Re: [Freesurfer] missing 3volreg.afni

2015-12-27 Thread Thục Trinh
My platform is centOS6.4 final 64bit. 3dvolreg.afni still works when I used FSv5.3. but when I update to FSv.6, I cannot use the 3dvolreg.afni. 2015-12-24 4:29 GMT+07:00 Douglas Greve : > what is your platform? Do you have AFNI installed and does it work? If so, > you can copy the 3dvolreg to 3dv

[Freesurfer] PhD position: MRI markers of neuroinflammation in treatment pharmacoresistant epilepsy

2015-12-27 Thread Barbara Kreilkamp
Dear Freesurfers, A PhD studentship „Identifying non-invasive imaging markers of neuroinflammation in treatment pharmacoresistant epilepsy“ is available in the Epilepsy Research Group (ERG) at the University of Liverpool, UK and is supervised by Dr Simon Keller and Prof Tony Marson. Please find a

Re: [Freesurfer] Integrating planes into a single volume?

2015-12-27 Thread Bruce Fischl
Hi John there are techniques around for integrating 3-plane, thick-ish slice data (3mm or so) into a single "highres" volume. We don't have any ourselves, but they are populat in the baby imaging world. You could try Colin Studholme's tool for this, for example: http://depts.washington.edu/bi

[Freesurfer] Integrating planes into a single volume?

2015-12-27 Thread John Benfield
Is there any way to integrate the information from axial, coronal and sagittal views into a single volume? I'm looking for ways to build a more accurate/comprehensive 3d model and I'm not having any luck finding workflows or tools that allow any sort of cross-plane refinement/interpolation. Any s

Re: [Freesurfer] R: Re: R: Re: R: Re: Recon-all error

2015-12-27 Thread Bruce Fischl
Hi Stefano do you have a license file? Does /Applications/freesurfer/license.txt exist? If so, can you send Zeke the contents of it. Make sure to do this offlist please. cheers Bruce On Sun, 27 Dec 2015, std...@virgilio.it wrote: Hi Zeke, please look this error. Thanks Stefano recon

[Freesurfer] R: Re: R: Re: R: Re: Recon-all error

2015-12-27 Thread stdp82
Hi Zeke, please look this error. Thanks Stefano recon-all -all -s 150706samspe/T1_STRUCT.nii.gz -i $SUBJECTS_DIR/150706samspe/T1_STRUCT.nii.gz -hippocampal-subfields-T1 Subject Stamp: freesurfer-Darwin-OSX-dev-20151214 Current Stamp: freesurfer-Darwin-OSX-dev-20151214 INFO: SUBJECTS_DIR is /Appli