Re: [Freesurfer] Problems Extending the Pial Surface

External Email - Use Caution Hi Bruce, I sent you the whole directory if one subject un which we had some problems extending the pial surface. Se would like extend the pial surface without affect the wm boundary. Did you have a chance to review It? Thanks in advance, Cheers,

[Freesurfer] differences between qdec display and summary file for monte carlo corrected results

External Email - Use Caution Hi, freesurfer experts, As I mentioned in my last email, I see no answer. I think it is possible that my description is not clear enough. I used qdec to compare the cortical thickness of two groups and tried to correct for multiple comparisons using

Re: [Freesurfer] correcting surface with optic chiam

Hi Jim it probably doesn't matter, except for aesthetics cheers Bruce On Fri, 11 May 2018, Alexopoulos, Dimitrios wrote: External Email - Use Caution In many of our studies there appears to be a pial/wm surface associated with the optic chiasm. (See attached). Do these ne

[Freesurfer] correcting surface with optic chiam

External Email - Use Caution In many of our studies there appears to be a pial/wm surface associated with the optic chiasm. (See attached). Do these need to be corrected? If so, is it best to remove from the brainmask.mgz or from the wm.mgz? Jim "The materials in this email are

Re: [Freesurfer] how to reinsert volume geometry information into surf

Hi Padma I think if you use mris_convert -vol-geom it will copy the voluem geometry from the mri volume you specify cheers Bruce On Fri, 11 May 2018, padma wrote: Hi, I exported a freesurfer mesh to PLY format to do some computation and have exported the PLY surface back to an fsmesh.

Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

Hi Ritesh you need to give us much more information if we are to be able to help you. We need the exact command you ran, the full screen output of the command, and the contents of the subjects recon-all.log file in /scripts/recon-all.log cheers Bruce On Fri, 11 May 2018, Ritesh Mahajan wrote:

[Freesurfer] mris_preproc error

Hi Freesurfers, I used the command mris_preproc to have all the surfaces of my cohort concatenated in fs average and I obtained this error message from several of my subjects: #@# 3/11 MS073_R01_05/Bay8_3T/fs/MS073_R01_05 Fri May 11 14:24:58 EDT 2018 -- --- mri_s

[Freesurfer] how to reinsert volume geometry information into surf

Hi, I exported a freesurfer mesh to PLY format to do some computation and have exported the PLY surface back to an fsmesh. How do I put back the volume geometry information into the mesh surface? Thanks, —Padma ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

External Email - Use Caution Hello Bruce, 1) I converted the my mri data from ALS to RAI orientation through command "mri_convert --out_orientation RAI inputALS.nii outputRAI.nii" 2) Then i gave a run for free-surfer, using recon-all command. After successful run of free-surfer

Re: [Freesurfer] V6 Stable OSX software error - multistrip flag - RESOLVED

External Email - Use Caution Hi Andrew, I installed the development version and everything ran correctly to completion as you suggested. Thanks, -Matt On Mon, May 7, 2018 at 1:08 PM, Hoopes, Andrew wrote: > Hi Matt, this issue should be fixed in the freesurfer development ver

[Freesurfer] Longitudinal LME cluster value extraction

External Email - Use Caution Dear FreeSurfer experts, Am analysing longitudinal structural data with the LME model algorithm. I will like to map the significant cluster after analysing the data to all subjects at all time points, extract the values for all and perform further stat