External Email - Use Caution
Hi Freesurfer, I am also experiencing the same problem and everything regarding FREESURFER path looks ok just getting error that says: Reading source surface /storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white MRISread(): could not open file No such file or directory mri_surfcluster: could not read surface /storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white No such file or directory I wonder if you found the reason and solution?
Best regards, Amirhossein Manzouri
On Thu, Dec 6, 2018 at 6:57 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
On 11/27/2018 06:46 AM, C.P.E. Rollins wrote:
External Email - Use Caution Hi Douglas,
Thanks a lot for your answers.
- For the permutations, would you recommend using this for
controlling for MC in cortical thickness analyses too?
Yes
Why is it recommended to use permutation simulation as opposed to Z Monte Carlo simulation for an LGI analysis?
Because the spatial correlations are very high (which makes MCZ less accurate)
- I've attached here the output from ls -Rl
$FREESURFER_HOME/subjects/fsaverage.
It looks like there is a difference in where you think FREESURFER_HOME is. Below, you say it is in /home/cper2/BeneMin/Freesurfer, but the attached file says it is in /applications/freesurfer/freesurfer_6.0.0. Which one is it?
Thanks again, Colleen
On 2018-11-23 16:26, C.P.E. Rollins wrote:
Dear Freesurfer Developers, I have a 2-part question:
- I was advised to use permutation to control for multiple
comparisons in an LGI analysis, would you mind elaborating how to do this in command line (in terms of command and parameters)? 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error (attached). I was wondering if you might have any advice? The file /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can view it in freeview.
Many thanks, Colleen
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