[Freesurfer] mesh referential

External Email - Use Caution Hello, I would like to know in which referential is the meshes ( lh.smoothwm for example). Is it RAS ? If not, how can we change the mesh referential in this referential. Thank you in advance for your time and answer. Best regards, Marion Taconné T

[Freesurfer] FreeSurfer 7.1.0 tkmedit not opening - please help

External Email - Use Caution Hello everyone, I'm having a problem with tkmedit on the pre-installed Freesurfer 7.1.0 version for as Ubuntu guest on a Windows 10 host (via Oracle VM). I did work with the 6.0 version before but changed to Freesurfer 7.1 and used the .vdi for Oracle

[Freesurfer] Fwd: Re: Segmentation with FreeSurfer 7.1

External Email - Use Caution Subject: Re: Re: [Freesurfer] Segmentation with FreeSurfer 7.1 Message-ID Hi, thanks a lot. What do you mean for topological default? We have checked our data, and there aren't any visible artifacts (if you were referring to this kind of things). Act

[Freesurfer] FreeSurfer 7.1.0 VirtualBox Installation password

External Email - Use Caution Hi, I followed the given instructions on this page (https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67) but could not find the README file to find the password to log in to the developer account. I've seen that other users in the archive received the p

[Freesurfer] Working with cortical surface area - parcellation size?

External Email - Use Caution Hi Freesurfer colleagues, I want to analyze regional profiles of differences in cortical surface area (SA). However, SA and its group differences in SA depend on parcellation size. In order to mitigate this effect, should I create a parcellation that

[Freesurfer] The input for Petsurfer

External Email - Use Caution Hello Freesurfer developers, I have PET images for brain and I want to analyze them with Petsurfer. But I don't have T1-weighted MRI of each subject. What should I do? Is it possible? Thank you in advance, Best regards, Hengameh ___

[Freesurfer] PETSurfer questions part III

External Email - Use Caution Hi Douglas, All the analyses have been run with FS version 6 indeed. If you confirm the commands below are correct, I therefore assume I should rerun all the analyses using FS 7.1. I just have few remaining questions: 1. Are there any other ROIs mo

Re: [Freesurfer] FS 7.1 update

External Email - Use Caution Hi Freesurfer experts, I'ld like to know whether it's possible to update a FS version (from 6.0 to 7.1) also remotely. Many thanks, Pilar > Il giorno 24 lug 2020, alle ore 4:27 PM, Ferraro, Pilar > ha scritto: > > Hi Douglas, > > All the anal

Re: [Freesurfer] Extract the cerebellum

Try mri_binarize --i aseg.mgz --match 7 8 46 47 --o cerebellum.nii.gz Those numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt On 7/23/2020 9:47 PM, Camargo, Aldo wrote: External Email - Use Caution Hi Freesurfer experts, I am trying to extract only the cerebellum and then save

Re: [Freesurfer] FreeSurfer 7.1.0 VirtualBox Installation password

External Email - Use Caution Hello Nuri, I am sending the password directly to your email. -R. On Jul 24, 2020, at 09:30, Choi, Nuri wrote:External Email - Use CautionHi,I followed the given instructions on this page (https://surfer.nmr.mgh

[Freesurfer] Question for Multiple Sclerosis

External Email - Use Caution Hey Freesurfer, I am new to Freesurfer. I wanting to use Freesurfer for measuring grey and white matter volumes in Multiple sclerosis. However I am wondering if there is a way to manually make a lesion mask for each individual and then use the mask

Re: [Freesurfer] mesh referential

The surface coordinates are in what we call "tkRegister space". Check out this page (and slide deck on this page) https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 7/24/2020 4:53 AM, TACONNE Marion (INTERN) wrote: External Email - Use Caution Hello, I would like to know

Re: [Freesurfer] Fwd: Re: Segmentation with FreeSurfer 7.1

Here is the page on topo defects https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefectV6.0 I can't answer your other questions because the previous emails are not in this one. If you repost with previous correspondance, then I can answer. On 7/24/2020 8:12 AM, Sara PONTICORVO

Re: [Freesurfer] The input for Petsurfer

It is not really possible. It is designed assuming you have MRIs. On 7/24/2020 10:06 AM, Hengameh Marzbani wrote: External Email - Use Caution Hello Freesurfer developers, I have PET images for brain and I want to analyze them with Petsurfer. But I don't have T1-weighted MRI of each s

Re: [Freesurfer] PETSurfer questions part III

On 7/24/2020 10:27 AM, Ferraro, Pilar wrote: > External Email - Use Caution > > Hi Douglas, > > All the analyses have been run with FS version 6 indeed. > If you confirm the commands below are correct, I therefore assume I should > rerun all the analyses using FS 7.1. > > I just have fe

Re: [Freesurfer] FS 7.1 update

I don't know what you mean. Do you want to install 7.1 on top of 6.0? That's probably not a good idea. They can exist on the same computer. Not sure what you mean by remotely On 7/24/2020 10:36 AM, Ferraro, Pilar wrote: > External Email - Use Caution > > Hi Freesurfer experts, > > I'ld

Re: [Freesurfer] Question for Multiple Sclerosis

Yes, just copy aseg.mgz and edit the copy. Then run mri_segstats. Look in recon-all.log for the mri_segstats command that is used to create the aseg.stats file. Adapt that command. The output will have an entry for the lesion (make sure to use code 99 for the label id). On 7/24/2020 1:43 PM, M

Re: [Freesurfer] FW: mri_fieldsign error

A few more questions 1. How much memory do you have on your system? You can find it from the first line of /proc/meminfo It should be something like "MemTotal:   131781468 kB" 2. What environmental limits do you have? Send the result of the "limit" unix command 3. I put a new version of

[Freesurfer] Coregistration to MNI

External Email - Use Caution Hi Freesurfer experts, I want to coregister a PET image to the MNI space, can I use mri_cvs_register ? Thanks a lot, Aldo Camargo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.