Re: [Freesurfer] Wm.mgz editing

Probably a topological defect but we would need the data to tell. Feel free to ftp it to us and we will take a look Cheers Bruce > On Feb 8, 2018, at 12:19 PM, Emily Schwartz > wrote: > > Hi FreeSurfer community, > > I am relatively new to manually editing and am having some questions dealing

[Freesurfer] smoothing command line- LGI

Hi, I am interested in looking at between-group differences in in LGI on Qdec (I will look at surface area as well later). I have a question regarding the smoothing stage. My recon-all for all subjects has completed, and I have LGI values for each subject. For smoothing, I was going to run the

Re: [Freesurfer] mri_segment error

looks like the acquisition is not what you would need to run FreeSurfer on. Looking at the log I think your input is a T2-weighted image (we require a T1) with a slice thickness of 9mm (we require all voxel dimensions to be <=1.5mm or so) cheers Bruce On Thu, 8 Feb 2018, Z Hessam wrote: s

Re: [Freesurfer] mri_segment error

when i use first code for another data set, it sent me an error: ERROR: /tmp/hessam91.tmp.decompressed.dcm.PV8Mal is not a dicom file why this error happens? On Thu, Feb 8, 2018 at 9:48 PM, Z Hessam wrote: > sure... > with first code i convert *.dcm files. > with second code i want to segment

Re: [Freesurfer] Cuda version > 5.0

Yes, Freesurfer 6 works well with CUDA 9.1. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Melanie Ganz Sent: Thursday, February 8, 2018 10:54 AM To: Freesurfer support list Subject: [Freesurfer] Cuda version > 5.0 Dear FS list, we just got a reall

[Freesurfer] Cuda version > 5.0

Dear FS list, we just got a really nice graphics card (Quadro P6000) that we also would like to use to speed up recon-all, preferably for running high-res data with FS version 6. Now we know that in the precompiled FS version 6 it still looks for cuda 5.0, but it seems like some people have got

Re: [Freesurfer] mri_segment error

can you send us the complete command you ran, the entire screen output and the recon-all.log file? cheers Bruce On Thu, 8 Feb 2018, Z Hessam wrote: Hello FreeSurfer develpers I'm attempting to run " recon-all " command on a file of dicom data, and encounter with an error command: recon-all -

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Hi Mohamed it depends on how you computed it. I believe that the one in the exvivo.stats file computes it directly from the surfaces (i.e. sum of the volumes of the tetrahedra or something like that). If you sample it into the volume and add up voxels you will get discretization artifacts that

Re: [Freesurfer] Extending pial surface to include excluded cortex

I agree that it looks like a topological defect that is fixed incorrectly. We can't tell from looking at the image of one slice though. If you gzip, tar and ftp the subject to us we will take a look cheers Bruce On Thu, 8 Feb 2018, Arsenije Subotic wrote: Hi Doug, I’ve notic

[Freesurfer] mri_segment error

Hello FreeSurfer develpers I'm attempting to run " recon-all " command on a file of dicom data, and encounter with an error command: recon-all -s dyegmoh exited with ERRORS at Thu Feb 8 17:08:16 +0330 2018 how can i understand why this error happens and what should i do to solve it? __

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Dear Bruce, Many thanks for you kind answer. I sampled the perirhinal roi label into the volume using the suggested command line: "mri_label2vol --subject s6904 --fill-ribbon --label lh.perirhinal.label --o lh.perirhinal.volume.nii --hemi lh --identity". The obtained mask seems to cover well th