcstats2table for white surface total area

External Email - Use Caution Hello, Forgive me, I'm new to FreeSurfer. I wish to collate values of white surface total area from all my subjects into a single table, so that I can control for this in my analyses. I understand this value is in the aparc.stats files for each part

Re: [Freesurfer] mri_compute_volume_fractions

hmmm, are you sure you are using an "o" and not a "0"? And the --regheader syntax different than I thought, it requires two argments, a subject name and a template volume (if you are using the anatomical space, any of the conformed volumes such as the norm.mgz should be fine). For example, I ru

Re: [Freesurfer] mri_compute_volume_fractions

External Email - Use Caution mri_compute_volume_fractions --o test --regheader unknown option --o If I am not giving any input before arguments, it is not taking them. Thanks, Dhivya From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfe

Re: [Freesurfer] mri_compute_volume_fractions

just run the command as I sent it: mri_compute_volume_fractions --o test --regheader the aseg is the default name. You are putting it in the wrong place and it thinks the aseg is a registration file On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: >External Email - Use Caution > > I am

Re: [Freesurfer] mri_compute_volume_fractions

External Email - Use Caution I am getting same Error with many permutations of arguments, mri_compute_volume_fractions 002_S/mri/aseg.mgz --o test --regheader identity.nofile arg = 6 reading registration file 002_S/mri/aseg.mgz regio_read_register(): Success Error reading inpla

Re: [Freesurfer] recon-all with T1 and T2 images

Hi Heidi it is easy to imagine there being a regionally specific bias between processing so you are better off doing them all the same way cheers Bruce On Wed, 25 Apr 2018, Heidi Lindroth wrote: External Email - Use Caution Hello,  I have processed the majority of my T1 i