Re: [Freesurfer] recon-all: too many levels of symbolic links

Hi Bruce, This is what I get: FreeSurfer:~/freesurfer/lindadata> ls -l drwxr-sr-x 42 virtualuser virtualuser 4096 2012-11-17 07:38 subjects FreeSurfer:~/freesurfer/lindadata> ls /subjects/lh.EC_average/surf ls: cannot access /subjects/lh.EC_average/surf: No such file or directory FreeSurfer:~/fre

Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all

Hi Tudor, I don't know how to solve this problem. Maybe Nick knows. doug On 12/19/12 6:59 AM, Tudor Popescu wrote: Hi Doug, thanks for replying, here is the file attached. In case the attachment doesn't go through please let me know if I should send it to a different address. Tudor On 18 Dec

Re: [Freesurfer] L-R Volume Flipping

Oh, right, that can be a problem. In 5.2, I've changed it to use nii by default. This breaks when spm2 is used, but then the user can spec to use img instead. doug On 12/19/12 5:38 PM, MCLAREN, Donald wrote: > When we added the --spm-nii option, the problem disappears. The > following thread

[Freesurfer] Diffusion Tensor Imaging

Dear Freesurfers, I am not very experienced with Freesurfer and would like to construct a Diffusion Tensor Image. I have the .bvecs, .bvals and .img files which I believe should suffice. I am aware that the format is slightly old but I believe it should still be fine. I attempted to use dt_rec

Re: [Freesurfer] tracula - posterior density just one-dimensional curve

Hi Andi - I managed to track this down by looking at the complete data set that you sent me. Your bvals file has no b=0, there's only b=2075 with some b=5 interspersed. The b=5 volumes must be your baseline volumes but unfortunately there's no way for the program to know this right now. As a

Re: [Freesurfer] L-R Volume Flipping

When we added the --spm-nii option, the problem disappears. The following thread is also relevant: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017981.html On Tue, Dec 18, 2012 at 8:26 PM, MCLAREN, Donald wrote: > Thanks, that's what I thought might be happening. I'll check

Re: [Freesurfer] space of T1.mgz

Hi there, Sorry, if my question is confusing. This is what I want to do, I have two groups of controls and patients and I've already run recon-all on them. I now want to know the head/body/tail volumes. What I did was: 1. used "mri_binarize" to get the right and left hippocampal masks from the cor

Re: [Freesurfer] recon-all: too many levels of symbolic links

ls -1 $FREESURFER_HOME/subjects cvs_avg35/ cvs_avg35_inMNI152/ fsaverage/ fsaverage3/ fsaverage4/ fsaverage5/ fsaverage6/ fsaverage_sym/ lh.EC_average/ README rh.EC_average/ sample-001.mgz sample-002.mgz surfer.log V1_average/ not sure why it thinks it doesn't exist. What are the permissions on

Re: [Freesurfer] mri_cc segfault

Bruce found that the data had the direction cosine wrong. I have fixed the direction and I'm running it again. I've put the data in the ftp - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilte

[Freesurfer] new atlas

Dear Freesurfers,Sorry for so many and basic questions lately.I'm working with my set of subjects (T1), and I'm looking for a different WM parcellation than the aseg.mgz, I have an atlas (JHU atlas in MNI space, Mori et al 1999, and some other in Colin27 space).I'm guessing I will have to use the F

Re: [Freesurfer] recon-all: too many levels of symbolic links

Dear all, I've run into the same error with recon-all -autorecon3. It could be that when I moved my data into the new SUBJECTS_DIR, I missed something out. What files should be in the $FREESURFER_HOME/subjects directory? The error reads as follows: #@# Ex-vivo Entorhinal Cortex Label lh Fri Dec