oh, sorry, you are completely right! What version are you using? If you tar and gzip the subject's dir we'll take a look. Has this happened on other datasets with these acquisition parameters? What sequence/coil/scanner are you using?
Bruce On Mon, 4 Apr 2011, Mayuresh K wrote: > 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 >> ***************************************** >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
