Re: [Freesurfer] Thalamic nuclei exited with ERRORS

2022-08-19 Thread Yann Quidé
External Email - Use Caution Not a good news for me, but thanks! Yann > On 20 Aug 2022, at 06:40, fsbuild wrote: > > Hello Yann, > > It looks like the system library, /usr/lib/libSystem.B.dylib, is too old on > your machine running MacOS (10.13) to work with the Matlab MCRv97

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

2022-08-19 Thread fsbuild
External Email - Use Caution Hello Yann, It looks like the system library, /usr/lib/libSystem.B.dylib, is too old on your machine running MacOS (10.13) to work with the Matlab MCRv97 runtime environment.   MacOS 10.13 (High Sierra), 10.14 (Mojave) - are no longer supported by Ap

Re: [Freesurfer] TRACULA - preprocessing error

2022-08-19 Thread Liliana Wu
External Email - Use Caution Here is the error log information: INFO: SUBJECTS_DIR is /home/lwu/Desktop/OIRM02/trc INFO: Diffusion root is /home/lwu/Desktop/OIRM02/trc/output Actual FREESURFER_HOME /usr/local/freesurfer trac-preproc -c /home/lwu/Desktop/OIRM02/trc/output/OIRM02/sc

[Freesurfer] TRACULA - preprocessing error

2022-08-19 Thread Liliana Wu
External Email - Use Caution Hi, I ran the preprocessing command trac-all -prep -c $SUBJECTS_DIR/script and I am getting the following error ERROR: fio_pushd: /home/lwu/Desktop/OIRM02/trc/OIRM02/dlabel/mni I don’t see the mni folder created in my files… I am trying to only reco

[Freesurfer] Segment subregion error

2022-08-19 Thread Md. Mamun Al-Amin
External Email - Use Caution Hi Freesurfer experts, I have been encountering following errors after running segment_subregions command. I am using freesurfer version 7.3.2, Recon -all -all has been done with the option -cm segment_subregions thalamus --cross sub-0049 Step 1: prep

[Freesurfer] Thalamic nuclei exited with ERRORS

2022-08-19 Thread Yann Quidé
External Email - Use Caution Hi team, I am trying to run the thalamic nuclei pipeline with FS7.3.2, on scans processed with recon-all from FS5.3 (mac OSX10.13). However, I receive the below error. Any idea how I could solve this? Thanks in advance. Yann ---

[Freesurfer] lesions number and lesion volume of MS with samseg

2022-08-19 Thread Dilek Özkan
External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I have ground truth values(binary mask), lesions number and lesion volume. I will compare these with the output of freesurfer-samseg. I am confused about the