[Freesurfer] problem saving in tkmedit

Hello freesurfer gurus, We are running into the following error when trying to save edits to the brainmask volume in tkmedit: % ERROR: opening pipe gzip -f -c > /study/midus/data/mri/processed/freesurfer/subject006/mri/brainmask.mgz, errno = 12 Cannot allocate memory mghWrite(/study/midus/data

[Freesurfer] how to use mri_surf2surf

Hi, there, mri_surf2surf resamples one CorticalSurface onto another. If I have two subjects from different time points (tp1 and tp2), I'd like to compare the FreeSurfer analyzed surface data. For example, could I use mri_surf2surf to resample the white matter surface of tp1 onto tp2, so I c

Re: [Freesurfer] GLOBAL region of the brain empty! error due to error in intensity normalization?

Hi Ana, that could be a problem as you don't have many bits of dynamic range if the image intensities are so low. You could try omitting the nu step and see if it resolves the problem. cheers, Bruce On Wed, 23 Sep 2009, Ana Catarino wrote: > Hello, > > > > I was just running autorecon1 on a

Re: [Freesurfer] how to use mri_compute_seg_overlap

Hi Guang, even in the longitudinal stream the asegs (and all images) are in the TP native space. They still need to be registered (either to each other or to the base space). The base space is recommended, because that way both images are treated the same (both are resampled). The registrations ar

[Freesurfer] GLOBAL region of the brain empty! error due to error in intensity normalization?

Hello, I was just running autorecon1 on a subject and I got the mri_watershed Error: GLOBAL region of the brain empty! I am aware that there was a bug in previous versions but I'm using v4.3.1, which I think it's not supposed to have that bug any longer. I tried running -skullstrip with the -no

Re: [Freesurfer] how to use mri_compute_seg_overlap

I think I still need register the second tp aseg.mgz to the first tp aseg.mgz, even they are longitudinal-stream analyzed. The dice coefficients are higher after registration. From: freesurfer...@hotmail.com To: ni...@nmr.mgh.harvard.edu Date: Wed, 23 Sep 2009 13:04:59 -0500 CC: freesurfer@nmr.

Re: [Freesurfer] how to use mri_compute_seg_overlap

Hello, Nick, Yes, I can get the results now, I set the wrong path. Just want to double check, I have send the two subjects (from different time points) to the FreeSurfer longitudinal stream, so the resulted two aseg.mgz files have been registered to the base-template, right? Thanks a lot! Gu

Re: [Freesurfer] how to use mri_compute_seg_overlap

Guang, So you did not get output that looked like this? logging overall Dice to text Jaccard Coefficients: correct ratio for label 2 = 1 correct ratio for label 41 = 1 . . correct ratio for label 44 = 1 mean +/- std = 1. +/- 0. Dice Coefficients: label 2 = 1 label 41 = 1 . . . label 44 =

Re: [Freesurfer] FSL to FreeSurfer registration

Estephan Moana wrote: > So what I need to do is to run the 1st level FEAT as usual for the FSL > pipeline, and repeat this analysis for FS with the only difference > been to set the "Spatial smoothing FWHM" to zero on the pre-stats tab > of the FEAT GUI? yes > > Also, can you explain if this s

Re: [Freesurfer] FSL to FreeSurfer registration

So what I need to do is to run the 1st level FEAT as usual for the FSL pipeline, and repeat this analysis for FS with the only difference been to set the "Spatial smoothing FWHM" to zero on the pre-stats tab of the FEAT GUI? Also, can you explain if this smoothing on the FEAT GUI is the 3D you

[Freesurfer] how to use mri_compute_seg_overlap

Hi, there, I have two subjects from two time points, I'd like to compare their overlap ratio of FreeSurfer segmented hippocampus. I try to use the command mri_compute_seg_overlap to do it, My command line is: mri_compute_seg_overlap -olog text tp1/mri/aseg.mgz tp2/mri/aseg.mgz Is it correct

Re: [Freesurfer] how to extract segmented hippocampus

photoshop? Sorry, I don't think there's an easy way to do it in tksurfer without making your own curv-format file. You could do it in freeview though if you want to mess around with it. cheers Bruce On Wed, 23 Sep 2009, Guang Zeng wrote: > > I loaded the left and right hippocampus mesh using t

Re: [Freesurfer] how to extract segmented hippocampus

I loaded the left and right hippocampus mesh using tksurfer, it works, Thanks! If I want to paint left hippocampus as yellow and right hippocampus as green after I load them using tksurfer, how could I do it? Thanks! Guang > Date: Thu, 17 Sep 2009 07:24:11 -0400 > From: fis...@nmr.mgh.harvard

Re: [Freesurfer] FSL to FreeSurfer registration

The example_func does not actually get smoothed, so smoothing itself will not affect the registration. 3D smoothing will smooth values from WM and CSF into gray and from across sulci into functionally distinct regions. For this reason we recommend not using 3D smoothing (or doing 2D smoothing o

Re: [Freesurfer] Using mris_preproc

If you just want to resample the ROI to the average subject, then use mri_vol2surf, something like mri_vol2surf --mov V1.nii --regheader --s SubjectX --hemi lh --projfrac 0.5 --trgsubject fsaverage --o lh.v1.fsa.mgh syntax might not be exactly right, check the help doug Holly Bridge wrote: >

Re: [Freesurfer] autorecon2 error

The error in the log says 'cannot restore segment prot after reloc: Permission denied', which has been appearing lately with the newest CentOS releases. Try typing this prior to running recon-all: /usr/sbin/setenforce 0 You have to run this command as root. Nick On Wed, 2009-09-23 at 09:51 +

[Freesurfer] Using mris_preproc

I am trying to register an anatomical ROI (V1Left.nii.gz) in the same volume space as brain.mgz for SubjectX using spherical registration to the average subject brain. I have used the following command mris_preproc --s SubjectX --out ~/SubjectX/lh.ave.v1.mgz --target average --hemi lh --ivp