Re: [Freesurfer] Preproc-sess failed

2015-06-25 Thread Thục Trinh
Hi, After complete install the suitable version of shared library as you suggested, I cannot find any file name libXpm.x86_64 to set the new path for shared library. Ps: Is there any differences between libXpm.x86_64 and libXp.x86_64 2015-06-24 16:03 GMT+07:00 Jalmar Teeuw : > That sounds more li

Re: [Freesurfer] Preproc-sess failed

2015-06-25 Thread Jalmar Teeuw
Is still gives you the same error? I'm not certain about libXpm; I recall having to install certain libraries on a slimmed down version of Centos 6.5, libXp and libXpm were amongst those libraries. For me, the lib files are stored in /usr/lib64 Try find /usr/lib64 -type f -iname "libXp*" -p

Re: [Freesurfer] Preproc-sess failed

2015-06-25 Thread Thục Trinh
the lib files are now in /usr/lib64, the ERROR still the same after I set a new path for shared lib with this command in .bashrc file *export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH* the Error still the same. *3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF class: ELF

Re: [Freesurfer] Freesurfer tool for children's data

2015-06-25 Thread Mayer Kristina
Hi Bruce, from 18-36 months of age. I got good results when adding some flags (adjustment of wsthresh, -bigventricles, -mprage) but still it is lot of work for adjustment, as the contrasts is slight different at that ageIs there a preliminary version I could try with? Would be great opportun

Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data

2015-06-25 Thread Falk Lüsebrink
Hi Thomas, this looks like a really nice script and a lot better than my own. In the upcoming release of FreeSurfer v.6 my work-around probably is not needed anymore. However, I haven’t been able to have a look at the dev release yet and whether the standard recon-all features a flag to process

[Freesurfer] Gray Matter: GM mask vs Surface

2015-06-25 Thread Mayer Kristina
Dear all, What is calculated in the aseg.stats cortical gray matter? As you see in the file attached, GM mask is integrating some of the skull (bad skull strip). But the surface line is correct. Do I have to adjust the segmentation for a correct value in the aseg.stats cortical grey matter or is

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

2015-06-25 Thread Z K
On 06/23/2015 04:52 PM, joseph veliz wrote: > Hello, > > > We are having issues installing Freeview on Macbook pro (2015) > > 2.2 GHz, 16GB DDR3, OSX 10.9.4, Integrated 1.5 GB intel iris pro graphic > processing. > > Installing lastest Freesurfer and Freeview downloads of Darwin lion v5.3.0. > >

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

2015-06-25 Thread joseph veliz
Positive we downloaded Freesurfer -Darwin - lion -dev.tar.gz On Thu, Jun 25, 2015 at 9:04 AM, Z K wrote: > > > On 06/23/2015 04:52 PM, joseph veliz wrote: > > Hello, > > > > > > We are having issues installing Freeview on Macbook pro (2015) > > > > 2.2 GHz, 16GB DDR3, OSX 10.9.4, Integrated 1.5

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

2015-06-25 Thread joseph veliz
Sorry that is an archive zip that i also downloaded The one installed is Freesurfer -Darwin -lion -stabel -pub-v5.3.0.dmg On Thu, Jun 25, 2015 at 10:36 AM, joseph veliz wrote: > Positive we downloaded Freesurfer -Darwin - lion -dev.tar.gz > > On Thu, Jun 25, 2015 at 9:04 AM, Z K wrote: > >>

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

2015-06-25 Thread Z K
H. Im not really sure how to proceed because you should not have that file. What does your build-stamp.txt file contain? Twice I have tested by downloading the lion OSX version of freesurfer from this page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download and never was a file called "free

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

2015-06-25 Thread Z K
Although I can confirm the issue with surface files. Please wait a day updating freeview. I will resolve the issue and email you and the list once it is resolved. Hopefully within the day. -Zeke On 06/25/2015 02:20 PM, Z K wrote: > H. Im not really sure how to proceed because you should not

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

2015-06-25 Thread joseph veliz
sorry for the confusion I assure it is the correct download installed Looking at the file again it does not have a '.bin' , but it is in the bin folder and is very small file 184 bytes the build-stamp.txt file say freesurfer-Darwin-lion-stable -pub-v5.3.0 On Thu, Jun 25, 2015 at 11:22 AM, Z K

Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data

2015-06-25 Thread Allison Moreau
Hi Falk and Thomas, We are actually working on testing the -hires flag now for the v6 release. We intend to release it with v6. -Allison On 06/25/2015 07:09 AM, Falk Lüsebrink wrote: Hi Thomas, this looks like a really nice script and a lot better than my own. In the upcoming release of F

[Freesurfer] Freeview surface misaligned with T1 - volume geometry missing

2015-06-25 Thread Hamilton, Liberty
Hello, I am having a similar problem to another user where I am trying to load a gifti surface in freeview, but it is misaligned with my T1 image and I get the error "Did not find any volume geometry information in the surface". When I load the surface in tkmedit it looks aligned. I saw that