[Freesurfer] Is there any way to measure the volume of substantia nigra and red nucleus via FS?

Hi, FreeSurfer experts, I would like to know is there any command to measure the volume of substantia nigra, red nucleus, and anyother nucleis in brainstem by using FS ? Thanks in advance, Nellie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] ROI NumVert

On 11/01/2016 05:58 PM, Daya P wrote: > Hi, > > I have gotten the lh and rh ROIs stats with mris_anatomical_stats > before, is there any statistical tests in particular that you > recommend for asymmetry? What I have done is a two-way anova and > paired t-test with Bonferroni correction. Would

Re: [Freesurfer] ROI NumVert

Hi, I have gotten the lh and rh ROIs stats with mris_anatomical_stats before, is there any statistical tests in particular that you recommend for asymmetry? What I have done is a two-way anova and paired t-test with Bonferroni correction. Would like to hear your opinion on that. Also, I would be

Re: [Freesurfer] ROI NumVert

You can certainly get the lh and rh ROI stats in table form and then do an asymmetry analysis. Or you can use the xhemi stream to do a vertex-wise analysis. the difference is the difference between ROI and map-based analysis On 11/01/2016 03:47 PM, Daya P wrote: > Thank you a lot! > > I will t

Re: [Freesurfer] ROI NumVert

Thank you a lot! I will try this. I had another question regarding statistical analysis for asymmetry. I have seen several papers that take the measures that come from freesurfer (i.e. cortical thickness of auditory cortex), and use MATLAB or SPSS to run statistical tests. I am looking at 13 regi

Re: [Freesurfer] Segmentation depends on image file format

We are preparing a large dataset for sharing. It has already been processed and edited through freesurfer with the dicom files. We would like to share the MR scans in Nifti format instead of dicom, however we are encountering this difference in results. We are using dcm2niix to convert. We would

[Freesurfer] White Matter Edits

Hello, I am a staff research associate for a group that specializes in MRI of Multiple Sclerosis. We use freesurfer's reconstruction approach, however the white matter masks are not very good for the MS disease population. We have combined the FreeSurfer algorithm with ANTS in order to get more

Re: [Freesurfer] mri_average vs mri_concat

Can you send me the mri_concat command and also upload the input files to our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2 On 11/01/2016 02:31 PM, Trisanna Sprung-Much wrote: > Does anyone know who wrote the script for mri_concat? I would really > like to get this figured out. > > thank

Re: [Freesurfer] BBR not recommended for PETSurfer?

I have to give credit to John Ashburner who's spm_coreg algorithm I shamelessly copied. On 11/01/2016 02:31 PM, Elijah Mak wrote: > Hi Christopher, > > We have very positive experiences with mri_coreg too. > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47135.html >

Re: [Freesurfer] mri_average vs mri_concat

Does anyone know who wrote the script for mri_concat? I would really like to get this figured out. thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Oct 21, 2016 at 12:13 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wr

Re: [Freesurfer] BBR not recommended for PETSurfer?

Hi Christopher, We have very positive experiences with mri_coreg too. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47135.html Quite a bit of manual tweaking had to be done along with BBR for our AV and PK BPnd data. It works just fine on the PIB SUVRs though. Then, we switched

Re: [Freesurfer] tkregister2 + mri_vol2vol do not transform

Thank you very much, I'll try it. 2016-11-01 13:17 GMT-04:00 Douglas N Greve : > tkregister is only for viewing and manually registering volumes. Try > mri_coreg which you can get from here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg > > > On 11/01/2016 01:16 PM, Chiara Giacosa

Re: [Freesurfer] fsaverage_sym LR-flipchecks

But how did you do the analysis on fsaverage_sym? Not that you cannot just supply fsaverage_sym to preproc-sess. It is unfortunately much more complicated than that. Before you use fsaverage_sym, you must first run the commands here: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi If you have

Re: [Freesurfer] tkregister2 + mri_vol2vol do not transform

tkregister is only for viewing and manually registering volumes. Try mri_coreg which you can get from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg On 11/01/2016 01:16 PM, Chiara Giacosa wrote: > The images that I see in tkregister are the original ones before any > transform

Re: [Freesurfer] tkregister2 + mri_vol2vol do not transform

The images that I see in tkregister are the original ones before any transformations. In this way I must do all the transformations manually, which is of course time consuming and user-driven; whereas my hope is to let the program do the transformations automatically, so that I have only to chec

Re: [Freesurfer] ROI NumVert

I've written a script that will come out with version 6, but I've put it here https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas I think it should work in 5.3, but I'm not sure. If not, you can download the dev version and make the atlas using that. Run it with --help to get i

Re: [Freesurfer] tkregister2 + mri_vol2vol do not transform

what do you mean "it does nothing" ? On 10/28/2016 04:41 PM, Chiara Giacosa wrote: > Thank you Douglas for your response. > > However I had already tried to check with tkregister without noedit > and it does nothing. I have to make the changes manually in order to > see differences in the image

Re: [Freesurfer] Questions about outputs in Longitudinal Stream

Thank you for the clarification Martin I have a follow-up question. When I load the base to make sure it doesn't look blurry, should I check the norm.mgz or brainmask.mgz? Online says norm.mgz but I just want to make sure. Similarly, when I open the base and the longitudinal runs to see whether

Re: [Freesurfer] BBR not recommended for PETSurfer?

Hi Christopher, yes, my position on BBR for PET has changed. I ran an analysis on FDG from an HR+ using BBR and coreg, and the results were not different enough to warrant choosing one over the other. However, coreg performed better on simulated FDG HR+ data, so I'm recommending coreg over BB

Re: [Freesurfer] Freesurfer recon-all error after installing

Hello Albert, The centos4 vs centos6 output you are seeing is not the problem. Log files get appended to (unless you use the -noappend option), so you'll actually see the proper FREESURFER_HOME value your expecting later in the file. The issue is that the version of the MNI tools shipped with

[Freesurfer] freesurfer preproc output

Dear all, after running a freesurfer preprocessing, in each subject subdirectory, the following files are produced: lh.avg_curv lh.curv lh.curv.pial (and the analogue for the right hemisphere) what is the content of these files? sure, I can guess they represent the local curvature. but

[Freesurfer] tksurfer viewing issues

Hi Bruce, I'm analyzing phase encoded retinotopy, and it is not clear to me how to load complex overlays in freeview. Perhaps I am missing something? Best, Paige Hi Paige we have stopped development and most support of tksurfer. Can you use freeview instead or is there still some functionalit