[Freesurfer] Trac -all error

Hi Anastasia: Sorry to bother you again. I ran trac all on our cluster but it gave me an error message. I have enclosed the text file. I used vim to see if I could decipher the error but I am not entirely sure what the problem is Please advice. thanks, Alan trac-all.o103866 Description: Bina

[Freesurfer] mri_surfcluster questions

Hi all, I experimented with the different flags for mri_surfcluster and have 2 issues that I don't understand, it would be great if somebody could enlighten me: 1) When I set --thmin (or --fdr) with --thsign abs, I get what I would expect, i.e., only clusters with a minimum vertex-wise p-value

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

Hi Andre - I'd go through the multimodal integration tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview a.y On Thu, 26 Feb 2015, André Schmidt wrote: Hi Anastasia, Thank you very much for your help. I have created such a label nii file, for example for ID 9,

Re: [Freesurfer] Tracula by-voxel tract profile

Hi Anastasia, I've looked at the tutorial webpage, which describes the usages and output from tract profile analysis. Instead I am more interested in how trac-all -stat does the processing to get the mean values of diffusion metrics along the pathways, such as registering a group of tracts, findin

[Freesurfer] Lta_convert

Hi, Is it possible to download lta_convert? Thanks, Xiaomin On Thu, Feb 26, 2015 at 9:35 AM -0800, "David Grayson" wrote: ok, great. so let's say I have a linear transformation or a full warp field to go between the freesurfer processed image and the unprocessed brain. is there a way that I

Re: [Freesurfer] warping segmentations onto unprocessed brain

ok, great. so let's say I have a linear transformation or a full warp field to go between the freesurfer processed image and the unprocessed brain. is there a way that I can propagate onto the unprocessed image the entire freesurfer contents including the "mri" and "label" and everything else, usi

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

Hi Anastasia, Thank you very much for your help. I have created such a label nii file, for example for ID 9, the left thalamus. Can you please help me how I can map that file into diffusion space using bbregister? I would like to use it then for probtrackx. Many thanks again. Andre ___

Re: [Freesurfer] Tracula by-voxel tract profile

Hi Ping - Have you looked at the tutorial? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics See: "Anisotropy and diffusivity along the trajectory of a pathway" a.y On Thu, 26 Feb 2015, Yeh, Ping-Hong wrote: Hi Anastasia and FS users,  Repost the mail:  I would l

Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer

Hi Bruce Thanks for your reply, I did use mri_vol2surf for the sampling mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi {hemi}--projfrac {0.8} --out {out file name} --out_type {mgz} I don't believe that I want to average within the ROI. I want to take any clusters of ac

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

Hi Andre - You find the ID number of each of the regions you're interested in, from $FREESURFER_HOME/FreeSurferColorLUT.txt. Then you run: mri_binarize --match ID --i aparc.a2009s+aseg.mgz --o yourlabel.nii.gz Then you'll have to map that label into DWI space. We recommend bbregister

Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer

Hi Sarah have you used mri_vol2surf to sample the data onto the surface? When you say "extract specific regions of functional data from a flat " do you want to average within the ROI? cheers Bruce On Thu, 26 Feb 2015, Sarah Finnegan wrote: I have a question about the equivalent of fslmaths

[Freesurfer] equivalent for fslmaths -mas option in freesurfer

I have a question about the equivalent of fslmaths -mas option in freesurfer. I have several manually defined labels in .label form that I want to use to extract specific regions of functional data from a flat patch. Ordinarily in fsl I would just use fslmaths -invol {functional_data} -mas {bin

Re: [Freesurfer] trac all -p

Thanks Anastasia. Your suggestion worked. On Wed, Feb 25, 2015 at 4:10 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Alan - It can't find the file. Check the error message, part of the > path to the file is repeated twice. I suspect you typed that part in both > dcmroot and

Re: [Freesurfer] recon-all and subcortical regions

Hi Andre sorry, I don't remember how many regions there are. Should be easy enough to count in matlab. For the tractography question you'll have to wait for Anastasia to respond Bruce On Thu, 26 Feb 2015, André Schmidt wrote: Hi Bruce, Thanks, yes I see these files in the mri folder. I li

Re: [Freesurfer] recon-all and subcortical regions

Hi Bruce, Thanks, yes I see these files in the mri folder. I like to use the apart.a2009s+aseg.mgz file (how many regions are included in this file?) now for tractography (every region as a seed mask) using probtrackx (sorry). How can I create a text file with all these seed regions (including

[Freesurfer] Tracula by-voxel tract profile

Hi Anastasia and FS users, Repost the mail: I would like to know the steps for creating the tract profile summary of diffusivity metrics along the trajectory of path. Is there any reference that I can refer to ? Will the codes be available to the public? If not, pseudo-codes summarizing the st

Re: [Freesurfer] warping segmentations onto unprocessed brain

Hi David yes, you can use bbregister to do the rigid alignment, then use it as initialization for mri_nl_align. I would think you are better off doing the surface recons and using cvs though. It's only computer time cheers Bruce On Wed, 25 Feb 2015, David Grayson wrote: > Hey Bruce, > Tha

Re: [Freesurfer] recon-all and subcortical regions

Hi Andre if you ran recon-all you will have created a volume file names aseg.mgz that has the subcortical segmentation (and an aparc+aseg.mgz that has both subcortical and cortical in it) cheers Bruce On Thu, 26 Feb 2015, André Schmidt wrote: Dear experts, I use recon-all for the parcella

[Freesurfer] recon-all and subcortical regions

Dear experts, I use recon-all for the parcellation of my MPRAGE. As far as I can see this procedure does not address subcortical regions - right? How can I additionally perform a parcellation of subcortical regions? Many thanks for your help Andre ___

Re: [Freesurfer] Analyze format

Hi Pablo I really don't know the analyze conventions or whether this will work. If you are sure of the orientation then convert it to mgz and check in tkmedit whether we got the orientation right (that is that the left side of the brain is properly identified as such in tkmedit/freeview) che

Re: [Freesurfer] Analyze format

Thank you Bruce for the piece of mind. The images were neurologically oriented (L=L) for analysis with SPM. Do you know if this helps at all? Thanks Pablo Date: Wed, 25 Feb 2015 10:44:48 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Analyze f

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

Dear freesurfer experts, I intend to use the aparc.a2009s.annot file as seed regions for a tractography analysis. I like to compute streamlines between every region in the annot file. Can you please guide me how I can create masks for every region in the annot file (or a text file with all seed

[Freesurfer] parcellation atlas

Dear experts, How many regions are included in the apart.annot and apart.a2009s.annot files, and which one do you recommend for later tractography analysis (using these regions as seeds)? Thank you BW Andre ___ Freesurfer mailing list Freesurfer@nmr.m