Freesurfer June 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

Corrections in Skull Stripping lead to changes in aseg.stats - underlying reasons
by Thomas Fink 28 Jun '12

28 Jun '12

Hello, After making some corrections to the skull stripping (by hand) and running recon-all I was really puzzled to notice that there had been changes in the aseg.stats. Here are the statistics: # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 222913.677586, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 223162.652586, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 446076.330172, mm^3 # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 197877.640625, mm^3 # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 199335.750000, mm^3 # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 397213.390625, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 172184.000000, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 618260.330172, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 976560.279689, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1340641.214487, mm^3 ---------------------- # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 221898.779029, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 221558.440924, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 443457.219953, mm^3 # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 196538.375000, mm^3 # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 199342.906250, mm^3 # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 395881.281250, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 172740.000000, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 616197.219953, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 974785.433550, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1340641.214487, mm^3 ---------------------- As you can see only the ICV stays the same but everything else changes: How can this be? Thank you very much for your answer in advance! Regards Thomas

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qdec Error
by Mohammed Goryawala 27 Jun '12

27 Jun '12

Hi, I am in the testing process of Freesurfer on a 64-bit Ubuntu installed personal computer. However when I run the qdec command as suggested in the testing stages I receive the following error. qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Please let me know a solution to fix this issue. Thank you for all you help. Mohammed Goryawala

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selxavg3-sess error
by Sam Cartmell 27 Jun '12

27 Jun '12

Hello, I'm trying to run selxavg3-sess with FS v4.5 for an FIR analysis where each trial is modeled as a separate condition. The command works smoothly for the majority of subjects, but for 2 different subjects, it exits with the following error: Saving X matrix to /home/sam/fMRIDATA/samstudies/SoCo/SoCo10/bold/Logit/Xtmp.mat XCond = 12220.6 (normalized) ERROR: design is ill-conditioned >> ------------------------------------------ ERROR: fast_selxavg3() failed\n details: I do not definite any contrasts, as I'm only running this command to generate trial specific betas for a separate analysis. Each trial lasts 18 seconds, followed by 4 seconds of fixation. Here is what part of a paradigm file looks like (the paradigm files are identical for all subjects): 4 1 18 1 22 0 4 1 26 2 18 1 44 0 4 1 48 3 18 1 66 0 4 1 70 4 18 1 88 0 4 1 92 5 18 1 110 0 4 1 114 6 18 1 132 0 4 1 136 7 18 1 154 0 4 1 here are the analysis.cfg and .info files: analysis analysis_name TR 2 fsd bold funcstem fmcsm4 tpexclude parname FIR_logit.par designtype event-related nconditions 96 -timewindow 20 -prestim 2 -acfbins 10 -fix-acf -noautostimdur -no-fsv3-st2fir -no-fsv3-whiten -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 the command which throws the error: selxavg3-sess -analysis analysis_name -s subject_name The strange part for me is that this only seems to be a problem with a couple subjects, despite the fact all the paradigm files are identical. After looking through the mailing archive, I tried playing around with the prestim window, but even it if is = 0, there is 1 subject that exits with an error when I run selxavg3-sess. Do you know what might be going on? Any guidance would be appreciated. Thanks, Sam

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DODS, DOSS, and interactions
by mdkruepke＠uwalumni.com 27 Jun '12

27 Jun '12

Freesurfers- Question, when looking for interactions to justify using DOSS say i am looking at cortical thickness and i have two discrete variables (G1 and G2) and 4 continious variables (V1, V2, V3, V4). My thinking is that i should look to see if there are interactions with the groups and each individual variable. However what if it is likely that an interaction of G1, G2, and V1 can be explained by V2? Michael -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

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error running FS on mac
by Dian "Oscar" Jiao 27 Jun '12

27 Jun '12

Hi, I just installed Freesurfer on my Mac Lion. When I ran recon-all, I got the following error. Can't locate MNI/Startup.pm in @INC (@INC contains:…………) at Applications/freesurfer/mni/bin/nu_coorect line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. Has this occurred to anyone before? How to fix it? Thanks DJ

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Correction of registration in preproc-sess stream
by Jörg Pfannmöller 27 Jun '12

27 Jun '12

Dear freesurfers, I have a simple question concerning the freesurfer 5.1 FSFAST preprocessing. In the preprocessing the functional images are registered to the anatomical ones using bbregister. This is the 3rd in a series of 8 preprocessing steps. If the preproc-sess registration fails it is possible to achieve a proper registration using various options of bbregister. Does it suffice to replace the register files created during the preprocessing with the ones received during the registration correction in order to attain proper preprocessed data or are there routines in steps 4 to 8 in the preprocessing which rely on the registration? Thanks in advance pfannmoe

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Hippocampal segmentation
by Gabriel Gonzalez Escamilla 27 Jun '12

27 Jun '12

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DTI question
by Drottar, Marie 27 Jun '12

27 Jun '12

I have a DTI dataset with 10 b0 and gradient 30 directions. I would like to remove one or two volumes from the dataset and then repackage the data. How do I do this? thank you Marie Drottar, MA Research Assistant Division of Newborn Medicine Fetal-Neonatal Neuroimaging & Developmental Science Center Boston Childrens Hospital 1 Autumn St Boston, MA 02115 http://childrenshospital.org/FNNDSC

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How to tackle large segmentation errors
by Richard Binney 26 Jun '12

26 Jun '12

Hi Freesurfers, I need some advice regarding the best approach to fixing some very large RECON errors in a highly lesioned brain. There are many problems in this RECON output, but I want to focus on one particularly bad one which is highlighted in the attached figure by yellow arrows but also have knock on effects in the ventricles. There are no examples in the tutorials or other docs that are quite like this. Can you tell me what the best approach to correcting this would be? Are WM.MGZ edits, as highlighted by purple arrows, the right approach? I can't help but feel there is a lot of room for error with this approach and it could be extremely time-consuming due to the need to accurately trace the basal surface or the subcortical mass. It is stated NOT to use control points in instances of white matter lesions. What about instances such as this? Clearly there is white and subcortical grey matter in this region - would placing control points in subcortical grey matter cause any problems? My take on control points is that it only informs the generation of the WM.MGZ image, which is not just white matter but generally all subcortical mass, and intensity changes instigated by them do not directly effect subcrotical parcellation - is this correct? If so, perhaps then control points would be OK to resolve this error. Please advise. Richard

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is it a bug of freeview? or wrong segmentation?
by Chao Suo 26 Jun '12

26 Jun '12

Hi all, I am new with freesurfer, and I found a problem when processing some data following the instruction online. When I checked the surfaces of these two timepoint together using freeview (follow the instruction online), it showed this abnormal spike on the white mater surface of my time point two scan. (fig 1, left, clear version: https://dl.dropbox.com/u/4825915/fig1.png) freeview -v SMART001aT1.long.SMART001T1/mri/norm.mgz \ SMART001bT1.long.SMART001T1/mri/norm.mgz \ -f SMART001aT1.long.SMART001T1/surf/lh.pial:edgecolor=red \ SMART001aT1.long.SMART001T1/surf/lh.white:edgecolor=blue \ SMART001bT1.long.SMART001T1/surf/lh.pial:edgecolor=255,128,128 \ SMART001bT1.long.SMART001T1/surf/lh.white:edgecolor=lightblue \ However, it was wired that I couldn't see this spike when I opened them in tkmedit. (fig1, right, https://dl.dropbox.com/u/4825915/fig1.png) tkmedit SMART001bT1.long.SMART001T1 brainmask.mgz -aux wm.mgz -surfs Further, if I inspected only the two surfaces of my time two data, there is no such spike at the same point. (fig2, clear version: https://dl.dropbox.com/u/4825915/fig2.png) freeview -v SMART001bT1.long.SMART001T1/mri/norm.mgz \ -f SMART001bT1.long.SMART001T1/surf/lh.pial:edgecolor=255,128,128 \ SMART001bT1.long.SMART001T1/surf/lh.white:edgecolor=lightblue \ So I am not sure whether these spikes are bugs when using freeview, or actually some registration error that need me to edit. Can some help me to confirm it? Or, did anyone come across this problem before? Thanks Chao Suo -------------------------------------------- PhD Candidate, School of Psychiatry, UNSW, Australia Brain & Mind Research Institute THE UNIVERSITY OF SYDNEY Room 401, Level 4, M02K | 100 Mallett St Camperdown | NSW | 2050 T +61 2 9351 0728 | F +61 2 9351 0551 |

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Freesurfer June 2012