Hi Dan and Bruce, Thanks for your getting back on the problem. My concern is more about the dura being incorrectly labeled - It appears to me that the grey-CSF boundary has been incorrectly labeled as the GM-WM boundary across the entire image. Any ideas what may have gone wrong?
Thanks, Mayuresh On Sat, Apr 2, 2011 at 3:28 AM, <freesurfer-requ...@nmr.mgh.harvard.edu>wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: incorrect GM/WM surfaces (Daniel G Wakeman) > 2. problems with loading a pial surface (Iris Steinmann) > 3. Re: incorrect GM/WM surfaces (Bruce Fischl) > 4. Re: problems with loading a pial surface (Bruce Fischl) > 5. preproc-sess OSX bug fix getrunlist (Juli Dolzhenko) > 6. MRI analyst position (Keith Schneider) > 7. Distance between two points along cortical (caoaize) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Apr 2011 05:53:20 +0100 > From: Daniel G Wakeman <daniel.wake...@mrc-cbu.cam.ac.uk> > Subject: Re: [Freesurfer] incorrect GM/WM surfaces > To: <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <471c0967-fe19-409e-8174-31fbb56cd...@mrc-cbu.cam.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Hi Mayuresh, > > I assume you are talking about the area in the posterior midline, where the > pial surface seems to go 'squiggly'. You also seem to have a problem with > the right hemisphere (left visually: I hate radiology ;)), where some dura > seems incorrectly labeled as pial surface (although the grey matter is very > difficult to see on this sequence/ at this setting). > > To fix these I recommend this wiki page: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits > > Good Luck! > Dan > > On 2011 Apr 1, at 05:08 , <freesurfer-requ...@nmr.mgh.harvard.edu> < > freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > > > Send Freesurfer mailing list submissions to > > freesurfer@nmr.mgh.harvard.edu > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > or, via email, send a message with subject or body 'help' to > > freesurfer-requ...@nmr.mgh.harvard.edu > > > > You can reach the person managing the list at > > freesurfer-ow...@nmr.mgh.harvard.edu > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Freesurfer digest..." > > > > > > Today's Topics: > > > > 1. incorrect GM/WM surfaces (Mayuresh K) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 1 Apr 2011 15:21:18 +1100 > > From: Mayuresh K <mayureshk...@gmail.com> > > Subject: [Freesurfer] incorrect GM/WM surfaces > > To: freesurfer@nmr.mgh.harvard.edu > > Message-ID: > > <AANLkTi=bltokkzngth5sxhsqvmfruhakzg9u07xzw...@mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hello freesurfer experts, > > > > I have successfully finished running the recon-all analysis without any > > errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM > > surfaces however look incorrect and I am not sure what may have gone > wrong. > > See attached screenshot from tkmedit. > > Any suggestions how to fix this would be helpful. > > > > I have processed other datasets collected from the same scanner using the > > same sequence which seem to have correctly identified the pial and > > grey-white boundaries. I am using > > freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1. > > > > Thanks, > > Mayuresh > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110401/f494b1a2/attachment.html > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: tkmedit ** brainmask.mgz ** (T1.mgz).png > > Type: image/png > > Size: 81386 bytes > > Desc: not available > > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110401/f494b1a2/attachment.png > > > > ------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > End of Freesurfer Digest, Vol 86, Issue 1 > > ***************************************** > > > > > > 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. > > > > > > > ------------------------------ > > Message: 2 > Date: Fri, 01 Apr 2011 09:42:47 +0200 > From: Iris Steinmann <iris.steinm...@uni-heidelberg.de> > Subject: [Freesurfer] problems with loading a pial surface > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <1301643767.2015.2.camel@steinmann> > Content-Type: text/plain; charset="UTF-8" > > Hello Freesurfers > > I still have the problem using a tcl script that should load the pial > surface on a patch in tksurfer. I tried to use the following three > commands: > > > 1. set gaLinkedVars(vertexset) 3 > SendLinkedVarGroup view > redraw > > > 2. read_pial_vertex_coordinates > redraw > > 3. read_surface_vertex_set 3 lh.pial > redraw > > > But none of them loaded the pial surface. I would be very thankful for > a solution ore a hint. > > Iris > > > > ------------------------------ > > Message: 3 > Date: Fri, 1 Apr 2011 08:27:58 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] incorrect GM/WM surfaces > To: Daniel G Wakeman <daniel.wake...@mrc-cbu.cam.ac.uk> > Cc: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <pine.lnx.4.62.1104010827050.28...@gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Mayuresh > > the "squiggly" stuff isn't necessarily a problem. You need to look at it in > a different view, but it can be a region in which the surface is nearly > paralell to the viewing plane to that it crosses back and forth a ton of > times in a small patch. > > cheers > Bruce > > > On Fri, 1 Apr 2011, Daniel G Wakeman wrote: > > > Hi Mayuresh, > > > > I assume you are talking about the area in the posterior midline, where > the pial surface seems to go 'squiggly'. You also seem to have a problem > with the right hemisphere (left visually: I hate radiology ;)), where some > dura seems incorrectly labeled as pial surface (although the grey matter is > very difficult to see on this sequence/ at this setting). > > > > To fix these I recommend this wiki page: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits > > > > Good Luck! > > Dan > > > > On 2011 Apr 1, at 05:08 , <freesurfer-requ...@nmr.mgh.harvard.edu> < > freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > > > >> Send Freesurfer mailing list submissions to > >> freesurfer@nmr.mgh.harvard.edu > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> or, via email, send a message with subject or body 'help' to > >> freesurfer-requ...@nmr.mgh.harvard.edu > >> > >> You can reach the person managing the list at > >> freesurfer-ow...@nmr.mgh.harvard.edu > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of Freesurfer digest..." > >> > >> > >> Today's Topics: > >> > >> 1. incorrect GM/WM surfaces (Mayuresh K) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Fri, 1 Apr 2011 15:21:18 +1100 > >> From: Mayuresh K <mayureshk...@gmail.com> > >> Subject: [Freesurfer] incorrect GM/WM surfaces > >> To: freesurfer@nmr.mgh.harvard.edu > >> Message-ID: > >> <AANLkTi=bltokkzngth5sxhsqvmfruhakzg9u07xzw...@mail.gmail.com> > >> Content-Type: text/plain; charset="iso-8859-1" > >> > >> Hello freesurfer experts, > >> > >> I have successfully finished running the recon-all analysis without any > >> errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM > >> surfaces however look incorrect and I am not sure what may have gone > wrong. > >> See attached screenshot from tkmedit. > >> Any suggestions how to fix this would be helpful. > >> > >> I have processed other datasets collected from the same scanner using > the > >> same sequence which seem to have correctly identified the pial and > >> grey-white boundaries. I am using > >> freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1. > >> > >> Thanks, > >> Mayuresh > >> -------------- next part -------------- > >> An HTML attachment was scrubbed... > >> URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110401/f494b1a2/attachment.html > >> -------------- next part -------------- > >> A non-text attachment was scrubbed... > >> Name: tkmedit ** brainmask.mgz ** (T1.mgz).png > >> Type: image/png > >> Size: 81386 bytes > >> Desc: not available > >> Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110401/f494b1a2/attachment.png > >> > >> ------------------------------ > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> End of Freesurfer Digest, Vol 86, Issue 1 > >> ***************************************** > >> > >> > >> 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 > > > > > > > > > ------------------------------ > > Message: 4 > Date: Fri, 1 Apr 2011 08:51:34 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] problems with loading a pial surface > To: Iris Steinmann <iris.steinm...@uni-heidelberg.de> > Cc: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <pine.lnx.4.62.1104010837040.28...@gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Iris, > > updating. I would try: > > > set_current_vertex_set 3 > UpdateLinkedVarGroup view > UpdateAndRedraw > > > if this doesn't work, tell us, and if you don't get a response in the next > day or so, can you repost in a week? We are flat out trying to prepare for > our upcoming course and also get 5.1 out the door. The tcl scripting is > confusing and could use serious > > cheers, > Bruce > > p.s. I am a bit confused about what you are trying to do though. Why do you > want only a patch of the pial surface? And not flattened I assume as I > don't even know what that would mean (it wouldn't be the pial surface > anymore). > > On Fri, 1 Apr 2011, Iris Steinmann wrote: > > > Hello Freesurfers > > > > I still have the problem using a tcl script that should load the pial > > surface on a patch in tksurfer. I tried to use the following three > > commands: > > > > > > 1. set gaLinkedVars(vertexset) 3 > > SendLinkedVarGroup view > > redraw > > > > > > 2. read_pial_vertex_coordinates > > redraw > > > > 3. read_surface_vertex_set 3 lh.pial > > redraw > > > > > > But none of them loaded the pial surface. I would be very thankful for > > a solution ore a hint. > > > > Iris > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > ------------------------------ > > Message: 5 > Date: Fri, 1 Apr 2011 12:00:17 -0400 (EDT) > From: "Juli Dolzhenko" <j...@nmr.mgh.harvard.edu> > Subject: [Freesurfer] preproc-sess OSX bug fix getrunlist > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <44911.68.162.255.42.1301673617.squir...@mail.nmr.mgh.harvard.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Hello, > > I am running into an issue with running preproc-sess on OSX as outlined > here: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15896.html > > I saw Doug posted a bug fix that should solve this problem, however, I am > unable to access it from: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/getrunlist > > Is there a way I can download this new version of getrunlist? > > Thanks so much, > Juli > > > > ------------------------------ > > Message: 6 > Date: Fri, 1 Apr 2011 12:26:03 -0400 > From: Keith Schneider <kei...@yorku.ca> > Subject: [Freesurfer] MRI analyst position > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <eafd6b8f-3d65-4ef3-af30-7d3938eba...@yorku.ca> > Content-Type: text/plain; charset=windows-1252 > > YORK UNIVERSITY > > Job Type: Contract > Location: Toronto, ON, CANADA; > Industry: Education > Company URL: http://www.yorku.ca > Date Posted: March 31, 2011 > > JOB TITLE: MRI Analyst, Neuroimaging Laboratory > > 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, with flexible work times > > CLOSING DATE FOR POSITION: April 14, 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, r?sum?, and > the names of at least two referees. > > By submitting an application package, you agree that your referees may be > contacted prior to any interview offer to gauge your suitability for the > position. > > 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 ? rsrch...@yorku.ca > > > ------------------------------ > > Message: 7 > Date: Sat, 2 Apr 2011 00:28:31 +0800 > From: caoaize <caoa...@hotmail.com> > Subject: [Freesurfer] Distance between two points along cortical > To: <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <snt103-w613dc3e0168318d3f2b966b5...@phx.gbl> > Content-Type: text/plain; charset="gb2312" > > > > Hello FS Experts, > > Suppose we have two points on the cortical surface (pial for example), we > want to know the distance between these two point along cortical surface > (not direct distance). Does FS report this kind of distance? Any suggestion > will be very appreciated. > > Aize > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110402/48f65e45/attachment.html > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 86, Issue 2 > ***************************************** >
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