Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30132 discussions

Job Opening, FreeSurfer Team, Software
by Nick Schmansky 12 Oct '10

12 Oct '10

Hello FreeSurfers, The always-busy FreeSurfer team is looking to add another team member with software skills to work in our lab. Our needs include someone to work on maintaining the existing software, to 'own' the build and release tasks, to maintain and create tests, to provide internal support to researchers within the center, to help others on the mailing list, to add to and improve our documentation, and to help in conducting courses. This opening is for someone with entry-level to five years of experience. Ideally, the candidate would have a computer science background, with C/C++ programming experience in Linux. Candidates from other backgrounds, such as psychology or cognitive science, but are comfortable with scripting or Matlab in Linux, and want to take-on a software role, will also be considered. If you are this person, or know of someone, please send a CV or resume to me at nicks(a)nmr.mgh.harvard.edu Sincerely, Nick Schmansky

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Fwd: RE: password for windows ubuntu to share folders:
by Krish Subramaniam 12 Oct '10

12 Oct '10

Hi, Also if feel the need to enable the root account for some reason, you can do sudo passwd root and enter a new password to begin using the account. -Krish -------- Original Message -------- Subject: RE: [Freesurfer] password for windows ubuntu to share folders: Date: Tue, 12 Oct 2010 10:58:37 -0500 From: Eggebrecht, Adam <eggebrechta(a)mir.wustl.edu> To: Krish Subramaniam <krish(a)nmr.mgh.harvard.edu> Ah, excellent. Thank you, Krish! -Adam Adam T. Eggebrecht, Ph.D. Dept. of Radiology Washington University School of Medicine St. Louis, MO 314-362-6942 ________________________________________ From: Krish Subramaniam [krish(a)nmr.mgh.harvard.edu] Sent: Monday, October 11, 2010 4:36 PM To: Eggebrecht, Adam Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] password for windows ubuntu to share folders: Hi Adam By default, the root account is locked in Ubuntu. See https://help.ubuntu.com/community/RootSudo You can do admin things by using "sudo" and entering the password when it prompts you. Krish On 10/11/10 5:32 PM, Eggebrecht, Adam wrote: > Hello Krish, > > Yes, that is the version of FreeSurfer. Alas, the password will not get me root access. > > -Adam > > Adam T. Eggebrecht, Ph.D. > Dept. of Radiology > Washington University School of Medicine > St. Louis, MO > 314-362-6942 > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of Krish Subramaniam [krish(a)nmr.mgh.harvard.edu] > Sent: Monday, October 11, 2010 4:12 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] password for windows ubuntu to share folders: > > Hi Adam > > Is this for the FreeSurfer 5.0.0 virtual machine? The password is > "freesurfer" ( without the quotes ). > > Cheers > Krish > > On 10/11/10 4:43 PM, Eggebrecht, Adam wrote: >> The README file explains how to gain access to a USB device, not how to internally mount the shared folder. >> The only ways I know how to finish mounting a shared folder include using root access. >> I tried brain2009 and other similar strings, but have had no luck cracking into root yet. >> >> Any other suggestions for the root password in the Ubuntu release? >> >> Many thanks, >> -Adam >> >> >> Adam T. Eggebrecht, Ph.D. >> Dept. of Radiology >> Washington University School of Medicine >> St. Louis, MO >> 314-362-6942 >> ________________________________________ >> From: Pedro Paulo de Magalhães Oliveira Junior [ppj(a)netfilter.com.br] >> Sent: Monday, October 11, 2010 12:39 PM >> To: Eggebrecht, Adam >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] password for windows ubuntu to share folders: >> >> It's in the README >> >> As far as I remember is brain2009 >> --------------------------------------------------------------------- >> Pedro Paulo de Magalhães Oliveira Junior >> Diretor de Operações >> Netfilter& SpeedComm Telecom >> -- www.netfilter.com.br<http://www.netfilter.com.br> >> -- For mobile: http://www.netfilter.com.br/mobile >> >> >> >> >> On Mon, Oct 11, 2010 at 14:15, Eggebrecht, Adam<eggebrechta(a)mir.wustl.edu<mailto:eggebrechta@mir.wustl.edu>> wrote: >> Hello there, >> >> I am using FreeSurfer in my XP box within its Ubuntu Virtual Box. >> It appears that everything is working just fine. >> I would like to make changes to the guest OS but need the password to do so. >> Can I please get this password? I am having trouble mounting my data folders to the guest OS without password or root privileges. >> >> Many thanks! >> -Adam >> >> >> Adam T. Eggebrecht, Ph.D. >> Dept. of Radiology >> Washington University School of Medicine >> St. Louis, MO >> 314-362-6942 >> >> The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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. >> >> >> >> The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Able to use bbregister to move from conformed space to diffusion space?
by Tanner,Jared J 12 Oct '10

12 Oct '10

Hi, Is there a way to use bbregister to register a FreeSurfer image (e.g., rawavg.mgz) to a diffusion image from the same participant? In other words, is there a way to specify --mov rawavg.mgz and make the target (template) image a b0 diffusion image? Or at least to perform an inverse transform on the rawavg image after registering the b0 to the rawavg? I plan on trying mris_cvs_register but I was wondering if bbregister can do what I want. I've used flirt, fnirt, and SyN registration methods but flirt isn't quite accurate enough for intra-subject, multi-modal registration, fnirt is better but still has troubles with cortical regions, and SyN has been too variable with results. Thank you, Jared Tanner PhD Candidate Clinical & Health Psychology University of Florida

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mri_label2label problem
by Ritobrato Datta 12 Oct '10

12 Oct '10

Hello All, I hand drew a label on subject X's inflated surface using the tools in tksurfer outlined in http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferWorkingWithD…, then I applied the label to Subject Y using mrilabel2label specifically - mri_label2label --srclabel ROI-subjX.label --srcsubject SubjX --trglabel ROI-subjY.label --trgsubject SubjY --regmethod surface --hemi lh The problem is on surface of subject Y, when I upload the label, I see these holes inside the label (please see figure attached). Can anyone tell how do I get rid of them ? Thanks much Ri

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QDEC Design tab interface options
by Jay Ives 12 Oct '10

12 Oct '10

Hi, I am wondering what is going on "under the hood" when one makes a choice under the Design tab in the Measure (Dependant Variable) box for Measure. For example if one chooses "Volume" instead of Thickness, what exactly is being used as volume? Where does the information on volume come from? I am hoping the answer will be the volume associated with each vertex, but where is this information? Thanks....J

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Left-Right Concern
by Jay Ives 11 Oct '10

11 Oct '10

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error loading averaged brain in QDEC
by Ilana Hairston 11 Oct '10

11 Oct '10

Hi there, I am trying to use and averaged subject instead of fsaverage for QDEC. I used make_average_subject to create the new template, which created a folder called avgsubject. Then i ran recon-all -s SUBJECTID -qcache -target avgsubject (on all subjects) In QDEC, in "Common-Space Subject" i typed the new averaged subject folder. But when trying to run analyses, i get an error message: Error in Analyze: Couldn't open file /usr/local/FS5/subjects/FS080920cr/surf/lh.thickness.fwhm10.avgsubject.mgh (where"avgsubject" was the output name of the averaged subject template). Indeed, there are only *h.*.fwhm*.fsaverage.mgh in my subject folders (presumably from the previous preproc), but no new ones with 'avgsubject'. What am i doing wrong? thanks ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Sentimental Insomnia and Nostalgia Disorders Sciences ********************

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password for windows ubuntu to share folders:
by Eggebrecht, Adam 11 Oct '10

11 Oct '10

Hello there, I am using FreeSurfer in my XP box within its Ubuntu Virtual Box. It appears that everything is working just fine. I would like to make changes to the guest OS but need the password to do so. Can I please get this password? I am having trouble mounting my data folders to the guest OS without password or root privileges. Many thanks! -Adam Adam T. Eggebrecht, Ph.D. Dept. of Radiology Washington University School of Medicine St. Louis, MO 314-362-6942 The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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uniform sampling of the sphere
by Ryan Muetzel 11 Oct '10

11 Oct '10

Hello, I was wondering if there was a way to uniformly parcellate the sphere into "n" regions, and ultimately apply this parcellation to the volume/native space to generate ROIs? Or perhaps output uniformly sampled sphere coordinates that could be converted to voxel coordinates? Thanks in advance! Ryan Muetzel University of Minnesota

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Setting lesion voxels
by Righart, Ruthger Dr. 11 Oct '10

11 Oct '10

Dear Freesurfers, I would like that surface analyses (i.e., cortical thickness) are not confounded by subcortical lesions in patients. Freesurfer provides a work-around in its release notes ( http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) which is to set lesion voxels in brainmask.mgz and norm.mgz to 110 and in aseg.mgz to 77 and then run recon-all -autorecon2-cp (see copy text underneath). As I have lesion masks of every patient I thought it would be best to automatize this step. In that case, I would like to bring mask images with white matter lesions of these patients in the same (freesurfer) space as my T1.mgz, with dimensions 256 x 256 x 256, spacing 1 x 1 x 1., and after that set the lesions to the aforementioned values. Is there a possibility to bring lesion mask of these patients in the same space as T1.mgz in freesurfer? I inspected the function bbregister and mri_convert but could not find a solution here. Any help or suggestions are appreciated! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany Ruthger.Righart(a)med.uni-muenchen.de http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes • mris_make_surfaces: where wm lesions exist, even if the lesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. A potential work-around is to set lesion voxels in brainmask.mgz and norm.mgz to 110 and lesions voxels in aseg.mgz to 77 (lesion mask can be derived manually or from an automated algorithm), then run recon-all -autorecon2-cp

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