Freesurfer October 2009

freesurfer@nmr.mgh.harvard.edu

99 participants
151 discussions

about the thalamus volume
by zhenxt03 30 Oct '09

30 Oct '09

Hi, I found Left-Thalamus-Proper volume and Right-Thalamus-Proper volume in the aseg.stats file. Do they have some difference between Left-Thalamus-Proper volume and Left thalamus volume? If not, can I use left or right thalamus proper volumes to do some statistics analysis between two groups? Thank you very much! Yours sincerely Xiantong Zhen

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structural morphometric analyses for 50 subjects
by Ritobrato Datta 30 Oct '09

30 Oct '09

Hello All, I have processed about 100 datasets with recon-all (autorecon1, 2and 3) There are 50 subjects, each subject is scanned twice, 19 months apart. So each subject acts as their own control. We only have structural data for these subjects only MPRAGES, one per each scan. No functional data. What kind of structural morphometric analyses can I do using freesurfer ? I mean if I want to see what has changed in each subject between the two sessions ? For each session, we have other data like their blood pressure, gender, age, ambient pressure, ambient temperature etc. For eg, there is a difference in ambient temperature between the first and second scans and I want to see if there is a structural morphometric change in each subject due to this temperature change, can that kind of statistics be done with freesurfer ? How do I remove the effect of other factors to see only the changes due to temperature change ? I have never done this kind of an analyses before, so so maybe freesurfer already has a pipe for this sort of analyses. I dont know. I am looking for any guidance I can get. Please let me know. Thanks a lot, Rito Ritobrato Datta, Ph.D. Post Doctoral Fellow Department of Neurology Center for Functional Neuroimaging University of Pennsylvania School of Medicine 3rd Floor Gates Building 3400 Spruce St. Philadelphia Pa 19104

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Fwd: FreeSurfer Error: bits = 0 not supported.
by Jordi Delgado 30 Oct '09

30 Oct '09

---------- Forwarded message ---------- From: Jordi Delgado <jordidem(a)pic.es> Date: 2009/10/30 Subject: FreeSurfer Error: bits = 0 not supported. To: freesurfer(a)nmr.mgh.harvard.edu Hello*, * My name is Jordi Delgado, I work with FreeSurfer on a cluster of machines. Yesterday I sent some subjects to process and for three of them I recived in the Output Log from PBS the following message: * Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.1 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.1 INFO: SUBJECTS_DIR is /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS Actual FREESURFER_HOME /nfs/arpon/SOFTWR/freesurfer Linux td172.pic.es 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030 mri_convert /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030/mri/orig/001.mgz mri_convert /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001... Starting DICOMRead2() dcmfile = /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 dcmdir = /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030 WARNING: tag ImageNumber not found WARNING: tag image orientation not found Ref Series No = 301 ERROR: bits = 0 not supported. Send email to freesurfer(a)nmr.mgh.harvard.edu Linux 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Oct 29 18:26:01 CET 2009* After revising the freesurfer implementation and verify that other subjects have been processed correctly I noted that three subjects start their slices numeration with 0001 up to 0172 and the rest started (the correctly finished subjects) by 0002 up to 0171. So I searched this error in the freeSurfer wiki and google and I didn't found anything. What is happening? Is an image problem? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Tel: +34 93 581 33 22 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Tel: +34 93 581 33 22 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

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PostDoc Positions at UCSD MultiModal Imaging Laboratory (MMIL)
by Don Hagler 29 Oct '09

29 Oct '09

Postdoctoral Research Scholar Position, Multimodal Imaging Laboratory, University of California, San Diego The Multimodal Imaging Laboratory (MMIL) at the University of California, San Diego invites applications for multiple postdoctoral research scholar positions under the direction of Dr. Anders Dale. The successful candidates will join a multi-disciplinary team of scientists, programmers, and support staff addressing a variety of neuroscience questions using multimodal brain imaging, electrophysiology, behavior, and genetics. An important component of the work done at MMIL, and the primary role for the currently announced positions, is the development and improvement of methods for the analysis of neuroimaging data. Postdoctoral researchers will receive training in brain imaging and methods development, and will be encouraged to develop their own research projects. The primary areas of development will include: 1. Segmentation of pediatric brain scans 2. Tractography and diffusion MRI analysis and modeling 3. Multispectral lesion segmentation and quantification 4. Longitudinal registration & analysis of contrast change 5. EEG/MEG/fMRI integration and modeling 6. Resting state fMRI & ASL analysis, quantification within anatomically-defined ROIs 7. Validation of non-invasive imaging measures using ex vivo histology and stereology Applicants for the position must have completed relevant Ph.D. research activities within the past five years. Applications from many disciplines may be considered, and the position is open to qualified international applicants. Experience or expertise in the following areas is highly desired: 1. computer programming experience (MATLAB, C/C++, Python, OpenGL, tcl/tk) 2. neuroimaging analysis methods (especially FreeSurfer) 3. structural MRI, DTI, fMRI, ASL 4. MRI physics and/or pulse programming 5. scientific writing This posting is for 2-year appointments beginning immediately. Salary will be consistent with the NIH/NRSA levels in accordance with the University of California, San Diego policies for Postdoctoral trainees. Compensation includes full staff benefits, including health insurance, and vacation time. Review of applications will begin immediately and will continue until the position is filled. To apply, please send your CV, a brief statement of research interests and goals, and any selected reprints to amdale(a)ucsd.edu with the subject line "MMIL postdoctoral position". Letters of reference will be required before final approval of hiring. Informal inquiries for more details are welcome. _________________________________________________________________ New Windows 7: Find the right PC for you. Learn more. http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID2472…

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effect of the radius on lGI
by Zhangyuanchao 29 Oct '09

29 Oct '09

Hi, expert, Could anyone tell me the effect of the radius on lGI. After reading the paper on lGI carefully, I still can not get a clear view of the effect of the radius on lGI. I still wonder why the default radius are chosen to be 25mm since there is very little discussion of the standard in choosing such a radius in the paper on TMI. When making group analysis, does the result vary greatly using different radii? and why is that? How to intepret the result obtained using different radii? Thank a lot! Best Regards ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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GLM question
by Mehul Sampat 29 Oct '09

29 Oct '09

Hi FS folks, I have a basic GLM question. I went through the tutorials online but I was not sure and wanted to check with someone. I am trying to compare the cortical thickness between a group of patients (n = 166) and controls (n = 76). For patients mean age is 49.8 +/- 9.1 and there are 55 Male; 111 Female For controls mean age is 40.5 +/- 11.4 and there are 26 Male; 50 Female If include gender as a fixed factor does the output of the GLM answer the following: 1. "Is the cortical thickness different between the patients and controls accounting for gender" 2. As I understand the GLM setup one can control for gender and other discrete factors but not for continuous co-variates such as age ? That is one can find the association between thickness and age and see if it is different for the two groups. However if the age distributions for the two groups are different one cannot control for it with GLM. is this interpretation correct ? If so, how would one control for age in such an analysis ? Any help is much appreciated. Thanks Mehul 2. For the correction of multiple comparisons, when should one use FDR as compared to monte-carlo simulations ? Thanks Mehul

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WM hypointensities in aseg vs wmparc
by Dankner, Nathan (NIH/NIMH) [F] 29 Oct '09

29 Oct '09

Hello all, I was curious as to whether it is preferable to use the wm hypointensities output from wmparc.stats or from aseg.stats or if there is no real difference. Also, I believe I've seen this answered elsewhere, but just to be clear, is it the case that there is currently no way to visualize/label these in tkmedit?

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Re: [Freesurfer] Recon-all exited with ERRORS
by Angie Morales 29 Oct '09

29 Oct '09

Hi, I'm trying to run the command: recon-all -subjid <subname> -autorecon1. I'm getting the an error message during skull stripping and the error log reads as follows: #@# Skull Stripping Wed Oct 28 12:29:47 PDT 2009 /space/raid7/data/london/data/ mri/other/angie/Freesurfer/SUBJECTS_DIR/5003/mri mri_em_register -skull nu.mgz /space/raid/fmri/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/space/raid/fmri/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=14.0 skull bounding box = (51, 40, 26) --> (206, 255, 255) using (103, 112, 141) as brain centroid... mean wm in atlas = 126, using box (84,85,113) --> (122, 138,169) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 initial log_p = -19541.4 ************************************************ First Search limited to translation only. ************************************************ using real data threshold=42.0 Found translation: (-1.1, 1.1, -17.0): log p = -17915.1 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Linux willis 2.6.27.25-0.1-default #1 SMP 2009-07-01 15:37:09 +0200 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Oct 28 14:45:19 PDT 2009 The error log simply states: CMD mri_watershed Any advice on how to troubleshoot this problem would be greatly appreciated. Angie

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building from source
by Michael Scheel 29 Oct '09

29 Oct '09

Hi everybody, I have the opportunity to run my analysis with freesurfer on a big computer-cluster that is running on AIX. However to install freesurfer there I need to build it from source. Is the source code available? I found some older entries in the archives and the issue seemed at that time rather complicated. Are there any news regarding building from source? Thanks, Michael

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question about load_segstats
by Mehul Sampat 29 Oct '09

29 Oct '09

Hi FS folks I was trying to use the load_segstats function to read aseg.stats and wmparc.stats It works well will these files but I get the following error if I try to read lh.aparc.stats or rh.aparc.stats [segname segindex segstats] = load_segstats('lh.aparc.stats','bert'); ??? Subscripted assignment dimension mismatch. Error in ==> load_segstats at 113 segstats(nthrow,:) = [nvox vol segmn segstd segmin segmax segrng]; Any suggestions on how I could fix the matlab function ? Thanks Mehul

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Freesurfer October 2009