Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

130 participants
211 discussions

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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Monte Carlo Simulation Precomputed Data
by Natasha Haris 27 Jan '14

27 Jan '14

Dear Freesurfers, I am slightly confused about the monte carlo simulation. First off, I only find a blob when I run the p<0.05 threshold level and don't see anything else when I run simulations with p less than that. What does this mean? Additionally, when I click on any question of interest after running this p<0.05 simulation (for ex. "Does the average thickness, accounting for Group, differ between male and female?" I get the same blobs that I found before I ran this precomputed simulation. Is the simulation not running correctly? Am I supposed to enter this threshold value (1.3) into the area marked Threshold min= and max=5. Thank you for your help! Natasha

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unable to download free surfer
by Davis, Peter 27 Jan '14

27 Jan '14

Hi, I am unable to download freesurfer. Is there a problem at the ftp? Thank you, Peter

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mri_glmfit-sim for volume data: GRF vs. simulation
by Susan Ruiz 27 Jan '14

27 Jan '14

Hi FreeSurfers, I was just reading this post to the archive (below) regarding using mri_glmfit-sim on volume data, and it suggests that using --grf rather than doing the simulation can be "inaccurate at low smoothness and low thresholds." At what smoothness values and threshold values should we opt to use the simulation over GRF for volume-based cluster corrections? Thanks, ~Sue Ruiz > Hi Yuko, it should be performing Gaussian Random Field (GRF) > cluster-wise correction. Based on the smoothness, the size of the search > space, and the voxel-wise threshold, it attempts to compute the p-value > of resulting clusters. The differences between GRF and doing the > simulation are that GRF runs almost instantly but it can be inaccurate > at low smoothnesses and low thresholds. It looks like the GRF was not > implemented until 5.1 doug yukoyy wrote: >* Dear all, *>>* I'm conducting volume based group analysis and corrections for multiple comparisons. *>* My environment :Mac OS 10.6.8, Freesurfer 5.0.0 *>>* I followed the instruction I found here: *>* http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel <http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel> *>>* When I first successfully ran: *>* mri_glmfit --y ces.005.nii --wls cesvar.005.nii --osgm --glmdir F2glm.wls --nii.gz *>* tkmedit fsaverage orig.mgz -aparc+aseg -overlay F2glm.wls/osgm/sig.nii.gz -fminmax 3 7 *>>* Then, I wanted to do corrections for multiple comparison. *>* mri_glmfit-sim --glmdir F2glm.wls --grf 3.0 pos --cwpvalthresh .0166 *>>* However, FreeSurfer does not seem to recognize --grf, and I don't understand what does grf do. *>* %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% *>* ERROR: Flag --grf unrecognized. *>* --glmdir F2glm.wls --grf 3.0 pos --cwpvalthresh .0166 *>* %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% *>>* I chose to use --grf because it was suggested in the tutorial, and in FreeSurfer mailing list archive. *>* http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20573.html <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20573.html> *>>* I am guessing that I cannot use --cache for volume analysis because I don't have *>* /Applications/freesurfer/average/mult-comp-cor/fsaverage/volume/cortex/fwhm12/pos/th30/mc-z.csd *>>* I also tried monte-carlo simulation, and it worked okay. *>>* So, here is my question. *>* What does --grf do? and Is there any documentation? *>>* Thank you! *>* Yuko Yotsumoto *>* yukoyy at a7.keio.jp <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>* _______________________________________________ *>* Freesurfer mailing list *>* Freesurfer at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>>> -- Douglas N. Greve, Ph.D. MGH-NMR Centergreve at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> Phone Number: 617-724-2358 Fax: 617-726-7422 -- * * ** *** ***** ******** ************* Susan Mosher Ruiz, Ph.D. Research Scientist Boston University School of Medicine Laboratory of Neuropsychology VA Boston Healthcare System smosher(a)bu.edu * * ** *** ***** ******** *************

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Inquiry about Choi's striatum parcellations.
by 조수연 27 Jan '14

27 Jan '14

p{margin:0;padding:0;} Hello, I'm a FreeSurfer beginner and would like to ask a question about Choi's stratium parcellations. I was doing a research to incoorporate the parcellations by Choi on my subjects' images to delve further to understand the distincitve characteristics of each parcels. I decided to use the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz. Since my images were on the standardized model from FSL, I transformed Choi's image to the MNI standard using FIRST of FSL. Since both images were now on the same MNI space, I viewed both of them on FSL to make sure that the Loose mask covered my image completely, but found that the tail bit of my image was a couple of pixels too longer than Choi's Loosened mask. Do you think there is a way that I can further "loosen" up Choi's image to fit my image? Or can you recommend me a different solution to this problem? I'll wait for your reply. Thanks! Sincerely, Sooyun Cho.

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Post-Doc position available at Aix-Marseille University
by Olivier Coulon 27 Jan '14

27 Jan '14

Dear all, a post-doc position is available at Aix-Marseille University, France, on the topic of "descriptors of cortical folding patterns in the developing brain". Please see document attached. If you are interested, please contact Dr Julien Lefèvre (julien.lefevre(a)univ-amu.fr) -- Olivier Coulon, CNRS research Fellow, olivier.coulon(a)univ-amu.fr <mailto:olivier.coulon@univmed.fr> Tel: +33491828527 fax: +33491828550 http://olivier.coulon.perso.esil.univmed.fr <http://olivier.coulon.perso.esil.univmed.fr/> LSIS Laboratory, I&M Team ESIL, Campus de Luminy, Case 925, 13288 Marseille cedex 09, FRANCE BrainMorph logo http://www.lsis.org/brainmorph

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Freesurfer January 2014