Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

TRACULA question: pathstats.overall.txt
by Minjie Wu 28 Jun '12

28 Jun '12

Dear TRACULA Developer & User, I am wondering if it is possible to add other DTI measurements to the pathstats.overall.txt along with those DTI parameters already included (FA, MD, AD, RD)? Thank you very much. Minjie

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Building ROI from SPM5 MNI results
by Kairys, Anson 28 Jun '12

28 Jun '12

Hi Everyone, I would like to "import" an ROI into a FS analysis and extract thickness measures form within this region. Is this at all possible? Thanks Anson K, ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Recent paper on FreeSurfer reliability
by Ed Gronenschild 28 Jun '12

28 Jun '12

Dear Bruce, Doug, Nick, and other co-workers, As authors of the recent paper “The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements” we would like to take the opportunity to respond to the numerous e-mails and reactions written on mailings lists and websites. We have never expected that our paper would have such an adverse impact. We have noticed that several so-called “journalists” have misinterpreted and erroneously extrapolated our conclusions. Even though this is not in our hands, we want to express our disappointment of these events and that we feel very uncomfortable with the created harassment. We want to stress that it has never been our intention to put FreeSurfer in a bad light or to blame its developers, rather we wanted to quantify the effects that you frequently warned the users about. The results of our study confirm your recommendations and increase the awareness of such effects to (novice) users. It is of course unavoidable that modifications to algorithms will produce different results; we, nevertheless, must admit that we were surprised that some effects were rather large. We are using FreeSurfer frequently for our MRI data and we definitely intend to do so in the future. We are impressed by the efforts of your team to improve the algorithms and to extend the capabilities of FreeSurfer. We are most grateful to you and the other developers because these continuing efforts enabled and will enable us to perform our research in a valid and proper manner. Unfortunately, the media attention gave the impression that our conclusions would only be directed to FreeSurfer. We have written in our discussion section that some of the conclusions may apply to other packages in the field of neuroimaging as well. We hope that you can acknowledge our sincere intention to examine and increase awareness of uncontrolled variation in MRI data analyses in general and not to pinpoint Freesurfer. Therefore, we have informed also the users and developers of FSL about possible similar effects. Ed Gronenschild, Petra Habets, Heidi Jacobs, Ron Mengelers, Nico Rozendaal, Jim van Os, Machteld Marcelis

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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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