Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

External Email - Use Caution Hi all, Thanks again for your help. We fixed the issue by adding user write permissions for the owner-user in the installation folder (note that the owner of the file in the installation folder is different from the users that we used for testing).

Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

the discussion.) Best, Jackson From: Iglesias Gonzalez, Juan E. Sent: Friday, December 22, 2023 10:18 AM To: Freesurfer support list Cc: Brouwer, I. (Iman) ; Gool, J.K. (Jari) ; Nolan, Jackson ; Dicamillo, Robert Subject: Re: [Freesurfer] SUBJECTS_DIR writing

Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Heese, E. van (Eva) Date: Friday, December 22, 2023 at 9:56 AM To: Freesurfer support list Cc: Brouwer, I. (Iman) , Gool, J.K. (Jari) Subject: Re: [Freesurfer] SUBJECTS_DIR writing permissions

Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

: freesurfer-boun...@nmr.mgh.harvard.edu Namens Iglesias Gonzalez, Juan E. Verzonden: vrijdag 22 december 2023 15:28 Aan: Freesurfer support list CC: Brouwer, I. (Iman) ; Gool, J.K. (Jari) Onderwerp: Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields Dear Eva

Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

, December 22, 2023 at 9:24 AM To: freesurfer@nmr.mgh.harvard.edu Cc: Brouwer, I. (Iman) , Gool, J.K. (Jari) Subject: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields External Email - Use Caution Dear FreeSurfer support team, I am running into some

[Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

External Email - Use Caution Dear FreeSurfer support team, I am running into some issues regarding the mandatory SUBJECTS_DIR writing permissions when running the hippocampal and amygdala subfields segmentation

Re: [Freesurfer] $SUBJECTS_DIR

There is already a label called ?h.cortex.label for all of cortex. For lobes, you can use mris_annotation2label to break up the annotation into its constituent labels, then use mri_mergelabels to combine subsets into a lobe, then use mris_label2annot to combine the lobes into a new annotation.

Re: [Freesurfer] $SUBJECTS_DIR

Thanks, any thoughts about Q#2:2-Also, Is there a way to segment the cortices as a whole, like left and right frontal cx, parietal cx, temporal cx, occipital cx? Thanks aj On Saturday, August 20, 2016 9:21 PM, "sha...@nmr.mgh.harvard.edu" wrote: Hi Adil,  

Re: [Freesurfer] $SUBJECTS_DIR

Hi Adil, My understanding is that, you can always change the location of SUBJECTS_DIR. Just use this command: setenv SUBJECTS_DIR You do not need to mention this new address in your recon-all command. Good luck > HI,1-I'm working with FreeSurfer that is on a server.  I don't have >

[Freesurfer] $SUBJECTS_DIR

HI,1-I'm working with FreeSurfer that is on a server.  I don't have permission to create files under the $SUBJECTS_DIR.  Is there any way I can specify -subject to be in a directory for which I do have permission? for example: recon-all -subject /location of the file or my own subject_dir

Re: [Freesurfer] subjects_dir

Hi Eric I think if FREESURFER_HOME is set properly recon-all will create the symlinks it needs so you won't have to do it yourself (including the fsaverage one - I just checked). cheers Bruce On Mon, 23 Nov 2015, Eric Cunningham wrote: > Other than fsaverage, are there any other files that

Re: [Freesurfer] subjects_dir

Hi Eric No, you can just symlink fsaverage and such Cheers Bruce > On Nov 23, 2015, at 9:40 PM, Eric Cunningham wrote: > > Greetings Freesurfer experts, > > The README file in the $SUBJECTS_DIR says that a different directory can be > specified by setting the env var

[Freesurfer] subjects_dir

Greetings Freesurfer experts, The README file in the $SUBJECTS_DIR says that a different directory can be specified by setting the env var SUBJECTS_DIR prior to the 'source $FREESURFER_HOME/FreeSurferEnv.csh' statement. Do the original contents of SUBJECTS_DIR (such as fsaverage) need to be

Re: [Freesurfer] subjects_dir

Other than fsaverage, are there any other files that need to be linked for recon-all to work? Thanks On Mon, Nov 23, 2015 at 4:57 PM, Bruce Fischl wrote: > Hi Eric > No, you can just symlink fsaverage and such > Cheers > Bruce > > > On Nov 23, 2015, at 9:40 PM, Eric

Re: [Freesurfer] SUBJECTS_DIR not defined in environment

Hi Matthew what shell are you using? If you type printenv SUBJECTS_DIR right before calling mri_segstats, what does it return? And when do you get that output? Are you sourcing the FreeSurferEnv.csh file? Don't execute it as otherwise it pushes a new shell, sets all that stuff, then pops

Re: [Freesurfer] SUBJECTS_DIR not defined in environment

Ok the main email is CC'd. Below is what I did and the output I received. The goal is to get a brain volume, Subdural space and/or a CSF volume to estimate how much room for displacement/deformation the brain has. Thanks in advance for your help. Matthews-MacBook-Pro-2:~] matthew% printenv