[Freesurfer] dcmunpack command not found

External Email - Use Caution Hello, i have been trying to use the dcmunpack command and it always says command not found, i searched in the archives and some said it could be because the tcsh or csh wasnt installed however i have both installed (which tcsh and which csh return t

[Freesurfer] PET image format

External Email - Use Caution Dear experts! I am using PetSurfer and I have a PET dataset that is in ecat format (.v). I would like to convert the images to nifti format to start processing the data. What function can I use to convert the images? How can I check that the left-right

Re: [Freesurfer] dcmunpack command not found

Hello Claudia, It may be due to FreeSurfer not being sourced properly within your terminal. If you are working in a Cshell environment, source FreeSurfer with these commands: You can make sure you’re in Cshell by typing tcsh. setenv FREESURFER_HOME /freesurfer source $FREESURFER_HOME/SetUpFreeS

[Freesurfer] mri_vol2surf

External Email - Use Caution Hello, I have a couple of questions: 1. I asked before how to obtain AAL labels on Freesurfer. I am following your instructions, but I don't know how to load the AAL onto my T1w template to ensure everything aligns 2. Secondly, I tried to run mri_vol2

Re: [Freesurfer] Mean thickness estimation

Hi Stephanie I think that is always a good idea, unless for some reason it isn’t possible Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Stephanie K Sent: Thursday, November 19, 2020 2:14 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mean thickness es

Re: [Freesurfer] extracting beta coefficients and p-values {Disarmed}

External Email - Use Caution Hi Dr. Greve, Sorry to bring this back up, but I didn't fully understand how to calculate the variance in order to get the confidence intervals for each covariate, so I wanted to double check the steps. A colleague in the lab is helping me to derive the

Re: [Freesurfer] Group Analysis

Hi Sara, You may want to use asegstats2table. Follow these links to learn more about mris_preproc, mri_glmfit, and asegstats2table: http://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit?highlight=%28asegstats%29 https://surfer.nmr.mgh.harvar

Re: [Freesurfer] Group Analysis {Disarmed}

External Email - Use Caution Hi Jocelyn, The links talk about measuring thickness and I’m trying to do a volumetric Group analysis using Glm. I was wondering if you could point me towards that. Sara On Thursday, November 19, 2020, Mora, Jocelyn S. wrote: > Hi Sara, > > You ma

Re: [Freesurfer] Group Analysis {Disarmed}

Sorry, meant to say instead of --meas thickness From: Greve, Douglas N.,Ph.D. Sent: Thursday, November 19, 2020 1:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] Group Analysis {Disarmed} Just use --meas volume instead of --meas area _

Re: [Freesurfer] Group Analysis {Disarmed}

Just use --meas volume instead of --meas area From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Sara Lyn Sent: Thursday, November 19, 2020 12:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] Group Analysis {Disarmed} External Email

[Freesurfer] Issue with custom label

External Email - Use Caution Hello, After running mri_vol2label I created a custom label named test.label. When I try to load the label onto lh.pial, I receive the following error: "Could not load label from ". The file is saved within the path folder itself. Within the terminal I

Re: [Freesurfer] Mean thickness estimation {Disarmed}

External Email - Use Caution Hi Bruce, Is it also necessary to remove outliers (eg. 3 SD from the mean) for Freesurfer structural measures of MRI images that have been visually inspected as a further data cleaning step? I really appreciate your help. Thanks On Thu, Nov 19, 202

Re: [Freesurfer] Mean thickness estimation {Disarmed}

Hi Stephanie Sorry, I think I misunderstood. If you have visually inspected the analysis results and think that they are accurate then you definitely should leave those subjects in Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Stephanie K Sent: Thursday, November 19,

[Freesurfer] Hypothalamic module fixed

Dear all, The problem in the volume estimates provided by the tool for segmentation of the hypothalamus and its nuclei has been fixed in the latest development version. Just to recap: if you downloaded the development version of FreeSurfer between September 18th and yesterday, the hypothalamic m

Re: [Freesurfer] -openmp vs -threads, -parallel options in recon-all

External Email - Use Caution Thanks. Just to confirm, the openmp reflects threads and not cores? In other words, on we have a 4 core machine with hyperthreading, so with 4 cores we have 8 threads available. In that scenario, would the -openmp 4 option reflect 4 cores/8 threads

[Freesurfer] License error on Windows Subsystem for Linux

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to use freesurfer 5.3.0 on Windows Subsystem for Linux (Ubuntu 20.04), but I got license error message as described below: -- ERROR: I

[Freesurfer] MNI Coordinates from the Destrieux Atlas and aseg.stats ROIs

External Email - Use Caution Hello Freesurfer developers, For the purpose of reporting ROIs in my article, I need a list of X Y Z coordinates in MNI space for all the labels in the Destrieux atlas. I came across a previous post with the following steps: Step 1: mri_annotation2l