[Freesurfer] R: Re: slice timing correction in preproc-sess

Ok.My acquisition slices interleaved.Should I add to the command line above the flag -sliceorder so odd preproc-sess -s Sess101 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder so but this is the error:3dvolreg.afni -verbose -dfile 001/fmcpr.mcdat -1Dmatrix_save 001/fmcpr.m

[Freesurfer] Supratentorial Volume

Dear all, I have 3 features which i want to display and visualize. -Supratentorial Volume -TotalGrayVol -rh-superiorTemporal Volume how can i do that??? Another thing how can i get the characteristic of these areas like which parts they have in brain and etc. Kind Regrds, ___

[Freesurfer] R: Re: qdec problem

In a precedent study that I've done with qdec, for a study with two groups, I saw that the effect of 'generate stats data table' tool is the creation of 'stats_table' directory in which it are produced these files: 1. one file of aseg.volume.stats.dat2. four files for emilate of each typ

Re: [Freesurfer] pial surface from one hemisphere is crossing the surface of other hemishpere

Dear Bruce, the subject with overlapping reconstructed pial surfaces is uploaded to surfer.nmr.mgh.harvard.edu/pub/transfer/incoming/20150727_overlap_hemispheres.tar.gz The problem appears at coronal slices 46-54. Thank you very much for your help. Regards, Antonin Skoch__

[Freesurfer] nlmefit

Hello, I was wondering if anyone has used the nlmefit function in Matlab to model longitudinal FreeSurfer data? If so, is there code available that could be shared? Regards, Sarah ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mai

Re: [Freesurfer] Using ROIs in SPM

Hi Doug, I solved the problem by using: bbregister --s subject --mov func_denoised/vol.nii --bold --init-spm --reg register.dat mri_label2vol --label mask.label --reg register.dat --temp func_denoised/vol.nii --o mask.nii Best regards, Amirhossein Manzouri On Mon, Jul 27, 2015 at 7:

Re: [Freesurfer] Huge difference ini area for the same subject

Hi Doug, As you can see in the image I attached the average area is different for the same set by two different editor. I wonder if there is any reason for this? Best regards, Amirhossein Manzouri On Mon, Jul 27, 2015 at 9:16 PM, amirhossein manzouri < a.h.manzo...@gmail.com> wrote: > Hi Doug

[Freesurfer] Error while using "mri_glmfit"

Dear Freesurfer's Experts, Please find below an error occuring when I use mri_glmfit : Design matrix -- 1.000 0.000 0.000 0.000 0.000 0.000 9.804 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0

[Freesurfer] single hemisphere analysis

Dear All, 1. Is it possible to run recon-all on only 1 hemisphere? 2. Is it possible to do longitudinal analysis on a single hemisphere? 3. How? We have big lesions in our patients in one of the hemispheres, so we would like to analyze the contralateral one. Thank you for your help in advance!

Re: [Freesurfer] Supratentorial Volume Versus Sum of Parts

Hello Douglas, Sorry about the delay. I was focusing on preparations for a conference. In the most current case, no, the regions that are supposed to make up the supratentorial volume do not add up to the volume displayed by freesurfer. The sum of the parts for supratentoral notvent seems to be a

[Freesurfer] mri_vol2vol from subject space to fsaverage space

Hi Freesurfer experts, We are analyzing data for a simultaneous PET-MRI study, and are having trouble registering individual subject BPnd maps to fsaverage space. I attached a photo of a post-registration subject (the left side is cut off). I had previously registered each individual BPnd volum

Re: [Freesurfer] Huge difference ini area for the same subject {Disarmed}

Doesn't that just mean your colleagues are editing the brains differently? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of amirhossein manzouri [a.h.manzo...@gmail.com] Sent: Tuesday, July 28, 2015 7:33 AM To: Do

Re: [Freesurfer] wm parcellation freesurfer

Hi, Is it possible to increase the number of parcellations when making the aparc+aseg file? I have a high resolution MRI, and one parcellation will match every three slides, but I want a better match overall. Thanks, Owais ___ Freesurfer mailing list F

[Freesurfer] dev version of mri_ca_label memory leak?

Devs, I'm running the CVS version of Freesurfer, checked out on 28/7/2015 (7/28/2015 for US people). I get to the -calabel step and mri_ca_label takes a *long* time (400 minutes) and uses a *lot* of memory. After it outputs "saving sequentially combined intensity scales to aseg.auto_noCCseg.lab

[Freesurfer] FreeSurfer 6.0 dev version Output

Hi, I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0 dev version. I used the following command: recon-all -i ${subject}.nii -subject ${subject} -all -hippocampal-subfields-T1. I can also view the segmented hippocampal regions using the command: freeview -v nu.mgz -v