Re: [Freesurfer] Error mri_surf2surf FS6

Dear Douglas thanks a lot for this information. Indeed, I thought we are sampling our data on the own average! Cheers Jürgen - University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychol

[Freesurfer] Error while attempting Segmentation

Hi, We have newly installed Freesurfer. We are a novice. We were trying to segment our data set. We used the following command. We attached the log. Command: recon-all -s testsample -all Output: [iplneurosurgery@localhost /]$ recon-all -s testsample -all Subject Stamp: freesurfer-Linux-cento

Re: [Freesurfer] Error while attempting Segmentation

Hi IPL Neurosurgery it seems that you have no read or write permission to the freesurfer tools. > /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission > denied. you can change the permission with sudo chmod -R 777 freesurfer Hope this helps Cheers Jürgen

[Freesurfer] How to check if FS are processing correctly.

Dear FS experts: I am using FS to analyze our MRI data. When I finished recon -all, there are following informaion: Started at Fri Mar 10 11:26:05 EST 2017 Ended at Fri Mar 10 18:26:51 EST 2017 #@#%# recon-all-run-time-hours 7.013 recon-all -s 10001 finished without error at Fri Mar 10 18:26:51

Re: [Freesurfer] Intensity normalization in longitudinal processing

HI Jaiashre is there a reason to mix versions? We always advise against this cheers Bruce On Fri, 10 Mar 2017, Jaiashre Sridhar wrote: Hello FreeSurfer Team,   For a longitudinal study, we processed the cross-sectional scans through FS v5.1 and ran the longitudinal stream in FS v6.0. The

Re: [Freesurfer] MRI intensity normalize

you can, but why do you need to do it outside of the recon-all stream? On Fri, 10 Mar 2017, shi yao wang wrote: Dear FS experts, I am wondering the process of MRI intensity normalization.  Before I am running recon -all, can I run following process to normalize our MRI images.  mri_normalize

[Freesurfer] -dura_thresh

Dear All, In FS6.0.0, this flag is added to manually adjust watershed threshold instead of its automatic calculation. I went back to the original paper by Segonne et al, and I could identify the prefllooding height h and the post watershed threshold t. I assume the flag refers to the latter. Since