[Freesurfer] Subfield parcellation in 1.5 T and 2.6 mm Thickness

? Hi FS developers, We were wondering whether a MRI scan that has 2.6 mm thickness + is 1.5 T would be sufficient for a subfield analysis (amygdala, hippocampus, thalamus). Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- This messag

[Freesurfer] Precise MNI152 space

External Email - Use Caution Dear FreeSurfer developers, Which MNI152 space is used within FreeSurfer? Is it the MNI152 nonlinear 6-th generation (as in, for example, FSL), or another one, like MNI152 nonlinear 2009a, 2009b or 2009c? I wasn’t able to find this information in th

Re: [Freesurfer] Brodmann area labels

External Email - Use Caution What do you mean with 'not working'? Is an incorrect area highlighted on the brain? Does some command you are using respond with an error message? Tim > On June 25, 2020 at 5:33 PM Peng Liu wrote: > > > External Email - Use Caution

Re: [Freesurfer] .IMA to NIFTI conversion using mri_convert

External Email - Use Caution Thank you very much, the modifications worked. On Thu, Jun 25, 2020 at 10:08 AM Douglas N. Greve wrote: > Try using dwi.nii > Also, you may want to remove -it siemens_dicom > > > On 6/24/2020 6:54 PM, Vinny K wrote: > > External Email - Use C

Re: [Freesurfer] Brodmann area labels

External Email - Use Caution I usually convert BA3b.label to a nifti mask with SPM to perform ROI analysis. But with exvivo label, the mask seems not working. Many Thanks PL On Thu, 25 Jun 2020 at 16:24, Fischl, Bruce wrote: > Can you elaborate? What do you mean it is not work

Re: [Freesurfer] Brodmann area labels

Can you elaborate? What do you mean it is not working as it should be? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Peng Liu Sent: Thursday, June 25, 2020 7:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Brodmann area labels External Email - Use Caution Hi Br

Re: [Freesurfer] .IMA to NIFTI conversion using mri_convert

Try using dwi.nii Also, you may want to remove -it siemens_dicom On 6/24/2020 6:54 PM, Vinny K wrote: External Email - Use Caution Hi, I have diffusion-weighted images (DWI) from a Siemens scanner in the .IMA format.  I used the following command in an attempt to convert the DWI se

Re: [Freesurfer] Brodmann area labels

External Email - Use Caution Hi Bruce, I have tried this label, but it seems not working as it should be. That is why I wanted to create labels like before. Thank you so much! PL On Wed, 24 Jun 2020 at 16:58, Fischl, Bruce wrote: > Hi Peng > > > > I think 'lh.BA3b*_exvivo*.la

Re: [Freesurfer] Brodmann area labels

External Email - Use Caution Hi Douglas, Previously, after I ran recon-all, I would get multiple labels for the same brain area. For example, for BA3b, I have BA3b.label, BA3b.hmap.label and BA3b.thresh.label for each hemisphere. However this time I only have BA3b_exvivo.label, I

Re: [Freesurfer] Extracting CRAS from nifti (mri_info)

External Email - Use Caution They are computed from the s-form/q-form in the NIFTI header. You can see how it's done in the FreeSurfer source code, which is available on github here: https://github.com/freesurfer/freesurfer It won't be done in 3 minutes, but I did it in R and it

Re: [Freesurfer] Nifti to gifti conversion {Disarmed}

External Email - Use Caution Thanks, Matt. Hopefully one of the developers picks up this thread and gets back to me. Doug, I cc’d you in case you have any thoughts on the issue? Cheers, Mason From: freesurfer-boun...@nmr.mgh.harvard.edu on beha