External Email - Use Caution Cause I segmented thalamus using only T1 image, I put the this command : quantifyThalamicNuclei.sh thalamus_nuclei_output_file.txt T1 But any file was not made after this command.
> On Aug 19, 2020, at 10:18 PM, Iglesias Gonzalez, Juan E. > <jiglesiasgonza...@mgh.harvard.edu> wrote: > > Dear HW, > What was the exact command you ran? > Cheers, > /Eugenio > > > Juan Eugenio Iglesias > Senior research fellow > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > http://www.jeiglesias.com <http://www.jeiglesias.com/> > > > > From: <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Haewon Roh > <rofree...@gmail.com <mailto:rofree...@gmail.com>> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Wednesday, August 19, 2020 at 03:26 > To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: [Freesurfer] " quantifyThalamicNuclei.sh" commend does not work.. > > External Email - Use Caution > > Hi team. > > I'd like to collect all kinds of volumes of subjects' thalamic nuclei but > the command " quantifyThalamicNuclei.sh" does not work in my mac book's > terminal window. > > (there's no error message but any file was not made after that command ; > please find attached screenshot showing the this problem) > > Before doing that command on terminal window, I made sure that every subject > file had three files (ThalamicNuclei.v12.T1.FSvoxelSpace.mgz, > ThalamicNuclei.v12.T1.mgz, ThalamicNuclei.v12.T1.volumes) after the process > of segmenting thalamus. > > > > But, for hippocampal and amygdala subsegmentations, command of > "quantifyHAsubregions.sh" is working well.. > > What is the difference between thalamic nuclei and hippoamygdala > substructures for gathering all volumes into tabelfile ? > > my subjects were preprocessed with freesurfer version 6.0 and their > substructure segmentations were made using freesurfer version 7.1. Does this > make this problem? > > I attached screenshot of my terminal window as below.. > > Thank you always !! > -- > Hae Won ROH, M.D. > > H.P: +82-10-4341-8142 > E-mail: rofree...@gmail.com > <mailto:rofree...@gmail.com>_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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