[Freesurfer] Stanford Postdoc opening: Simultaneous Spinal Cord/Brain fMRI

External Email - Use Caution The Systems Neuroscience and Pain Laboratory at Stanford University is currently accepting applications for a postdoctoral fellow for neuroimaging research in chronic pain. Funded by NIH (co-PIs Sean Mackey, Gary Glover), this project's overall goal

[Freesurfer] qdec and mris_anatomical_stats help

External Email - Use Caution Dear Freesurfer experts, Hope everyone is doing well! Could someone please clarify some things about mris_anatomical_stats, done after running qdec + mapping label to all subjects? From what I can understand, the following code should be used: mris_a

Re: [Freesurfer] LGI problem

External Email - Use Caution Hi doug, I tried to re-run 3 or 4 times and always failed at the segmentation stage… I have no linux machine, but I can try in a mac computer with a different OS... thank you! Angela > Il giorno 15 mag 2020, alle ore 23:08, Douglas N. Greve > ha s

Re: [Freesurfer] Group Analysis Covariates

There is not an easy way to do it, but you can do it in matlab cd glmdir X = load('Xg.dat'); y = load('perm.th30.abs.y.ocn.dat'); beta = inv(X'*X)*X'*y; yhat = X(:,[i j k ...]*beta([i j k ...]) where i j k ... indicate the factors you want keep in your data. Each factor gets a column in the desi

Re: [Freesurfer] LGI problem

Hi Angela, I cannot replicate this error. If you re-run, does it always exit with error? You can try this quickly be running setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/Aachen cd /Users/angelafavaro/Desktop/Aachen/subj220/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Users/a

Re: [Freesurfer] error in TRACUAL : preprocessing step.

It can't find the freesurfer recon of your subject. Your SUBJECTS_DIR is /Users/ahn/Downloads/9211720/ and your subject name is freesurfer. This means that you have saved the output from running recon-all on this subject's T1 scan at this location: /Users/ahn/Downloads/9211720/freesurfer/ ___

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters. The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the adjusted values acc

Re: [Freesurfer] LGI problem

External Email - Use Caution I have uploaded to you the data using the Martinos Center FileDrop Hope is a good option for you Thank you Angela > Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro > ha scritto: > > External Email - Use Caution > > > Hi Doug,

Re: [Freesurfer] LGI problem

External Email - Use Caution Hi Doug, I have some problem in uploading my subj.tar.gz using ftp. I am using a MacOs Catalina and, although I am able to connect to the FTP site and open the incoming window (also in binary mode), commands are not working... I am trying to overcom

[Freesurfer] error in TRACUAL : preprocessing step.

External Email - Use Caution Hello? Freesurfer developer. I am attempting to run Tracula and follow the tutorial step using my own data but failed in 1st step, preprocessing. I modified configuration file fit to my pathway Command I used : trac