Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

longitudinal processing error
by Rashmi Singh 21 May '12

21 May '12

Hello, I am running longitudinal stream processing on mprage scans of some subjects who have been scanned multiple times using the same sequence with 32 NOVA channels on GE scanner. For most subjects the base run exited without error, however for few error was reported in the runs. The error was with Tailarach failure. When I looked at the recon-all runs of the individual tps for those subjects, there was no error and recon-all had completed the runs without error on these timepoints. Why am I getting the error on base run when there was no error in the recon –all run ? And and how do I correct it? Please advise. Thanks, Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

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trac-all -path error
by Kiely Donnelly 21 May '12

21 May '12

Hello-- I have run Tracula successfully for ~75 healthy subjects. However, the pathway reconstruction seems to fail for a handful of people. I've attached the log file for one of these subjects. It appears that the control points are not within the dwi. A similar problem occurred in a subject with substantial signal loss in the dwi, but that doesn't seem to be the case for this particular person. I have been creating the entire set of tracts, but at this point, I'm only interested in the SLFt and SLFp. Thanks, Kiely

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trac-all -bedp error
by Sarina Sacco 21 May '12

21 May '12

Hi, tracula users I run the trac-all bedp process and resulted this error: 74 slices processed 75 slices processed 76 slices processed Queuing post processing stage 80 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. I look the processed data in dmri.bedpostx,but I don't identify the problem. help me plese. I run -path process and in this moment not created problem,but is not terminated.I fear that the information is incomplete.

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Rejoindre mon réseau sur LinkedIn
by Mohan Boddu via LinkedIn 21 May '12

21 May '12

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GLUT Error
by Tate, David Franklin 21 May '12

21 May '12

I am running FreeSurfer 5.1 on a Mac Pro intel using Snow Leopard (OS X 10.6). I am getting the following GLUT error message: GLUT: Fatal Error in tkmedit.bin: could not open display: :0.0 GLUT: Fatal Error in tksurfer.bin: could not open display: :0.0 when trying to run tkmedit or tksurfer. Freeview seems to work without any issue. I have tried to run it in both the x11 window and the terminal window with the same results. The messages on the message board seem to raise the issue but the appeared to not answer the issue completely. Any help would be greatly appreciated.

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How to edit the pial surface
by 李盟 21 May '12

21 May '12

Hi professor, The attachment is the subject after running the recon-all command. MR data were obtained on a 1.5T Philips Achieva Nova Dual MR scanner. the sequence name is T1W.3D.FFE.SENSE and the voxel size is 0.90*0.90*1mm. how should I fix the poor quality surface reconstruction? Thanks a lot for your help. Meng Li At 2012-05-19 23:10:31,"Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >p.s. looks like an intensity normalization failure. Can you give us details >of the acquisition? Sequence name, voxel resolution, etc....? If you upload >the subject I'll take a look > >cheers >Bruce > >On Sat, 19 May 2012, >limengsecret wrote: > >> Hi Professor, >> The image blow shows the problems which occur. >> color lines representing the surfaces (pial and white) were not along the >> folding pattern, and the distance between the two sufaces was rather short. >> How to deal with these problems? >> [IMAGE] >> Thanks. >> >> Meng Li >> >> >> ____________________________________________________________________________ >> limengsecret >> >> From: Bruce Fischl >> Date: 2012-05-19 22:08 >> To: ?? >> CC: freesurfer >> Subject: Re: [Freesurfer] how to edit the pial surface >> Hi Meng >> >> 1. Not positive I understand, but I don't think it should matter. >> >> 2. we'll need to see some data to diagnose this. >> >> cheers >> Bruce >> >> >> On Sat, 19 May 2012, ?? wrote: >> >> > >> > Hi FreeSurfer Experts, >> > >> > I had 2 question about the output troubleshooting. >> > >> > ? >> > >> > 1)?? when I used the mri_convert command, the format of the input image I >> > choosed was 4D nii format, but not the original dicom format, which would >> > affect the result of reconstruction? >> > >> > 2)?? When I checked the quality of output using tksurfer, I found the >> > color line representing the surface (pial and white) were not along the >> > folding pattern, and the distance between the two sufaces was rather shor >> t. >> > Whether or not it was caused by the bad GM/WM contrast? What is the best >?? ?way >> > to deal with them? >> > >> > ? >> > >> > Thanks. >> > >> > ? >> > >> > Meng Li >> > >> > >> > >> > >> > >> >> >> The information in this e-mail is intended only for the person to whom it i >> s >> addressed. If you believe this e-mail was sent to you in error and the e-ma >> il >> contains patient information, please contact the Partners Compliance HelpLi >> ne at >> http://www.partners.org/complianceline . If the e-mail was sent to you in e >> rror >> but does not contain patient information, please contact the sender and pro >> perly >> dispose of the e-mail. >> >> >> 从QQ邮箱发来的超大附件 Sub.rar (262MB, 2012年06月19日 12:40 到期) 进入下载页面：http://mail.qq.com/cgi-bin/ftnExs_download?k=0d636362224297d81b96735…

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Re: [Freesurfer] Freeview chrash
by Focke, Niels 21 May '12

21 May '12

Hi Ruopeng, yep, this fixes the problem and explains the user specificity. Excellent work! Many thanks, Niels __________________________________________________________________________ Dr. Niels Focke Klinische Neurophysiologie UMG - Universitätsmedizin Göttingen -----Ursprüngliche Nachricht----- Von: Ruopeng Wang [mailto:rpwang@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 16. Mai 2012 18:30 An: Focke, Niels Betreff: Re: AW: [Freesurfer] Freeview chrash Hi Niels, Are you using non-English terminals? I think we found the reason. But no fix yet. The work around is to set your terminal to English before running freeview. You can run something like this: setenv LANG en Then run freeview. Let me know if that works. Ruopeng On 05/10/2012 10:28 AM, Focke, Niels wrote: > Hi Ruopeng, > > any success/ideas yet? > > > Thanks, > > > Niels > > > ______________________________________________________________________ > ____ > > Dr. Niels Focke > Klinische Neurophysiologie > UMG - Universitätsmedizin Göttingen > > > -----Ursprüngliche Nachricht----- > Von: Ruopeng Wang [mailto:rpwang@nmr.mgh.harvard.edu] > Gesendet: Donnerstag, 3. Mai 2012 18:23 > An: Alexandre Gramfort > Cc: freesurfer(a)nmr.mgh.harvard.edu; Focke, Niels > Betreff: Re: [Freesurfer] Freeview chrash > > This is too strange. I logged into the same machine. Both stable and > dev version load the surface file without any problem... We will investigate. > > Ruopeng > > On 05/03/2012 12:12 PM, Alexandre Gramfort wrote: >>> Alex, since you're in the Martinos center, can you try source the >>> dev version just to see if the same problem exists? >> I just tried after sourcing /usr/local/freesurfer/nmr-dev-env >> >> and got the same segfault with MatrixMultiply: m2 is null! >> >> I tried on the machine: megmix >> >> Alex >> >> > > > 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 error on lesioned brain
by octavian lie 20 May '12

20 May '12

Dear All, > > I processed a MR brain after temporal lobe resection. While brainmask.mgz, > and brain.mgz include the temporal remnant (correctly), the calculated pial > surface excludes it (see attached). How, and at what step can I edit the > image so that the pial surface (red line) is inclusive of the postop > temporal lobe? Again, this is not a problem with skull extraction, and > overall I am happy with brainmask.mgz as is, but not with subsequent pial > calculations. Setting the volume brush to clone from brainmask.mgz the > temporal remnant does not seem to help, I may be doing smth wrong. > Please advise, thank you very much. > > Octavian. >

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Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
by Xue, Feng 19 May '12

19 May '12

Sorry, I didn't notice that the reply address was not the list, I've done re-post it. Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings. It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script. On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > can you post this to the list? There are others better qualified to say > what's going on. But if everything finished ok is there really a problem? > Maybe this is just a warning? > On Sun, 14 Mar 2010, Xue, Feng wrote: > >> Hi Bruce, >> >> Thanks for your reply. The recon-all.log said it finished without >> error. please find the whole scripts root in the attachment. >> I'm also running a raw testing with one subject and without SGEяяMaybe >> I can report the result the day after tomorrow. >> >> BTW, I found in my 64bit Debian nodes, I repeated got the error as below >> (standard_in) 2: Error: comparison in expression >> but in 32bit, I met both. >> >> for the GMail security restriction, I changed recon-all.cmd in the >> attachment to recon-all.cmds. >> >> On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>> what does the recon-all.log say? Did the recon finish correctly? Does >>> this >>> happen if you just run it on the command line? >>> Bruce >>> >>> On Sat, 13 Mar 2010, Xue, Feng wrote: >>> >>>> Dear Bruce & FS experts, >>>> >>>> Please forgive my re-post, for I havn't got any response from last post. >>>> I do appreciate if anyone could give me a hint or suggestion. >>>> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>> >>>> We are running freesurfer with Sun GridEngine. Currently, we >>>> repeatedly got this error in SGE's job error log file on some data >>>> when doing recon_all: >>>> >>>> $ cat recon_xf.e437 >>>> (standard_in) 2: Error: comparison in expression >>>> $ cat recon_xf.e431 >>>> (standard_in) 2: comparison in expression >>>> >>>> I also checked the recon-all-status.log file, but not error was found. >>>> >>>> Has anyone met this problem? Is it critical? >>>> Thanks in advance. >>>> >>>> -- >>>> Best Regards >>>> >>>> Xue, Feng Phd. candidate >>>> Major in Developmental Cognitive Neuroscience >>>> >>>> National Key Laboratory of Cognitive Neuroscience and Learning >>>> Beijing Normal University >>>> Beijing, China. 100875 >>>> Tel: +86-13810154455 >>>> web: http://psychbrain.bnu.edu.cn >>>> ============================================== >>>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University >>>> telnet://bbs.mdjs.org >>>> http://bbs.mdjs.org >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)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. >>> >>> >> >> >> > -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

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Re: [Freesurfer] 回复: Re: how to edit the pial surface
by Bruce Fischl 19 May '12

19 May '12

p.s. looks like an intensity normalization failure. Can you give us details of the acquisition? Sequence name, voxel resolution, etc....? If you upload the subject I'll take a look cheers Bruce On Sat, 19 May 2012, limengsecret wrote: > Hi Professor, > The image blow shows the problems which occur. > color lines representing the surfaces (pial and white) were not along the > folding pattern, and the distance between the two sufaces was rather short. > How to deal with these problems? > [IMAGE] > Thanks. > > Meng Li > > > ____________________________________________________________________________ > limengsecret > > From: Bruce Fischl > Date: 2012-05-19 22:08 > To: ?? > CC: freesurfer > Subject: Re: [Freesurfer] how to edit the pial surface > Hi Meng > > 1. Not positive I understand, but I don't think it should matter. > > 2. we'll need to see some data to diagnose this. > > cheers > Bruce > > > On Sat, 19 May 2012, ?? wrote: > > > > > Hi FreeSurfer Experts, > > > > I had 2 question about the output troubleshooting. > > > > ? > > > > 1)?? when I used the mri_convert command, the format of the input image I > > choosed was 4D nii format, but not the original dicom format, which would > > affect the result of reconstruction? > > > > 2)?? When I checked the quality of output using tksurfer, I found the > > color line representing the surface (pial and white) were not along the > > folding pattern, and the distance between the two sufaces was rather shor > t. > > Whether or not it was caused by the bad GM/WM contrast? What is the best ?? ?way > > to deal with them? > > > > ? > > > > Thanks. > > > > ? > > > > Meng Li > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom it i > s > addressed. If you believe this e-mail was sent to you in error and the e-ma > il > contains patient information, please contact the Partners Compliance HelpLi > ne at > http://www.partners.org/complianceline . If the e-mail was sent to you in e > rror > but does not contain patient information, please contact the sender and pro > perly > dispose of the e-mail. > > >

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Freesurfer