Re: [Freesurfer] username and password

External Email - Use Caution Hi, I am just writing to ask whether you have time to look into the maillist redirecting issue? It would be very helpful to be able to read the existing questions in the maillist. Are there any other ways to search and access the previous QnA emails?

Re: [Freesurfer] view labels in native space

Hi Doug Thanks for your reply. Could you pleas let me know how I can solve this issue? How should I view those labels on the subject’s native space? Thanks Mona On Oct 28, 2019, at 10:18 AM, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: yes, the vertices in one subject do not

Re: [Freesurfer] mri_glmfit ill-conditioned matrix question

My guess is that your covariates have almost no range to them and so look like constant (similar to columns 1 and 2). You can try demeaning and rescaling the covariates. You can do this by hand and create a new FSGD file or you can add the following lines anywhere in the fsgd: RescaleFlag 1

Re: [Freesurfer] view labels in native space

Hi Tim Thanks for you reply. I did use the command you recommended ( tksurfer subject23 lh inflated -ov sig.nii.gz ) But, I don't see any activation on it. However, when I use ( tksurfer fsaverage lh inflated -ov sig.nii.gz ), I see patches of activation. Is it because my whole

Re: [Freesurfer] view labels in native space

yes, the vertices in one subject do not have any correspondence to vertices in an other subject On 10/25/19 12:08 PM, Nasiriavanaki, Zahra wrote: Hi Freesurfer experts I have a few labels that correspond to activation clusters in fsaverage space for an individual subject. I used

Re: [Freesurfer] b0 to T1’s co-registration without b0 inhommogeneities

12 DOF is probably not going to help much. I vaguely remember that there were some tools out there that would attempt to fit the non-linear parts of the B0 map. Maybe in fmriprep? Sorry, can't give you more guidance than that. On 10/26/19 10:56 AM, Daniel Callow wrote: External Email -

Re: [Freesurfer] Error in glmfit-sim cache

Which version of FS are you using? One thing you can try is setenv LANG en_US.UTF-8 or if you on bash export LANG=en_US.UTF-8 On 10/26/19 2:56 PM, Renew Andrade wrote: External Email - Use Caution I don’t know what do you mean by not knowing what it means. I said that I have tried all

Re: [Freesurfer] recon-all at native resolution

Yes, this is the issue we have with the high res stream in v6. As I said, you can use the patch that I pointed to below to get better surfaces. On 10/25/19 12:30 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Opps, here are the snapshots. The aseg subcortical look good

Re: [Freesurfer] Vertex and voxel-wise linear regression in Freesurfer

what is your request? On 10/26/19 1:20 PM, Larry Lai wrote: External Email - Use Caution Hello FreeSurfer Users I'm attempting to explore the correlations between the surface-based and voxel-based values and adjusted for nuisance covariate in FreeSurfer. Correlational study: A.

Re: [Freesurfer] recon-all -skullstrip issues

Did you run recon-all from the beginning? It needs to create those files On 10/27/19 3:18 PM, Adam Rytina wrote: External Email - Use Caution Hello all, I´m struggling with running "recon-all -skullstrip", in general with "recon-all". I added NIfTI series file to a new directory "QWE"

Re: [Freesurfer] view labels in native space

External Email - Use Caution If I get the question correctly, all you have to do is: 1) not run mri_label2label at all 2) replace 'fsaverage' with the subject identifier in the command, e.g.: tksurfer subject23 lh inflated -ov sig.nii.gz Best, Tim > On October 28, 2019

Re: [Freesurfer] recon-all at native resolution

External Email - Use Caution Thanx Doug. Tried the patch and got similar results to -hires. Must be the data and tissue contrast in that region where WM is difficult to discern. These are 2yo subjects. We also tried baby freesurfer with poorer results. Jim From:

Re: [Freesurfer] mri_cvs_register error while diffusion imaging processing

Hi Andrade, This probably has to do with SIP being enabled, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best, Andrew

Re: [Freesurfer] username and password

Hi Rachel, the mailing list archives are available to search through at https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ Best, Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Rachel S Sent: Monday, October 28, 2019 10:08

Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}

Yes On 10/28/19 1:04 PM, Nillo, Ryan Michael R wrote: > Am I correct in assuming this results in z-scoring/normalizing the > covariates? > > Ryan Michael Nillo > Staff Research Associate I > University of California San Francisco > Department of Radiology and Biomedical Imaging > >> On Oct 28,

Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}

Am I correct in assuming this results in z-scoring/normalizing the covariates? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On Oct 28, 2019, at 7:33 AM, Greve, Douglas N.,Ph.D. > wrote: > > My guess is

Re: [Freesurfer] recon-all -skullstrip issues

External Email - Use Caution Hello, what do you mean by the beginning? You mean to download the tutorial set and run recon-all on that? Thanks Adam Od: freesurfer-boun...@nmr.mgh.harvard.edu za uživatele Greve, Douglas N.,Ph.D. Odesláno:

[Freesurfer] FW: Mapping coordinates from sphere file to ?h.white

External Email - Use Caution From: Timothy Coalson Reply-To: Timothy Coalson Date: Monday, October 28, 2019 at 8:21 PM To: "Glasser, Matthew" Subject: Re: FW: [Freesurfer] Mapping coordinates from sphere file to ?h.white That is not a sphere of fs_LR coordinates (in fact,

[Freesurfer] Mapping coordinates from sphere file to ?h.white

External Email - Use Caution Dear experts, In the context of the BIDS transforms extension and the ".x5" format we chatted about in the workshop we made in March at MIT, we are addressing the following question. We have a sphere of fsLR coordinates in fsaverage space (e.g.,

Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels

External Email - Use Caution Hi Kersten, Did you recieve the files I dropped to [ mailto:mreu...@nmr.mgh.harvard.edu | mreu...@nmr.mgh.harvard.edu ] on the 16th of October (titled 'BAR_Sydney_FSIssues_SurfThreshLabels.zip')? Kind regards, Bronwyn Overs Research

Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}

External Email - Use Caution Thanks, Doug. One more question: I want to see how correlated my covariate ROI is with LGI and compare the correlation maps between the two groups. Is my glmfit command the correct setup? I have tried running glmfit on a different fsgd and contrast