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Problems segmenting monkey brain
by Srihasam, Krishna 08 Apr '10

08 Apr '10

Hi, I have a (0.35 mm)^3 resolution monkey brain which I am trying to segment. I am unable to get the frontal cortex to segment properly. My WM.mgz looks good ( I think), but after I do "recon-all -autorecon2-wm ", the surf that gets created has no frontal cortex. I have attached two pictures of one slice, with generated surface overlaid on WM.mgz ( WM_Surf133.jpg) and the same generated surface on T1 image (NU-Surf133.jpg). I tried adding control points, I manually edited the WM.mgz and nothing works. Any help will be appreciated.. regards, Krishna Srihasam Postdoctoral Fellow Livingstone Lab 220 Longwood Avenue, WAS 232 Boston, MA 02115

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Re: [Freesurfer] Freesurfer Digest, Vol 74, Issue 13
by Sebastian Moeller 07 Apr '10

07 Apr '10

Hi Krishna, how does your brainmask look? In my experience, if you use bet to create a brainmask for monkeys, occasionally the brain center is positioned to far posterior. This seems to cause to a loss of frontal gray & white matter in the brainmask. That in turn, would "crop" these parts away from what is considered for the reconstruction. Then since I have no clue about your workflow an procedere this might not actually be helpful... Nevertheless Best Regards Sebastian On Apr 7, 2010, at 1:05 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Wed, 7 Apr 2010 16:06:31 -0400 > From: "Srihasam, Krishna" <Krishna_Srihasam(a)hms.harvard.edu> > Subject: [Freesurfer] Problems segmenting monkey brain > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <97172F7B8A916A44BF05EA8D13905ECE50C293CA0F(a)ITCCRMAIL02.MED.HARVARD.EDU> > > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I have a (0.35 mm)^3 resolution monkey brain which I am trying to segment. I am unable to get the frontal cortex to segment properly. My WM.mgz looks good ( I think), but after I do "recon-all -autorecon2-wm ", the surf that gets created has no frontal cortex. I have attached two pictures of one slice, with generated surface overlaid on WM.mgz ( WM_Surf133.jpg) and the same generated surface on T1 image (NU-Surf133.jpg). I tried adding control points, I manually edited the WM.mgz and nothing works. Any help will be appreciated.. > > > regards, > Krishna Srihasam > Postdoctoral Fellow > Livingstone Lab > 220 Longwood Avenue, WAS 232 > Boston, MA 02115 > >

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Re: [Freesurfer] Pial Surfaces Cutting off Gyri
by Sherri Novis 07 Apr '10

07 Apr '10

Thank you Bruce. I've had this prob randomly before - but recently it's been each of the last 10 datasets - so I think its a process issue that I introduced - but would love help from any direction. If I use the upload site - which files to you need? will send wm.mgz, ?h.orig surface - any others? Thank you - Sherri -----Original Message----- >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >Sent: Apr 7, 2010 1:15 PM >To: Sherri Novis <echotalk(a)earthlink.net> >Cc: Sita Kakunoori <sita(a)nmr.mgh.harvard.edu>, freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Pial Surfaces Cutting off Gyri > >Hi Sherri, > >you may also have a topological defect near those control points, which >is causing the surfaces to lose the wm (and hence the gm also). What does >the wm.mgz look like there? Is the wm segmented correctly but not >included in the ?h.orig surface? If you upload this data we can take a >look, if you want. >Bruce > > >On Wed, 7 Apr 2010, Sherri Novis wrote: > >> Thanks Sita. I have struggled with how to capture very ghostly gray matter. Sometimes throwing a CP in it works (I understand now this may be hosing it sometimes) - if AR2-cp w/CPs in white matter is not driving the pial surfaces to capture all the gray - is the only way to capture the ghostly gray matter to directly edit the pial surface? >> >> I was trying to avoid that. I was told don't ever edit the pial surfaces - not sure why though. Will manual edits of the pial surfaces cause other problems in getting surface segmentation stats? >> >> Thank you - >> Sherri >> >> -----Original Message----- >>> From: Sita Kakunoori <sita(a)nmr.mgh.harvard.edu> >>> Sent: Apr 7, 2010 12:55 PM >>> To: Sherri Novis <echotalk(a)earthlink.net> >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Pial Surfaces Cutting off Gyri >>> >>> >>> Hi Sherri, >>> >>> one of the control points seems to be in gray matter, which is probably >>> causing this. Please try deleting it and rerunning autorecon2-cp. >>> >>> Sita. >>> >>> >>> On Tue, 6 Apr 2010, Sherri Novis wrote: >>> >>>> Hello brilliant and generous FS people, >>>> >>>> I have introduced a problem I cannot solve. I am simply trying to capture as much gray matter as possible. We have some very bad constrast images (ghostly edeges where the gray matter should be). I'm adding control points to try to capture - however, now when I run AR2-cp, the pial surfaces go haywire on the superior borders of the slices. >>>> >>>> Attached are two images displaying the problem. >>>> >>>> I have edited wm.mgz to fill in the ventricles because I was getting islands, and I manually edited the brainmask to remove some vasculature that was being included in the pial surfaces. >>>> >>>> Can you tell me where I introduced this instability? >>>> >>>> Best Regards, >>>> Sherri >>> >>> >>> 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(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>

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Re: [Freesurfer] Pial Surfaces Cutting off Gyri
by Sherri Novis 07 Apr '10

07 Apr '10

Thanks Sita. I have struggled with how to capture very ghostly gray matter. Sometimes throwing a CP in it works (I understand now this may be hosing it sometimes) - if AR2-cp w/CPs in white matter is not driving the pial surfaces to capture all the gray - is the only way to capture the ghostly gray matter to directly edit the pial surface? I was trying to avoid that. I was told don't ever edit the pial surfaces - not sure why though. Will manual edits of the pial surfaces cause other problems in getting surface segmentation stats? Thank you - Sherri -----Original Message----- >From: Sita Kakunoori <sita(a)nmr.mgh.harvard.edu> >Sent: Apr 7, 2010 12:55 PM >To: Sherri Novis <echotalk(a)earthlink.net> >Cc: freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Pial Surfaces Cutting off Gyri > > >Hi Sherri, > >one of the control points seems to be in gray matter, which is probably >causing this. Please try deleting it and rerunning autorecon2-cp. > >Sita. > > >On Tue, 6 Apr 2010, Sherri Novis wrote: > >> Hello brilliant and generous FS people, >> >> I have introduced a problem I cannot solve. I am simply trying to capture as much gray matter as possible. We have some very bad constrast images (ghostly edeges where the gray matter should be). I'm adding control points to try to capture - however, now when I run AR2-cp, the pial surfaces go haywire on the superior borders of the slices. >> >> Attached are two images displaying the problem. >> >> I have edited wm.mgz to fill in the ventricles because I was getting islands, and I manually edited the brainmask to remove some vasculature that was being included in the pial surfaces. >> >> Can you tell me where I introduced this instability? >> >> Best Regards, >> Sherri > > >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. >

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Pial Surfaces Cutting off Gyri
by Sherri Novis 07 Apr '10

07 Apr '10

Hello brilliant and generous FS people, I have introduced a problem I cannot solve. I am simply trying to capture as much gray matter as possible. We have some very bad constrast images (ghostly edeges where the gray matter should be). I'm adding control points to try to capture - however, now when I run AR2-cp, the pial surfaces go haywire on the superior borders of the slices. Attached are two images displaying the problem. I have edited wm.mgz to fill in the ventricles because I was getting islands, and I manually edited the brainmask to remove some vasculature that was being included in the pial surfaces. Can you tell me where I introduced this instability? Best Regards, Sherri

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2005 vs 2009 parcellations
by Frida Polli 07 Apr '10

07 Apr '10

hi aside from new ROIS (i.e. the cingulate being divided into 3 parts), the 2009 looks like it has smoother/different boundaries than the 2005 one, even for ROIs that remain the same as the 2005. what is that a result of? thanks, frida -- Frida E. Polli, PhD Postdoctoral Fellow Brain & Cognitive Sciences, MIT 43 Vassar St., Room 46-4033 Cambridge, MA 02139 email: fpolli(a)mit.edu tel: (617) 324 2897

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Re: [Freesurfer] Optseq2 - Incorporate sequential order of trials as a factor
by Gaber, Tilman 07 Apr '10

07 Apr '10

Thank you for your quick response. Initially I had the same idea. Unfortunately, this easy solution does not work. All trials are successor of the previous and predecessor of the following trial. Therefore we can't just randomly distribute pairs of trials. The whole chain of trials has to be in proper order. ([A-B-A-A-B-B-B-A-...] = [AB BA AA AB BB BA ...]) My thinking was to somehow add these restrictions to the initial part of optseq2 algorithm and fix for null event interuptions afterwards... Tilman --------------------------------------------------------------------------------- Tilman J. Gaber, Dipl.Psych. Translational Neuroscience in Psychiatry and Neurology Dpt. of Child and Adolescent Psychiatry and Psychotherapy RWTH Aachen University Neuenhofer Weg 21 52074 Aachen Germany PHONE: +49-(0)241-80.85347 FAX: +49-(0)241-80.3335070 Email: tgaber(a)ukaachen.de ________________________________________ Von: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Gesendet: Freitag, 26. Februar 2010 18:56 An: Gaber, Tilman Cc: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Optseq2 - Incorporate sequential order of trials as a factor You can specify that there are 4 trial types (AA, AB, BA, BB), and give the duration twice that of the individual. doug Gaber, Tilman wrote: > Dear mailinglist recipients, > > I am currently planning an optimized experiment using optseq2 and a 2x2 factors behavioral response task (Simon-task). > The task consists of a pseudo-randomized series of two kinds of trials (congruent and incongruent). > In addition there is a sequential factor, i.e. it is of interest whether a trial follows a trial of the same or the opposite kind. In other words there are (2x2) four different conditions where trials relate to precedent trials (AA,AB,BB,BA). > Would it be possible to incorporate this sequential factor into the optseq2? > I am aware that null events will fall between trials and thus interrupt trial sequences. Trials following null events would therefore be treated separately (i.e. for data analysis). In order to obtain an equal number of trials per condition, this would require increasing the number of trials depending on the number and order of null events. > Currently I am able to produce a randomized order of equally balanced trials regarding trial type and sequential order (AA,AB,BB,BA). > Any thoughts or suggestions are more than welcome! > > Best, > Tilman > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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flattening occipital lobe results in closed patch
by Vadim Axel 07 Apr '10

07 Apr '10

Dear all, For one of my brains I fail to flatten correctly occipital lobe neither for rh, nor for lh (I get 'closed' patch). I tried to make several cut planes with different calcarine cut lines, but the result was the same. I attach a screenshot of rh with three of my attempts and the reconstructed full brain (resized it a little to fit the screenshot).I run: mris_flatten -w 0 -distances 20 20 command. Any idea what exactly might have gone wrong? How crucial is to have the calcarine cut and cut plane to be exactly on its place in order to achieve successful flattening procedure? I am using Ubuntu VirtualBox FreeSurfer v4.5 version. Thanks a lot, Vadim

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Rawavg wrong
by Janani Dhinakaran 07 Apr '10

07 Apr '10

Hello, I was wondering whether you could help me wit this. I had reported a talairach error during recon and was asked to check what the rawavg looked like. Sagital is shown instead of Coronal, and upside down at that! Clearly, there is some formatting error. Is there a way to fix this within Freesurfer or would you recommend I use Analyze to reformat, flip and then introduce the newly saved copy as the subject files? Are there any other options? Thank you for your help Jan -- I am the Sun, I know no darkness.

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scripting get label form talirach point
by Ben Hamida Cammoun Leila Faiza 07 Apr '10

07 Apr '10

Hello, I am trying to check if some talairach coordinates of AI (auditory primary) (from paper) are in the transverstamporal label, on am subjects. To do this, and thanks to your answers I used the commands line in tksurfer: select_talairach_coordinate x y z mark_vertex $select 1 and I can read: the vertex number and the label but I have to get the vertex number and the label for 5 points and 40 subjects, do you know how to get the vertex number and the label in a script? I tried func_select_label which gives me the label in the command line but I don't know how to get it in a file. Thanks a lot for this help

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