Re: [Freesurfer] View Results: Paired T-Test

Have you looked at the tutorial? https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel On 7/20/2019 4:59 PM, FAST Study wrote: External Email - Use Caution Dear Dr. Greve, Will you please help me learn how to view the output of the paired t-test - via mri_glmfi

Re: [Freesurfer] region mask creation

Use mri_binarize --match segid --i aseg.mgz --o mask.mgz where segid is the segmentation code (eg, left hippo is 17) from $FREESURFER_HOME/FreeSurferColorLUT.txt On 7/21/2019 2:09 AM, Dandil dNd wrote: External Email - Use Caution Hi Bruce, Thank you for your reply. I want to create a

Re: [Freesurfer] freesurfer stopped

There is nothing in the log file that indicates a problem. Was there anything else printed to the screen? Try running this command to see if it works cd Users/adomas/Desktop/test/Subj001/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere On 7/21/2019 8:54 AM, Adomas Bunevicius

[Freesurfer] mri_robust_template always fails in fmriprep when aligning multiple T1 images (Return code: -9)

Dear Freesurfer experts, I’m running into a problem with mri_robust_template when trying to align multiple T1 images (this is with Freesurfer 6.0.1). I’m using fmriprep 1.4.1 to preprocess subjects from the OASIS3 dataset (or at least, attempting to). Each subject has 5-7 T1 scans over 3-4 tim

[Freesurfer] Combining white/pial surfaces created during separate runs of autorecon2

External Email - Use Caution Hello Freesurfer support team, I am trying to create accurate white/pial surfaces, however, due to signal drop-out, Freesurfer is consistently underestimating the pial surface -- a problem which I am only able to fix using control points. Unfortunately

Re: [Freesurfer] Mass-Univariate LME - help please!

External Email - Use Caution Hi Tom, basically most of it looks OK to me, just a few remarks: I assume that you deliberately chose the plain mass-univariate approach instead of the potentially more powerful spatiotemporal mass-univariate approach. For the interpretation of the

Re: [Freesurfer] Resending question about Freesurfer LME analysis

External Email - Use Caution Hi Bronwyn, sorry for the late reply, and thanks for the detailed mail. I have to admit that at the moment I do not see anything obvious. If you can share it, you might upload a Matlab mat file with one or more 'F_lhstats' and 'F_rhstats' example

[Freesurfer] transformation question

External Email - Use Caution Hi, I would like to create a registration matrix from orig.mgz to diffusion space. I created a reg file with bbregister --t2 --init-fsl --reg /data/FS/sub01/reg.dat --mov /data/FS/sub01/B0.nii.gz --s sub001 but how can I invert this registration so th

Re: [Freesurfer] transformation question

In most of the tools there is an option to invert the matrix before you apply it. If you save the registration matrix as an LTA instead of DAT, then most of the tools will figure out the directionality. On 7/22/19 4:24 PM, Sam W. wrote: > > External Email - Use Caution > > Hi, > I would

Re: [Freesurfer] transformation question

External Email - Use Caution Thanks Doug! I'll use lta then, but which tool do you recommend I use for inverting the matrix in order to have a freesurfer-to-diffusion registration matrix? bbregister does not seem to offer the option to invert matrices. Is tkregister2 the preferable

Re: [Freesurfer] transformation question

Use lta_convert with --invert. BTW, the registration matrix is already anat-to-diffusion On 7/22/2019 7:50 PM, Sam W. wrote: External Email - Use Caution Thanks Doug! I'll use lta then, but which tool do you recommend I use for inverting the matrix in order to have a freesurfer-to-diff