Re: [Freesurfer] Tracula: missing or incomplete tracts

What about: freeview -v FA.nii.gz -v V1.nii.gz:vector=yes From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Tuesday, March 17, 2015 11:57 AM To: Freesu

Re: [Freesurfer] segmentation

I don't think it does. On 03/16/2015 10:36 PM, Mauricio Anés wrote: > Dear Freesurfer users, > > Does anybody knows if the steps after the segmentation have some > impact in subcortical structures volume? If it does, how can I have > this measurements back even if I had already run recon-all? >

Re: [Freesurfer] Drawing ROIs using coordinates in another space?

You can try putting them into a label file and displaying them on fsaverage. If there is a template brain used by BV, then you can try running that through recon-all. If that works, you can create a label file for the BV template, then map it to fsaverage or other subjects using mri_label2labe

Re: [Freesurfer] aparc superior occipital lobe labeled as superior parietal (fwd)

Hi Raul, Thank you for your answer. Yes, the aparc2009 should work fine. But if I may suggest something, I think that just changing the label name to Sup. Parietal + Sup. Occipital Cortex would be a good way to warn the users about the extend of this label. Best Regards. Paulo - Mensage

Re: [Freesurfer] Multiple and equidistant circular ROIs on the surface

that's what I was going to suggest. cheers Bruce On Tue, 17 Mar 2015, Douglas N Greve wrote: > Bruce may know better, but mris_make_face_parcellation will may do what > you need. You'll need to choose an icosohedron order based on the number > of ROIs ("vertices" below) you want. > > >

Re: [Freesurfer] Using a2009s.annot as seed masks for tractography

Hi Andre - There is no way for us to guess what went wrong if we don't know the output of the command that you're trying to run. For example, "something went wrong" could mean that that the command failed without creating any volume, that the volume was created but it doesn't look right, etc.

Re: [Freesurfer] Multiple and equidistant circular ROIs on the surface

Bruce may know better, but mris_make_face_parcellation will may do what you need. You'll need to choose an icosohedron order based on the number of ROIs ("vertices" below) you want. Order Number of Vertices 0 12 1 42

Re: [Freesurfer] Multiple and equidistant circular ROIs on the surface

Hi Doug, We conducted a cortical thickness analysis in patients versus controls and generated a group atrophy map. We additionally conducted a resting state functional connectivity study in volume space using healthy controls. Ideally we would like to create a series of circular ROIs evenly distr

Re: [Freesurfer] Using a2009s.annot as seed masks for tractography

Hi Anatasia, I was able to create a registration.dat with bbregister now ("bbregister --s HC001 --mov HC001/mri/bo_brain.nii.gz --reg HC001/mri/registration2b0.dat --dti --init-fsl"). However, I got an error message after using mri_label2vol - ERROR reading left_accumbens.nii.gz I think someth

Re: [Freesurfer] Multiple and equidistant circular ROIs on the surface

what do you mean by equidistant distance? On 3/17/15 12:54 PM, Victor Montal Blancafort wrote: Hi FS expert, I was wondering if it is possible to create multiple "circular" ROIs on a surface with equidistant distance. Since the distance between vertex is not constant, it works if the number o

[Freesurfer] Multiple and equidistant circular ROIs on the surface

Hi FS expert, I was wondering if it is possible to create multiple "circular" ROIs on a surface with equidistant distance. Since the distance between vertex is not constant, it works if the number of vertices between ROIs it is the same. Any suggestion will be very appreciated! Thank you in advan

[Freesurfer] Scale Factor Question

Hi FreeSurfer Experts, I am trying to use mri_label_volume to correct for head size differences in volumetric outputs. I know that this command needs a scale factor. Where do I find this scale factor? Is this scale factor different for each participant? I read through the eTIV wiki information

Re: [Freesurfer] Using a2009s.annot as seed masks for tractography

Hi Andre - What do you mean by diffusion file? The registration file that transforms between diffusion and anatomical space is output by bbregister (see part A of the tutorial that I mentioned below). a.y On Tue, 17 Mar 2015, André Schmidt wrote: Hi Anastasia, I intend to use mri_label2vo

Re: [Freesurfer] Tracula: missing or incomplete tracts

Hi Amelia - Sorry, not that I know of. Perhaps this can be a feature request for Ruopeng to add to freeview :) BTW, freeview in 5.3 had a bug with the vector display for some input image orientations, but this has been fixed in the dev version (that you can download on the web site). a.y

[Freesurfer] Cognitive neuroscientist wanted for open position in drug discovery (Cambridge, MA)

Dear Freesurfers, We are looking for a cognitive neuroscientist to join our growing team in the Neurocognition and Functional Imaging group at Pfizer (Cambridge, MA). Please feel free to forward this listing to interested parties or other lists. See the full job posting or apply via https://www.l

[Freesurfer] ERROR: talairach_afd: Talairach Transform

Hi, I'm using FreeSurfer for analyses on lesioned brains, and so far it has worked well for most of my patient group and control group. However, for a few subjects (lesion size does not seem to be the case here) the recon-all stream crashes at the stage of talairach_afd. Here is the exact error lo

[Freesurfer] Fwd: Postdoc position in biostatistics in Copenhagen, Denmark, available

anyone interested, please contact Gitte directly doug Forwarded Message Subject: Postdoc position in biostatistics in Copenhagen, Denmark, available Date: Tue, 17 Mar 2015 14:35:36 +0100 From: Gitte Moos Knudsen To: Douglas N Greve Hi Doug Hope things are we

Re: [Freesurfer] Thin Surface

Hi Pedro they should be based on the input to mris_make_surfaces, which I believe is brain.finalsurfs.mgz cheers Bruce On Tue, 17 Mar 2015, Pedro Rosa wrote: Hi, Bruce. I tried several thresholds in some subjects and it seems to work reallh well. Thanks for the help! However, I would like t

Re: [Freesurfer] Using a2009s.annot as seed masks for tractography

Hi Anastasia, I intend to use mri_label2vol to map the label file into the diffusion space. Can you say me what for a diffusion file I can use for that and where I can find it? Thanks again for your help Andre Von: freesurfer-boun...@nmr.mgh.harvard.edu