Freesurfer May 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
219 discussions

Freesurfer Cerebellum Overgrab
by Burgess, Leah Lanette 22 May '17

22 May '17

Hi FreeSurfer experts, We recently finished a twin study with 450 participants. Most of the FreeSurfer issues have been common and fixable. However, we have two sessions that have a similar issue that I have not been able to find a solution to using the forums. Could you please advise us on how to correct these problems? Please see attached screenshots: 114147 - aparc+aseg and brainmask are grabbing the cerebellum 116336 - aparc+aseg is over grabbing the brainstem when tracing the cerebellum (the brainmask is fine on this one). I made edits to aparc+aseg and aseg and reprocessed with no change, however, since these are not common edits the processor may not have uploaded/taken these edits correctly. We use a service at the university Center for Computational Imaging called XNAT. The lab who runs this processor writes spiders for us to process everything so I have limited access to the scripts. However, on past projects I have used terminal for FreeSurfer processing. If I can fix this problem with a terminal script, then upload it to XNAT for normal FreeSurfer processing, it may correct the issue. I haven't been able to figure out a correct terminal script to correct the issue on my own though. Any help is appreciated. Sincerely, Leah Burgess Leah Burgess Research Analyst Department of Psychology Vanderbilt University 219 Wilson Hall 111 21st Avenue South Nashville, TN 37240 (615) 343-1446<tel:%28615%29%20343-1446> NOTE: This e-mail transmission, including any attachments, is intended only for the named recipient(s) and may contain information that is privileged, confidential and/or exempt from disclosure under applicable law. If you have received this transmission in error, or are not the named recipient(s), please notify the sender immediately by return e-mail and permanently delete this transmission, including any attachments.

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Importing external statistical map and overlaying over freesurfer anatomical
by Jerry Jeyachandra 22 May '17

22 May '17

Hi Freesurfer list, I have a statistical map (.nii format) produced from analysis performed in BrainVoyager that I'd like to register with the anatomical model produced with Freesurfer's recon-all, this is on a single-subject basis from the same raw data. I have several questions with respect to this (hopefully possible) process: 1. I've noticed that using mri_info (and loading into freeview on top of orig.mgz) that the coordinate spaces do not match, does freesurfer have a process to align the statistical map to orig.mgz? 2. Currently, loading in the .nii image is interpreted as an anatomical image, is there any way I can indicate to freesurfer that it is a functional map such that I can work with thresholding? 3. When aligned with the orig.mgz anatomical image, is there a process that will allow me to project it onto the segmented model? Specifically, I'd like to extract plial surface coordinates associated with the regions of BOLD activation. Thanks, Jerry Jeyachandra

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Contrast matrix regressing out effect of diagnosis and age
by Erik Lindberg 22 May '17

22 May '17

Dear Freesurfer experts, I am running a GLM-model in which I have 6 classes (diagnosis) and two covariates age and variable X). I want to look at mean correlation of variable X. My contrast matrix is as follows: 0 0 0 0 0 0 0 0 0 0 0 0 0.17 0.17 0.17 0.17 0.17 0.17 0.17 (approx. 1/6) Did I get this right? Thanks Eric

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3D conversion of Desikan-Killiany Atlas
by Kwangyeol Baek 22 May '17

22 May '17

Hi, all. Is there a 3D MNeI space version of Desikan-Killiany Atlas? (e.g. a sample 3D parcellation using MNI152 brain) Please let me know where I can find it or how I can get it in using Freesurfer. Thank you very much! Sincerely, Kwangyeol Baek

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local gyrification index (lGI) Error in Design
by Katherine Damme 22 May '17

22 May '17

Hello FreeSurfer Group I would like to make a two group comparison controlling for both gender and medication status. The only way that I have sorted out doing this is to make eight groups (ClinicalGroup x Sex x Meds) but I get an error that my design is poorly scaled: -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.lgi.mgh --fsgd FSGD_GroupSexTP_AntiPsych.txt --glmdir lh.lgi.glmdir --surf average lh --C contrast.txt 2. The FSGD file (if using one) 3. And the design matrix above

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Thresholding sig.mgh with cluster extent K > 20 voxels
by Elijah Mak 22 May '17

22 May '17

Hi Everyone, How may I threshold the sig.mgh (p<0.001) with a cluster extent K > 20 voxels? Is it possible to do this in Freesurfer? Thanks. Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry, Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

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Extracting fMRI mean time series from Desikan ROIs
by Elijah Mak 22 May '17

22 May '17

Hello Freesurfer Experts, I have a question to ask about extracting the mean time series from resting-state fMRI (239 volumes). I have used bbregister to bring the 4D fMRI data into T1 space. My next objective is to project the data onto the fsaverage surface, and then extract the mean time series for each ROI. These are my steps so far. Can anyone let me know if I am on the right/wrong track? bbregister --s $i --mov ${i}_medn.nii (fMRI resting-state) --init-fsl --t2 --reg ${i}/fmri/fmri_t1.dat --o ${i}/fmri/fmri_t1.mgz mri_vol2surf --src ${i}/fmri/fmri_t1.mgz --out ${i}/surf/lh.fmri.mgh --hemi lh --projfrac 0.5 --interp nearest --regheader ${i} --trgsubject fsaverage mri_segstats --i ${i}/surf/lh.fmri.mgh --annot fsaverage lh aparc --sum ${i}/stats/lh.fmri_aparc.sum Ultimately, how may I derive a 239 (volumes) x 34 (ROIs per hemisphere) matrix of the data? Appreciate your help. Thanks! Best Wishes, Elijah Elijah Mak, Research Associate Department of Psychiatry, Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK

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Recon-all error: -autrecon2 unrecognized
by Gwang-Won Kim 22 May '17

22 May '17

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[How to transform the statistical map from the average surfaces into the individual subject's surfaces]
by 김정식 22 May '17

22 May '17

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Error in hippocampal subfield segmentation
by Md. Mamun Al-Amin 22 May '17

22 May '17

Hello FreeSurfer Developers, I'm attempting to compute hippocampal subfield segmentation. Unfortunatelty I found following errors. ------------------------------------------------------------------------ Segmentation violation detected at Sat May 20 10:45:37 2017 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Current Visual : None Default Encoding: ISO-8859-1 MATLAB Root : /Applications/freesurfer/MCRv80 MATLAB Version : 8.0.0.783 (R2012b) Operating System: Darwin 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 58 Stepping 9, GenuineIntel Window System : No active display Fault Count: 1 Abnormal termination: Segmentation violation Register State (from fault): RAX = 0000000000000000 RBX = 0000000103310000 RCX = 0000000000000006 RDX = 0000000103313a00 RSP = 000000010fc39e80 RBP = 000000d0ffffffff RSI = ffffffffffffffff RDI = 0000000000000005 R8 = 0000000000000000 R9 = 0000000110323852 R10 = 0000700002d27480 R11 = 0000700002d274e0 R12 = 0000000000000005 R13 = 000000001c004121 R14 = 0000000000000246 R15 = 0000000110500160 RIP = 0000700002d27b98 RFL = 0000700002d27b60 CS = 000000010f91fd54 FS = 0000700002d27360 GS = 0000000000000005 Stack Trace (from fault): [ 0] 0x0000000101e61e46 /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00036422 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+000150 [ 1] 0x0000000101e62af1 /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00039665 fl_diag_terminate+000321 [ 2] 0x0000000101e64c34 /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00048180 _ZN2fl4diag13terminate_logEPKcRKNS0_14thread_contextE+000100 [ 3] 0x0000000105ed825e /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00315998 mnTrapCtrlc+000254 [ 4] 0x0000000105ed9d24 /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00322852 _Z32mnRunPathDependentInitializationv+003492 [ 5] 0x0000000105eda13d /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00323901 _Z32mnRunPathDependentInitializationv+004541 [ 6] 0x0000000105eda7f5 /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00325621 _Z32mnRunPathDependentInitializationv+006261 [ 7] 0x0000000105eda945 /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00325957 mnFatalSignalHandler+000149 [ 8] 0x00007fffa5b60b3a /usr/lib/system/libsystem_platform.dylib+00011066 _sigtramp+000026 [ 9] 0x00000004ffffffff /usr/lib/system/libsystem_platform.dylib+18446603359210840063 If this problem is reproducible, please submit a Service Request via: http://www.mathworks.com/support/contact_us/ A technical support engineer might contact you with further information. Thank you for your help.** This crash report has been saved to disk as /Users/mdmamunalamin/matlab_crash_dump.5756-1 ** MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 38: 5756 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $a I would like to draw your kind attention regarding this. -- Kind regards Md. Mamun Al-Amin ------------------------------ PhD Candidate, Queensland Brain Institute Building 79, St Lucia QLD 4072

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Freesurfer May 2017