Hi Bruce, Thanks for offering to take a look at the data. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1. Yes I have had this problem on a few other data-sets - more like 1 every 8 datasets. Teh data is collected using a 3D SPGR scan (TR=13, TE=6.2, flip=20, sagittal, 256*256, 1mm slice thickness, isotropic voxels), HNS head coil, on a 1.5 clinical GE scanner.
How should I send you the subject's processed dir? Its a bit big to email after tar and gzip. Regards, Mayuresh On Mon, Apr 4, 2011 at 11:11 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > 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 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.
