[Freesurfer] acces to virtual machine archive

External Email - Use Caution Hello, I have just downloaded the virtual machine and ubuntu package. Could you send me a password for unpack archive with virtual machine image, and for ubuntu account? Thanks so much in advance! ___ Freesur

[Freesurfer] Request: Password VirtualBox Vm Images

External Email - Use Caution Dear all, I would like to kindly ask for the password related to the VM zip archive: https://secure-web.cisco.com/1f7WVlIuUEn_Vllgaj670_9Zm1yN5Kl0O5jr8VA3slmuHCi0ayOLU0D8lg6uA4oAh3LEWrrr-MvAi_m1NQ6Loo-cv50TtO9lErg7hHVTLwxFygKiwFoVX2UJJ5Q1NOKCo_C3v53

Re: [Freesurfer] Segmentation fault (core dumped)

External Email - Use Caution As Yujing said, the 5.1.0 release is quite old (dating back to CentOS4) and binary backwards compatibility cannot be expected to work indefinitely going forwards to newer versions of the OS.  I ran a simple mri_surf2surf command from 5.1.0 on CentOS7

Re: [Freesurfer] Fwd: Segmentation fault (core dumped)

Hi Tracy, I looked at your recon-all.log. There are total of 19 runs. The first 4 runs from 2015 and 2016 finished without errors. They were all run on hippocampus.umd.edu. The later failed ones with segmentation fault were run a different machine - seahorse.umd.edu. Since you are using Frees

[Freesurfer] mri_glmfit with age-squared

External Email - Use Caution Hello Freesurfer experts, I am attempting to run the command mri_glmfit --y lh.RBS_ADRC_N0_control.10.mgh --fsgd RBS_ADRC_APOE_age22.fsgd dods --C APOE_ageINT.mtx --surf fsaverage lh --cortex --glmdir lh.RBS_ADRC_N0.glmdir On this .fsgd file: “RBS_

Re: [Freesurfer] Substantia nigra segmentation status

External Email - Use Caution Good luck. It requires a 7T to separate the compacta and reticulata. Localizing the the substantia nigra is impossible with standard MPRAGES but can be done if you modify the sequence or use a adequate T2 . There are papers that discuss how to locali

Re: [Freesurfer] recon-all not parcellating

Hi Carlos, Can you send recon-all.log as attachment? So, we can have a better understanding of what happened. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Carlos Estévez Fraga Sent: Thursday, March 9, 2023 9:33 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesur

[Freesurfer] recon-all not parcellating

External Email - Use Caution Dear Freesurfer team, I am trying to run recon-all -all in the cluster but unfortunately I am unable to obtain the parcellated images (exact command is recon-all -parallel -openmp $NSLOTS -s ${j} -i ${j}_corrected.nii.gz -all -cw256) I have run the s

Re: [Freesurfer] freesurfer could not parse freeview-loadable surface label

External Email - Use Caution Hi Yujing I figured it out – it turns out the R package shifts vertex indices by 1 by default, I was able to fix the problem by changing the option to stop the index adjustment because I was merging information from two recon-all outputs so the vert

[Freesurfer] password to unzip virtual machine

External Email - Use Caution I would like the password to unzip the virtual machine installation -- Ing. Pierpaolo Croce, PhD. Institute for Advanced Biomedical Technologies - ITAB and Department of Neuroscience and Imaging University of Chieti "G. D'Annunzio" Via dei Vestini, 3