[Freesurfer] Again: Confusion about discrete variable in the FSGD file

External Email - Use Caution Dear FreeSurfer users, I am not sure whether my question was posted, so I will just ask it again. I am interested in cortical thickness differences between preterm (PT) and fullterm (FT) individuals. I have used DODS with mri_glmfit and wanted to

[Freesurfer] Brain Volume Extraction

External Email - Use Caution Hello, I am new to FreeSurfer and I have a question regarding brain volume extraction. When I run recon-all on a patient, once the entire process is done, I get the brain volume levels from aseg.stats. I would like to know if there are any ways to d

Re: [Freesurfer] mri_label2label issues

Try this: register the old/1st recon to the second with bbregister --mov old/mri/nu.mgz --targ newsubject --t1 --reg reg.lta Map the old surface into the new space mris_apply_reg --lta reg.lta old/surf/lh.white newsubject/surf/lh.white.old Verify that the old surface overlays on the new volume Map

Re: [Freesurfer] tksurfer

You can use tksurferfv (this is a frontend for freeview that takes most of the original tksurfer options) On 11/3/2021 1:11 PM, Fischl, Bruce wrote: Hi Arian Tksurfer has been deprecated for a long time. Can you try freeview instead? Bruce *From:* freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] adding covariates to a longitudinal glmfit model

On 10/29/2021 10:39 PM, Zeng, Qi wrote: External Email - Use Caution Hi Experts, After completing long_mris_slopes to get the rate of change and then concatenating them into one.mgh file for group analysis (mris_preproc). I am finally getting to mris_glmfit. Got a couple of questi

Re: [Freesurfer] Confusion about discrete variable in the FSGD file

On 10/27/2021 11:39 AM, Douglas N. Greve wrote: Dealing with discrete variables as discrete is the way I would do it as you would not have any reason to think that there is some linear relationship between your the (arbitrary) values you assign to discrete variables and thickness. Age is no

Re: [Freesurfer] recon-all stuck at -fill on AWS batch processing

External Email - Use Caution Hi Xin, If I understand correctly, recon-all runs successfully in your docker container when testing it on an EC2 instance, but when trying to run the same container on AWS batch or fargate, it doesn't make it past the `-fill` step. Is that correct?

Re: [Freesurfer] Aseg and wm edits? + white/pial overlap near subcortical structures

On 10/29/2021 10:46 AM, Kang, Jee Won wrote: External Email - Use Caution Hello all, There are two topics I would appreciate your expert advice on: Topic 1: Aseg and wm edits I was going through the wiki and the archive of past inquiries and was unable to find a clear answer to

Re: [Freesurfer] Brain Volume Extraction

You could run it up to the skull stripping (-autorecon1), then compute the brain volume yourself from the skull-stripped image. You could also use samseg; samseg only takes an hour or so to run and outputs a measure of total intracranial volume, but you could also extract total brain volume fro

Re: [Freesurfer] Brain Volume Extraction

External Email - Use Caution Since I am using FreeSurfer v6 I do not have access to samseg. How can I compute the brain volume myself from the skull-stripped image? Get Outlook for iOS

Re: [Freesurfer] crash

External Email - Use Caution Hello, Thank you for your help! I have an old intel mac (not M1). I allowed Freeview to access all my disk. I also put the license file and run the export commands (but not sure if it useful to run freeview.app?). But still it crashes when I try to op

Re: [Freesurfer] recon-all stuck at -fill on AWS batch processing

External Email - Use Caution Dear Paul: Thank you so much for your quick response and we will test on your suggestion! Best regards Xin On Mon, Nov 8, 2021 at 1:15 PM Paul Wighton wrote: > External Email - Use Caution > > Hi Xin, > > If I understand correctly, recon-al

Re: [Freesurfer] mri_label2label issues

External Email - Use Caution Hi Doug THIS WORKED!!! Thank you so much for all your help! Trisanna -- From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Monday, November 8, 2021 1:35 PM To: freesurfer@nmr.mgh.h

Re: [Freesurfer] crash (on MacOS)

External Email - Use Caution Hello Nikolai, You could let us know what version of MacOS you are running, e.g., $ sw_versProductName: Mac OS X ProductVersion: 10.15.7 BuildVersion: 19H1419 I would try setting the environment variable FS_LICENSE to the absolute path of your lic

[Freesurfer] Matlab Runtime download error

External Email - Use Caution Greetings Freesurfer Team, I am working on a new Macbook with the M1 chip. So far, I've had little issue with installation (7.2.0) and running recon-all. I am trying to run the thalmic nuclei and brainstem segmentations in preparation for running TRACU

Re: [Freesurfer] Matlab Runtime download error (on MacOS)

External Email - Use Caution Hello Stephanie, If you installed 7.2.0 using the Mac pkg installer, then FREESURFER_HOME is /Applications/freesurfer/7.2.0.  If you installed elsewhere however, then change FREESURFER_HOME in the command below to the appropriate path for your setup

[Freesurfer] Clinical research coordinator positions at MGH - Boston

External Email - Use Caution Clinical Research Coordinator positions at the Department of Radiology, Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and H

Re: [Freesurfer] crash (on MacOS)

External Email - Use Caution Hello, Thanks a lot! When I do things like this, I am able to run freeview from the terminal and the nii file loads without any issue! When I run Freeview.app, by clicking on it in the mac os GUI, it crashes when I try to load the nii file. So that it