Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

set a breakpoint in malloc_error_break to debug Bus error in recon-all
by pietro de rossi 15 Oct '12

15 Oct '12

Hi free surfer users and developers, for the first time I got this error after running recon-all: CORRECTING DEFECT 76 (vertices=36299, convex hull=8085) mris_fix_topology(74305) malloc: *** mmap(size=1148719104) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error Darwin HG-01881507-DM7.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 recon-all -s 122 exited with ERRORS at Sat Oct 13 22:31:01 EDT 2012 What can I do to fix the problem? Thanks in advance, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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ERROR: inputs have mismatched dimensions! when running recon -i dicom -i dicom -s
by Knut J Bjuland 15 Oct '12

15 Oct '12

Hi, When I import one subject with recon -i dicom -i dicom -s subjec, I get this error message ERROR: inputs have mismatched dimensions! I think it is caused by the fact that there is a different number of slices into the two series. One series has 256x256x125 white the other has 256x256x128. How can I detect if there is missing slices in the series with 125 slices? What would you recommend me to do? Is is possible to ask recon-all to bypass this error message and import both series? Knut J output k_ras = (-1, 0, 0) writing to /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz... ERROR: inputs have mismatched dimensions! /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100 is 256 x 256 x 125 while /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235 is 256 x 256 x 128 Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

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Tksurfer display issue
by leemon albert 15 Oct '12

15 Oct '12

Hi, everyone. The tksurfer can't initial a window in iOS 10.7.5. Has anyone met this before? Last login: Mon Oct 15 10:57:04 on ttys001 -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl $ system_profiler SPSoftwareDataTypeSoftware: System Software Overview: System Version: Mac OS X 10.7.5 (11G63) Kernel Version: Darwin 11.4.2 Boot Volume: Macintosh HD Boot Mode: Normal Secure Virtual Memory: Enabled 64-bit Kernel and Extensions: Yes Time since boot: 1:56 $ tksurfer bert lh pial subject is bert hemi is lh surface is pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/canlab06 checking for nofix files in 'pial' Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=132501, faces=264998 surfer: single buffered window surfer: tkoInitWindow(bert) then it stopped here and does#t have any respond. I tried several times with different subjects, but failed with the same issue. Does anyone have any ideas? Thanks a lot. Best Wishes Meng

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Error with mris_calc
by Christopher Coello 15 Oct '12

15 Oct '12

Dear Freesurfer community, Using freeview, I can visualize that two binary volumes are overlaying in some parts. freeview -v binF1.mgz -v binF2.mgz When using the command mris_calc -o out.mgz binF1.mgz mul binF2.mgz to create the intersection of these two volumes, I obtain a file with only zeros. To debug, I added the two volumes mris_calc -o out.mgz binF1.mgz add binF2.mgz I was surprise to see that one of the volumes (binF1) is shifted of tens of voxels along an axis. When doing mris_calc -o out.mgz binF2.mgz add binF1.mgz, the binF2 is shifted. Is that a bug ? mris_calc : v.1.37.2.4 2011/04/04 freeview : v1.0 2011/05/22 Best, Christopher -- Christopher Coello, Ph.D. Preclinical PET/CT unit http://www.med.uio.no/imb/english/research/about/infrastructure/pet/ Institute of Basic Medical Sciences Faculty of Medicine, University of Oslo tel. +4745154516

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Re: [Freesurfer] WM/GM boundary changes and control points
by EK Kim 15 Oct '12

15 Oct '12

I've been struggling to upload the file to the ftp server, but failed in several times. Sorry for bothering you, but I will send an e-mail when the uploading is done. Best, EK 2012/10/14 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > I found EK_test.zip, but neither tar nor unzip knows how to uncomress it. > What format is it? Or maybe it's corrupted... > > > On Sat, 13 Oct 2012, EK Kim wrote: > > Bruce, and other experts, thank you for your time :) >> >> I'm now uploading the data folder (before cp and after cp) to the >> freesurfer incoming directory. >> >> >> We obtained the 3D-SPGR axial images using 3T GE system which have >> 8HRBRAIN receiving coil. >> Data acquisition matrix is 320-by192, FOV is 200-by-200. >> >> Other parameters; >> slice thickness =1.5 >> TR=5.924 >> TE=1.472 >> Flip angle: 20 >> Inversion Time=400 >> Imaging Frequency 127.88 >> Percent Phase FOV =80 >> >> Sincerely, >> >> EK >> >> >> >> 2012/10/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi EK >> >> that is a really low-contrast image. Can you tell me about the >> acquisition parameters and resolution? Also, I can't >> diagnose your problem from just the volume I'll need the entire >> (tarred and gzipped) subject directory. Finally, >> please cc the list on these emails so that others can help you! >> >> Bruce >> On Thu, 11 Oct 2012, EK Kim wrote: >> >> I uploaded the files to transfer/incoming folder. >> >> >> Best, >> >> EK >> >> 2012/10/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> If you upload the subject to our FTP site I will take a >> look >> Bruce >> >> >> >> On Oct 10, 2012, at 9:29 PM, EK Kim <ksea03(a)gmail.com> wrote: >> >> Thank you for your answer. >> I'm not sure I understand your question right, >> but I just processed the file using following procedures. >> 1. recon-all -autorecon1 -nuintensitycor-3T (because mine was >> 3T) >> 2. skullstripping brain mask using gcuts >> 3. adding control points (only on the left hemisphere) >> 4. recon-all -autorecon2-cp >> and this figure was made by a commnad line, [tkmedit wm.mgz >> -aux >> brain.mgz -surfs]. >> Best, >> EK. >> >> 2012/10/10 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> what was the name of the file that you transferred? >> On Wed, 10 Oct 2012, EK Kim wrote: >> >> I already uploaded this problem 2 days >> ago, reprocessing the subject to make >> sure about control points. >> However when I added the control points >> to the left hemisphere, >> the right hemisphere surface was changed >> severely. >> I used the command line, recon-all >> -autorecon2-cp -s subjectID. >> Could you tell me why does it occur and >> how to deal with it? >> >> >> Best, >> >> EK >> >> >> >> >> 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. >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >> >> >>

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Re: [Freesurfer] WM/GM boundary changes and control points
by EK Kim 13 Oct '12

13 Oct '12

Bruce, and other experts, thank you for your time :) I'm now uploading the data folder (before cp and after cp) to the freesurfer incoming directory. We obtained the 3D-SPGR axial images using 3T GE system which have 8HRBRAIN receiving coil. Data acquisition matrix is 320-by192, FOV is 200-by-200. Other parameters; slice thickness =1.5 TR=5.924 TE=1.472 Flip angle: 20 Inversion Time=400 Imaging Frequency 127.88 Percent Phase FOV =80 Sincerely, EK 2012/10/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi EK > > that is a really low-contrast image. Can you tell me about the acquisition > parameters and resolution? Also, I can't diagnose your problem from just > the volume I'll need the entire (tarred and gzipped) subject directory. > Finally, please cc the list on these emails so that others can help you! > > Bruce > > On Thu, 11 Oct 2012, EK Kim wrote: > > I uploaded the files to transfer/incoming folder. >> >> >> Best, >> >> EK >> >> 2012/10/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> If you upload the subject to our FTP site I will take a look >> Bruce >> >> >> >> On Oct 10, 2012, at 9:29 PM, EK Kim <ksea03(a)gmail.com> wrote: >> >> Thank you for your answer. >> I'm not sure I understand your question right, >> but I just processed the file using following procedures. >> 1. recon-all -autorecon1 -nuintensitycor-3T (because mine was >> 3T) >> 2. skullstripping brain mask using gcuts >> 3. adding control points (only on the left hemisphere) >> 4. recon-all -autorecon2-cp >> and this figure was made by a commnad line, [tkmedit wm.mgz -aux >> brain.mgz -surfs]. >> Best, >> EK. >> >> 2012/10/10 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> what was the name of the file that you transferred? >> On Wed, 10 Oct 2012, EK Kim wrote: >> >> I already uploaded this problem 2 days >> ago, reprocessing the subject to make >> sure about control points. >> However when I added the control points >> to the left hemisphere, >> the right hemisphere surface was changed >> severely. >> I used the command line, recon-all >> -autorecon2-cp -s subjectID. >> Could you tell me why does it occur and >> how to deal with it? >> >> >> Best, >> >> EK >> >> >> >> >> 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. >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >>

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talairach.xfm error frequency
by Eric Cunningham 12 Oct '12

12 Oct '12

Greetings, I am trying to determine how bad a talairach.xfm registration has to be to warrant a manual edit. I have found that even minor edits can have noticable (9%) effects on major subcortical volumes (such as thalamus or hippocampus). Very few registrations seem to have completely failed, but most seem like they could be made better by a tweak here or there. At what point would I just be adding randomness by manually editing? About what percent of a given dataset would you expect to manually edit? Much appreciated, -Eric Cunningham

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Re: [Freesurfer] volumes per lobe
by MAHINDA YOGARAJAH 12 Oct '12

12 Oct '12

Dear Experts, As an addendum to the last post I made here are the commands I propose to use to extract lobar measures for GM and WM. I would be grateful for input. GM Lobar Values (1) mri_annotation2label --subject subject1 --hemi ?h --lobesStrict lobesfile (2) mri_anatomical_stats –mgz –cortex ../label/?h.cortex.label –f ../stats/?h.lobesfiles.stats –b –a ../label/?h.lobesfile.annot subject1 ?h white Q: Is this valid? Q:Do I need to include that part of the command in italics - is it not redundant given the use of the ?h.lobesfile.annot - using one or the other does give a different result at the top of the stats file (namely NumVert, WhiteSurfArea, and mean thickness which disappears if ?h.cortex.label is not passed) - why is this ? WM Lobar Values (1) mri_annotation2label --subject subject1 –hemi ?h --lobesStrict lobesfile (2) mri_aparc2seg --s subject1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.lobar.mgz --ctxseg aparc+aseg.mgz --annot ?h.lobesfile.annot Q: Is this valid ? Q: Do I need all the items in italics - they are present in the recon-all logfile but not in some forum posts on similar topics. (3a) mri_segstats --seg mri/wmparc.lobar.mgz --sum stats/wmparc.lobar.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject1 --surf-wm-vol --surf-ctx-vol --totalgray --ctab newcolourtable --etiv OR (3b) mri_segstats --seg mri/wmparc.lobar.mgz --sum stats/wmparc.lobar.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/norm.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject1 --surf-wm-vol --ctab newcolourtable --etiv Q: Which of these should I be using - the latter is based on the recon-all log file, while the former is based on forum posts - what are the differences (as highlighted in italics). Thanks. Mahinda

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mri_ms_fitparms?
by dgw 12 Oct '12

12 Oct '12

Hi, >From the wiki (http://www.freesurfer.net/fswiki/mri_ms_fitparms) I can see that mri_ms_fitparms can accept and afi map. Can someone tell me what assumptions the -afi subcommand makes about the position of the afi map relative to the flash volumes? does it calculate everything in scanner coordinates, or do I need to register them to one another? Thanks, D

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Re: [Freesurfer] volumes per lobe
by MAHINDA YOGARAJAH 12 Oct '12

12 Oct '12

Dear FreeSurfer Experts, I write in regard to the posting on calculating GM measures on a lobar basis. I had a couple of quick questions: 1) Having derived a lobesfile using mri_annotation2label --subject <name> --hemi lh --lobesStrict lobesfile one uses mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.lobesfile.stats -b -a ../label/lh.lobesfile.annot subject lh white a) Why is the -cortex ../label/lh.cortex.label option needed ? I thought this is needed if one wants to pass cortical label for computing statisitcs across all of the cortex ? When I repeat the command without it the stats at the bottom of the lobar stats file are the same. However the total number of vertices and white surface area total at the top of the stats file are different and without the -cortex option the average thickness at the top disappears - why is this ? Should the cortex flag be included or not for lobar GM volumes b) Does the flag white refer to areas based on white matter in which case if one wants areas based on pial surface should pial flag be used ? 2) What would the approach be to get lobar measures as above but for white matter instead ? Thanks. Mahinda

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Freesurfer October 2012