Re: [Freesurfer] Amygdala Segmentation T1.v20 Command

Thanks, Wisteria. Can you please send us the list of files under the mri directory of any subject? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Deng, Yushan Wisteria" Reply-To: Freesurfer sup

[Freesurfer] RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca public permissions

External Email - Use Caution Dear Freesurfer experts, I am trying to compile freesurfer from source. It is nicely performed expect the "git annex get ." command which fails in these two files, RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca. I searched github's annex br

[Freesurfer] Projection on fsaverage5

External Email - Use Caution Dear Freesurfer experts, I would like to convert the individual preprocessed EPI volume (that it is normalized to MNI152 space and without smoothing) to surface and project it on fsaverage5. I used the following command: mri_vol2surf --mov EPI.nii --r

Re: [Freesurfer] Projection on fsaverage5

Hi Marina how do you project to fsaverage5? cheers Bruce On Wed, 8 Jan 2020, Marina Fernández wrote: External Email - Use Caution Dear Freesurfer experts, I would like to convert the individual preprocessed EPI volume (that it is normalized to MNI152 space and without smoothin

Re: [Freesurfer] Projection on fsaverage5

Use --trgsubject fsaverage5 (you might have to link it to your SUBJECTS_DIR). Also, how did you compute the register.dat? If you've normalized it to MNI152, that will complicate things. Was the normalization linear and nonlinear? On 1/8/20 8:03 AM, Marina Fernández wrote: > > External E

[Freesurfer] FsFast Question

External Email - Use Caution Hello, I am new to fmri processing/FsFast and I had a question on creating nuisance variables. Is it possible to set a block-design task fMRI paradigm file as a nuisance variable, so that it can be inputted at a .dat file for the mkanalysis-sess co

Re: [Freesurfer] (no subject)

External Email - Use Caution Ok. i figured it out. The problem was just that you can not specify the file type - so .mgz in BN_Atlas_subcotex.mgz was actually the problem. Now I run in a new issue: gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz --ctx-annot BN

Re: [Freesurfer] FsFast Question

Not directly as an external regressor. You would have to extract the info and create a waveform, one value for each TR in the external regressor file. You might also want to convolve it with a hemodynamic response function On 1/8/20 11:15 AM, Swetara Joshi wrote: > > External Email - Us

[Freesurfer] Projection on fsaverage5

External Email - Use Caution Hi Bruce, Thanks for the quick response. I found that the problem was the input. If I use the EPI that it is coregistered to the T1 of Freesurfer instead of the EPI that it is also normalized to the MNI space, it works and I can project the surface (t

Re: [Freesurfer] Projection on fsaverage5

I think that should work, but I have not used the "ico" subject in a long time. It would be safer to use --trgsubject fsaverage. But you can also verify that they give the samme thing On 1/8/20 12:12 PM, Marina Fernández wrote: > > External Email - Use Caution > > Hi Bruce, > > Thanks fo

Re: [Freesurfer] RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca public permissions

Hi Kostakis, sorry about that - should be fixed now! Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Kostakis Gkiatis Sent: Wednesday, January 8, 2020 5:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] RB_all_2020-01-02.gc

Re: [Freesurfer] Recommendation for CFT and CWT FreeSurfer analysis

External Email - Use Caution Hi, I have follow-up concerns. I also ran PALM as following to check my results: palm -i y.mgh -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh -d X.csv -t C1.csv -m mask.mgh -o plm -C 1.95996 -Cstat extent -twotail -n 5000 Interestin

[Freesurfer] funcroi-sess annotation issue

Hello Freesurfer Team, I am running the fsfast analysis stream for resting state data and recently came across an issue with the funcroi-sess command. I originally used funcroi-config to configure the rois with the -annot aparc.a2009s $ROI flag to seed each of the regions from the 2009 annotati

[Freesurfer] single-trial analysis of BOLD data in FSFAST

Dear Doug, I would like to perform GLM on a trial-by-trial basis in FSFAST. That is, I'm interested in obtaining beta estimates per trial and using them as input for group-level analyses of activation patterns (e.g., MVPA) or functional connectivity (e.g., beta series correlations). I've done t

Re: [Freesurfer] RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca public permissions

External Email - Use Caution Dear Andrew, Thank you for your quick response. It works perfectly now. Kostakis --- Electrical and Computer Engineer Phd Candidate in Brain Imaging Medical Image Processing, Algorithms and Applications National Technical University of Athens 9,Iroon P

[Freesurfer] mri_glmfit with flag -pvr

External Email - Use Caution Dear Freesurfer team, I am running the glm analysis on CBF maps. I have two class and I want to see the group difference regressing out the cortex thickness. I know that I can add the average cortical thickness as one covariable in FSDG file. However,