[Freesurfer] timeseries question

Hi Freesurferes I have extracted timeseries from a task fMRI using the command below: mri_segstats --i fmcpr.sm0.self.rh.nii.gz --slabel $subj rh rh.label --id 1 --avgwf-remove-mean --avgwf ./rh.txt My question is: Is the temporal drift being counted in considering that I used preprocessed dat

Re: [Freesurfer] group analysis for same group in 2 conditions

External Email - Use Caution Thanks for your support. Here my "mkanalysis-sess" command: mkanalysis-sess -a rtopy.self.?h.ng -surface self ?h -paradigm rtopy.par > -retinotopy 41 -TR 2.5 -fsd bold -fwhm 5 -per-run I run this command for both no goggles condition (rtopy.self.?h.n

Re: [Freesurfer] Issue with BBR and Applying CVS Warps to Diffusion Data

External Email - Use Caution The b0-to-anat look fine. I’m using mri_vol2vol with trilinear interpolation to apply the CVS warps. Thanks, -Austin From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Friday, February 28, 2020 at 3:18 PM To: "freesurfe

Re: [Freesurfer] Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary

Sorry, I don't know what else to tell you. On 2/28/2020 9:59 AM, CiRong Liu wrote: External Email - Use Caution Hi, Douglas, Thank you for your reply. I tried adding -max XXX. If I set the "-max 5" as the default values, the mris_mask_surfaces would finish running. However, if

Re: [Freesurfer] group analysis for same group in 2 conditions

What quantity from the retinotopy analysis do you want to compare across subjects? Eg, the phase? Can you send your mkanalysis-sess command? On 2/28/2020 8:17 AM, Marco Ninghetto wrote: External Email - Use Caution Dear experts, I'm performing a study on visual pathways, in which each

Re: [Freesurfer] mri_vol2surf produces invalid surface

mri_vol2surf does not actually produce a surface, it produces a surface overlay (ie, a value for each vertex). You can to run recon-all to produce a surface On 2/27/2020 4:49 AM, Shuntaro Aoki wrote: > External Email - Use Caution > > Dear mailing list, > > I was trying to convert a vol

Re: [Freesurfer] Issue with BBR and Applying CVS Warps to Diffusion Data

So the B0-to-Anat registration is ok? What command are you using to map the B0s into the CVS space? On 2/26/2020 3:50 PM, Austin Patrick wrote: External Email - Use Caution Dear All, I have used CVS to align around 180 scans to a single, representative subject. I have then used BBR

Re: [Freesurfer] make_average_subject

Look at the release notes for how to resolve this http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes On 2/26/2020 4:34 AM, Benjamin Ineichen wrote: External Email - Use Caution Dear Freesurfer experts, I want to create a new standard template from my study population. For this, I

Re: [Freesurfer] beta testing FreeSurfer v7 beta: recon-all-status.log, samseg

Yes, if you want to run it now, use samseg --i orig.mgz --i T2.mgz --o samsegdir And don't use the T1.mgz I have fixed this bug in the version that we will release. I mostly wanted to make sure that samseg itself would run. On 2/25/2020 3:08 PM, Antonin Skoch wrote: External Email -

Re: [Freesurfer] DOSS questions

answers below On 2/25/2020 4:36 AM, Ferraro, Pilar wrote: External Email - Use Caution Thank you so much for all the help! Below you can find few remaining questions I have following your suggestions! Message: 6 Date: Mon, 24 Feb 2020 09:24:00 -0500 From: "Douglas N. Greve"

Re: [Freesurfer] Registration error

Hi Tim, Did you use an auto-completion plugin to fill out the webform? If so, can you disable it and try again? We have a fairly ~old-fashioned~ spam detector that checks for completed entries in hidden fields. best, Andrew From: on behalf of "Harrigan, Timothy P." Reply-To: FS Help Date:

Re: [Freesurfer] MNI coordinates from Thalamic nuclei

Hi Corinna, You can compute label centroids from a segmentation using mri_segcentroids, and you can map them into any space with the --lta flag. best Andrew From: on behalf of Corinna Bauer Reply-To: FS Help Date: Friday, February 28, 2020 at 10:48 AM To: FS Help Subject: Re: [Freesurfer]

[Freesurfer] OHBM Brainhack 2020

External Email - Use Caution Hello all, The OHBM Open Science Special Interest Group is very happy to announce that the 8th Annual OHBM Brainhack will be held June 23-25 at Phi Centre in Montreal. A hackathon? For who? At the OHBM Brainhack, member

Re: [Freesurfer] MNI coordinates from Thalamic nuclei

External Email - Use Caution I have them already ask masks in subject space, but I am doing connectivity analysis on a few of them and would need the MNI coordinates of the centroids for visualizing those results. Thanks! On Fri, Feb 28, 2020 at 10:29 AM Glasser, Matthew wrot

Re: [Freesurfer] MNI coordinates from Thalamic nuclei

External Email - Use Caution Why not represent thalamic nuclei as the actual masks? Thalamic nuclei are not single points. Matt. From: on behalf of Corinna Bauer Reply-To: Freesurfer support list Date: Friday, February 28, 2020 at 9:26 AM To: Mailing Freesurfer List Subjec

[Freesurfer] MNI coordinates from Thalamic nuclei

External Email - Use Caution Hi all, Is there a way to obtain the MNI coordinates for the thalamic nuclei? Thanks Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

Re: [Freesurfer] Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary

External Email - Use Caution Hi, Douglas, Thank you for your reply. I tried adding -max XXX. If I set the "-max 5" as the default values, the mris_mask_surfaces would finish running. However, if I set the "-max" more than 5, the mris_mask_surfaces would crash during the runn

[Freesurfer] group analysis for same group in 2 conditions

External Email - Use Caution Dear experts, I'm performing a study on visual pathways, in which each participant undergoes to 2 different conditions. One in normal sight (NG, i.e.: No Goggles) and second in narrowed sight using special goggles (YG, i.e.: Yes Goggles). I'd like to co