Re: [Freesurfer] regions of Yeo 17 networks in fast

External Email - Use Caution Dear Freesurfer users, We have fixed the issue. In our previous Yeo2011 split components parcellation (version b in Ruby’s email), the colortable inside these annot files contain ROIs from both hemisphere. This will cause some problems when you want t

[Freesurfer] Where is the BrainVolStatsFixed patch?

External Email - Use Caution Dear Freesurfers, I just read the page about “Fixing of Morphometry Stats and Global Measure of Volume” on the freesurfer website . I am, however, a bit confused about the location of the

[Freesurfer] convert aseg to functional space

External Email - Use Caution Hi, I just finished reconall and now I'd like to convert the aseg.mgz to native functional space. My first thought was to simply convert the aseg.mgz to native functional space with mri_vol2vol: mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func

Re: [Freesurfer] Holes in labels (Brainnetome) after conversion from surface to volumetric space

External Email - Use Caution Now, I understand! Thank you so much for your help !! ;-) Carolin On Tue, Apr 16, 2019 at 4:07 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > A voxel is a 3D cube. The surface is a 2D sheet. The surface may pass > through the cube in s

[Freesurfer] same aparc ROI with mri_label2vol?

External Email - Use Caution Hi, I created a series of labels with mri_annotation2label (aparc.a2009s labels) and then created a reg file with: tkregister2 --mov mri/rawavg.mgz --noedit --s bert --regheader --reg register.dat and the volume: mri_label2vol --label labels/lh.G_cingul

Re: [Freesurfer] same output with vol2vol and label2vol

External Email - Use Caution Thank you Douglas. So that means I can basically use either one for freesurfer to native space conversion, is that right? Is there any case in which label2vol should definitely be used instead of vol2vol? Best regards, Sam On Tue, Apr 16, 2019 at 10:1

Re: [Freesurfer] Holes in labels (Brainnetome) after conversion from surface to volumetric space

A voxel is a 3D cube. The surface is a 2D sheet. The surface may pass through the cube in several ways. It might pass right through middle or just  nick one of the corners. When we select whether the voxel is inside or outside of the surface, we have to handle these cases where it is partially

Re: [Freesurfer] Holes in labels (Brainnetome) after conversion from surface to volumetric space

External Email - Use Caution Could you explain a little more what you mean with "even if the surface just barely goes through it"? I assume that this is something I would understand when I look in more detail on how the conversion is done from surface to volumetric space? Carolin

Re: [Freesurfer] Holes in labels (Brainnetome) after conversion from surface to volumetric space

I think what is happening is that when you use the --annot option, it will fill in a voxel even if the surface just barely goes through it. With --fill-ribbon, it will only fill in a voxel if that voxel is labeled as ribbon in the ribbon.mgz file. The --fill-ribbon is probably going to be more

Re: [Freesurfer] Followup on the mystery of the missing mcprextreg file

Can you upload the functional volume to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is On 4/16/19 5:55 PM, Mcnorgan, Christopher wrote: > > External Email - Use Caution > > Hi Doug, > > For some reason I’m having a problem replyin

[Freesurfer] Followup on the mystery of the missing mcprextreg file

External Email - Use Caution Hi Doug, For some reason I’m having a problem replying to this list with my reply to your reply. To recap: some of my functional runs are missing the mcprextreg file, and so the GLM with the motion correction parameters is failing. You had asked whe

Re: [Freesurfer] same output with vol2vol and label2vol

Are they exactly the same? Try mri_diff file1.mgz file2.mgz I would not expect them to be all that different, just a few voxels here and there On 4/16/19 3:47 PM, Sam W. wrote: > > External Email - Use Caution > > Hi, > In a Freesurfer help webpage it says that to convert an image (eg >

[Freesurfer] same output with vol2vol and label2vol

External Email - Use Caution Hi, In a Freesurfer help webpage it says that to convert an image (eg brain.mgz) from freesurfer to anatomical native space (eg rawavg.mgz) we should use mri_vol2vol, but for a segmentation (aseg.mgz) we should use mri_label2vol. I converted the aseg.mg

Re: [Freesurfer] mri_surf2surf help

So do you still have an issue that needs to be solved? Can't quite tell from your email. I've fixed the webpage to add a template volume in the mri_surf2surf command, thanks for pointing out. On 4/16/19 3:15 PM, Larson, Kathleen E wrote: > External Email - Use Caution > > Thank you! Yes

Re: [Freesurfer] mri_surf2surf help

External Email - Use Caution Thank you! Yes, I was able to figure it out. However, even when I swap the moving/target inputs, the surface is still not in the correct anatomical space. Also, just so you are aware, the instructions on the website you gave me aren't up to date... t

Re: [Freesurfer] Including a hyperintensity in wm surface

Can you send a picture? On 4/16/19 2:07 PM, Rachel Hoel wrote: > > External Email - Use Caution > > Dear Freesurfer Developers, > > Our study is using the longitudinal processing pipeline with version > 6.0. We have one subject where there is a hyperintenisty in the right > temporal lobe

Re: [Freesurfer] Problems with recon-all -s soft and hard fallures

Unfortunately, it usually means that you need to go in and manually fix the problems that you are seeing. Probably the best thing is to look at the aseg.presurf.mgz to see how the WM lesions are getting labeled. You may have to go in an label them manually. Can you upload a case or two here ftp

[Freesurfer] Including a hyperintensity in wm surface

External Email - Use Caution Dear Freesurfer Developers, Our study is using the longitudinal processing pipeline with version 6.0. We have one subject where there is a hyperintenisty in the right temporal lobe, and even after adding several control points and running recon-all,

Re: [Freesurfer] MP-RAGE protocol

Hi Mustafa, why not just run recon-all on the data you have and see whether it looks ok? On 4/15/19 7:06 AM, mustafa amin wrote: > External Email - Use Caution > > Hi Bruce, > > I’ve talked to the MRI operator and she told me that the best thing to do the > MP-RAGE protocol is doing the

Re: [Freesurfer] Holes in labels (Brainnetome) after conversion from surface to volumetric space

I think this is probably coming down to partial volume effects. Can you look at  the underlying image to see whether cortex actually extends into the brown voxels? On 4/15/19 3:54 PM, Caroline Chwiesko wrote: > > External Email - Use Caution > > Hello Douglas, > > that you very much for

Re: [Freesurfer] Resampling anatomical ROI to the functional images

If  you want to upsample to the anatomical space, use mri_vol2vol (run with --help to get examples) On 4/16/19 5:54 AM, Juhyoung Ryu wrote: > External Email - Use Caution > > Hi Douglas, > Thank you for the response. > > I tried to figure out your suggestion, but as i understand about bb

Re: [Freesurfer] Nucleus Accumbens Area or Volume

Hi Bruce, Got it- thank you for clarifying. best, arkadiy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Nucleus Accumbens Area or Volume

Hi Arkadiy we do generate the volume of the "nucleus accumbens area". It is called this as the accumbens doesn't have clean contrast boundaries on all sides cheers Bruce On Tue, 16 Apr 2019, Maksimovskiy, Arkadiy wrote: > Dear Experts, > > My apologies for the very basic question. I wanted

[Freesurfer] Nucleus Accumbens Area or Volume

Dear Experts, My apologies for the very basic question. I wanted to ask, because it keeps coming up in literature, and I wanted to make sure that I am not mistaken. Based on the documentation, my understanding is that Freesurfer ROI's do not generate Nucleus Accumbens volume, but just NAcc area

Re: [Freesurfer] Resampling anatomical ROI to the functional images

External Email - Use Caution Hi Douglas, Thank you for the response. I tried to figure out your suggestion, but as i understand about bbregister, it provides registration of functional space to anatomical space in $subjects_dir. As what i want to do is registration of anatomical