[Freesurfer] Primary slice direction and image origin?

External Email - Use Caution Dear all, This is not directly related to FreeSurfer, however, can anyone tell me how the primary slice direction and image origin is determined from the DICOM header as displayed for example using mri_info? Best, Falk ...

[Freesurfer] freeview parcellation error

External Email - Use Caution Hi FreeSurfer Developers, I'm attempting to perform a freeview visualisation and parcellation to my data on Linux. I can open freeview and load surfaces and volumes.But when I want to load a label for parcellation on freeview ,it can not load label.

Re: [Freesurfer] freeview parcellation error

Hi Ebru are you sure yo uare loading a label and not a color lut? What is the name of the file you are trying to load? cheers Bruce On Thu, 2 May 2019, Ebru Ayyürek wrote: External Email - Use Caution Hi FreeSurfer Developers, I'm attempting to perform a freeview visual

[Freesurfer] inaccurate segmentation from recon-all

Hi Freesurfer team, I have a question about segmentation. I am working with scans of patients with Down syndrome and the segmentation (aseg.presurf.mgz and aseg.mgz) for a few subjects is slightly inaccurate. It mostly affects the areas that we are specifically interested in - basal ganglia and

[Freesurfer] Postdoc position available

External Email - Use Caution Dear all, We are looking for a postdoc in our ERC project, with two main purposes. First, to improve the 3D histology reconstruction tools that we have been developing to build an ultra-high resolution atlas of the brain using histology. And second,

Re: [Freesurfer] inaccurate segmentation from recon-all

Hi Anna can you send us some images of upload a subject so we can see what you mean? cheers Bruce On Thu, 2 May 2019, Mun, Anna wrote: Hi Freesurfer team, I have a question about segmentation. I am working with scans of patients with Down syndrome and the segmentation (aseg.presurf.mgz a

Re: [Freesurfer] Primary slice direction and image origin?

You can use --slicedirection to get the slice direction (it will also get printed out by just running mri_info on a file). What do you mean by the image origin? On 5/2/19 7:16 AM, falk.luesebr...@med.ovgu.de wrote: > > External Email - Use Caution > > Dear all, > > This is not directly r

Re: [Freesurfer] ERROR! FOV=265.909 > 256

Can you send your command line (with -cw256) and the recon-all.log file? On 4/23/19 6:54 AM, Anik Dar wrote: > > External Email - Use Caution > > Hello All, > > I am running recon-all highres on 10 7T MP2RAGE datasets that has been > skull striped and in two subjects, I get the following

Re: [Freesurfer] inaccurate segmentation from recon-all

Bruce, I have uploaded files via FileDrop, I was not able to use freesurfer@nmr.mgh.harvard.edu as a recipient and I used your email instead. Please let me know if you are able to access the files. Thank you! Best, Anna From: freesurfer-boun...@nmr.mgh.harvard.

[Freesurfer] Research Assistant for Brain Imaging Studies @ Albert Einstein College of Medicine {Disarmed}

External Email - Use Caution The Position: The Research Assistant will work in the Division of Cognitive and Motor Aging to acquire, manage and process behavioral and brain imaging data in ongoing neuroimaging studies of older adults. Responsibilities • Recruit, screen and

[Freesurfer] resampling to native space for recons with multiple T1s

External Email - Use Caution Hi Freesurfers, What’s the best way to resample recon data such as aparc+aseg.mgz into scanner space for recons with multiple T1s? Right now I’m using mri_vol2vol with –regheader to resample from orig space to rawavg, then using mri_vol2vol again w

Re: [Freesurfer] resampling to native space for recons with multiple T1s

First, create an LTA to go from the orig to rawavg space: tkregister2 --noedit --mov orig.mgz --targ rawavg.mgz --reg deleteme.dat --ltaout reg.orig-to-rawavg.lta --regheader Then concatenate with the input volume lta, eg, mri_concatenate_lta  -invert2 reg.orig-to-rawavg.lta 001.lta reg.orig-to-0

Re: [Freesurfer] Failure to import cortical surface extracted with Freesurfer into Matlab using ft_read_headshape

Hi Darinka what is fieldtrip? I don't think it is anything of ours. What happens if you call read_surf directly? cheers Bruce On Wed, 1 May 2019, Darinka Trübutschek wrote: External Email - Use Caution Dear freesurfer community, I am currently trying to import cortical su

Re: [Freesurfer] [External] Re: resampling to native space for recons with multiple T1s

External Email - Use Caution Thanks, I'll give this a shot. On 5/2/19, 4:39 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D." wrote: First, create an LTA to go from the orig to rawavg space: tkregister2 --noedit --mov orig.mgz --targ ra