Re: [Freesurfer] starting longitudinal pipeline after mri_robust_template

External Email - Use Caution Hi Martin, Thank you for your email! What is the best way to stop the long pipeline after a certain step in a way that allows continuing from there? Best, Marisa Am Do., 22. Okt. 2020 um 11:54 Uhr schrieb Martin Reuter < mreu...@mgh.harvard.edu>: >

[Freesurfer] Open a Pre-doc position in Spain

External Email - Use Caution Dear FreeSurfer forum, Sorry for the cross posting. We are looking to cover a position for a* pre-doc* student working in the field of life sciences (medical doctor, biologist, psychologist) to work on a project about arteriopathies and atherosclerosi

Re: [Freesurfer] eTIV=0.0 on volumes where control points have been added manually

External Email - Use Caution Hi, Thank you for your help. Best regards, Julia Lam 12 jan. 2021 kl. 16:56 skrev Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>>: Hi Julia, this is a bug. We've fixed it in our development version, but for you there are a few option. One is

Re: [Freesurfer] Desikan Killiany Atlas Node Coordinates

If you want the coordinates, you can also run mri_segcentroids on the aparc+aseg.mgz in fsaverage. Or, if you want them in mni152 space, you can run the 152 through recon-all and then run mri_segcentroids on the resulting aparc+aseg.mgz On 1/5/2021 11:01 AM, Mora, Jocelyn S. wrote: Hi Jessica,

Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

When you use --cache, mri_glmfit-sim will use precomputed (ie, "cached") CSD files as found in $FREESURFER_HOME/average/mult-comp-cor On 1/5/2021 4:55 PM, Na, Xiaoxu wrote: External Email - Use Caution Dear Freesurfer Experts, I’ve all the subjects successfully done recon-all, lgi befo

Re: [Freesurfer] Editing Recon-all on Different Computers

Yes, i think that is still fine On 1/5/2021 8:18 PM, Boa Sorte Silva, Narlon wrote: External Email - Use Caution Hi Allison As a follow-up to this question Applying gcut to improve skull stripping when making the manual edits on a different computer be a problem (still same FS version

Re: [Freesurfer] parcellation-based connectome viewing in freeview.

this might be something you can do in matlab with the function below (found in $FREESURFER_HOME/matlab) function surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile) % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile) % % Example: % I have three annotations % ann

Re: [Freesurfer] mincRead error in recon-all

Hi Michele, Looks like the base error here is: ncopen: filename "./tmp.mri_nu_correct.mni.6973/nu1.mnc": Not a netCDF file My immediate guess is this is a version incompatibility. You mentioned that you reinstalled minc tools? How so and with what version? Also, what was the previous nu_correct

Re: [Freesurfer] Non-uniform voxel size

I've just created a new version of gtmstats2table (attached). This will take a --volume flag to report the volume of the ROIs instead of the uptake On 1/6/2021 6:00 PM, Julie Ottoy wrote: External Email - Use Caution Thank you Doug! I have another question related to voxel size. In th

Re: [Freesurfer] freesurfer flag for multiple edited volumes

Greetings Aylin, If you have made edits to both the brainmask.mgz and wm.mgz files, I would recommend running recon-all with the -autorecon2 and -autorecon3 flags. Each step in the FreeSurfer recon-all process draws on files generated in previous steps. So, if you have made edits to the wm.mgz

Re: [Freesurfer] Non-uniform voxel size

External Email - Use Caution Thank you Doug, this is great! On Wed, 13 Jan 2021 at 10:41, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > I've just created a new version of gtmstats2table (attached). This will > take a --volume flag to report the volume of the ROIs in

Re: [Freesurfer] freesurfer flag for multiple edited volumes

External Email - Use Caution Hi Jackson, Thank you for the reply! I appreciate the explanation. It makes sense the wm.mgz edits need to be run before the brainmask.mgz edits through the recon-all pipeline. Just to clarify, would it be preferred to run: "recon-all -s subject -a

Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

External Email - Use Caution Thank you for your confirmation! I tried the -perm as well and this error wouldn't show after using the csd files generated from permutation. However, I have one more question. Shall I use -perm first in order to use -cache? If this is the case, the

Re: [Freesurfer] Post-Doctoral position available in human neuroimaging and sensory testing at the University of Minnesota School of Dentistry

External Email - Use Caution A gentle reminder that this post doctoral position is still open for applications. Thank you. On Mon, Sep 14, 2020 at 2:28 PM Estephan Moana Filho wrote: > *POSITION OVERVIEW* > > > > The Division of TMD & Orofacial Pain (OFP) at the University of Mi

Re: [Freesurfer] freesurfer flag for multiple edited volumes

Hello Aylin, You should be fine running 'recon-all -autorecon2-wm -autorecon3' FreeSurfer will not overwrite or ignore the manual edits you have made, even if you begin processing before that volume is created (i.e. edits made to brainmask.mgz will be considered if you run -autorecon2, or the e

Re: [Freesurfer] parcellation-based connectome viewing in freeview.

External Email - Use Caution Thank you, this is very helpful. Octavian On Wed, Jan 13, 2021 at 9:19 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > this might be something you can do in matlab with the function below > (found in $FREESURFER_HOME/matlab) > > > functi