[Freesurfer] calculation of the volume in mm3

External Email - Use Caution Hello FreeSurfer Developers, I was wondering about the volume calculation of the structures in the aseg.stats file. VoxelVolume_mm3 0.512 NVoxels 8616Volume_mm3 4312.4 StructName Right-Hippocampus After my calculation of NVoxels * VoxelVolume

[Freesurfer] Ynt: recon-all error

External Email - Use Caution Yes I have been try to processes other subjects in Freesurfer,I have installed freesurfer a little while ago and to test my installation,I did full recon-all to single subject T1w data but I get an error like this.But I solved the problem.I used free

Re: [Freesurfer] ERROR: flirt in bbr Matlab Execution

Thank you. Now I understand the last changes to this functionality. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Wednesday, April 24, 2019 9:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR: flir

Re: [Freesurfer] calculation of the volume in mm3

Hi René our volume calculation corrects for partial volume effects, so it does more than just counting voxels. cheers Bruce On Thu, 25 Apr 2019, Schranzer René wrote: External Email - Use Caution Hello FreeSurfer Developers,   I was wondering about the volume calculation

Re: [Freesurfer] recon-all stops in CORRECTING DEFECT

Hi Marina there is a tutorial on fixing defects you can look at here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview?highlight=%28tutorial%29%7C%28topology%29 I find the best way to do this is to load the lh.orig.nofix and lh.inflated.nofix (or the rh), then lo

[Freesurfer] pvc error

External Email - Use Caution Dear freesurfer experts, I am running the rbv pvc correction on a mac system and encountered the following error. mghRead(/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz, -1): c

Re: [Freesurfer] CORRECTING DEFECT 1 problem

External Email - Use Caution Hello, Have you got some time to check my data? I appreciate if you can give me some advices. Thank you very much. Ruwan On Tue, Apr 23, 2019 at 7:41 PM Pradeepa Ruwan < pradee.wanniarach...@gmail.com> wrote: > Dear Prof.Bruce, > > I am sending my ra

[Freesurfer] Questions about multiple test correction and quality assurance

External Email - Use Caution Dear FreeSurfer experts, I am reading your work 'False positive rates in surface-based anatomical analysis' and having several questions about multiple test correction in mri_glmfit-sim: 1. The permutation is permuting the design matrix, but how to pe

Re: [Freesurfer] pvc error

can you send command line and terminal output? On 4/25/19 10:37 AM, Donatienne Van Weehaeghe wrote: > > External Email - Use Caution > > Dear freesurfer experts, > > I am running the rbv pvc correction on a mac system and encountered > the following error. > > mghRead(/Volumes/DATA_PETMR/

Re: [Freesurfer] Questions about multiple test correction and quality assurance

On 4/25/19 10:54 AM, Zhi Li wrote: > > External Email - Use Caution > > Dear FreeSurfer experts, > > I am reading your work 'False positive rates in surface-based > anatomical analysis' and having several questions about multiple test > correction in mri_glmfit-sim: > > 1. The permutati

Re: [Freesurfer] fsaverage error with recon-all

What is the output of running: ls -ld /home/dujiachen/HCP/human_connectome/female_processed/fsaverage From: on behalf of chen <824247...@qq.com> Reply-To: FS Help Date: Thursday, April 25, 2019 at 7:46 AM To: FS Help Subject: [Freesurfer] fsaverage error with recon-all External Email

[Freesurfer] mri_convert : Error while loading library libGLdispatch.so.0

External Email - Use Caution Dear all, I am trying to convert .mgz file to nii.gz using mri_convert command mri_convert filename.mgz filename.nii.gz but i am getting an error "mri_convert: error while loading shared libraries: libGLdispatch.so.0: cannot open shared object file:

Re: [Freesurfer] mri_convert : Error while loading library libGLdispatch.so.0

Hi Vasudev, are you using an old dev distribution? This was an issue a while back, but it’s fixed now. Andrew From: on behalf of Dev vasu Reply-To: FS Help Date: Thursday, April 25, 2019 at 3:30 PM To: FS Help Subject: [Freesurfer] mri_convert : Error while loading library libGLdispatch.so.

Re: [Freesurfer] pvc error

External Email - Use Caution Dear Dough, The terminal output: HV_02_11_p2x7 mghRead(/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz, -1): could not open file ERROR: loading /Volumes/DATA_PETMR/data_donatienn