Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

(no subject)
by Angela Cosentino 14 Feb '11

14 Feb '11

Salve! Sto utilizzando freesurfer per un lavoro di tesi e ho incontrato problemi per la fase di preprocessing. Allora ho ricevuto dei file in fomrato ".nii" e li ho converiti con il comando: "recon-all -i "file_name.nii" -s "nuovo_nome". Ora dovrei processarli, tramite il comando "recon-all -i file_name.dcm -s subject_name -all. Potreste dirmi cosa evo mettere di preciso al posto del campo "file_name.dcm"; mi dà sempre errore. Sto utilizzando la versione 5 di FreeSurfer, su Linux. Grazie!

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Blocked Design
by Mandy Nagy 14 Feb '11

14 Feb '11

Hello, We are attempting to run an analysis using selxavg3-sess but keep getting an error. We are using: freesurfer v5 Our subjects directory: /cluster/manoach/milton/subjects Command that was run: selxavg3-sess -analysis mandylh2 -fwhm -s PAMST06 Output that was given: Creating Design Matrix ... creation time = 0.006 sec DoMCFit = 1 ntptot = 250, nX = 5, DOF = 245 Saving X matrix to /autofs/cluster/manoach/milton/subjects/PAMST06/bold/mandylh2/Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg3 at 256 XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Do you know what might cause this? Thanks! --Mandy

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FreeSurfer coordinates
by Douglas N Greve 14 Feb '11

14 Feb '11

I have created some use cases on how to transform coordinates in one space to those in another space (eg, a point on the surface to MNI305 space or to the col, row, slice of a functional volume). Let me know if you have any questions or have other use cases you'd like me to add. http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Segmentation into native space
by Yolanda Vives 14 Feb '11

14 Feb '11

Dear freesurfer's, I have run a conventional recon-all process and I am interested in isolating the caudate from my subjects. I have applied the following commands: *./mri_label2vol --seg $SUBJECTS_DIR/$subj/mri/aseg.mgz --temp $SUBJECTS_DIR/$subj/mri/rawavg.mgz --o $SUBJECTS_DIR/$subj/mri/aseg-in-rawavg.mgz --regheader $SUBJECTS_DIR/$subj/mri/aseg.mgz * *./mri_extract_label $SUBJECTS_DIR/$subj/mri/aseg-in-rawavg.mgz 11 $PROJDIR/$subj.nii.gz * I had seen in the wiki that these commands should be used when we need the images in native space. ¿Does it mean that my caudates are "denormalized" or on the contrary, that the images have only been resliced to the original size? If it is the second case, how could I obtain the caudates from the original image? Thank you for your help, Yolanda

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Opening positions
by Xinian Zuo 11 Feb '11

11 Feb '11

Opening positions (postdoc, research assistant, or professorship) for collaborative projects from the Center for Human Brain Research, Hangzhou Normal University (Professor WENG Xuchu, wengxc(a)psych.ac.cn) Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University (Professor ZANG Yufeng, zangyf(a)gmail.com) and Institute of Psychology, Chinese Academy of Science (Professor ZUO Xi-Nian, zuoxinian(a)gmail.com) Any applicant with relevant neuroimaging background is welcome, including neuroscience, medicine, psychology, biology, physics, mathematics, computer and information science, and so on. Salary and compensation are almost the best in China. Please send your CV to any of the three e-mail addresses listed above if you are interested in these jobs. -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn)

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position ad for image analysis
by Bruce Fischl 11 Feb '11

11 Feb '11

A full-time position as image analysis specialist is available at the Section of Biomedical Image Analysis (SBIA), of the Department of Radiology, University of Pennsylvania. The successful candidate must have a Bachelor's or Master's degree in Electrical or Biomedical Engineering, or Computer Science, or related field. Experience with medical images is a plus. The work will involve applying, testing and extending image processing algorithms and protocols on medical images. SBIA has been a dynamically growing medical image analysis group (www.rad.upenn.edu/sbia) including 40 researchers and many collaborators from diverse fields. Please e-mail or mail CV's to christos(a)rad.upenn.edu Christos Davatzikos, Ph.D. Professor of Radiology, and Electrical and Systems Engineering, Director, Section of Biomedical Image Analysis Joint Affiliations: Bioengineering and Applied Math graduate groups University of Pennsylvania 3600 Market street, Suite 380 Tel.: 215-349-8587 Email: christos(a)rad.upenn.edu http://www.rad.upenn.edu/sbia Christos Davatzikos 3600 Market street, Suite 380 Philadelphia, PA 19104 The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.

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DCM filename problems with recon-all
by Joakim Vinberg 11 Feb '11

11 Feb '11

Hi everybody, I have several older anatomical series that I would like to run through recon-all. Unfortunately, the DCM files were pulled down with an older filename convention that seems to trip mri_convert immediately, and I'm having some trouble interpreting the error. Can anybody shed any light on this one? The filenames were pulled down from the scanner in the E8846S5I%d.MR format are still in this format, so I'm not immediately sure what's going on. Thanks in advance for all of the help! Joakim /Volumes/192.168.1.10/projects/freesurfer/0029 \n mri_convert /Volumes/192.168.1.10/projects/freesurfer/0029/dcm/E8846S5I1.MR /Volumes/192.168.1.10/projects/freesurfer/0029/mri/orig/001.mgz \n mri_convert /Volumes/192.168.1.10/projects/freesurfer/0029/dcm/E8846S5I1.MR /Volumes/192.168.1.10/projects/freesurfer/0029/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /Volumes/192.168.1.10/projects/freesurfer/0029/dcm/E8846S5I1.MR... MRIalloc(1229409857, 0, 124): bad parm fname_format : /Volumes/192.168.1.10/projects/freesurfer/0029/dcm/E8846S5I%d.MR fname_format2 : /Volumes/192.168.1.10/projects/freesurfer/0029/dcm/E8846S5I%03d.MR multi-echo genesis file detected (26981 echoes)... No such file or directory Darwin sam 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:19:13 PDT 2010; root:xnu-1504.9.17~1/RELEASE_X86_64 x86_64 recon-all -s 0029 exited with ERRORS at Fri Feb 11 12:06:11 PST 2011

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Segmentation problem
by XJ Kang 11 Feb '11

11 Feb '11

Hi, I have a brain segmentation problem. Scanner: Siemens 3T Verio Sequence: MPrage, TR=1900ms, TE=2.45ms, TI=900ms, Voxel: 1x1x1mm, 192 sagittal slices. Problem: The lay of dura mater between brain and skull is bright (See attached brain.jpg). As a result, the segmented brain.mgz has a "cap", and the pial surface and GM/WM surface will "leak" to the dura layer somewhere (see the red dots in surfaces.jpg). This happened to some places and needs a lot of manual work to remove the connection between the brain and dura. I tried to increase the TR to 3000ms. Still some connection somewhere, although the results are much better. Anybody optimized the mprage sequence to minimize the problem? Thank you. XJ Kang

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Memory allocation problem with mri_robust_template
by Mahen 11 Feb '11

11 Feb '11

Hi all, Since upgrading to Freesurfer v5.0, I have been unable to complete the first step of recon-all ('recon-all -autorecon1 -subjid ...') when using 5 anatomical datasets (our typical load for surface reconstruction). The problem seems to come when the third dataset is being registered, at which point recon-all exits with the following error message: ========================= Resolution: 0 Iteration(single-prec): 1 (subsample 200) mri_robust_template(47536) malloc: *** mmap(size=921600) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(480, 480, 248): could not allocate 921600 bytes for 207th slice Cannot allocate memory /Users/mahen/fMRI/Surfaces/cck_kmu \n mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz /Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform \n mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz /Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform mghRead(/Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz, -1): could not open file $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz... Darwin MahenWillEatYourChildren.local 10.6.0 Darwin Kernel Version 10.6.0: Wed Nov 10 18:13:17 PST 2010; root:xnu-1504.9.26~3/RELEASE_I386 i386 recon-all -s cck_kmu exited with ERRORS at Tue Feb 8 20:50:00 CST 2011 ===================== My machine has 4gb of RAM, and I've ssh'd into my advisor's machine (which has 16gb) and had the same problem. I tryed updating the binaries for recon-all and mri_robust_template (from http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-in…) but the problem remained unsolved. My advisor informs me that it is now running with version 4.5 (all 5 anatomicals); I'd still like to know what's going on. I have tried running it on version 5 with just 2 anatomical datasets, and it works just fine. Here is the output of bugr: FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 Kernel info: Darwin 10.6.0 i386 Thanks in advance, Mahen

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confusion about look up table labels...
by Joe Andreano 11 Feb '11

11 Feb '11

Hi, I'm looking at the list of anatomical regions (found here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurfe…) and I notice that there are two separate sets of coordinates in the same hemisphere for rostral ACC: 1201, G_cingulate-rostral_ACC, and 1206, S_cingulate-rostral_ACC. Can someone tell me the difference, and what the G and S stand for? Thanks, Joe Andreano _________________________________ Joseph M. Andreano, PhD Research Fellow Interdisciplinary Affective Science Lab Massachusetts General Hospital _________________________________

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Freesurfer