Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

how to map the anatomical to the diffusion space
by 李盟 22 May '12

22 May '12

Hi FreeSurfer Experts, Using the mri_surfcluster command, I got the labels of the significant regions from qdec comparisons of thickness between two groups. The diffusion data was not processed using the dt_recon, but DTI-studio. So how can I map the significant regions to the individual diffusion space? Thanks a lot. Meng Li

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Nipype connectivity workshop 2012
by Chris Filo Gorgolewski 22 May '12

22 May '12

Dear fellow neuroimagers, I am very excited to announce the second Nipype workshop which will take place on 8-9 September 2012 in Magdeburg, Germany. For those who have not heard about Nipype it is a framework which helps designing, maintaining, sharing and executing data processing workflows. It allows you to combine existing data processing solutions (such as FSL, SPM, FreeSurfer and many others), cache partial results, do parameter space exploration and run workflows in parallel (both locally and on clusters). You can read more about Nipype at http://nipy.org/nipype . This year the workshop is going to be a satellite event to the Third Biennial Conference on Resting State Brain Connectivity and therefore focus of the covered analyses will follow the theme of brain connectivity. To learn more about the workshop and register (make sure to be quick - we have limited number of spaces) go to http://nipype.blogspot.com On behalf of the Nipype team, Chris Gorgolewski

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question about reconstructing surface on monkeys
by Leon 21 May '12

21 May '12

Hi, FreeSurfer experts I have some problems reconstructing a wm surface out of a monkey template and would appreciate help from you all. Basically, I try to reconstruct a surface based on the average T1 images of a group of monkeys (see the attached figure). The original surface (?h.orig) looks fine, following the filled.mgz and wm.mgz very well. However, the wm and pial surfaces look messed up, not following the wm.mgz at all and the white matter surface and pial surface almost overlap on each other (i.e., almost zero thickness). I have reconstructed ~6 individual subjects' surfaces in which the T1 image was used to derive the template mentioned above and I have never seen this type of error. I ran the recon-all twice and the results were almost identical. So, I wonder if anyone would tell me what is causing this and possible directions for avoiding such problems. Many thanks in advanceLeon

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label shape with mris_divide_parcellation
by Linda Douw 21 May '12

21 May '12

Hi all, I would like to make a fine-grained surface parcellation from aparc - let's say 500 labels, and I would like the labels to be more or less isometric. When subdividing the parcellation with mris_divide_parcellation, the labels become very stretched instead of isometric. Is there a way to get a different result? Thanks! -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129

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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

LinkedIn ------------ Mohan Boddu souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Mohan Boddu http://www.linkedin.com/e/-qq80um-h2hmte6k-5g/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Mohan Boddu http://www.linkedin.com/e/-qq80um-h2hmte6k-5g/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ Quel est l'intérêt de faire partie du réseau de Mohan Boddu ? Le réseau de Mohan Boddu développera votre propre réseau : Si vous acceptez l'invitation de Mohan Boddu, vous pourrez voir qui vous connaissez dans son réseau et demander à Mohan Boddu de vous présenter. Appartenir à un réseau est toujours un plus pour votre carrière. -- (c) 2012, LinkedIn Corporation

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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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Freesurfer May 2012