Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

DEFECT 57
by Varghese Chikku 21 Feb '13

21 Feb '13

Hi all, One of my subject exited with error after 5 days of processing. This is what it said, CORRECTING DEFECT 57 (vertices=101022, convex hull=10822) Excessive topologic defect encountered: could not allocate 536232126 edges for retessellation Cannot allocate memory Darwin chikkus-MacBook-Pro.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 recon-all -s onco4 exited with ERRORS at Fri Feb 15 12:17:05 CET 2013 My question is this much edges normal and how much memory i need allocate to process this. Many Thanks Chikku

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Invitation to publish in a Frontiers Research Topic
by Jürgen Hänggi 21 Feb '13

21 Feb '13

Dear colleagues we are hosting the Frontiers Research Topic entitled: Relationship between structural and functional brain connectivity. The description of the Research Topic, the publications of which will be published in Frontiers in Human Neuroscience, is described in the attached PDF file. We are seeking for potential contributors. If you are interested to publish in this Frontiers Research Topic, please fill in the attached Excel file and send it back to us. Please note that your consent to participate in the Research Topic is not binding. Thanks a lot for intending to participate. Best regards in the name of all hosting editors Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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unusually long running time in autorecon2
by Dawei Liu 20 Feb '13

20 Feb '13

Dear Freesurfer experts, I am running autorecon2 using Freesurfer verion 5.1.0 on Linux. For some subjects, it looks that the pipeline stucked in the middle of mri_cc and keeps running for days (without any error message). Last time when it occurred I thought it may be caused by some hardware-related problem, so I killed these jobs and re-launched recon-all -autorecon2 on a different machine. Now these jobs have been running for over 40 hours and they are still running. Do you know why they take so long? For your reference, I copied the most recent processing information below: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/transforms/cc_up.lta 0057_34479 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/transforms/cc_up.lta reading aseg from /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/aseg.auto_noCCseg.mgz reading norm from /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/norm.mgz 24076 voxels in left wm, 23641 in right wm, xrange [73, 130] searching rotation angles z=[65 79], y=[-54 -40] searching scale 1 Z rot 75.6 global minimum found at slice 103.0, rotations (-50.09, 68.60) final transformation (x=103.0, yr=-50.093, zr=68.597): 0.234 -0.931 -0.280 230.831; 0.597 0.365 -0.714 75.219; 0.767 -0.000 0.642 3.440; 0.000 0.000 0.000 1.000; Thanks in advance for your help! Dawei

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changes in tracula in the upcoming freesurfer release 5.2
by Anastasia Yendiki 20 Feb '13

20 Feb '13

Dear all - For those who have been using TRACULA or are considering using it in the future, it is strongly recommended to use the new (and hopefully improved) version that will come out shortly with FreeSurfer 5.2. For those who fear change and need some time to adjust, here's what to expect: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates Best, a.y

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Gray Matter probabilistic Segmentation
by Vincent Koppelmans 20 Feb '13

20 Feb '13

Dear FreeSurfer experts, I have some experience with FSL and SPM, but not a lot with FreeSurfer, so please bear with me. When I observe FreeSurfer segmentations, I see that images are binary (either a voxel belongs to a tissue class, or it does not) and not probabilistic. I want to obtain total gray matter volume from the FreeSurfer segmentation, so I searched the forum and came across the following post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11790.html I followed directions which resulted in three whole-brain gray-matter probabilistic map: https://dl.dropbox.com/u/6747155/FS_GM_prob.png The three maps end in 000.mgz, 001.mgz, and 002.mgz. >> Could Somebody explain to me the differences between these images? Furthermore, the intensity range in the maps goes from 0 to 40 (as can be observed from the histogram). How do I convert this image to probabilities 0-1? I don't believe dividing by 40 is correct, because that would mean that the very few voxels will have a probability of being grey matter higher than 50% (see the histogram). Thanks in advance, Vincent

1 0

Postdoctoral position in Cognitive Neuroscience and Reading Disability
by Peter J. Molfese 20 Feb '13

20 Feb '13

Postdoctoral position in Cognitive Neuroscience and Reading Disability Haskins Laboratories (PI: Dr. Julie A. Van Dyke), New Haven, CT Application deadline: April 15, 2013 Applications are solicited for a postdoctoral fellowship in Cognitive Neuroscience at Haskins Laboratories. Applicants should have a Ph.D. in psychology, linguistics, cognitive neuroscience, or a related field. The selected candidate will contribute to a recently funded NIH study of the role of memory interference in comprehension ability. This exciting new study will explore the relationships between the mechanisms of memory and language processing as they contribute to (dis)ability in spoken and written language comprehension. Prior experience in language processing or memory research using fMRI is required. Responsibilities will include assistance with designing fMRI and behavioral experiments; fMRI data analysis (preferably using AFNI); formulating and participating in writing of scientific papers as part of the research team; and developing independent projects investigating memory, language, and reading. An additional focus of this project involves structural MRI analysis, using both volumetric and DTI techniques to identify the grey and white-matter brain networks that support resolution of lexical and syntactic interference during single word and whole sentence reading. Additional desirable, but not necessary qualifications include: - Experience with fMRI software: AFNI, FSL, SPM, Freesurfer, or Nipy - Previous research experience or interest in EEG/ERP analysis (this project also includes EEG data collection) - Strong analytical skills and demonstrated expertise in statistics such as multivariate statistics, mixed-effects modeling, SEM, or MLM/HLM - Strong computer skills using Mac OS X and UNIX/Linux - Programming Skills (Python, R, MATLAB, C/C++ and or JAVA) The successful applicant will join Haskins Laboratories (www.haskins.yale.edu) a private, non- profit research institute located in downtown New Haven, CT. Founded in 1935, our primary focus is on speech, language, reading, and their biological bases. Haskins Laboratories has long- standing, formal affiliations with the University of Connecticut and Yale University. We are also actively engaged in research collaborations and partnerships with institutions, groups, and individuals around the world. We house facilities for conducting eye tracking, including 3 Eyelink 1000 eye-trackers, EEG/ERP (both Biosemi and EGI systems), ultrasound and NIRS technology, and a mock fMRI scanner, which exactly replicates the 3T scanner used for fMRI research at Yale University. Interested applicants should contact Dr. Julie Van Dyke (jvandyke(a)haskins.yale.edu) with cover letter, statement of research interests, CV, and three letters of recommendation. The appointment will be made for two years (with the possibility of renewal for a third year), beginning in Summer/Fall 2013. Applications should be submitted by April 15, 2013, but the application process will be ongoing until the position is filled. International applicants are welcome. Haskins Laboratories is an Equal Opportunity Employer.

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Virtual Machine Disk Image Space
by Kristina Nalbandian 20 Feb '13

20 Feb '13

Hello, I recently posted on the FreeSurfer mailing list, but received no reply. The main problem I am having is due to my virtual machine disk image, there isn't enough space. The virtual machine allows me to store up to four patient files, but there are some processes on FreeSurfer that require all the data to be in the freesurfer directory. Is there anyway to increase the size of the virtual machine disk image? We are using the Xubuntu Box as recommended on the FreeSurfer installation webpage. Thank you for your help, Kristina

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MRInormalize: could not find any valid peaks
by Eli Fredman 20 Feb '13

20 Feb '13

Hi Bruce, After exhausting all of our options, Tali Swisher informed me that I should contact you. I have been trying to run freesurfer on a brain and have been running into a lot of problems. After first running: recon-all -i nifti-files/002-t1w-realign-masked.nii.gz -autorecon1 -noskullstrip -subjid 002 && cp subjects/002/mri/T1.mgz subjects/002/mri/brainmask.mgz && recon-all -autorecon2 -subjid 002 && recon-all -autorecon3 -subjid 002 the process stopped within 10 minutes with a talairach_afd error. I followed our instructions ( https://intweb.spl.harvard.edu/Freesurfer_Notes#Stopping_after_talairach_afd) to create the xformed-t1w.xfm file, and compared it with the talairach.xfm file in the subjects/002/mri/transforms folder. Since they were different, I replaced the values in the talairach.xfm file with the ones from the xformed-t1w.xfm file (side note: the xformed-t1w is 4x4 and talairach.xfm is 3x4-- i attempted both including the last line and excluding it; to no avail). Afterwards, I ran the script: recon-all -autorecon1 -notal-check -noskullstrip -subjid 002 && cp subjects/002/mri/T1.mgz subjects/002/mri/brainmask.mgz && recon-all -autorecon2 -subjid 002 && recon-all -autorecon3 -subjid 002 and while I got past the initial 20 minutes, I ended up exiting with errors. I have included the entire process below, but highlighted areas I believe to be problems: <121> pnl-d6-4 /projects/schiz/ra/eli/ freesurfer5.1 % source SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /projects/schiz/ra/eli/freesurfer5.1 FSFAST_HOME /projects/schiz/ra/eli/freesurfer5.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /projects/schiz/ra/eli/freesurfer5.1/subjects MNI_DIR /projects/schiz/ra/eli/freesurfer5.1/mni FSL_DIR /projects/schiz/software/fsl-4.1-64bit <122> pnl-d6-4 /projects/schiz/ra/eli/freesurfer5.1 % recon-all -autorecon1 -notal-check -noskullstrip -subjid 002 && cp subjects/002/mri/T1.mgz subjects/002/mri/brainmask.mgz && recon-all -autorecon2 -subjid 002 && recon-all -autorecon3 -subjid 002 Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /projects/schiz/ra/eli/freesurfer5.1/subjects Actual FREESURFER_HOME /projects/schiz/ra/eli/freesurfer5.1 -rw-rw-r-- 1 eli schiz 22143 Feb 19 19:37 /projects/schiz/ra/eli/freesurfer5.1/subjects/002/scripts/recon-all.log Linux pnl-d6-4.bwh.harvard.edu 2.6.34.9-69.fc13.x86_64 #1 SMP Tue May 3 09:23:03 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Wed Feb 20 13:31:51 EST 2013 Found 1 runs /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig/001.mgz /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/rawavg.mgz /projects/schiz/ra/eli/freesurfer5.1/subjects/002 mri_convert /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/rawavg.mgz /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig.mgz --conform mri_convert /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/rawavg.mgz /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -0.989776, -0.142629) j_ras = (0, 0.142629, -0.989776) k_ras = (1, 0, 0) Original Data has (1, 1, 1) mm size and (216, 220, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig.mgz... mri_add_xform_to_header -c /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/transforms/talairach.xfm /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig.mgz /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Feb 20 13:32:06 EST 2013 /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Nu Intensity Correction Wed Feb 20 13:33:08 EST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri /projects/schiz/ra/eli/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux pnl-d6-4.bwh.harvard.edu 2.6.34.9-69.fc13.x86_64 #1 SMP Tue May 3 09:23:03 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux Wed Feb 20 13:33:08 EST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.24409 /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24409/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24409/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (2.38419e-07, 0, -1) k_ras = (-1.93715e-07, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.24409/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Feb 20 13:33:15 EST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.24409/nu0.mnc ./tmp.mri_nu_correct.mni.24409/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24409/0/ [eli@pnl-d6-4.bwh.harvard.edu:/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/] [2013-02-20 13:33:15] running: /projects/schiz/ra/eli/freesurfer5.1/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24409/0/ ./tmp.mri_nu_correct.mni.24409/nu0.mnc ./tmp.mri_nu_correct.mni.24409/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 3 CV of field change: 0.000383553 [eli@pnl-d6-4.bwh.harvard.edu:/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/] [2013-02-20 13:33:21] running: /projects/schiz/ra/eli/freesurfer5.1/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24409/nu0.mnc ./tmp.mri_nu_correct.mni.24409/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Wed Feb 20 13:33:31 EST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.24409/nu1.mnc ./tmp.mri_nu_correct.mni.24409/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.24409/1/ [eli@pnl-d6-4.bwh.harvard.edu:/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/] [2013-02-20 13:33:31] running: /projects/schiz/ra/eli/freesurfer5.1/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24409/1/ ./tmp.mri_nu_correct.mni.24409/nu1.mnc ./tmp.mri_nu_correct.mni.24409/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 2 CV of field change: 0.000575678 [eli@pnl-d6-4.bwh.harvard.edu:/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/] [2013-02-20 13:33:36] running: /projects/schiz/ra/eli/freesurfer5.1/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24409/nu1.mnc ./tmp.mri_nu_correct.mni.24409/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.24409/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24409/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.24409/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24409/ones.mgz sysname Linux hostname pnl-d6-4.bwh.harvard.edu machine x86_64 user eli input ./tmp.mri_nu_correct.mni.24409/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.24409/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24409/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24409/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24409/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24409/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24409/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24409/input.mean.dat sysname Linux hostname pnl-d6-4.bwh.harvard.edu machine x86_64 user eli Loading ./tmp.mri_nu_correct.mni.24409/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.24409/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24409/ones.mgz --i ./tmp.mri_nu_correct.mni.24409/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24409/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24409/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24409/ones.mgz --i ./tmp.mri_nu_correct.mni.24409/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24409/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24409/output.mean.dat sysname Linux hostname pnl-d6-4.bwh.harvard.edu machine x86_64 user eli Loading ./tmp.mri_nu_correct.mni.24409/ones.mgz Loading ./tmp.mri_nu_correct.mni.24409/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.24409/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.24409/nu2.mnc ./tmp.mri_nu_correct.mni.24409/nu2.mnc mul .98003231285471643398 Saving result to './tmp.mri_nu_correct.mni.24409/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.24409/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.24409/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.24409/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (2.38419e-07, 0, -1) k_ras = (-1.93715e-07, 1, 0) INFO: transform src into the like-volume: orig.mgz Reslicing using trilinear interpolation writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 11 seconds. mapping ( 0, 0) to ( 3, 110) Wed Feb 20 13:35:04 EST 2013 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Wed Feb 20 13:35:04 EST 2013 /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... MRInormalize: could not find any valid peaks. Make sure the Talairach alignment is correct! building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 6 minutes and 5 seconds. 1d normalization failed - trying no1d... white matter peak found at -nan white matter peak found at 0 gm peak at 0 (0), valley at 0 (-10) csf peak at 0, setting threshold to 0 white matter peak found at -nan white matter peak found at 0 gm peak at 0 (0), valley at 0 (-10) csf peak at 0, setting threshold to 0 #------------------------------------------ recon-all -s 002 finished without error at Wed Feb 20 13:41:11 EST 2013 done Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /projects/schiz/ra/eli/freesurfer5.1/subjects Actual FREESURFER_HOME /projects/schiz/ra/eli/freesurfer5.1 -rw-rw-r-- 1 eli schiz 50049 Feb 20 13:41 /projects/schiz/ra/eli/freesurfer5.1/subjects/002/scripts/recon-all.log Linux pnl-d6-4.bwh.harvard.edu 2.6.34.9-69.fc13.x86_64 #1 SMP Tue May 3 09:23:03 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux #------------------------------------- #@# EM Registration Wed Feb 20 13:41:16 EST 2013 /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /projects/schiz/ra/eli/freesurfer5.1/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/projects/schiz/ra/eli/freesurfer5.1/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=0.0 skull bounding box = (0, 0, 0) --> (255, 255, 255) using (85, 85, 128) as brain centroid... mean wm in atlas = 107, using box (53,53,96) --> (116, 116,159) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf Linux pnl-d6-4.bwh.harvard.edu 2.6.34.9-69.fc13.x86_64 #1 SMP Tue May 3 09:23:03 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 002 exited with ERRORS at Wed Feb 20 13:41:52 EST 2013 For more details, see the log file /projects/schiz/ra/eli/freesurfer5.1/subjects/002/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting *The only thing I am not sure about, is maybe I needed to edit the talairach.auto.xfm file as well? I haven't tried that because I am not sure if there would be unintended consequences. Thanks, Eli * -- Eli Fredman, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6118 Cell: (314) 952-8098 Fax: (617) 525-6150

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Re: [Freesurfer] extracting hand drawn ROIs to Afni space
by Paul Beach 20 Feb '13

20 Feb '13

Hi Ziad, Thank you so much for the suggestions. However, I'm not really sure how to utilize any of them...So I guess more detailed help would be necessary for me to follow these suggestions. Sorry. I've also never actually used SUMA. Previously I was just using a 3dcalc command to bring aseg ROIs into AFNI space. I'm not sure if this will make a difference, but I'm dealing with an averaged subject made with the 'make_average_subject' command (rather than fsaverage). Paul On Tue, Feb 19, 2013 at 10:42 PM, ziad <ziad.ss(a)gmail.com> wrote: > Hello Paul, > > There are a couple of ways I can think of bringing the new ROIs to AFNI > land from FreeSurfer. I can suggest the following, with the assumption that > you seek to dump the average time series from single-subject data using an > ROI defined on the FS average surface. > > 1- Get a list from FreeSurfer of the nodes indices that constitute the ROI > on the FS average surface. That list can take the form of a dataset, that > we'll call ROI_dset_avg. Use GFTI/NIFTI for surface/volume exchange format > between FreeSurfer and AFNI. > 2- Create a standard mesh version of the FS average surface, assuming you > don't have one already. You can do that much as you would for a regular > subject using @SUMA_Make_Spec_FS. > 3- Use SurfToSurf, or MapIcosahedron to map the ROI_dset_avg from the > original fsaverage surface mesh onto any of the standard-mesh versions of > fsaverage. We'll call that dataset ROI_dset_avg_std. > This new dataset can now be used on any of your subject's standardized > meshes, as long as you use the same icosahedral mesh. > 4- Create for each subject a volumetric mask of ROI_dset_avg_std > with 3dSurf2Vol > > I don't know how well you know how to use the SUMA tools I mentioned > above, but if you need more detailed help let me know. > > cheers, > Ziad > > On Feb 18, 2013, at 4:39 PM, Paul Beach wrote: > > Thank you for forwarding this. > > I realize I need to further clarify my issue as well. > > With the help of Doug Greve I've taken hand made ROIs in tksurfer, > repackaged them into a new annotation, and repackaged that into a new aseg > file for an average subject. Now (and this is where I'm stuck) I'm trying > to take those newly minted ROIs, place them onto individual subjects' > brains and THEN send them to Afni for each of those subjects (before doing > seed correlation analysis). > > Previously I had been using mri_label2label to place the averaged subject > ROI into single subjects' folders and then mri_label2vol to get them ready > to send to Afni. However, this method was not producing ROIs that covered > the extent of a region's gray matter. Thus, Doug's solution of > re-annotating and re-segmenting. > > Hopefully that makes things a bit easier. > > > Thanks again for your help! > Paul > > > On Mon, Feb 18, 2013 at 3:13 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> Hi Paul >> >> we usually call those labels and have an ascii label file format. Not >> sure how to get that into AFNI, but I'm zure Ziad (ccd) knows. >> >> cheers >> Bruce >> >> On Mon, 18 Feb 2013, Paul Beach wrote: >> >> Hi there, >>> Through the help of the Freesurfer Q&A staff I've been able to get ROIs >>> drawn in tksurfer into an augmented aparc+aseg file of an averaged >>> subject. >>> I need to be able to get those ROIs, which are not part of the color LUT, >>> into Afni space. >>> >>> For ROIs that are already in the LUT, getting them to Afni is no >>> problem, I >>> simply use a 3dcalc command. However, I have the problem of needing to >>> export newly parcellated and segmented ROIs that aren't in the Freesurfer >>> LUT to Afni space. >>> >>> Is there a way to do this short of creating a new "spot" for them in our >>> LUT? If not, how does one go about adding ROIs to the LUT and/or >>> creating a >>> LUT specific to my needs (since the Wiki suggests not fussing with the >>> original LUT)? >>> >>> >>> Thanks, >>> Paul >>> -- >>> >>> >>> >>> >> >> 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<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. >> > > > > -- > Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist Association, MSU COM Chapter > > > -- Paul Beach DO/PhD candidate - Year V Michigan State University - College of Osteopathic Medicine - OMS V - Neuroscience Program - Bozoki Lab: Neurology/Radiology - President: American Physician Scientist Association, MSU COM Chapter

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Longitudinal processing error
by Sabin Khadka 20 Feb '13

20 Feb '13

Hi all, I am running longitudinal processing and it keeps on crashing with no error message whatsoever in middle of one or the other processing steps. I am not sure if this is an memory issue. Any thoughts/suggestions would be helpful. I have attached error log as well. -Sabin

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Freesurfer February 2013