Re: [Freesurfer] mri_robust_template - MyMatrix::RotationMean Error

Have you looked at the images in freeview to verify that they both look ok (eg, one is not all 1s or 0s or missing half the brain or misoriented)? Can you try to run it with the unmasked data as a test? On 7/4/2022 4:24 PM, Andrew Beaudin wrote: External Email - Use Caution Hello

Re: [Freesurfer] recon-all error: mri_cc

Not sure what is happening. Does it work if you restart the long time point from scratch (ie, remove the folder that is there)? On 6/29/2022 5:49 PM, coope...@student.unimelb.edu.au wrote: External Email - Use Caution Dear FreeSurfer developers, I’m attempting to run recon-all with

Re: [Freesurfer] How is cache.th40.pos.sig.voxel.mgh computed, exactly?

On 6/30/2022 2:31 PM, Mark Ebden wrote: External Email - Use Caution Hi Douglas, Thank you. From your explanation, the software's numbers from 0 to 1 aren't corrected p-values -- specifically, they aren't corrections in the well-accepted sense of Bonferroni corrections or other

Re: [Freesurfer] FW: How to project SPM image

First, what is rReslice_Combined_roi_meanRD.nii? How was it created? If that is you lesion map, then it is  not the right input to BBR. I can't remember, but if the AAL is in the MNI152 space, then it will be easier to just run recon-all on the MNI152 ( or whatever the atnatomical reference is

Re: [Freesurfer] Cohen's D from selxavg3-sess output

You can use ces/rstd On 7/5/2022 10:50 AM, Caspar M. Schwiedrzik wrote: External Email - Use Caution Hi! I would like to compute Cohen's D for individual subjects. I was wondering whether I can use the output from selxavg3-sess for this: ces./rstd Or does this only work with gamma

Re: [Freesurfer] Interpretation of intergroup comparisons

I'm having problems following your narrative. Can you send the fsgd and contrast files? On 7/4/2022 5:37 PM, Adriana Cannizzaro wrote: External Email - Use Caution Hello Freesurfers, We performed a whole-brain analysis using general linear model analysis with FreeSurfer mri_glmfit

Re: [Freesurfer] Problem with sxconcat-sess

These dof files are created by selxavg3-sess. If they are not there, then that program must have failed in some way On 6/29/2022 4:10 PM, Shapiro, Noah Lorenz wrote: Hi Paul, Thanks for your suggestion. I examined all files within the /script directory from recon-all from two subjects where

Re: [Freesurfer] Tksurfer Error

External Email - Use Caution Thanks very much Dr. Greve! Just had another question for you, if you have the time! I am currently working on displaying my SPM overlay on a 3D brain volume, using bbregister, and am getting this:

Re: [Freesurfer] Tksurfer Error

tksurfer is depracated. Try using tksurferfv instead On 6/29/2022 4:33 PM, Rachel Wagner wrote: External Email - Use Caution Hello, I am attempting to paint my spm functional data onto freesurfer’s anatomical image. I ran this code: tksurfer bert lh inflated -overlay updated.img

Re: [Freesurfer] mri_concat killed

Maybe it is running out of memory? Can you try it reducing the number of inputs? On 6/29/2022 2:42 PM, Benjamin Deck wrote: External Email - Use Caution Hi there, I am attempting to concat a number of volume files that are filled cortical ribbons from a series of label files. My

Re: [Freesurfer] Segmentation Mistakes

what are you using as input? I can't tell from the image you sent, but it looks pretty blurry. What is the resolution? What kind of acquistion? On 6/28/2022 11:38 PM, Wang, Yu wrote: External Email - Use Caution Hello FreeSurfer Developers, I used the _recon-all -s c1NT816 -i

Re: [Freesurfer] Command Not Found

Sorry, orig.mgz should exist in mri not mri/orig On 7/10/2022 4:04 PM, Douglas N. Greve wrote: Does orig.mgz exist in /usr/local/freesurfer/7.2.0/subjects/home/mri/orig? Also be aware that we are phasing out register.dat files in favor or using lta files. Also, the tk tools (tkregister2,

Re: [Freesurfer] Command Not Found

Does orig.mgz exist in /usr/local/freesurfer/7.2.0/subjects/home/mri/orig? Also be aware that we are phasing out register.dat files in favor or using lta files. Also, the tk tools (tkregister2, tkmedit, tksurfer) are officially depricated. Try using tkregisterfv instead. On 6/28/2022 4:38 PM,

Re: [Freesurfer] aseg.presurf edits are undone or incomplete when brainmask.mgz edits are involved

I'm just reading this more carefully. It looks like you made edits to the aparc+aseg. Is that right? Those edits will definitely be erased when you rerun. You are supposed to make them on the aseg.presurf. If you did  make them on the aparc+aseg, then we can figure out a way to transfer them

Re: [Freesurfer] aseg.presurf edits are undone or incomplete when brainmask.mgz edits are involved

Hi, I see the locations of interest, but can you send a freeview command line that will load up the two volumes as well? On 6/28/2022 6:34 PM, Keefe, Sarah wrote: External Email - Use Caution Hi, Thank you for the response! I just sent a file via FTP:

Re: [Freesurfer] Convert coordinates from FreeSurfer space to Native space

Have you seen this page? https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 7/7/2022 12:18 PM, Yiyu wrote: External Email - Use Caution Thank you, Bruce If possible, I would like to transform an individual coordinate (x,y,z) from FreeSurfer space to the native space.