[Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

Hi, I have run a number of cases through the FS6 hippocampal longitudinal processing steps listed at https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing It seems that all steps completed, but when it came

Re: [Freesurfer] Fwd: wm edits not incorporated

Thank you, this is very helpful. Octavian On Thu, Apr 13, 2017 at 12:19 PM, Antonin Skoch wrote: > Dear Octavian, > > the current philosophy with wm.mgz edits is not to directly affect voxel > values in original T1 image. > > The wm.mgz serves as starting point for the white

Re: [Freesurfer] Freeview - corrupted pixel values after saving volume (via save as) when images with mutually different geometry are simultaneously loaded

Dear Ruopeng, thank you for the feedback. Yes, the behavior is exacly like you described. I suspected that this has something to do with resampling but I was not sure. The stripes were result of nearest-neighbor interpolation. Antonin Hi Antonin, When you load two images like that, the

Re: [Freesurfer] Surface down sample by taking cortical vertices only

Hi It is for computing sources correlation with symmetrical orthogonalized correlations which is dependent on the rank of the data, so I am limited to the number of sensors I use for estimating sources. I would appreciate to know if there is any method to get about a 100 cortical vertices in the

Re: [Freesurfer] Fwd: wm edits not incorporated

Dear Octavian, the current philosophy with wm.mgz edits is not to directly affect voxel values in original T1 image. The wm.mgz serves as starting point for the white surface estimation. The ?h.white surface is estimated according gradient in voxel values in brain.finalsurfs.mgz (which is,

Re: [Freesurfer] Freeview - corrupted pixel values after saving volume (via save as) when images with mutually different geometry are simultaneously loaded

Hi Antonin, When you load two images like that, the second image will be resampled, using nearest neighbor method by default. And when you save, it will be resampled back to its original space. So there will be shifted voxels depending how oblique it is to the first image. So I think what you

Re: [Freesurfer] manual edits

Dear John, David, To great summarization of David, I would add following: My personal preference is to run whole -autorecon2 -autorecon3 after editing of the brainmask.mgz. Early stages of -autorecon2 (normalization, registration, volumetric labeling) use brainmask.mgz, therefore I believe

[Freesurfer] Freeview - corrupted pixel values after saving volume (via save as) when images with mutually different geometry are simultaneously loaded

Dear experts, I encountered following issue with freeview: When two images with mutually different geometry are simultaneously loaded and one of them is saved (via save as), its pixel values get somewhat corrupted. There are strips in image with modified pixel values. It seems to affect only

Re: [Freesurfer] trac-all -stat

OK, thanks Amelia. That's interesting - keep me posted if you run into this with 6.0 in any new data set. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Versace, Amelia [versa...@upmc.edu] Sent:

Re: [Freesurfer] trac-all -stat

Thanks, Anastasia!! It should be it. I had run the same command before with slightly fewer subjects in my "set subjlist" and it did work fine. Then I rerun the -path (and added extra 18 subjects) to update the tracts with the recent implementation that you have done (FS 6). After, started

Re: [Freesurfer] Bits of dura being captured as GM ..

Hi Shane by far the best way to do this is if you have a T2 or FLAIR scan that is high-enough resolution (i.e. around 1mm isotropic). If not, you can try the graph cuts skull stripping option in recon-all. It is more aggressive than the watershed (which is the default). cheers Bruce On

[Freesurfer] mri_watershed script not working

Hello FreeSurfer Developers and experts, I am trying to run our FSPGR sequences using the -mri_watershed script, but I am not able to set and vary the -t threshold. The aim of my work is to calculate the BPF in order to quantify parenchymal atrophy in patients with Multiple Sclerosis. Instead

Re: [Freesurfer] Using own parcellation atlas

Hi Julie what space is the Gordon Parcellation in? Did they use FreeSurfer? If so, then you just need to map it to each of your subjects. And how is a surface-based parcellation stored in a nifti file? cheers Bruce On Wed, 12 Apr 2017, Julie Hall wrote: Hi experts, I would like to

Re: [Freesurfer] mris_ca_label giving error CTABfindAnnotation: ct was NULL

Thanks . Its working now. ___T_ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 11 April 2017 16:48 To: Freesurfer support list Subject: Re: [Freesurfer]

Re: [Freesurfer] manual edits

Hi David, Thank you for the feedback! I followed your advice's and everything has been resolved. Highly appreciated! Cheers, John Sent with [ProtonMail](https://protonmail.com) Secure Email. Original Message Subject: Re: [Freesurfer] manual edits Local Time: April 12, 2017

Re: [Freesurfer] Longitudinal Pipeline

Yes, that is why it is experimental. However, global atrophy will affect the ventricles (they are growing) which is an effect in the opposite direction, so maybe it cancels out to some extend. Best, Martin > On 12 Apr 2017, at 23:55, Arman Eshaghi wrote: > > Thanks