Announcement!
There is a new release of FreeSurfer, v5.0.0!
Features and fixes are described in the ReleaseNotes page:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
It is available for download at:
http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
Please pose questions about the release to the freesurfer mailing list.
The FreeSurfer Team
Hi Nick,
pretty cool. It looks like this is the real deal :). I noticed something weird on macosx 10.6.4 (x86_64 kernel). The simple inflated surgace is not rendered smoothly but shows recognizable steps in the gray values. Attached an png showing the effect (I hope this is small enough to make it to the list). (This shows up with X11 set to millions or thousands of colors, tksurfer will not start with 256 colors, but you knew that :)). I hope that this is easy to fix. Thanks a lot for supplying this great tool!
Best Sebastian
Here is bugr: ---------------------------------------------------------------------
FREESURFER_HOME: /opt/freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Kernel info: Darwin 10.4.0 x86_64
--------------------------------------------------------------------- Please include the following additional information in your report:
1) subject name bert
2) the entire command-line executed tksurfer bert lh inflated
3) the error message generated none, just the display has too little colors...
4) optionally include the subject's /script/recon-all.log
On Aug 16, 2010, at 9:04 , Nick Schmansky wrote:
Announcement!
There is a new release of FreeSurfer, v5.0.0!
Features and fixes are described in the ReleaseNotes page:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
It is available for download at:
http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
Please pose questions about the release to the freesurfer mailing list.
The FreeSurfer Team
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
sebastian,
snow leopard has given us a number of headaches in the freesurfer gui department, and it may take a while to sort them out. the gray scale issue is one of them. freeview not working is another.
n.
On Mon, 2010-08-16 at 11:35 -0700, Sebastian Moeller wrote:
Hi Nick,
pretty cool. It looks like this is the real deal :). I noticed something weird on macosx 10.6.4 (x86_64 kernel). The simple inflated surgace is not rendered smoothly but shows recognizable steps in the gray values. Attached an png showing the effect (I hope this is small enough to make it to the list). (This shows up with X11 set to millions or thousands of colors, tksurfer will not start with 256 colors, but you knew that :)). I hope that this is easy to fix. Thanks a lot for supplying this great tool!
Best Sebastian
Here is bugr:
FREESURFER_HOME: /opt/freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Kernel info: Darwin 10.4.0 x86_64
Please include the following additional information in your report:
- subject name
bert
- the entire command-line executed
tksurfer bert lh inflated
- the error message generated
none, just the display has too little colors...
- optionally include the subject's /script/recon-all.log
On Aug 16, 2010, at 9:04 , Nick Schmansky wrote:
Announcement!
There is a new release of FreeSurfer, v5.0.0!
Features and fixes are described in the ReleaseNotes page:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
It is available for download at:
http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
Please pose questions about the release to the freesurfer mailing list.
The FreeSurfer Team
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Nick,
On Aug 16, 2010, at 14:47 , Nick Schmansky wrote:
sebastian,
snow leopard has given us a number of headaches in the freesurfer gui department, and it may take a while to sort them out. the gray scale issue is one of them. freeview not working is another.
Ah, too bad I already switched to snow leopard then ;). Well, I will just continue doing my real work on Linux... (Especially since the macosx build seems 32 bit)
Best Sebastian
n.
On Mon, 2010-08-16 at 11:35 -0700, Sebastian Moeller wrote:
Hi Nick,
pretty cool. It looks like this is the real deal :). I noticed something weird on macosx 10.6.4 (x86_64 kernel). The simple inflated surgace is not rendered smoothly but shows recognizable steps in the gray values. Attached an png showing the effect (I hope this is small enough to make it to the list). (This shows up with X11 set to millions or thousands of colors, tksurfer will not start with 256 colors, but you knew that :)). I hope that this is easy to fix. Thanks a lot for supplying this great tool!
Best Sebastian
Here is bugr:
FREESURFER_HOME: /opt/freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Kernel info: Darwin 10.4.0 x86_64
Please include the following additional information in your report:
- subject name
bert
- the entire command-line executed
tksurfer bert lh inflated
- the error message generated
none, just the display has too little colors...
- optionally include the subject's /script/recon-all.log
On Aug 16, 2010, at 9:04 , Nick Schmansky wrote:
Announcement!
There is a new release of FreeSurfer, v5.0.0!
Features and fixes are described in the ReleaseNotes page:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
It is available for download at:
http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
Please pose questions about the release to the freesurfer mailing list.
The FreeSurfer Team
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi all,
Can I simply rerun recon-all -s -all on datasets already processed in a previous version?
Cheers,
Diederick
On 16 aug 2010, at 18:04, Nick Schmansky wrote:
Announcement!
There is a new release of FreeSurfer, v5.0.0!
Features and fixes are described in the ReleaseNotes page:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
It is available for download at:
http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
Please pose questions about the release to the freesurfer mailing list.
The FreeSurfer Team
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
yes, but dont mix results from different versions if conducting a group study.
n.
On Mon, 2010-08-16 at 21:29 +0200, Diederick Stoffers wrote:
Hi all,
Can I simply rerun recon-all -s -all on datasets already processed in a previous version?
Cheers,
Diederick
On 16 aug 2010, at 18:04, Nick Schmansky wrote:
Announcement!
There is a new release of FreeSurfer, v5.0.0!
Features and fixes are described in the ReleaseNotes page:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
It is available for download at:
http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
Please pose questions about the release to the freesurfer mailing list.
The FreeSurfer Team
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This is very nice. I just tried to do an analysis in the new release under Mac OS X (10.6.4, Intel). However, retinotopic mapping would not run. I did "sfa-sess -a rtopy -sf sessid -df sessdir". The error message says "sfa-sess: Command not found." Any idea why this is the case? Thanks.
-Yuhong
On Mon, Aug 16, 2010 at 11:04 AM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
Announcement!
There is a new release of FreeSurfer, v5.0.0!
Features and fixes are described in the ReleaseNotes page:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
It is available for download at:
http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
Please pose questions about the release to the freesurfer mailing list.
The FreeSurfer Team
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
There is a new retinotopic mapping stream. I have not fully documented it yet. You now analyze the retinotopy data like you would other functional analysis in fsfast. First create an "analysis" with mkanalysis-sess. Run it with -help to get info on retinotopy-specific parameters. Eg,
# Create analysis for the left hemi (30 sec period), 5mm surface-based smoothing mkanalysis-sess -a rtopy.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par -fwhm 5 # Create analysis for the right hemi mkanalysis-sess -a rtopy.rh -surface self rh -TR 2 \ -retinotopy 30 -paradigm rtopy.par -fwhm 5
# Analyze both (this will do preprocessing too) selxavg3-sess -a rtopy.lh -sf ... selxavg3-sess -a rtopy.rh -sf ...
# diplay sig maps tksurfer-sess -a rtopy.lh -s sessid
# display raw angle tksurfer-sess -a rtopy.lh -s sessid -map angle
# display raw angle tksurfer-sess -a rtopy.lh -s sessid -map angle.masked
# create the field sign fieldsign-sess -a rtopy.lh -s sessid -occip
# display the field sign tksurfer-sess -a rtopy.lh -s sessid -fieldsign
Yuhong Jiang wrote:
This is very nice. I just tried to do an analysis in the new release under Mac OS X (10.6.4, Intel). However, retinotopic mapping would not run. I did "sfa-sess -a rtopy -sf sessid -df sessdir". The error message says "sfa-sess: Command not found." Any idea why this is the case? Thanks.
-Yuhong
On Mon, Aug 16, 2010 at 11:04 AM, Nick Schmansky <nicks@nmr.mgh.harvard.edu mailto:nicks@nmr.mgh.harvard.edu> wrote:
Announcement! There is a new release of FreeSurfer, v5.0.0! Features and fixes are described in the ReleaseNotes page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes It is available for download at: http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall Please pose questions about the release to the freesurfer mailing list. The FreeSurfer Team _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Job Type: Contract Location: Toronto, ON, CANADA; Industry: Education Company URL: http://www.yorku.ca Date Posted: January 27, 2011
JOB TITLE: MRI Analyst, Centre for Vision Research TYPE OF POSITION: Contract – 1 year contract with a possibility of renewal SALARY: $60,000 - $75,000 per annum plus benefits HOURS: 35 hours per week – flexible work times CLOSING DATE FOR POSITION: February 3, 2011
JOB PURPOSE:
Reporting to the Director of the Neuroimaging Laboratory, the MRI Analyst will serve as the primary support person for the computational and analytical needs of the Neuroimaging Laboratory.
The Neuroimaging Laboratory at York University with a research-dedicated Siemens Trio MRI scanner is part of York’s world-class Centre for Vision Research. Located at the Sherman Health Science Research Centre, the MRI Analyst is a key component of this new unit.
FUNCTIONS/DUTIES:
1. Consult with users of the Neuroimaging Laboratory to help them design and program experimental paradigms and assist in analyzing their MRI data 2. Develop new data analysis tools and write scripts to efficiently implement existing tools 3. Manage the MRI data server 4. Manage the Analysis Lab computer network 5. Assist with programming for the Neuroimaging Laboratory website 6. Provide IT support 7. Assist users of the Neuroimaging Laboratory with the design and fabrication of new stimulus equipment
EDUCATIONAL REQUIREMENTS: University undergraduate degree in science or engineering required, Master's degree preferred.
EXPERIENCE REQUIREMENTS: Experience with the analysis of MRI data desirable. Experience with parallel processing on CPU clusters and/or GPUs is desirable. Experience with system administration and network management is desirable.
SKILLS (Specialized knowledge): Superior interpersonal skills and the ability to deal courteously and effectively with a wide range of people; excellent oral and written communication skills; demonstrated ability in exercising good judgment and initiative; excellent troubleshooting and problem-solving skills; ability to prioritize and work with deadlines; good organizational skills; ability to administer Mac and Linux computers; ability to utilize neuroimaging programs and statistical packages; computer programming (C, Matlab, shell scripts and/or other languages); ability to assess computer/network security, identify security risks and implement appropriate solutions.
Application Process Details
Your complete application package must include a cover letter, résumé, and the names of at least two referees.
The closing date for applications — which must be submitted by mail, e-mail or fax ONLY — is Wednesday, February 3, 2011.
Please ensure that “MRI Analyst” is quoted in e-mail subject lines and all hard copy applications.
Only those selected for an interview will be contacted. Priority consideration is given to Canadian citizens and permanent residents in Canada. York University is committed to Employment Equity and encourages applications from all qualified candidates.
Applications should be submitted to:
MRI Analyst Hiring Committee The Office of the Vice-President, Research & Innovation Fifth Floor, York Research Tower York University 4700 Keele Street Toronto, Ontario, Canada, M3J 1P3 Fax — 416-650-8197 Email — rsrchjbs@yorku.ca
freesurfer@nmr.mgh.harvard.edu
-
Diederick Stoffers -
Douglas N Greve -
Keith Schneider -
Nick Schmansky -
Sebastian Moeller -
Yuhong Jiang