[Freesurfer] Different aseg and aparc stats with Freesurfer 5.3 and 6.0

External Email - Use Caution Hello Experts, I was working with some data pre-processed using freesurfer v5.3 - i think this was done on linux. Recently I pre-processed the dataset using v6.0 on an imac. I extracted cortical thickness and surface area from both hemispheres. The

[Freesurfer] Makefile for Tracula

External Email - Use Caution Hi everyone! Firstly - and most importantly - thank you for the awesome tool, and for all your help in using it! I'm re-processing (and re-quality controll-ing) data that was formatted in v5.3 into v6 and I've come to re-running trac-all. I've been

[Freesurfer] segmentHA_T2.sh hippo stream fails and doesn't recon both side, using 2019-02-03 dev version, centos6

External Email - Use Caution Hi Freesurfer, I’m running the dev version of freesurfer (cent06 from website, dated 2019-02-03) after seeing the (volumesAmygdala.txt error) message thread of https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59610.html But it still

Re: [Freesurfer] partial FoV - registration failure

External Email - Use Caution Thank you! Unfortunately, I don't have any whole brain scan. I registered the template and all the runs with tkregisterfv and the I run bbregsiter. Now, should I just re-run selxavg3-sess? Thanks Best Il giorno lun 26 nov 2018 alle ore 22:31 Greve,

Re: [Freesurfer] mri_segstat: same output with two different label

External Email - Use Caution Thanks! There was a mistake in the contrasts indeed. Best Il giorno lun 11 feb 2019 alle ore 18:59 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > > If mri_diff says that there is no difference, then there is something > wrong.

Re: [Freesurfer] registration and resampling in native space

Hi Francesca sorry, I defer to Doug on the details of mri_vol2vol. cheers Bruce On Tue, 12 Feb 2019, Francesca Strappini wrote: External Email - Use Caution Thank you for the reply! I run: mri_vol2vol --reg register.dat --mov func_data.nii.gz --targ

Re: [Freesurfer] MRISalloc error during automatic reconstruction

Hi Julia can you send us the recon-all.log file? cheers Bruce On Tue, 12 Feb 2019, Julia Ströhlein wrote: External Email - Use Caution Dear experts, while running one of my subjects, I got this error:   MRISalloc(732595, 480): could not allocate vertices Cannot

[Freesurfer] mris_preproc calling on incorrect target surface

External Email - Use Caution Hi Freesurfer Pros, I'm trying to perform mris_preproc with an average subject that I created called 'avgsubject.Patients_EB', as my target. Although it appears to take avgsubject.Patients_EB as the target subject, and VIPD_010 (the first

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution Thank you for the reply! I run: mri_vol2vol --reg register.dat --mov func_data.nii.gz --targ /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o func_data_registered2T1.nii.gz --no-resample Then I checked the registration and it seems that the original