Re: [Freesurfer] Installing Freesurfer

External Email - Use Caution Hello Rio, I’m not sure why the paths you list include "$home/username”. Usually the absolute path listed by the environment variable HOME ends with the subdirectory named with your username.  So your Downloads folder is usually referenced as $HOME/D

[Freesurfer] display results with tksurfer

External Email - Use Caution Dear Freesurfer experts, I would like to modify the values of the colorbar scale to display results in the inflated surface with tksurfer, in such a way that displayed values in the colorbar range from the minimum t- value detected to the maximum t val

Re: [Freesurfer] Installing Freesurfer

External Email - Use Caution ... Sorry, I should have said - if you expanded the tar archive under $HOME/Downloads, then $ ls $HOME/Downloads/freesurfer … would show you something like … ASegStatsLUT.txt  diffusion/              FreeSurferEnv.sh  mni@                  SetUpFreeS

Re: [Freesurfer] Freesurfer 7.1.1: locale bug and workaround

External Email - Use Caution Hi, Thanks for your response. Yes: the errors appear for the individual commands specified, for example: alex@fmri-proc1:~$ mri_ca_label --help error: No such file or directory error: Could not set locale sysname  Linux hostname fmri-p

[Freesurfer] Moving .nii atlas to surface space and create .annot file

External Email - Use Caution Dear Freesurfer Team, I need to move an atlas file, Shen268 in 2mm (https://www.nitrc.org/frs/download.php/7977/shen_2mm_268_parcellation.nii.gz) from volumetric into surface space in order to do some analysis in MATLAB with it. Specifically, I need

Re: [Freesurfer] Freesurfer 7.1.1: locale bug and workaround {Disarmed}

External Email - Use Caution Hello Alex, Thanks for the additional command output.  If a machine does not have certain locale files installed, then I’m not sure what can be done apart from our having a (Debian) linux installer that might update them.   Basically I think this is

[Freesurfer] asegstats2table error with options --etiv and --no-vol-extras

External Email - Use Caution Hello, when using asegstats2table with the two flags --etiv and --no-vol- extras, I get the following error: ERROR: --etiv, cannot find EstimatedTotalIntraCranialVol in list It seems computing the ratio of volumes to etiv needs etiv to be included in

[Freesurfer] Put the updated vertex_label into .annotation

External Email - Use Caution hello, After I updated the vertex_label of rh.aparc.a2009s.annot with an algorithm, now I want to replace the vertex_label in the .annot with the updated vertex_label, mainly to see the effect of the segmentation, do you know what to do ? if you know

[Freesurfer] The usage about annotation view

External Email - Use Caution hello, FreeSurfer  I have loaded rh.pial and rh.aparc.2009s.annot, why my version does not have the label view option that can see the annotation? Is it a version issue? My FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

[Freesurfer] Open the .annotation file with Notepad is garbled

External Email - Use Caution Hello, FreeSurfer Why is it garbled when I open the .annotation file with Notepad? Is there any solution?  Looking forward to your reply___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail

[Freesurfer] Qdec - talairach to vertex for display purposes

External Email - Use Caution Dear Freesurfer community, I have an experiment in which participants received brain stimulation using anatomical coordinates which I have in talairach space. I have run a whole-brain analysis using qdec, and I have a surviving cluster. For display pu

[Freesurfer] amygdala segmentation on anatomy

External Email - Use Caution Dear freesurfer, This is Elena Aggius Vella. I'm writing to ask for your help. I need to do amygdala segmentation based on anatomy I see freesurfer has a nice tool to do it, but i'm new in freesurfer. Is it possible to have any help on this? many

[Freesurfer] Estimating the memory footprint of Longitudinal Stream?

External Email - Use Caution Hi FreeSurfers, Is there any guidance on how to estimate the memory footprint of the Longitudinal steam? We are trying to process the MacLaren test-retest dataset [1] (40 timepoints per subject) with the longitudinal stream in v7.1.1 and are running i

Re: [Freesurfer] Open the .annotation file with Notepad is garbled

You can’t open an annotation as a plain text file – it’s a custom binary structure. You can visualize it on top of a surface in freeview. Something like: freeview -f surf/lh.inflated:annot=label/lh.aparc.annot From: on behalf of 1248742467 <1248742...@qq.com> Reply-To: FS Help Date: Tuesday, O

Re: [Freesurfer] error trac all prep

Hi Ileana - It looks like it fails on the left uncinate. Is there any artifact or missing part of the brain or brain mask, either in the diffusion scan or the T1 scan, in a location that would affect the uncinate? Anastasia. From: freesurfer-boun...@nmr.mgh.harva

[Freesurfer] Postdoc and PhD positions @ BrainLENS Lab w/ Fumiko Hoeft {Disarmed}

External Email - Use Caution Hi All, *We have openings for Postdoc and PhD positions @ UConn brainLENS Lab: **https://www.brainlens.org/employment * *Fumiko Hoeft MD PhD*, Professor of the Departments of Psychological Sciences, Mathematics, N

[Freesurfer] Help with creating contrast matrix - 6 classes and 3 variables

External Email - Use Caution Dear Freesurfer community, I am having trouble with my contrast matrix, and would greatly appreciate any help with this. I have 2 categorical variables, sex (2 levels) and training type (3 levels). I also have three (continuous) variables: Age, perce