Freesurfer July 2007

freesurfer@nmr.mgh.harvard.edu

61 participants
99 discussions

Recon-all
by Sharon Ruso 25 Jul '07

25 Jul '07

Dear Freesurfers. I am facing a crucial point.:)and I need your help. After examining most of our subjects, we decided that there is no need to run all the procedures- work flow, since our data is not prone to too many failures, and just start with recon-all-all, get all the data and then start editing. Usually we have to add very few cp and to do some pial edits (not in all the cases).However, our talairach looks good, no skull striping problems and wm is also ok. I was wondering if running recon-all-all, and then fixing the i.e. cp , or the pial surface when repeating autorecon2-cp, or autorecon2-pial-autorecon3, is it harmful? Does this mass my analysis , or it's ok? Thank You Sharon

2 1

about mris_make_surfaces
by Ning Liu 24 Jul '07

24 Jul '07

Hi all, I am trying to use mris_make_surfaces to create the final surface. Is aseg.mgz necessary for running this command? If not, how can I let this command skip this file? Thanks. Ning -- When was the last time you had a conversation with the moon or made a wish on a falling star? The time is now.

2 1

Problems still with recon-all
by Andrew Ellison 24 Jul '07

24 Jul '07

Hey all so when i run recon-all after ive set up all my subjects directories (previous issue) i am told the following [root@ebrcb-dhcp-240-47 freesurfer]# recon-all -autorecon1 -subjid 060615_26SS INFO: SUBJECTS_DIR is /usr/subjects/athpro/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 7014 Jul 24 11:58 /usr/subjects/athpro/freesurfer/060615_26SS/scripts/recon-all.log Linux ebrcb-dhcp-240-47.bumc.bu.edu 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux mri_convert: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_convert: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory strings: 'mritotal:': No such file strings: 'Command': No such file strings: 'not': No such file strings: 'found.': No such file nu_correct: Command not found. mri_normalize: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_watershed: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_segment: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_fill: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_tessellate: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_smooth: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_inflate: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_sphere: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_fix_topology: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_euler_number: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_make_surfaces: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_register: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mrisp_paint: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_label2label: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_em_register: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_ca_normalize: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_ca_register: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_ca_label: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory #-------------------------------------------- #@# MotionCor Tue Jul 24 12:06:18 EDT 2007 ERROR: no run data found in /usr/subjects/athpro/freesurfer/060615_26SS/mri. Make sure to have a volume called 001.mgz in /usr/subjects/athpro/freesurfer/060615_26SS/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux ebrcb-dhcp-240-47.bumc.bu.edu 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue Jul 24 12:06:18 EDT 2007 although the gsl is in its proper place and when i manually setenv it still claims cannot open shared object and what not, any help? thanks Andy i think im posting this, apologies if im not

2 1

mris_wm_volume
by Morgan Hough 24 Jul '07

24 Jul '07

Would it be possible to post binaries of mris_wm_volume again? I believe this is the preferred tool to calculate the total white matter volume over the current aseg output. Thanks in advance. Cheers, -Morgan

3 12

Problems with recon-all
by Andrew Ellison 24 Jul '07

24 Jul '07

Hey everyone, seems that when I run recon-all it almost immediatly tells me I am missing a COR-.info file. I am using Par/Rec data that i converted into Analyze 7.5(.hdr, .img) is this not compatible for use in recon-all? corRead(): can't open file /usr/subjects/athpro/Swimmers_Jun06/060615_26SS/COR-.info Thanks

2 1

Annotations II
by Claus Reinsberger 24 Jul '07

24 Jul '07

Sorry - I forgot to provide the other details.... machine: tkmeg environment: nmrenv Subjects-Dir: /autofs/space/megraid_083/MEG-MRI/seder/freesurfer current working directory: subjects-dir command line: tksurfer nmr00192 xh pial (+loading the annotations) Thanks again for helping, Claus

1 0

annotations
by Claus Reinsberger 24 Jul '07

24 Jul '07

Hi everybody, when I try to load annotations (xh.aparc.annot) in one of the scans in tksurfer, I always get this error (on both hemispheres): CTABreadFrom: could not allocate -2 bin table Cannot allocate memory Hemispheres match and I already re-ran autorecon-3, which went fine according to the log-file. Would anybody have any ideas about that error? Thanks a lot, Claus

1 0

corpus callosum
by Morgan Hough 24 Jul '07

24 Jul '07

I was wondering if I can use the surface area estimate of the aparc corpus callosum label as a decent subject specific measurement of its cross-sectional area. Thanks in advance. Cheers, -Morgan

2 3

Help with surface parcellation
by Sharon Ruso 24 Jul '07

24 Jul '07

Hello Everyone. I have a subject that throughout all the process "looked pretty good", however, when I reached the final process of checking surfaces and loading the aparc.annot file, I paid attention that all my "unknown area" , covers my -almost fully my "corpus callosum" label. What should I do, is there a way to fix it? Thanks Sharon

2 1

Another question
by Sharon Ruso 24 Jul '07

24 Jul '07

Dear Freesurfers Another problem that I'm facing while checking my surfaces is: when I load the aparc.annot I get a mass with the colors, which I assume can be a result of either loading the wrong lh/rh, on the original surface , or a result of noise. How can I fix it? Thanks again Sharon

2 1

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Freesurfer July 2007