[Freesurfer] Getting from MNI152 to fsaverage

External Email - Use Caution Dear experts, I am comparing freesurfer mri_vol2surf to nilearn surface.vol_to_surf. I am finding large differences so I just wanted to get this command absolutely right before making any sort of conclusions. I would love if someone could confirm t

[Freesurfer] mris_convert to gifti

e issue is. I am running this version of freesurfer: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b Could someone provide an example how this is done? Thank you so much! Lauri Tuominen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

Re: [Freesurfer] Longitudinal stream bug ?

messed things up, maybe. Have a nice day! Lauri From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lauri Tuominen Sent: November-03-22 2:39 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal stream bug ? CAUTION: External Mail. Do

[Freesurfer] Longitudinal stream bug ?

r this error but did not see anything. Would anyone have any thoughts on how to fix this? Thanks in advance Lauri Tuominen? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The infor

[Freesurfer] Fully funded postdoctoral fellowship in Ottawa, Canada

External Email - Use Caution Drs. Lauri Tuominen and Sara Tremblay at the Institute of Mental Health Research in Ottawa are looking for a postdoctoral fellow. The candidate should have strong experimental skills in resting state fMRI to be able to develop and implement an fMRI

[Freesurfer] Integrating glmsingle with freesurfer and mri_glmfit

? Thank you again! Lauri Tuominen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If yo

[Freesurfer] Issue with tksurfer-sess

External Email - Use Caution Dear Surfers, I ran into a problem with tksurfer-sess. See below. I have a mac big sur. I wonder if there is a bug. Any help would be appreciated. Thank you Lauri Tuominen tksurfer-sess -s subj1 -d ../subjects -analysis ftap.sm05.rh -c ftap

[Freesurfer] FSFAST (mkcontrast-sess) with Octave

out? Am I missing a file or a path? Thank you so much Lauri Tuominen INFO: Found 2 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1. 0 mkcontrast2 -config ../mkanalysis/ftap.sm05.lh/ftap.config -anadir ../mkanalysis/ftap.sm05.lh -wcond 1. 0

[Freesurfer] time point exlusion file exceed nframes

outliers. So my tpef file includes numbers 478.4 and 480.7. When I run selxavg3-sess, I get the error time point exlusion file exceed nframes. I can’t figure out where the bug might be. So once again I would really appreciate your help! Thanks Lauri Tuominen

[Freesurfer] fsaverage label into functional space

dof6.lta And I get exactly the same ROI in the volume. So just to confirm, is this what I want for the fcseed -commands? Thank you so much again! Lauri Tuominen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard

[Freesurfer] Conversions between MNI152, MNI305 & surface

External Email - Use Caution Hello! I keep having 2 somewhat related problems: 1. How to convert a single coordinate from MNI305 to surface. Previosly Doug suggested to try the example 8b in https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems. However, that one is about

[Freesurfer] MNI target to surface

5mm radius sphere. Thank you so much! Lauri Tuominen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Group level T map

, which I take means that it is the beta coefficient map. Which one would be the t-value map or should I calculate this separately? Thank you so much!! Lauri Tuominen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] How to use FIR to get HRF shape

events with the TR. Am I completely lost here? Cheers! Lauri Hi Lauri, what is non-ideal about it? doug On 12/06/2018 05:30 PM, Lauri Tuominen wrote: > External Email - Use Caution > > Hi there, > > I would like to know if a condition leads to a delayed HRF peaking. &g

[Freesurfer] How to use FIR to get HRF shape

other workaround / analysis? Or do I need to collect the data in some other way, i.e somehow sliding the TR-event locking? Additional question: what is in cesmag.nii.gz, cesmagpct.nii.gz, iminsig.nii.gz and minsig.nii.gz? Thanks so much again for the help Lauri Tuominen

[Freesurfer] pcc.nii.gz vs z.nii.gz resting state

are extremely high, i.e. > 4. Am I doing something totally wrong? My understanding was that z = arctanh(r). Thank you so much again! Lauri Tuominen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mail

[Freesurfer] Error running hippocampal segmentation with FS6

Dear freesurfers, I tried running hippocampal segmentation using the Dev version 6 on launchpad. I get the following error message: I ran the recon-all command yesterday and it worked fine. Cheers! Lauri Tuominen INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux

[Freesurfer] mri_glmfit-sim

ance! Lauri Tuominen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail