Re: [Freesurfer] talairach.xfm error frequency

2012-10-12 Thread Eric Cunningham
Would you recommend subjects through autorecon1 in freesurfer 5.0 and then through autorecon2 and autorecon3 in 5.1? Thanks, -Eric On Wed, Oct 10, 2012 at 4:35 PM, Eric Cunningham wrote: > Hi all, > Ah, good to know that there is a Talairach accuracy problem. What have > other groups been doing

Re: [Freesurfer] mri_ms_fitparms?

2012-10-12 Thread Bruce Fischl
You can ignore that Bruce On Oct 12, 2012, at 5:24 PM, dgw wrote: > Hi, > > Thank you for the advice. I have a follow-up question. I seem to be > getting a warning: > non-equal flip_angle found for the volume 1. > Flip_angle is set to zero. > The full log is at the bottom. Using > free

Re: [Freesurfer] volumes per lobe

2012-10-12 Thread MAHINDA YOGARAJAH
Dear FreeSurfer Experts, I write in regard to the posting on calculating GM measures on a lobar basis. I had a couple of quick questions: 1) Having derived a lobesfile using mri_annotation2label --subject --hemi lh --lobesStrict lobesfile one uses mris_anatomical_stats -mgz -cortex ../labe

Re: [Freesurfer] mri_ms_fitparms?

2012-10-12 Thread dgw
Hi, Thank you for the advice. I have a follow-up question. I seem to be getting a warning: non-equal flip_angle found for the volume 1. Flip_angle is set to zero. The full log is at the bottom. Using freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514 Setting up environment fo

Re: [Freesurfer] unpacksdcmdir error

2012-10-12 Thread Douglas N Greve
Hi Jeff, use -run 9 instead of -run 009 doug On 10/12/2012 10:58 AM, jwa...@nmr.mgh.harvard.edu wrote: > Dear Freesurfer community, > > I am using the unpacksdcmdir command as part of a DTI analysis in stable51: > > unpacksdcmdir -src > /space/archive/60/siemens/Allegra-20401-20051011-143458-528

Re: [Freesurfer] Error with mris_calc

2012-10-12 Thread Rudolph Pienaar
In your use case below, the output volumes in each case are 'out.mgz'. There should be *no* modifications to binF1.mgz or binF2.mgz. 'mris_calc' in fact only reads from those files, it does not write to or manipulate them in any way. So I don't completely understand how their contents can be mo

[Freesurfer] unpacksdcmdir error

2012-10-12 Thread jwaugh
Dear Freesurfer community, I am using the unpacksdcmdir command as part of a DTI analysis in stable51: unpacksdcmdir -src /space/archive/60/siemens/Allegra-20401-20051011-143458-528000 -targ ./ -run 009 dti NII CD_cerv_ctrl2_sess2_dti.nii -unpackerr and am getting the following error: ERROR: n

Re: [Freesurfer] Error with mris_calc

2012-10-12 Thread Bruce Fischl
Hi Christophe what does mri_info tell you about them? Are they the same geometry? Bruce On Fri, 12 Oct 2012, Christopher Coello wrote: > Dear Freesurfer community, > > Using freeview, I can visualize that two binary volumes are overlaying > in some parts. > freeview -v binF1.mgz -v binF2.mgz > >

[Freesurfer] Error with mris_calc

2012-10-12 Thread Christopher Coello
Dear Freesurfer community, Using freeview, I can visualize that two binary volumes are overlaying in some parts. freeview -v binF1.mgz -v binF2.mgz When using the command mris_calc -o out.mgz binF1.mgz mul binF2.mgz to create the intersection of these two volumes, I obtain a file with only zero