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30132 discussions

z-test differences from fscalc and mri_glmfit
by Jonathan DuBois 05 Nov '13

05 Nov '13

Hi All, In a previous post Doug suggested two methods for generating voxel-wise z-score maps, one using glmfit with one subject in one group and the second using fscalc.fsl. Link to post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-June/014673.html I have tried both methods using PET data registered to the surface, but get very different results from fscalc and mri_glmfit. The results I expect are given by fscalc, but I would also like to run the Monte Carlo-based MCC, which requires a glmdir. Is there another way to run MC MCC on the z-map generated by fscal or alternatively, is the code that I am using for glmfit wrong? A simplified version of the code for both analyses is below. I am using FS 5.3 with the fsl binaries from the release notes on mac OS 10.8. Thanks for your help Jon ----------------------------------mri_glmfit: for h in rh lh; do mris_preproc --target fsaverage --hemi $h --iv nc01_mrispace_pet.mgz nc01_mrispace_pet_2_T1_register.dat --iv nc02_mrispace_pet.mgz nc02_mrispace_pet_2_T1_register.dat --iv nc03_mrispace_pet.mgz nc03_mrispace_pet_2_T1_register.dat --iv pat01_mrispace_pet.mgz pat01_mrispace_pet_2_T1_register.dat --pf 0.5 --out ${h}.pat01_allcontrols_pet_ztest_pf05_fsaverage.mgh for h in rh lh; do mri_surf2surf --hemi $h --s fsaverage --fwhm 10 --cortex --sval ${h}.${s}pat01_allcontrols_pet_ztest_pf05_fsaverage.mgh --tval ${h}.${s}pat01_allcontrols_pet_ztest_pf05_fsaverage_fwhm10.mgh; done for h in rh lh; do mri_glmfit --y ${h}.${s}pat01_allcontrols_pet_ztest_pf05_fsaverage_fwhm10.mgh --fsgd patient1_allcontrols_ztest.fsgd dods --C group2_cov0_diff.mtx --surf fsaverage $h --cortex --glmdir ${h}.${s}pat01_allcontrols_pet_ztest_pf05_fsaverage_fwhm10.glmdir *patient1_allcontrols_ztest.fsgd*: GroupDescriptorFile 1 Title patient01_ztest Class Patient Class Control Input pat01 Patient Input nc01 Control Input nc02 Control Input nc03 Control *group2_cov0_diff.mtx*: -1 1 ----------------------------------fscalc.fsl: for h in rh lh; do mris_preproc --target fsaverage --hemi $h --iv nc01_mrispace_pet.mgz nc01_mrispace_pet_2_T1_register.dat --iv nc02_mrispace_pet.mgz nc02_mrispace_pet_2_T1_register.dat --iv nc03_mrispace_pet.mgz nc03_mrispace_pet_2_T1_register.dat --pf 0.5 --out ${h}.allcontrols_pet_ztest_pf05_fsaverage.mgh for h in rh lh; do mris_preproc --target fsaverage --hemi $h --iv pat01_mrispace_pet.mgz pat01_mrispace_pet_2_T1_register.dat --pf 0.5 --out ${h}.patient01_pet_ztest_pf05_fsaverage.mgh for h in rh lh; do for stat in mean std; do mri_concat ${h}.allcontrols_pet_ztest_pf05_fsaverage.mgh --o ${h}.allcontrols_pet_ztest_pf05_fsaverage_${stat}.mgh --${stat}; done; done for h in rh lh; do fscalc.fsl --surf fsaverage $h ${h}.patient01_pet_ztest_pf05_fsaverage.mgh -sub ${h}.allcontrols_pet_ztest_pf05_fsaverage_mean.mgh -div ${h}.allcontrols_pet_ztest_pf05_fsaverage_std.mgh ${h}.patient01_vs_allcontrols_pet_ztest_pf05_fsaverage_zmap.mgh; done

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Seg fault with mri_segstats?
by Michael Waskom 05 Nov '13

05 Nov '13

Hi Doug, I'm running into a strange seg fault when trying to use mri_segstats (it's actually ocurring within mri_glmfit-sim, but I can reproduce it manually) This is the line that fails (stripping the leading paths for readability): mri_segstats --seg cache.th20.pos.sig.ocn.mgh --exclude 0 --i concat_output.nii.gz --sum mri_glmfit-sim.junk.84357 --avgwf cache.th20.pos.y.ocn.dat With the log: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg /Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/osgm/cache.th20.pos.sig.ocn.mgh --exclude 0 --i /Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/concat_output.nii.gz --sum mri_glmfit-sim.junk.84357 --avgwf cache.th20.pos.y.ocn.dat sysname Darwin hostname ben-octocore.stanford.edu machine i386 user mwaskom UseRobust 0 Loading /Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/osgm/cache.th20.pos.sig.ocn.mgh Loading /Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/concat_output.nii.gz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 5 segmentations Computing statistics for each segmentation 1 1 10934 10934.000 2 2 2409 2409.000 3 3 1620 1620.000 4 4 2044 2044.000 Reporting on 4 segmentations Computing spatial average of each frame 0 1 2 3Segmentation fault Intriguingly, it does not segfault if I remove the --avgwf parameter OR the --exclude 0 parameter. It does segfault if I use --avgwfvol instead of --avgwf I'm not too sure what's going on, I can otherwise read the segmentation file and --y file and do statistical operations on them, and I can write other files to the directory I'm testing this in. Here's my system info: FREESURFER_HOME: /usr/local/freesurfer/5.3.0 Build stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Kernel info: Darwin 10.8.0 i386 Any thoughts? Michael

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Extract voxel time series from subcortical segmentation (without averaging)
by Martin Luessi 05 Nov '13

05 Nov '13

Hi, I have fMRI data which has been co-registered with the FS reconstruction using "bbregister". I would like to extract the voxel time series for the voxels in the subcortical labels from the "aseg" subcortical segmentation. I know that "mri_segstats" can be used with the "--avgwf" option to extract an average time series for each label, but is there a way to extract a time series for each voxel inside each label without averaging? Thanks, Martin

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visualizing a surface below the WM surface
by celine＠nmr.mgh.harvard.edu 05 Nov '13

05 Nov '13

Hi Freesurfer team We are sampling diffusion images below the WM surface , and would like to visualize with tkmedit or freeview the surface itself to see if it is appropriate to our analysis (not the surface overlay, but the surface as a line like the one that are on the surfs directory). I couldn't find how to do it but maybe I didn't choose the correct keywords in the archives! Thanks so much for you help! Céline -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

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Fwd: using matched pairs in QDEC?
by christian buhl 05 Nov '13

05 Nov '13

Hi - Thank you for a fantastic piece of software :-) - I have en one question: - In the GUI-module QDEC, is it possible to adjust the GLM-model to account for a pair-matched cohort? (diabetes vs non-diabetes - matched pairwise by age, sex and bmi) Kind regards Christian, Denmark Christian Buhl Medical Doctor (MD), PhD-student Institute of Biomedicine, Pharmacology Aarhus University Wilhem Meyers Allé 4, Bldg. 1240 DK-8000 Aarhus C Tel: +45 2986 9829

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Re: [Freesurfer] mri_segment WM/GM limits
by Jonathan Holt 05 Nov '13

05 Nov '13

Also, quick question . . . How exactly do you run a recon from scratch without nifti images? I’d always delete the directory and restart with mri_convert -i … Jon On Nov 5, 2013, at 10:40 AM, Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> wrote: > Hi Jon, > I see the area you are talking about. I'm rerunning the recon from scratch to start with a clean copy since the case you sent has been rerun multiple times and there are a bunch of control points. The fact that the rh.orig.nofix looks good makes me optimistic that this can be fixed. > > I'll get back to you soon. > -Louis > > On Mon, 4 Nov 2013, Louis Nicholas Vinke wrote: > >> Got it, I'll take a look. >> >> On Mon, 4 Nov 2013, Jonathan Holt wrote: >> >>> OK, >>> >>> been uploaded as JONbrain.tar >>> >>> Please let me know! >>> >>> >>> On Nov 4, 2013, at 1:15 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>>> Hi Jon >>>> >>>> maybe you should upload your data and we'll take a look >>>> >>>> cheers >>>> Bruce >>>> On Mon, 4 Nov 2013, >>>> Jonathan Holt wrote: >>>> >>>>> Bruce, >>>>> >>>>> If I understand you correctly, you?re saying I should tweak my expert options? Should I further change the limits, how so? You previously advised that I not adjust the -p threshold, is this still the case? >>>>> >>>>> Basically, I?m still confused after your response. >>>>> >>>>> Sorry to bother, >>>>> Jon >>>>> On Nov 4, 2013, at 12:52 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>>>> >>>>>> Hi Jon >>>>>> >>>>>> this is almost certainly due to a topological defect. Improving the >>>>>> segmentation quality can frequently reduce the # of defects and get rid of >>>>>> big ones, so if you find that the wm segmentation isn't as visually >>>>>> accurate as is usually the case, using expert opts to improve its quality >>>>>> may also get rid of the problem you are seeing >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> >>>>>> On Mon, 4 Nov 2013, Jonathan Holt wrote: >>>>>> >>>>>>> Hey Louis, >>>>>>> >>>>>>> thanks for your response. It?s actually a bit different, in my case an entire sulcus, including the empty space within it has been segmented and surfaced as white matter. I?m trying to reduce the WM surface such that the empty space is not included. I?ve tried removing segmentation manually and running >>>>>>> >>>>>>> recon-all -autorecon2-noaseg -subjid <SUBJID> >>>>>>> >>>>>>> that doesn?t work, the empty space is simply resegmented and the surface doesn?t change.. I should note that this has worked for me in the past on some brains. >>>>>>> >>>>>>> Since there are no WM voxels to remove I didn?t bother with removing any of them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s <subjID> with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn?t worked? >>>>>>> >>>>>>> I?m open for ideas. >>>>>>> >>>>>>> I should also note that this problem is not an issue in rh.orig.nofix >>>>>>> >>>>>>> (sorry about duplicate email, Louis) >>>>>>> >>>>>>> >>>>>>> On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> wrote: >>>>>>> >>>>>>>> Hi Jon, >>>>>>>> The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense (<< 110). >>>>>>>> -Louis >>>>>>>> >>>>>>>> On Thu, 31 Oct 2013, Jonathan Holt wrote: >>>>>>>> >>>>>>>>> HI experts, >>>>>>>>> >>>>>>>>> I?m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number? >>>>>>>>> >>>>>>>>> Jon >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> The information in this e-mail is intended only for the person to whom it is >>>>>>>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>>>>>>> contains patient information, please contact the Partners Compliance HelpLine at >>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in error >>>>>>>> but does not contain patient information, please contact the sender and properly >>>>>>>> dispose of the e-mail. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>

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MRISread error
by Anita van Loenhoud 05 Nov '13

05 Nov '13

Hi everyone, I run into an error when I try to do the tutorial on ROI group analysis. I downloaded the tutorial set, but did not put it into FREESURFER_HOME/subjects, because my computer doesn't allow it. I made my own folder and copied everything in there. The error arises when I try to map a label from the fsaverage subject to a target subject: mri_label2label \ > --srcsubject fsaverage \ > --srclabel fsaverage/label/lh.BA45.label \ > --trgsubject 004 \ > --trglabel 004/label/lh.BA45.label \ > --hemi lh \ > --regmethod surface srclabel = fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = 004 trglabel = 004/label/lh.BA45.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/group_analysis_tutorial FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.sphere.reg MRISread(Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.sphere.reg): could not open file No such file or directory ERROR: could not read Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.sphere.reg In related posts I read that it might have to do with the creation of symbolic links. I made sure that in my SUBJECTS_DIR, fsaverage is a symbolic link to my FREESURFER_HOME/subjects directory, in which surf/lh.sphere.reg etc are stored. What am I doing wrong? Does it still have to do with the fact that I put the tutorial data in another folder? Hope you can help me, Thanks in advance, Anita

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Literature values of cortical thickness
by Emma Biondetti 05 Nov '13

05 Nov '13

Dear Freesurfers, I need to compare the cortical thickness values, obtained from a data set of 32 healthy subjects, with some reference literature values of cortical thickness. I'd like to check the values of mean and standard deviation for each one of the 32 cortical parcellations automatically generated by Freesurfer. This is to decide if the data set can be used for the following steps of my work or not. On the mailing list, I read an old thread that talks about the existence of a set of literature reference values, obtained by Rauhl Desikan. Would it be possible to access those data? Thank you Emma Biondetti

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fMRI postdoc, Center for Mind/Brain Sciences, University of Trento, Italy
by Angelika Lingnau 05 Nov '13

05 Nov '13

*fMRI postdoc* At the Center for Mind/ Brain Sciences (CIMeC, www.unitn.it/en/cimec) University of Trento, Italy, there will soon be an opening for a postdoc position to work with Angelika Lingnau ( https://sites.google.com/site/angelikalingnau/) in collaboration with Carlo Marzi, University of Verona. The ideal applicant will have completed their PhD (Cognitive Neuroscience, Computer Science, Psychology, Physics, or a related discipline), experience with fMRI design and analysis methods (in particular MVPA), and programming experience with Matlab or C. Additional experience with real-time fMRI and/ or connectivity analyses is very desirable. The CIMeC has been recently ranked as the leading Cognitive Neuroscience research unit in Italy. It offers an international and vibrant research setting with access to state-of-the-art neuroimaging methodologies, including a research-only 4T MRI scanner, MEG, EEG and TMS, as well as behavioral, eye tracking and motion tracking laboratories. English is the official language of the CIMeC, where a large proportion of the faculty, post-docs and students come from a wide range of countries outside of Italy. If you wish to receive further information please contact Angelika Lingnau ( angelika.lingnau(a)gmail.com) or meet her at the SfN Meeting (Poster Board Number BBB19, presentation 273.18).

1 0

LGI path problem
by Linn Mittlestein 05 Nov '13

05 Nov '13

Hi, I am trying to compute lgi measures, and I think my problem lies in the fact that the matlab path is not set correctly; it is calling an older version of matlab however I need it to point to matlab2013b. I have tried numerous things like changing the startup.m file, the .bashrc file and exporting the matlab path, however It keeps calling another version of Matlab. Can someone please tell me how exactly the path is set and where? Best Wishes and thank you, Linn

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