[Freesurfer] DPABISurf V1.2 Is Released

External Email - Use Caution Dear Colleagues, We are pleased to announce the release of DPABISurf V1.2! DPABISurf is a surface-based resting-state fMRI data analysis toolbox evolved from DPABI/DPARSF, as easy-to-use as DPABI/DPARSF. DPABISurf is based on fMRIPprep 1.5.0 (Esteban

Re: [Freesurfer] issue with lesions

mri_coreg should have printed out tkregisterfv command. Try running that to see if the registration is accurate. What is the nature of anat.nii? On 9/20/2019 4:41 PM, Sam W wrote: External Email - Use Caution Thanks Doug, I'll try that. How would you register the lesion image (which is

Re: [Freesurfer] mri_glmfit: don't display "positive"

In freeview, you can select with sign you want to view (I think it is called "truncation"). Is that what you mean? On 9/20/2019 2:48 PM, Rockers, Elijah D. wrote: External Email - Use Caution Hello, with Qdec, there was an option to "remove" positive (or negative) results from the

Re: [Freesurfer] Keep manual edits of older freesurfer versions?

Hi Joëlle I don't think so, but I guess you could run a subject with 6.0 from scratch, and remove any file in your rerun subjects that doesn't appear in the 6.0 analysis cheers Bruce On Mon, 23 Sep 2019, Joëlle Ismay Rosanne Van Der Molen wrote: External Email - Use Caution 

Re: [Freesurfer] GLM analysis question

On 9/23/2019 10:54 AM, Ferraro, Pilar wrote: > External Email - Use Caution > > To the kind attention of the FreeSurfer team, > > I have some questions concerning a GLM analysis I’m running and any help > would be greatly appreciated! > I’m interested in identifying cortical regions

Re: [Freesurfer] Keep manual edits of older freesurfer versions?

External Email - Use Caution Hi Bruce, Perfect, indeed this is what I was planning to do. Do I need to be concerned about old FS5.1 files that are not updated anymore in the FS6 run (i.e., should I make sure to remove them once FS6 has run)? In other words, there is no risk

Re: [Freesurfer] Keep manual edits of older freesurfer versions?

Hi Joëlle why not cp the whole 5.1 dir to a 6.0 dir, then run recon-all in the 6.0 dir (so all the directories are prepopulated with the 5.1 edits so they can be preserved) cheers Bruce On Mon, 23 Sep 2019, Joëlle Ismay Rosanne Van Der Molen wrote: External Email - Use Caution  

Re: [Freesurfer] talairach.m3z not found

Hi Vasudev that means recon-all didn't complete. Try rerunning with -make all cheers Bruce On Mon, 23 Sep 2019, Dev vasu wrote: External Email - Use Caution Dear all, When i run recon-all , i am encountering an error transforms/ talairach.m3z not found during registration

[Freesurfer] talairach.m3z not found

External Email - Use Caution Dear all, When i run recon-all , i am encountering an error transforms/ talairach.m3z not found during registration phase, could some one please let me know how to resolve this?. Thanks Vasudev ___

[Freesurfer] Keep manual edits of older freesurfer versions?

External Email - Use Caution Dear FreeSurfer experts, I have a question regarding manual edits and change of FreeSurfer version. In our lab, we have thus far processed most of our T1 scans using FS version 5.1 and have performed manual edits when needed. We are now updating

[Freesurfer] GLM analysis question

External Email - Use Caution To the kind attention of the FreeSurfer team, I have some questions concerning a GLM analysis I’m running and any help would be greatly appreciated! I’m interested in identifying cortical regions where older age is associated with greater atrophy.

Re: [Freesurfer] Fwd: Talairach Failure Dection error for recon-all

Hi Hang have you looked at the talairach transform? If it is accurate you can just tell recon-all to ignore it. If it is not, maybe you can run the SPM bias correction later in the stream? cheers Bruce On Mon, 23 Sep 2019, Hang Zeng wrote: External Email - Use Caution

Re: [Freesurfer] freeview command line options

Hi Eli, The bug has been fixed. You can follow these steps to update freeview to the latest dev build: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best, Ruopeng On 9/20/19 4:14 PM, Rockers, Elijah D. wrote: External Email - Use Caution Hello, it's possible I

[Freesurfer] Fwd: Talairach Failure Dection error for recon-all

External Email - Use Caution mT1.nii Dear Freesurfer users, I am trying to run the recon-all command for a T1 imge. The image is bias corrected using spm-segmentation (see attached). And the

Re: [Freesurfer] help! Hippocampal subfield segmentation with FS development version

Dear Liwen, We rebuilt the atlas and there were also minor changes in the code, so the volume won’t be exactly the same. Having said that, if you plot 6 vs dev volumes, they should be highly correlated. Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL

[Freesurfer] Hippocampal Subfields Atlas

External Email - Use Caution Dear Freesurfer developer: I have a group of multimode MRI data, including functional MRI, T1WI and diffusion MRI. We want to analyze the functional and structual connectivity between the hippocampal subregions. Now, we have obtained