Re: [Freesurfer] hippocampal subfields downsampling question

Great question! El 26/10/2017 17:09, "NIELS JANSSEN ." escribió: > In the mri output folder, I noticed that both the 0.33 mm and 1 mm > (voxelspace) maps have subfields that do not overlap in space, meaning that > each subfield occupies a unique location in space that does

Re: [Freesurfer] Preproc-sess Error

You can put it somewhere in your path On 10/26/2017 10:35 AM, Hsu, Eugene wrote: > > Dear Dr. Greve, > > > I checked $FREESURFER_HOME/bin in Stable 6 and 3dvolreg.afni is indeed > missing but I found it in 5.3. > > > However, I don't have permission to copy the file from 5.3 over to > Stable

Re: [Freesurfer] freesurfer errors-windows bash

Dear Alexandre, It seems that problem is that you need the latest dev version to use this feature. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: Alexandre

Re: [Freesurfer] freesurfer errors-windows bash

Dear Eugenio, The freesurfer version commands tells me that I run the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version. Before using segmentHA_T1.sh command, I run the recon-all -all -s bert one and it worked. Of course, recon-all also worked, telling be how to use it properly.

Re: [Freesurfer] freesurfer errors-windows bash

Dear Alexandre, You need to download the latest dev version to have access to the new hippocampus/amygdala segmentation. The other potential problem is that FreeSurfer is not sourced properly. Do other FreeSurfer commands work? E.g. do you get an output when you type: recon-all Cheers,

Re: [Freesurfer] hippocampal subfields downsampling question

Hi Niels, The code works at .33 mm and ends up with a soft segmentation for each voxel, i.e., each voxel has a vector of probabilities corresponding to the different structures. So, they DO overlap. However, we don’t write those probabilities by default. Instead, we take the most likely label

[Freesurfer] freesurfer errors-windows bash

Dear all, I'm would like to run a hippocampal segmentation on my data. However, I'm a beginner with freesurfer thus, I juste try to run the commands with subject training data. I first try to run commands following the recent development (

[Freesurfer] hippocampal subfields downsampling question

In the mri output folder, I noticed that both the 0.33 mm and 1 mm (voxelspace) maps have subfields that do not overlap in space, meaning that each subfield occupies a unique location in space that does not overlap with other subfields (i.e., 12 subfields and 12 unique voxel intensities). I am

Re: [Freesurfer] Preproc-sess Error

Dear Dr. Greve, I checked $FREESURFER_HOME/bin in Stable 6 and 3dvolreg.afni is indeed missing but I found it in 5.3. However, I don't have permission to copy the file from 5.3 over to Stable 6: cannot create regular file

[Freesurfer] Postdoctoral Fellow Positions in a longitudinal birth cohort imaging study

Postdoctoral Fellow Positions Job description: Growing Up in Singapore Towards Healthy Outcomes (GUSTO) is the most comprehensive birth cohort study over the world. The GUSTO mothers were recruited during pregnancy between 2009 and 2010. We have followed the GUSTO family since then. The GUSTO

[Freesurfer] Errors in LGI computation

Dear Freesurfers, I try computing the local gyrification index following the method developed by Marie Schaer and her colleagues. The process itself finishes without errors, yet there remain large grey areas of variable size on the cortex, indicating errors in the computation of the