Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

dt_recon error
by Ritobrato Datta 11 Aug '14

11 Aug '14

Hi All, I ran dt_recon and got the following error. Can someone suggest how to fix this ? I have attached the dwi-infodump.dat file for more information. Thanks a lot for the help. Best Rito #@#------------------------------- Fitting Tensors Mon Aug 11 07:29:29 EDT 2014 cd /Users/iron/rito/VisualMeasures-CHOP/VisionMeasures-003 mri_glmfit --y /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii --glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon --dti /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /Users/iron/rito/VisualMeasures-CHOP/VisionMeasures-003 cmdline mri_glmfit --y /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii --glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon --dti /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat sysname Darwin hostname magi-2-balthasar.uphs.upenn.edu machine x86_64 user iron FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii logyflag 1 X /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat usedti 1 glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon Loading y from /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii Using DTI bValue = 1000 ERROR: cannot extract sWiPMemBlock.alFree[8] from /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat

2 1

midline cortical thickness
by Ivanka Savic Berglund 11 Aug '14

11 Aug '14

Question regarding reliability of midline cortical regions by Amir - it refers to the cingulate cortex, the cuneus, precuneus. Sincerely Ivanka Savic M.D., PhD > Professor of Neurology > Karolinska Institute > Dept of Women’s and Children’s Health > and Neurology Clinic,Karolinska Hospital, Q2:07 > SE-171 76 STOCKHOLM, Sweden > > Telephone +46 8 517 773 41 > +46 709 38 07 38 > Fax +46 8 517 773 49 > ivanka.savic-berglund(a)ki.se

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lobes gyrification
by melinda dora 11 Aug '14

11 Aug '14

Dear freesurfer group, is there a command to extract lobar gyrification values for each subject? If so please what are the steps? if Ive already created the lobar annotation labels, can I extract gyrifaction with these if I have already passed the gyrification command? Best, Melly

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Any good cortical segmentation methods for brains with infarct or tumors?
by Salil Soman 11 Aug '14

11 Aug '14

Hi, Does anyone have recommendations for good automated cortical segmentation tools for brains with infarct (so some brain missing) or tumors? I am under the impression that FreeSurfer is not reliable in these cases. If I am incorrect, any pointers on how to use FreeSurfer in these cases would be very helpful. Thank you. Salil Thanks

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Recon-all Error
by Esha Mehta 09 Aug '14

09 Aug '14

Hello, I am extremely new FreeSurfer user, and have hit a bump in the road while trying to run -autorecon1 and -autorecon2. The process seemed to be running smoothly until I got the following warning messages for every file number, and then it was randomly killed- * WARNING: TP 890 to 1 did not converge !! * WARNING: TP 891 to 1 did not converge !! * WARNING: TP 892 to 1 did not converge !! mapping movs and creating initial template... allow intensity scaling Linux login4 2.6.32-431.5.1.el6.x86_64 #1 SMP Fri Jan 10 14:46:43 EST 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s DNS_highRes_N892 exited with ERRORS at Mon Jul 21 10:48:23 EDT 2014 Within the error log, there was also an extremely lengthy command, and I believe could have been part of the issue as well. It is way to long to post here, but here is how it begins and ends- CMD mri_robust_template --mov /groups/wallacegrp/DNS_highRes_N892/mri/orig/000.mgz /groups/wallacegrp/DNS_highRes_N892/mri/orig/001.mgz /groups/wallacegrp/DNS_highRes_N892/mri/orig/002.mgz ... /groups/wallacegrp/DNS_highRes_N892/mri/orig/888.lta /groups/wallacegrp/DNS_highRes_N892/mri/orig/889.lta /groups/wallacegrp/DNS_highRes_N892/mri/orig/890.lta /groups/wallacegrp/DNS_highRes_N892/mri/orig/891.lta I was hoping you could give me some advice on how to deal with this error, or help me determine whether this is a freesurfer error, or has to do with something else. Thanks so much! -- Esha Mehta 585-967-7223 emehta15(a)gwu.edu George Washington University, Class of 2017

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tksurfer tool "graph marked vertices avg" not active
by Katharina Zech 09 Aug '14

09 Aug '14

Dear all, I have a problem regarding tksurfer ROI cluster extraction after full mc-simulation: I marked my cluster of interest as described in the freesurfer tutorial. But when I choose Tools --> Group, "Graph marked vertices avg" is not selectable. Is this due to a license or package problem? Best, Katharina <https://mail.google.com/mail/u/0/?ui=2&ik=fca2d919c7&view=att&th=14791a8926…>

2 5

insula on medial surface
by Harms, Michael 09 Aug '14

09 Aug '14

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What is the best method to calculate cohenD or any other map of effective size with lme?
by Knut J Bjuland 09 Aug '14

09 Aug '14

Dear FreeSurfer expert I have calculated the residuals as y-x*beta as described in (Bernal-Rusiel et al., 2012). What is the best method to calculate cohenD or any other map of effective size with lme? Can I calculate cohenD as R=y-desingmatrix*Bhat cohenD=gamma./(sqrt(sum(r.^2)/df2-1)) Reference Bernal-Rusiel, J.L., et al., 2012. Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models. Neuroimage. 66C, 249-260. Best regards Knut Jørgen

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Cortical Thickness Correction Factor
by David Tate 08 Aug '14

08 Aug '14

We are working on a study that includes data from multiple scanners and initial indication suggest that there may be small differences in cortical thickness measures that are scanner related (human and other phantom data were acquired at both sites). Is it possible to include a correction factor adjusting for the scanner differences when using glmfit or qdec? Thanks, David David F. Tate, Ph.D. Research Neuropsychologist Defense and Veterans Brain Injury Center Contractor, General Dynamics Information Technology Brooke Army Medical Center MCHE MDU (DVBIC) 3551 Roger Brooke Drive JSBA Ft. Sam Houston, TX 78234-4504 Office (210) 916-8090

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Update to Tracula longitudinal?
by Chung, Yoonho 08 Aug '14

08 Aug '14

Dear Freesurfer Experts We decided to reprocess our T1 and DTI data with the latest stream v.5.3 – we would like to give TRACULA longitudinal stream a try. Before we go ahead and reprocess our recons and DTI data with FS v 5.3 we were wondering if you plan to release a new version of the TRACULA DTI longitudinal stream anytime soon. I think I saw somewhere in the email chain that this is likely to happen soon with additional features and bug fixes. If so, I think it would be worth a wait. Thank you! Yoon

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