Re: [Freesurfer] Freeview quit unexpectedly

surfer@nmr.mgh.harvard.edu Cc: Addison, Reuben Subject: Re: [Freesurfer] Freeview quit unexpectedly External Email - Use Caution By crashing from the GUI do you mean that you when you try to navigate to open a file, e.g., $SUBJECTS_DIR/bert/mri/brain.mgz, using the freeview GUI Open->

Re: [Freesurfer] Freeview quit unexpectedly

Please ignore the previous email. Apparently when I type the command it works but the issue is with using the gui Reuben A. Get Outlook for iOS<https://aka.ms/o0ukef> From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Addison, Reuben Sent:

Re: [Freesurfer] Freeview quit unexpectedly

@nmr.mgh.harvard.edu Cc: Addison, Reuben Subject: Re: [Freesurfer] Freeview quit unexpectedly External Email - Use Caution Please try the following: 1) Open a new terminal window and run the bash shell as, $ arch -arm64 /bin/bash 2) set FS_LICENSE to point to your license.txt file. Say it is in your

[Freesurfer] Freeview quit unexpectedly

I am trying to use freeview to load a volume. I am using freesurfer 7.3.2 on the new M1 mac pro with ios ventura. Please view below the error report I am getting. Is there any work around it? I have tried different volumes but same issues Translated Report (Full Report Below)

Re: [Freesurfer] acompcor in fsfast

, specify the number of components you want when specify -nuisreg On 10/26/2022 6:29 PM, Addison, Reuben wrote: Hi, I am running resting State functional connectivity and I want to run everything in freesurfer and fsfast. I wanted to know is it is possible to run acompcor in fsfast. If so, how do I

[Freesurfer] acompcor in fsfast

Hi, I am running resting State functional connectivity and I want to run everything in freesurfer and fsfast. I wanted to know is it is possible to run acompcor in fsfast. If so, how do I go about it. Thanks. Get Outlook for iOS

[Freesurfer] B0 distortion correction (a clearer question)

I sent a question earlier on but I do don’t think I was clearer the first time. I am trying to do a distortion correction using (epidewarp.fsl) epidewarp.fsl \ --mag mag.nii.gz \ --dph dphase.nii.gz \ --tediff YOUR_TE_DIFF --esp YOUR_ESP \ --vsm bold/b0dcmap.nii.gz The issue we

[Freesurfer] Creating a seed sphere using MNI coordinate

1. I am planning to add a seed sphere 6mm cortical and 4 millimeters subcortical and I want to do this with Fsfast using given MNI coordinates from a previous study. I am wondering if there is a command on fsfast to achieve that, I have gone through the connectivity analysis but couldn't

[Freesurfer] B0 distortion correction using 2. FSL epidewarp script

Hi, I am new to fsfast and I trying to create a field map using the AP and PA spin echo maps for B0 distortion correction using the FSL epidewarp script I have two fieldmaps PA_spinecho.nii and AP_spinecho.nii 1. First I want tow know if my code below is about right epidewarp.fsl --mag

Re: [Freesurfer] Freeview quits unexpectedly on macOS Big Sur

Sara, do you have a double screen by any chance ? Reuben A. Get Outlook for iOS From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Sara Sanchez-Alonso Sent: Monday, August 15, 2022 5:07:01 PM To: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Parcellation issue

lation issue External Email - Use Caution Hi Reuben, What template are you trying to use? Regards, Thomas On Tue, Aug 9, 2022 at 8:39 PM Addison, Reuben mailto:raddi...@mghihp.edu>> wrote: I want to use a different template apart from the MNI for my

[Freesurfer] Parcellation issue

I want to use a different template apart from the MNI for my parcellation (Yeo_JNeurophysiol11_FreeSurfer.zip). Below are the instructions given in the readme. My question is – do I need to run this code before Recon-all or after In terminal (ASSUMING shell is bash), a) "cd" to unzipped

Re: [Freesurfer] Rookie question

I have a rookie question regarding free surfer after going through the excellent course on youtube First time I know the free surfer does the reconstruction on the anatomical scan (eg., T1t1_mprage_sag_p2_iso.nii) I see 3 other files in my data that were never used in the tutorials