Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] Fwd: Corrections to the segmentation lead to giant defects
by Thomas Fink 28 Jan '14

28 Jan '14

Yes, all we did in this case was change amygdala to hippocampus and in other cases white matter to hippocampus or vice versa. Thomas Fink Doktorand & wiss. Mitarb. Lehrstuhl für Neuropsychologie Mail: Thomas.Fink(a)psy.lmu.de Phone: +49(0)89/2180-3123 On Tue, Jan 28, 2014 at 2:32 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > can you cc the list? So all you did was change some voxels from > hippocampus to amygdala? > > > On Tue, 28 Jan 2014, Thomas Fink wrote: > > Hi Bruce, >> >> Sorry, these were .tifs. Now they are... >> >> Thanks >> >> On Mon, Jan 27, 2014 at 11:48 PM, Bruce Fischl < >> fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Thomas >> >> what format are these in? Can you include extensions in the >> files you send in the future? >> >> thanks >> Bruce >> On Mon, 27 Jan 2014, Thomas Fink wrote: >> >> Hi Bruce, >> >> At the moment we are interested in the volumes and >> thus we checked and >> corrected the aseg-file (corrections done as >> described in the >> RecommendedReconstructions). >> In the first attachment you can see the incorrect >> automatic segementation of >> the hippocampus and in the second what it looked >> like after our corrections, >> but before the new recon with the giant defect. >> >> Cheerio, >> Thomas >> >> On Thu, Jan 23, 2014 at 10:39 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Thomas >> >> when you say errors in the hippocampus do you >> mean the aseg or >> the surfaces? If the surfaces, don't worry >> about them as they >> are not used in the hippocampal region. You >> are probably >> connecting the temporal lobe to the main body >> of the white >> matter creating a giant defect. >> >> cheers >> Bruce >> On Mon, 20 Jan 2014, Thomas Fink wrote: >> >> >> Dear Freesurfer experts, >> >> We are using FS 5.1 and have several >> participants >> with errors in the >> segmentation of the hippocampus and >> other regions of >> the cortex. So far we >> did corrections to the hippocampus but >> in 10 out of >> 13 participants we got >> error messages listed below: >> >> Seven participants: >> >> ----- >> >> CORRECTING DEFECT 0 (vertices=74686, >> convex >> hull=1605) >> >> Excessive topologic defect encountered: >> could not >> allocate 390335770 edges >> for retessellation >> >> Cannot allocate memory >> >> Darwin NPSY.local 12.4.0 Darwin Kernel >> Version >> 12.4.0: Wed May 1 17:57:12 >> PDT 2013; >> root:xnu-2050.24.15~1/RELEASE_X86_64 >> x86_64 >> >> ----- >> >> One participant: >> >> ----- >> >> mhtVoxelList_Add(189, 240, 290, 260205): >> complete >> list too big! >> >> mhtVoxelList_Add(189, 240, 290, 260205): >> complete >> list too big! >> >> No such file or directory >> >> marking ambiguous vertices... >> >> Too many intersected faces for face >> 255461 (126442, >> 128896, 128873) >> >> No such file or directory >> >> Darwin NPSY.local 12.4.0 Darwin Kernel >> Version >> 12.4.0: Wed May 1 17:57:12 >> PDT 2013; >> root:xnu-2050.24.15~1/RELEASE_X86_64 >> x86_64 >> >> ----- >> >> One participant: >> >> ----- >> >> CORRECTING DEFECT 14 (vertices=33317, >> convex >> hull=1285) >> >> mris_fix_topology(26738) malloc: *** >> mmap(size=1212047360) failed (error >> code=12) >> >> *** error: can't allocate region >> >> *** set a breakpoint in >> malloc_error_break to debug >> >> Bus error >> >> Darwin NPSY.local 12.4.0 Darwin Kernel >> Version >> 12.4.0: Wed May 1 17:57:12 >> PDT 2013; >> root:xnu-2050.24.15~1/RELEASE_X86_64 >> x86_64 >> >> ----- >> >> One participant: >> >> ----- >> >> Correction of the Topology >> >> Finding true center and radius of >> Spherical >> Surface...done >> >> Surface centered at (0,0,0) with radius >> 100.0 in 11 >> iterations >> >> marking ambiguous vertices... >> >> 414500 ambiguous faces found in >> tessellation >> >> segmenting defects... >> >> Bus error >> >> Darwin NPSY.local 12.4.0 Darwin Kernel >> Version >> 12.4.0: Wed May 1 17:57:12 >> PDT 2013; >> root:xnu-2050.24.15~1/RELEASE_X86_64 >> x86_64 >> >> ----- >> >> The error log says in all cases that >> there is >> something wrong with the >> cerebellum. When we open the ?h >> inflated.nofix file >> then we see the >> cerebellum added (see attached file) in >> the >> hemisphere we made the edits. >> >> We have no clue if or what we are doing >> wrong and >> here are the steps we >> did: >> >> - open the files (tkmedit subject >> norm.mgz >> -aseg.mgz >> >> - Tool -> Configure Segmentation Brush >> info -> >> select the hippocampus -> add >> voxels >> >> - File -> save segmentation >> >> - run recon with "recon-all -autorecon2 >> -noaseg >> -autorecon3 -subjid subject >> -nuintensitycor-3T" >> >> So far we had no problems with our >> subjects for all >> the previous steps >> (recon after wm, pial, .... edits) and >> it did run >> smoothly. >> >> >> Any help would be greatly appreciated. >> >> Thomas Fink Mail: Thomas.Fink(a)psy.lmu.de >> >> >> >> >> 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 . 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. >> >> >> >> >> >> >>

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Postdoc: Neuroimaging
by Direktion, Institut f. Schlaganfall- und Demenzforschung 28 Jan '14

28 Jan '14

The Hospital of the University of Munich, Germany, is one of the largest and most competitive university hospitals in Germany and Europe. 45 specialized hospitals, departments and institutions harboring excellent research and education provide patient care at the highest medical level with approximately 10.000 employees. The Institute for Stroke and Dementia Research at the Ludwig Maximilian University of Munich offers: Postdoc: Neuroimaging (m/f) RESEARCH FOCUS and RESPONSIBILITIES: The postdoc will work on disease crossing mechanisms of neurodegeneration and cognitive decline using multimodal MRI data acquired through prospective longitudinal studies. Our protocols include repeat structural and functional MRI together with amyloid PET and detailed cognitive testing. The study is funded by the German Center for Neurodegenerative Diseases (DZNE) and embedded in an ambitious imaging program on disease crossing mechanisms. The postdoc will work in a highly dynamic neuroimaging team and is encouraged to bring in own research ideas. REQUIREMENTS: The candidate should hold a PhD, MD or equivalent degree in relevant disciplines (informatics, engineering, mathematics, neuroscience), should be familiar with state of the art structural and functional imaging techniques as documented by relevant publications. Solid knowledge of programming and statistics is a plus. An enthusiastic, independent work style will provide a good fit for our team. OFFER: We offer an excellent multidisciplinary environment with expertise in neuroimaging, neuropsychology, bioinformatics, epidemiology and state of the art multimodal neuroimaging equipment (3T MRI, high-density fMRI compatible EEG, molecular PET, IT infrastructure). The research team is embedded in the Munich Cluster for Systems Neurology, which is funded by the German Excellence Initiative. The research fellow will draw on a comprehensive database and technical support to facilitate efficient work conditions. He/she will work in a young and highly productive team at the Institute for Stroke and Dementia Research. The Ludwig Maximilian University of Munich (LMU) (http://www.en.uni-muenchen.de/index.html) Germany, and its hospitals figure among Germany's premier and internationally competitive biomedical research sites and are funded by the government's Excellence Initiative. Salary is according to TV-L. The position is limited for two years, with a possible extension. Disabled persons will be preferentially considered in case of equal qualification. Presentation costs can not be refunded. HOW TO APPLY: Your application - preferably in electronic form - with the usual documents indicating the earliest possible starting date should be directed to: Klinikum der Universität München, Institute for Stroke and Dementia Research Prof. Dr. Martin Dichgans Marchioninistr. 15 81377 Munich | Germany Send application by email to: Mrs. Lilo Thomas E-Mail: isd(a)med.uni-muenchen.de

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Fast subcoritcal segmentation
by Thomas Fink 28 Jan '14

28 Jan '14

Dear experts, We have a pool of 490 subjects and will work on a linux grid for the recon. For this analysis we are only interested in subcortical areas. Question: Is it possible to run only the subcortical segmentation (and leave out the cortical segmentation)? (Is it possible to run the -subcortseg of recon without any other processing?) What flag would be used for this instead of the -all option, or is a different general command available that limits the segmentation to the subcortical areas only? Thank you very much in advance, Thomas

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Comparing aparc+aseg.mgz and aparc.a2009s+aseg.mgz
by Mehul Sampat 27 Jan '14

27 Jan '14

Hi Folks, I have two questions related to aparc.a2009s+aseg.mgz: 1. I was wondering if there is a mapping between structures in aparc+aseg.mgz & aparc.a2009s+aseg.mgz ? For example I would like to know what "isthmuscingulate" in aparc+aseg maps to in aparc.a2009s+aseg.mgz. 2. I could find a lobe mapping for aparc+aseg.mgz here: http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation Is there a similar lobe mapping for aparc.a2009s+aseg.mgz ? Thanks Mehul

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mris_preproc questions
by Pedro Rosa 27 Jan '14

27 Jan '14

Pedro Rosa Hi, I have a couple of questions about the mris_preproc: 1) Can I include all subjects in the qdec.table, but afterwards exclude some of them (based on a determined categorial variable) during the statistical analysis? I understood that the script assembles thickness / area data into a single file, but individual data is not changed depending of other subjects’ data (it assembles individual data independently of other subjects into common-space fsaverage). Am I mistaken? 2) In a longitudinal study, should I include the .base. folders in the qdec-long.table (variable 2), or is it the same to include only the .long. folders in the qdec.table (below fsid)? Thanks a lot, Pedro.

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Re: [Freesurfer] Fwd: Corrections to the segmentation lead to giant defects
by Bruce Fischl 27 Jan '14

27 Jan '14

Hi Thomas what format are these in? Can you include extensions in the files you send in the future? thanks Bruce On Mon, 27 Jan 2014, Thomas Fink wrote: > Hi Bruce, > > At the moment we are interested in the volumes and thus we checked and > corrected the aseg-file (corrections done as described in the > RecommendedReconstructions). > In the first attachment you can see the incorrect automatic segementation of > the hippocampus and in the second what it looked like after our corrections, > but before the new recon with the giant defect. > > Cheerio, > Thomas > > On Thu, Jan 23, 2014 at 10:39 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Thomas > > when you say errors in the hippocampus do you mean the aseg or > the surfaces? If the surfaces, don't worry about them as they > are not used in the hippocampal region. You are probably > connecting the temporal lobe to the main body of the white > matter creating a giant defect. > > cheers > Bruce > On Mon, 20 Jan 2014, Thomas Fink wrote: > > > Dear Freesurfer experts, > > We are using FS 5.1 and have several participants > with errors in the > segmentation of the hippocampus and other regions of > the cortex. So far we > did corrections to the hippocampus but in 10 out of > 13 participants we got > error messages listed below: > > Seven participants: > > ----- > > CORRECTING DEFECT 0 (vertices=74686, convex > hull=1605) > > Excessive topologic defect encountered: could not > allocate 390335770 edges > for retessellation > > Cannot allocate memory > > Darwin NPSY.local 12.4.0 Darwin Kernel Version > 12.4.0: Wed May 1 17:57:12 > PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 > x86_64 > > ----- > > One participant: > > ----- > > mhtVoxelList_Add(189, 240, 290, 260205): complete > list too big! > > mhtVoxelList_Add(189, 240, 290, 260205): complete > list too big! > > No such file or directory > > marking ambiguous vertices... > > Too many intersected faces for face 255461 (126442, > 128896, 128873) > > No such file or directory > > Darwin NPSY.local 12.4.0 Darwin Kernel Version > 12.4.0: Wed May 1 17:57:12 > PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 > x86_64 > > ----- > > One participant: > > ----- > > CORRECTING DEFECT 14 (vertices=33317, convex > hull=1285) > > mris_fix_topology(26738) malloc: *** > mmap(size=1212047360) failed (error > code=12) > > *** error: can't allocate region > > *** set a breakpoint in malloc_error_break to debug > > Bus error > > Darwin NPSY.local 12.4.0 Darwin Kernel Version > 12.4.0: Wed May 1 17:57:12 > PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 > x86_64 > > ----- > > One participant: > > ----- > > Correction of the Topology > > Finding true center and radius of Spherical > Surface...done > > Surface centered at (0,0,0) with radius 100.0 in 11 > iterations > > marking ambiguous vertices... > > 414500 ambiguous faces found in tessellation > > segmenting defects... > > Bus error > > Darwin NPSY.local 12.4.0 Darwin Kernel Version > 12.4.0: Wed May 1 17:57:12 > PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 > x86_64 > > ----- > > The error log says in all cases that there is > something wrong with the > cerebellum. When we open the ?h inflated.nofix file > then we see the > cerebellum added (see attached file) in the > hemisphere we made the edits. > > We have no clue if or what we are doing wrong and > here are the steps we > did: > > - open the files (tkmedit subject norm.mgz > -aseg.mgz > > - Tool -> Configure Segmentation Brush info -> > select the hippocampus -> add > voxels > > - File -> save segmentation > > - run recon with "recon-all -autorecon2 -noaseg > –autorecon3 -subjid subject > -nuintensitycor-3T" > > So far we had no problems with our subjects for all > the previous steps > (recon after wm, pial, .... edits) and it did run > smoothly. > > > Any help would be greatly appreciated. > > Thomas Fink Mail: Thomas.Fink(a)psy.lmu.de > > > > > 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 . 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. > > > > >

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QDEC error loading y
by Wanda Truong 27 Jan '14

27 Jan '14

Hi all, I am running surface area analysis in qdec and I get this error: $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /Users/vinagoghari/Documents/Wanda/Wanda_SFS cmdline mri_glmfit --y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh --fsgd /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/qdec.fsgd dods --glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates --surf fsaverage lh --label /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/contrasts/lh-Avg-Intercept-area.mat --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/contrasts/lh-Diff-Control-Proband-Intercept-area.mat sysname Darwin hostname Vinas-iMac.local machine x86_64 user vinagoghari FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh logyflag 0 usedti 0 FSGD /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/qdec.fsgd labelmask /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label maskinv 0 glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates Loading y from /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh mghRead(/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh): could not read 655368 bytes at slice 0 File exists ERROR: loading y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh Any insights? Thanks very much for your help, Wanda -- Wanda Truong, MSc

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Monte-Carlo Cluster Correction
by Cat Chong 27 Jan '14

27 Jan '14

Dear Experts, I was wondering if you could possibly help me with a reviewer-related question: We conducted a between-group-analysis estimating the interaction between cortical thickness and age. In summary, we wanted to investigate whether the interaction between cortical thickness and age is stronger for one group relative to another (using a DODS design). We cluster-corrected our results using a Monte Carlo cluster correction of p<0.01 and attained significant group differences for several areas over the left and right hemisphere. One of the reviewer commented that although group differences were estimated for each hemisphere separately, they ought to have been cluster-corrected for both hemispheres. Would you be able to tell me whether or not cluster-correcting for both hemispheres is a necessity, or help me understand the possible implications of not having cluster-corrected for both hemispheres? Very Best Regards, Catherine

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tkmedit - display reconstruction toolbar by default
by Chris Adamson 27 Jan '14

27 Jan '14

All, Is there any configuration file/source code file that can be edited to display the reconstruction toolbar by default in tkmedit? Thank you. Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.au<http://www.mcri.edu.au/> E chris.adamson(a)mcri.edu.au T 03 9936 6780 ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Re: [Freesurfer] Fwd: QDEC error
by Douglas N Greve 27 Jan '14

27 Jan '14

Perhaps try saving it as a txt file directly from excel instead of doing the cut and paste On 01/23/2014 08:14 PM, Wanda Truong wrote: > Hi Doug, > > This was all done on a mac. What would be the best way to recreate it? > Was the above mentioned excel method adequate? > > Wanda > > > On 23 January 2014 17:13, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > there is something wrong with the format. did you make your qdec table > on a windows machine? If so, convert it to linux format or recreate it > on a linux/mac machine > > doug > > On 01/23/2014 07:02 PM, Wanda Truong wrote: > > > > > > ---------- Forwarded message ---------- > > From: *Wanda Truong* <wanda.truong.87(a)gmail.com > <mailto:wanda.truong.87@gmail.com> > > <mailto:wanda.truong.87@gmail.com > <mailto:wanda.truong.87@gmail.com>>> > > Date: 23 January 2014 16:57 > > Subject: QDEC error > > To: freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > > > > Hello, > > > > I am having trouble with my group analysis using QDEC. I have 3 > > groups, 72 subjects, and 4 covariates. This is the error I get: > > > > Loading data table > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/qdec.table.dat... > > Number of columns: 438 > > fsid column: 1 > > Number of factors: 437 > > Number of subjects: 0 > > ERROR: QdecDataTable::Load: number of subjects = 0 > > Error loading the data table. > > > > I've attached my qdec.table.dat file and fsgd file as well. I > > initially created the columns using excel and I copied and pasted it > > into a .txt. file. Could this be the problem? If so, what would be a > > better method? > > > > Thanks very much, > > Wanda > > -- > > Wanda Truong, MSc > > > > > > > > -- > > Wanda Truong, MSc > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 . 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. > > > > > -- > Wanda Truong, MSc -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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