Hi to all,
there are still correction problems after recon-all!
After recon-all not all of the corrections are visible???????
I corrected e.g. 10 slices. I deleted some voxels in wm.mgz as aux volume, non-white matter classified as white matter. I saved the aux volume and i startet recon-all! After running without errors, i checked in tkmedit. There were 5 of 10 slices corrected, but not the others???? With means there are still 5 slices of the previous corrected including some non-white matter classified as white matter! When i open the cor files for these slice, the corrections are visible!!
please help to find the bug
Best Mareen
-------- Original-Nachricht --------
Datum: Fri, 13 Aug 2010 11:38:01 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: Mareen Kussatz mareenkussatz@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] autorecon2
Hi Maureen,
if you exit tkmedit and reload the wm.mgz before rerunning recon-all are your edits in it? It shouldn't matter whether you edit/save in the main or aux volume.
cheers Bruce
On Wed, 11 Aug 2010, Mareen Kussatz wrote:
Hi to all,
after correcting white matter problems, we saved the wm as aux volume
and we tried also to save it as main volume. And than, we started recon-all -autorecon2-wm -subjid (subject file name). The process ends without any error for both conditions but after checking the tkmedit, there weren´t any corrections visible and actually there were no change at all.???
We just want to know if it is a syntax problem or if there is something
wrong with the freesurfer itself.
thanks and best regards.
Mareen Kussatz
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Mareen,
when you say the corrections are not visible, doo you mean the surfaces are still in the wrong place? Does the wm.mgz show the corrections? If so, then the edits you made didn't fix the underlying problem, possibly a topological defect. If you want to upload the data we'll take a look.
cheers Bruce
On Mon, 30 Aug 2010, Mareen Kussatz wrote:
Hi to all,
there are still correction problems after recon-all!
After recon-all not all of the corrections are visible???????
I corrected e.g. 10 slices. I deleted some voxels in wm.mgz as aux volume, non-white matter classified as white matter. I saved the aux volume and i startet recon-all! After running without errors, i checked in tkmedit. There were 5 of 10 slices corrected, but not the others???? With means there are still 5 slices of the previous corrected including some non-white matter classified as white matter! When i open the cor files for these slice, the corrections are visible!!
please help to find the bug
Best Mareen
-------- Original-Nachricht --------
Datum: Fri, 13 Aug 2010 11:38:01 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: Mareen Kussatz mareenkussatz@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] autorecon2
Hi Maureen,
if you exit tkmedit and reload the wm.mgz before rerunning recon-all are your edits in it? It shouldn't matter whether you edit/save in the main or aux volume.
cheers Bruce
On Wed, 11 Aug 2010, Mareen Kussatz wrote:
Hi to all,
after correcting white matter problems, we saved the wm as aux volume
and we tried also to save it as main volume. And than, we started recon-all -autorecon2-wm -subjid (subject file name). The process ends without any error for both conditions but after checking the tkmedit, there weren´t any corrections visible and actually there were no change at all.???
We just want to know if it is a syntax problem or if there is something
wrong with the freesurfer itself.
thanks and best regards.
Mareen Kussatz
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
HUMAN NEUROSCIENCE/BRAIN IMAGING. The Department of Psychology at The OHIO STATE UNIVERSITY seeks outstanding candidates to fill 2-3 positions over the next few years in human neuroscience with an emphasis on brain imaging methodologies. Pending availability of funds, these positions are expected to be at the Assistant or early Associate Professor levels. Candidates in any area of psychology (i.e., behavioral neuroscience, clinical, cognitive, developmental, quantitative, or social) who use functional magnetic resonance imaging (fMRI) as a core methodological tool are encouraged to apply. The department is opening an MRI facility with a research dedicated Siemens Trio scanner within its building in January, 2011. All applicants are expected to have strong and fundable research programs and to contribute to both graduate and undergraduate supervision and instruction. Prospective candidates should send a letter of application, statements of research and teaching interests, a vita, selected reprints, and three letters of recommendation to the Human Neuroscience Search Committee, Department of Psychology, Ohio State University, 1835 Neil Avenue, Columbus, OH 43210-1222. To ensure consideration, application materials must be received by October 1, 2010, but applications will be reviewed until the position is filled. Electronic applications will not be accepted. For more information about the department, visit: www.psy.ohio- state.edu. Ohio State is an EEO/AA Employer. To build a diverse workforce, women, minorities, veterans, and individuals with disabilities are encouraged to apply.
OPEN RANK, PSYCHOPATHOLOGY. Pending the availability of funds, the Department of Psychology at The OHIO STATE UNIVERSITY invites applications for a tenure track position. Rank is open, with preference for a candidate at the Associate Professor or early Full Professor level. We are seeking a scholar with an established program of research broadly focused on psychopathology, who has achieved national visibility and external research funding. The candidate’s program of research may use human or animal models. Candidates whose interests complement existing strengths in or bridge between our clinical psychology and behavioral neuroscience areas will be especially attractive. Responsibilities include graduate and undergraduate teaching, and research mentorship. Although not required, candidates with clinical training who are license eligible in Ohio are desired. Review of applications will begin on October 1, 2010, and continue until the position is filled. Electronic applications will not be accepted. Prospective candidates should submit a letter of interest, vita, statements of research and teaching interests, selected reprints, and three letters of recommendation to Michael Vasey, Chair, Psychopathology Search Committee, Department of Psychology, The Ohio State University, 1835 Neil Avenue, Columbus, OH 43210-1222. Ohio State is an EEO/AA Employer. To build a diverse workforce, women, minorities, veterans, and individuals with disabilities are encouraged to apply.
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