[Freesurfer] Color map - color bar

External Email - Use Caution Hello all, I did the post-processing on brain images in Freesurfer. I changed the color coding to display where MR signals values are higher or lower. I need to add the color bar onto the image in order to easily identify what "blue" or "red" color

Re: [Freesurfer] field inhomogeneities and eddy current correction evaluation

External Email - Use Caution Hello all, does anyone know whether it is possible to evaluate the field inhomogeneities and eddy current correction I performed on my DWI images? Thanks Od: Adam Rytina Odesláno: středa 26. února 2020 19:56 Komu

[Freesurfer] field inhomogeneities and eddy current correction evaluation

External Email - Use Caution Hello all, how can I evaluate the field inhomogeneities and eddy current correction I performed on my DWI images? Does any metric exist to do so? Thanks a lot in advance Regards Adam ___ Freesurfer mailing

Re: [Freesurfer] Apply transformation

on structural image? I am still struggling with the transformation of my binary mask as explained below. Thanks a lot Regards Adam Od: Adam Rytina Odesláno: středa 19. února 2020 8:11 Komu: Greve, Douglas N.,Ph.D. Předmět: Fw: [Freesurfer] Apply

Re: [Freesurfer] Apply transformation

External Email - Use Caution Hello, please, could you help me with this case? What am I doing wrong? Thanks a lot Od: freesurfer-boun...@nmr.mgh.harvard.edu za uživatele Adam Rytina Odesláno: sobota 15. února 2020 19:52 Komu: Freesurfer

[Freesurfer] Skull stripping quality assessment

External Email - Use Caution Hello all, I want to assess the skull stripping quality performed in Freesurfer (autorecon1) and in FSL. Does any program enable to evaluate the skull stripping quality? If so, which metric is used for an evaluation? ___

Re: [Freesurfer] Apply transformation

:15 Komu: freesurfer@nmr.mgh.harvard.edu Předmět: Re: [Freesurfer] Apply transformation Yes, mri_vol2vol On 2/15/20 11:07 AM, Adam Rytina wrote: External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatom

[Freesurfer] Apply transformation

External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxel

Re: [Freesurfer] DWI EPI correction

ort list Subject: Re: [Freesurfer] DWI EPI correction In that case, you'll want to use the topup tool in FSL. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Adam Rytina Sent: Thursday, February 6, 2020 3:32 PM To: Freesurfer support list Subject

[Freesurfer] Affine registration 2 input images

External Email - Use Caution Hello all, I need to perform an affine registration between two input images. Please, which Freesurfer tool does enable to perform affine registration (12 DOF) ? Does the command mri_robust_register enable to do that? Thanks a lot Regards Adam __

Re: [Freesurfer] DWI EPI correction

tool in FSL. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Adam Rytina Sent: Thursday, February 6, 2020 3:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] DWI EPI correction External Email - Use Caution I´m sorry I didn´t specify my data. I didn´t acquire

Re: [Freesurfer] DWI EPI correction

r-boun...@nmr.mgh.harvard.edu on behalf of Adam Rytina Sent: Thursday, February 6, 2020 2:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] DWI EPI correction External Email - Use Caution Hello all, I have an input DWI dataset and wanna perform the diffusion data correction (mg suscepti

[Freesurfer] DWI EPI correction

External Email - Use Caution Hello all, I have an input DWI dataset and wanna perform the diffusion data correction (mg susceptibility induced distortion correction, geometric correction...). Does Freesurfer enable to perform the diffusion correction? Does recon-all include thi

Re: [Freesurfer] Noise reduction + Eddy current reduction

rents in a typical T1 or FLAIR On 1/10/2020 2:53 PM, Adam Rytina wrote: External Email - Use Caution Hello all, I want to apply the denoising and eddy current reduction on input images 3DT1 and 3D Flair. Are there any algorithms in Freesurfer to perform the noise and eddy current reduc

[Freesurfer] Noise reduction + Eddy current reduction

External Email - Use Caution Hello all, I want to apply the denoising and eddy current reduction on input images 3DT1 and 3D Flair. Are there any algorithms in Freesurfer to perform the noise and eddy current reduction? Does recon-all involve denoising and eddy current reductio

Re: [Freesurfer] bias field correction Freesurfer

there a reason you don't want to just let recon-all run them in the way it usually does? cheers Bruce On Fri, 15 Nov 2019, Adam Rytina wrote: > > External Email - Use Caution > > Hello all, > > I have an input MR T1w series of images. I want to apply the bias field >

[Freesurfer] bias field correction Freesurfer

External Email - Use Caution Hello all, I have an input MR T1w series of images. I want to apply the bias field correction. According to some articles that I´ve read, bias field correction is automatically done in the standard "recon-all". Is that right - in which of 31 stages

Re: [Freesurfer] recon-all -skullstrip issues

: pondělí 28. října 2019 15:34 Komu: freesurfer@nmr.mgh.harvard.edu Předmět: Re: [Freesurfer] recon-all -skullstrip issues Did you run recon-all from the beginning? It needs to create those files On 10/27/19 3:18 PM, Adam Rytina wrote: External Email - Use Caution Hello all, I´m struggling

[Freesurfer] recon-all -skullstrip issues

External Email - Use Caution Hello all, I´m struggling with running "recon-all -skullstrip", in general with "recon-all". I added NIfTI series file to a new directory "QWE" (/usr/local/freesurfer/subjects/QWE) and running the skull stripping "mri_watershed /usr/local/freesurfer

Re: [Freesurfer] can´t open an image in Freeview {Disarmed}

to try and improve its performance. You could also try setting this on the command line for the vtk libs - but it may not fix the graphics getting greyed out. $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FREESURFER_HOME/lib/vtk/lib/vtk5.6 - R. On Oct 22, 2019, at 14:46, Adam Rytina wrote

Re: [Freesurfer] can´t open an image in Freeview

lo Adam, Please check if you have a “freeview.bin” program. $ which freeview.bin If you get a path back with freeview.bin in it, e.g. something like /usr/local/freesurfer/bin/freeview.bin - then try the ldd command on freeview.bin, $ ldd `which freeview.bin` | grep not - then see if it l

Re: [Freesurfer] can´t open an image in Freeview

ldd `which freeview` | grep not Adam Rytina<mailto:adam.ryt...@outlook.cz> October 18, 2019 at 14:31 External Email - Use Caution Hello all, I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machin

[Freesurfer] FreeSurfer mal list - please remove me

External Email - Use Caution Hello all, few days ago I subscribed to the FreeSurfer list in order to get e-mails regarding the FreeSurfer issues. I will not use FreeSurfer anymore. Hence, please, could you remove me from this list? Thanks a lot Adam