[Freesurfer] error in hippocampal subfields and nuclei of amygdala segmentation

External Email - Use Caution Dear freesurfer experts, I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala with segmentHA_T1.sh command. I already run segmentation of hippocampal subfields and nuclei of amygdala several times, however, after segment

Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}

External Email - Use Caution Hi Martin, Thanks for the input! It worked perfectly. A follow up question: I understand that for T1 hippocampal subfield segmentation, Freesurfer has a longitudinal module for it (segmentHA_T1.long.sh) Does freesurfer have a longitudinal module

Re: [Freesurfer] Segmentation fault

External Email - Use Caution ​Hello Jon, Looks like you are already running with -debug and -allowcoredump option, and the shell limits do not look like they are too small to allow the coredump to be written. I don't know offhand if that coredump option causes a file to be

Re: [Freesurfer] Cortical Parcellation: ROIs not covering gray matter in depth direction

Hi Yixin check to see if the lh.pial and rh.pial surfaces are accurate. cheers Bruce On Mon, 29 Oct 2018, Yixin Ma wrote: External Email - Use Caution Hi, I’m writing to ask about cortical parcellation (Desikan-Killiany and Destrieux), which do not work well on my recent

Re: [Freesurfer] resampling data onto cortical surface

Hi Greg, yes, that sounds correct cheers Bruce On Mon, 29 Oct 2018, GREGORY R KIRK wrote: External Email - Use Caution there is some misunderstanding ? I said to resample onto the cortical surface not into a volume you say Use --s subject instead of --reg (run mri_vol2vol

Re: [Freesurfer] freeview libpng12.so.0 error

External Email - Use Caution ​Hello Ashesh, You need to install the "gdebi" command on your Ubuntu machine. Then download and install the libpng12 package from, http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb Then install that

[Freesurfer] freeview libpng12.so.0 error

External Email - Use Caution Dear FreeSurfer Team, I'm running FreeSurfer on a 64-bit Linux machine running Ubuntu 18.04 LTS. Here is my config: ashesh@ashesh-gpu:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Re: [Freesurfer] resampling data onto cortical surface

External Email - Use Caution there is some misunderstanding ? I said to resample onto the cortical surface not into a volume you say Use --s subject instead of --reg (run mri_vol2vol with --help to get more info). but this is not mri_vol2surf mri_vol2surf does not have --s as

Re: [Freesurfer] Freeview coordinates

glad to hear it Bruce On Mon, 29 Oct 2018, k3...@free.fr wrote: External Email - Use Caution Hi Ruopen and Bruce, indeed I fixed the transform multiplication and now I am able to get the good coordinates. Thanks for your help! Best, Florent - Mail original - De: "Ruopeng

Re: [Freesurfer] Freeview coordinates

External Email - Use Caution Hi Ruopen and Bruce, indeed I fixed the transform multiplication and now I am able to get the good coordinates. Thanks for your help! Best, Florent - Mail original - De: "Ruopeng Wang" À: freesurfer@nmr.mgh.harvard.edu Envoyé: Vendredi 26

Re: [Freesurfer] cavum septum pellucidum

Hi Sarah can you upload your subject processed with both version? There isn't anything explicit we have done that would change the 5th ventricle segmentation as far as I know. 5.2 was an orphan version, so hopefully we can sort this out and you can stop using it cheers Bruce On Mon, 29

[Freesurfer] cavum septum pellucidum

External Email - Use Caution HI, wondering if there are thoughts on this question I posted a week ago? Repeated here: I'm comparing output of Freesurfer5.2 to 6 on the same set of brains. The "5th ventricle" (Cavum septum pellucidum) is not being detected by 6. I had eyeballed

[Freesurfer] Research Opportunity

External Email - Use Caution UCSF, Dept. of Radiology & Biomedical Imaging is seeking a Postdoctoral Scholar for The Laboratory for Precision Neuroimaging We are seeking a postdoctoral candidate with a strong background in genetics human imaging and a desire to use a

Re: [Freesurfer] cluster failing on HCP freesurfer script

External Email - Use Caution Thanks Matt The Environment script actually sets up: freesurfer-Darwin-lion-stable-pub-v5.3.0-HCP From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Glasser, Matthew Sent: Friday, October 26, 2018

Re: [Freesurfer] mris_apply_reg failing for area/volume

Hi James can you verify that the various files (e.g. /cluster/projects/p23/projects/Memory_Project/James/AgeSym/long_recons_FXhemi/010_NDev/1000409_02_10_02_11.long.base_1000409_11/surf/rh.area) are intact by loading them into freeview? For the area file you will of course have to load it as

Re: [Freesurfer] subfield normalization vs. covarying for whole hippocampal volume

External Email - Use Caution Dear Lauren, This is a very interesting question! Site harmonization matters aside (there’s a vast literature on it), whether you correct by ICV or whole hippocampal volume essentially answers to different questions: - ICV: you’re asking whether

[Freesurfer] mris_apply_reg failing for area/volume

External Email - Use Caution ? Dear freesurfer experts I'm running the following commands to register RH area and volume files per sub to both hemispheres of a symmetrical template following Xhemi routines. The commands have already worked for many subs, but are failing to