Freesurfer March 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
247 discussions

White matter edits
by Eleanor Stahura 26 Mar '14

26 Mar '14

Hello, I am visually checking wm.mgz after running recon-all. There seems to be a pattern where I'm seeing white matter "bleed" past the (correct) white matter surface and into gray matter or appear in the sagittal sinus/dura. However, when I look at wmparc.mgz, the problem is no longer there and the white/gray matter is correctly segmented. Even if the wmparc volume is correct, do I need to do white matter edits? Thanks, Elle

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removal oblique sforms
by Righart, Ruthger 26 Mar '14

26 Mar '14

Dear Freesurfers, To obtain an accurate volume-surface alignment of Freesurfer surfaces in Caret, it is advised that oblique sforms should be removed from the header of the t1w images. I tried to remove the sform (using sform_code='0' and qform='1') and changed the nii header using fslcreatehd. However, something seems to go wrong, as my thickness data of the same subject are different than the thickness data from the original t1w images. In addition, alignment in Caret is still poor. I am puzzled and I would be happy to have your suggestions about removing sforms. Thank you very much in advance! FS 5.3. was run on a Linux machine x86_64. Ruthger

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norm2b, norm2n
by Jason Tourville 26 Mar '14

26 Mar '14

Greetings, I am working with pediatric data and have some early evidence that running recon-all with the flag -norm2-b 20 -norm2-n 5 improves the anterior temporal lobe segmention as suggested in the v5.2 release notes (I am running this with v5.3). I'd like to experiment more with this parameters to see if I can further improve the segmentation but have been unable to find a a description of how these parameters influence the 2nd norm. Can someone point me to such a description? Thanks, Jason Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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Thickness analysis on fetal brain
by stdp82＠virgilio.it 26 Mar '14

26 Mar '14

Hi list, we would like to perform cortical thickness analysis on fetal brain. We have a single shot T2 image (good quality) and T1 image (poor quality). All images are in 2D with overlapping and they are acquired by using 1.5 tesla. We have some questions: 1. Do you know a post-processing way to trasform 2D in 3D images and to reduce motion artifacts? 2. Is adapt single shot T2 image to measure the thickness? 3. Given that we are still acquiring data, do you advise a specific protocol to improve T1 or other sequences? Thank you very much, Stefano

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fsaverage -> fsaverage3
by Itamar Kahn 26 Mar '14

26 Mar '14

Greetings, We would like to downsample surfaces (e.g. using mris_decimate) but we want to duplicate the way it was done with fsaverage (namely, find out how fsaverage3/4/5 were created from the original fsaverage). Also, we wish to be able to project using mri_surf2surf but we don’t have sphere registration available (these are fetal imaging surfaces). Thanks, Itamar _________________________________________________ Itamar Kahn, Ph. D., Assistant Professor Department of Physiology and Biophysics The Ruth and Bruce Rappaport Faculty of Medicine Technion – Israel Institute of Technology POB 9649 Bat Galim Haifa 31096 Israel (o) 972-4-829-5461 http://kahnlab.technion.ac.il/ _________________________________________________

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missing codecs for mne_make_movie
by Joseph Dien 26 Mar '14

26 Mar '14

Hi, I tried to use mne_make_movie but got the following error: Movie production selected (from data)... Scanning /Applications/MNE-2.7.3-3268-MacOSX-i386/lib for plugins Found lqt_mjpeg.so...Getting codec info from module Trying to load /Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so... dlopen failed for /Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so: dlopen(/Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so, 2): Library not loaded: /opt/local/lib/libjpeg.62.dylib Referenced from: /Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so Reason: image not found ERROR: lqt_find_video_codec failed to find codecs! The command was: mne_make_movie --inv RPforMNE-eeg-inv.fif --meas RPforMNE.fif --tmin 0 --tmax 250 --tstep 10 --stc RPforMNE --view lat --mov RPforMNE I’m using MNE 2.7.3 under OS X 10.9.2. Any help would be appreciated. Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist Maryland Neuroimaging Center University of Maryland E-mail: jdien07(a)mac.com Phone: 202-297-8117 http://joedien.com

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example in mris_label2annot's help
by Carl Anderson 25 Mar '14

25 Mar '14

Dear list, I tried runing the example in mris_label2annot's help: mris_label2annot --s bert --h lh --ctab aparc.annot.ctab --a myaparc --l lh.unknown.label --l lh.bankssts.label --l lh.caudalanteriorcingulate.label --nhits nhits.mgh got the following result: ERROR: cannot find or read aparc.annot.ctab aparc.annot.ctab is in bert and here is my setup: -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl could this be a bash vs tcsh problem as I am using bash? -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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Re: [Freesurfer] glmfit with correlated covariates
by L. Schweren 25 Mar '14

25 Mar '14

Dear FreeSurfer experts, Thank you for your fast reply. We are extracting cortical thickness values for statistical sub-analyses in SPSS (due to corrections required with regard to family relatedness within the data); therefore we want to be a 100% certain that the statistical model we use in SPSS is identical to the model used by mri_glmfit. Can you confirm that, out of the multiple linear regression types listed below, mri_glmfit makes use of the Direct (or Standard) regression model? Type Characteristics Direct (or Standard) . All IVs are entered simultaneously Hierarchical . IVs are entered in steps, i.e., some before others . Interpret: R2 change, F change Forward . The software enters IVs one by one until there are no more significant IVs to be entered Backward . The software removes IVs one to one until there are no more non-significant IVs to removed Stepwise . A combination of Forward and Backward MLR Thank you again for your help, Best wishes, Lizanne Date: Wed, 12 Mar 2014 11:04:00 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] glmfit with correlated covariates To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <53207760.8010809(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" It is just a standard multiple regression analysis where all regressors are fit simultaneously. One weight does not include that of another weight. doug On 3/12/14 5:16 AM, L. Schweren wrote: > > Dear FreeSurfer experts, > > I am attempting to disentangle the effects of different features of > pharmacological treatment on cortical thickness. > > I am running glmfit from the commandline, with multiple covariates > (a.o. Z_Age, Z_TreatmentDuration and Z_StartAge) in the fsgd-file. > These covariates are correlated up to approximately 0.6 , which to my > understanding is not ideal yet not inducing collinearity. Running > glmfit, I do not get any errors such as ill-designed matrix or so. > > My question regards the way the different regression weights are > calculated in each voxel. If I test the variance in CT of voxel A > explained by for example TreatmentDuration, and part of the variance > in voxel A is explained by both TreatmentDuration and StartAge, will > the regression weigth of TreatmentDuration than include the part that > is also explained by StartAge? Or are all other covariates first > "regressed out" of the variance, such that the variable I test can > only explain the variance that was not explained by any of the other > covariates? > > Thank you very much, your help is very much appreciated! > > Best wishes, > > Lizanne > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Percent signal change after resampling and combining FEAT analyses
by Manuel Spitschan 25 Mar '14

25 Mar '14

Dear FreeSurfer experts, I've performed a few first-level analyses of BOLD data with FSL, and have followed the instructions on the FS Wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat) to sample the COPEs of each run to a common surface (fsaverage) and run a fixed-effects analyses using 'mri_glmfit' across the runs. The resulting gamma.mgh contains the COPEs per vertex across the runs. How would I find out the appropriate scaling factor and the baseline image to calculate percent signal change per vertex following these analysis steps? Any help would be appreciated. Thanks in advance, Manuel Spitschan

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thickness for "subcortical structures"
by Francesco Puccettone 25 Mar '14

25 Mar '14

Hello, I've read that cortical thickness analyses are limited to the cortex and cannot be used to examine subcortical grey matter. But does "subcortical grey matter" refer to deep gray matter structures such as the hippocampus, the basal ganglia or the nucleus accumbens - all of which are still technically part of the "cerebral cortex" - or does it in fact refer to gray matter nuclei surrounded by white matter, for which it would not be possible to model a white & a pial surface? Thank you! Francesco

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Freesurfer March 2014