Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Lateral Geniculate Nucleus (LGN) roi or volume measures?
by Yash Patel 18 Apr '18

18 Apr '18

Hi all, Is there any way to obtain (automatically, n~1000 subjects), LGN volumes from the Freesurfer set of tools? Or somehow transform the ROI from an atlas into subject space, then extract volume data? Thanks, Yash

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HCP Course 2018 at Oxford: Final Course Schedule posted -- Register Now!
by Jennifer Elam 18 Apr '18

18 Apr '18

Faculty listings and the full schedule of covered topics <https://store.humanconnectome.org/courses/2018/exploring-the-human-connecto…> are now available for the *2018 HCP Course: "Exploring the Human Connectome" <http://store.humanconnectome.org/courses/2018/exploring-the-human-connectom…>*, to be held *June 25 – 29, 2018* at the Blavatnik School of Government <https://www.bsg.ox.ac.uk/partner/contact-us>, at the University of Oxford <http://www.ox.ac.uk/>, in Oxford, UK! FreeSurfer is a major part of the HCP structural processing pipeline, has been critical to the processing of the HCP Young Adult project's over 1100 released high quality imaging datasets, and continues to be used in the processing of forthcoming Lifespan HCP data. The 5-day intensive HCP course is a great opportunity to learn directly from HCP investigators and gain practical experience with the Human Connectome Project's approach to multimodal whole brain imaging acquisition, processing, analysis, visualization, and sharing of data and results. For more info and to register visit the HCP Course 2018 website <http://store.humanconnectome.org/courses/2018/exploring-the-human-connectom…> . Don't delay, registration is limited, and the course is filling up fast! Nearby affordable accommodations are available at Worcester College at Oxford by selecting registration with accommodations on the site. If you have any questions, please contact us at: hcpcourse@humanconnectome. org We look forward to seeing you in Oxford! Best, 2018 HCP Course Staff -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam(a)wustl.edu www.humanconnectome.org

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problem with mri_label2vol for aseg
by Michelle VanTieghem 17 Apr '18

17 Apr '18

Hi Freesurfer experts, I am trying to convert the aseg back into native space of the anatomical T1 image. I followed the instructions as in the webpage: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat specifically this line of code: cd $SUBJECTS_DIR/<subjid>/mri mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz However, the result is very odd. The aseg boundaries appear correct in the subcortical regions. however, at the gray mater boundaries, there are single voxels incorrectly labeled as different subcortical-regions. As a result, in the viewer, the gray matter boundaries look multicolored. This is problematic, as I would like to extract a mask of specific ROIs (e.g. right amygdala) but there are many other voxels labeled '54' in addition to the right amygdala. See attached images. I would greatly appreciate your assistance!! Thank you, Michelle -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

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Map the vertices that show a relationship between the FC (obtained by FS-FAST)
by Piero Chiacchiaretta 17 Apr '18

17 Apr '18

Hi there, I wonder if the fsgd file and the command lines listed below are corrected. My sample included 4 groups with different diagnosis (g1, g2, g3, g4). I'm interested to map the vertices that show a relationship between the FC (obtained by FS-FAST) and cortical thickeness, regressing out the diagnosis. To this aim I used the --pvr option: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Thickness.wls --nii.gz --fsgd g4v1_thickness.fsgd --C intercept.mtx --C slope.mtx --pvr $SUBJECTS_DIR/rh.thickness.10B.mgh The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship FC-thick reg out dignosis Class g1 Class g2 Class g3 Class g4 Input XX1 g1 Input XX2 g1 ... Input YY1 g2 Input XX2 g2 ... Input XY1 g3 Input XY2 g3 ... Input YX1 g4 Input YX2 g4 ... -------------------------------------------------------------- intercept.mtx 0.25 0.25 0.25 0.25 0 slope.mtx 0 0 0 0 1 thanks piero Piero Chiacchiaretta, PhD Institute for Advanced Biomedical Technologies - ITAB - University “G. d’Annunzio” of Chieti - Pescara Department of Neuroscience, Imaging and Clinical Sciences Via dei Vestini, 31 66013 Chieti, Italy tel: 39-0871-3556919 fax: 39-0871-3556930 e-mail: p.chiacchiaretta(a)unich.it

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FSFAST, Beta values and Percent Signal Change questions
by Sarah Cole 17 Apr '18

17 Apr '18

Hi Doug, I need your recommendations on two topics. I really appreciate your help. 1.) I have two runs of the same experiment, each for about 12 minutes. These 2 runs are different only in the presentation order of the stimuli. I also have one localizer session which first, I calculated my contrasts in it, found the active voxels with positive values, and made a mask of those voxels. Then, mapped the masks on those 2 runs and got the raw data within those voxels. So far, so good. Now, I am looking at the Beta values in these 2 runs for those active voxels, they are very different from each other. For example, in the first run, they are mostly positive but in the second run, they are mostly negative. My intuition was that they should be in the same ballpark. I cannot make sense of this. Do you have any suggestions on why this is happening? 2.) To calculate the % signal change, is it ok to pick the baseline whatever is suitable to my research question. For example, if I need to know the % signal change relative to* the average signal in the first TR of a specific block*, can I use that as a baseline? Or does it always need to be the rest or the mean? Thank you so much and looking forward to hearing from you. Sarah

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mri_anatomical_stats with lobeStrict annot for multiple subjects
by Fernanda Hansen P. de Moraes 17 Apr '18

17 Apr '18

Good night, I would like some help to extract mri_anatomical_stats with lobeStrict annot for multiple subjects in a table format, with the results for all subjects there. I've already tried aparcstats2table and I don't got how to insert the lobeStrict annot there. Thank you very much, Fernanda Moraes -- Fernanda Hansen P. de Moraes Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz

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how to use annotation file in FSFAST for seed based analysis
by Sims, Sara A 17 Apr '18

17 Apr '18

Hello, I am trying to use Glasser’s parcellation to create a correlation matrix that compares all parcels to all parcels. I am new to FSFAST, but so far I have gotten the data preprocessed and ready to go. But I am unsure how to proceed. I have rh and lh annotation files of the parcellation in fsaverage space and I am not sure what to do to them to get to the point that I can use “fcseed-sess”? Should I convert them to labels and then put them on each subject? But what do I do after that? Help please, Sara Sims

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mri_deface keeps seg faulting
by Warner, Graham Cary 17 Apr '18

17 Apr '18

Hi, I'm trying to deface an MEMPRAGE dataset using the following command: [jazz:test_deface] (nmr-stable53-env) mri_deface outSubDir/mri/orig/001.mgz talairach_mixed_with_skull.gca face.gca sample_T1_input_defaced.mgz and am getting the output: logging results to sample_T1_input_defaced.log reading 'talairach_mixed_with_skull.gca'... reading 'outSubDir/mri/orig/001.mgz'... changing type of input volume to 8 bits/voxel... MRIchangeType: Building histogram Segmentation fault (core dumped) I'm using the Martinos center's default version of mri_deface located at /usr/local/freesurfer/stable5_3_0/bin/mri_deface. I'm using the talairach_mixed_with_skull.gca and face.gca sample files found on https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface but the actual input mgz came from a scanner here at the center. Maybe this is a CentOS 7 compatibility problem? Please let me know if there is any other information I can provide. Thank you, Graham

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Group Analysis Contrast (Follow-up)
by David S Lee 17 Apr '18

17 Apr '18

Hi Douglas, Thank you for your reply. To follow up, I am setting up GLM analysis with 1 categorical variable and 1 continuous variable (age X weight). My fsgd looks like this: *GroupDescriptorFile 1* *Title Cortical Thickness Interaction between Age and Weight* *Class class1 plus blue* *Class class2 circle green* *Variable Demean Age X Demean Weight* *Input 001 Class1 500* *Input 002 Class2 433* *...* I want to test for an interaction between age and weight while controlling for group. Instead of putting-in age and weight separately, I multiply them to test for interaction. Can you tell me if following contrast vector will correctly test for this? *0 0 0.5 0.5* Thank you for your time, -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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Non-rigid registration approaches
by Hedyeh Javaheri 17 Apr '18

17 Apr '18

Hello all, I am performing DTI analysis and wanted to know if Freesurfer has a tool for non-rigid registration. I performed recon-all and dt_recon on my subject and then used the register.dat file that was generated by dt_recon to convert the dt_recon output files back into the space of my orig.nii file from the recon-all output. Now I need to register the files in the orig.nii space back onto the T1 MRI that is in native space. I have tried using mri_vol2vol to get the files in the orig.nii (recon-all) space into the T1 native space without using a registration file (I used --regheader) and now the registration matrix of my file is the same as the native space, but when I use rview to visualize the registration there are flaws. I've also tried this co-registration using tkregister2 to create a registration file called register.native.dat, and then used mri_vol2vol with register.native.dat; and the results were the same as when I used mri_vol2vol with --regheader. Is there a tool to do actual manual registration in Freesurfer? Using tkregister2 I cannot perform localized changes; and the global changes it is capable of do not improve on the coregistration. Here is a breakdown of what I have done: subject in Native space to Freesurfer conformed space using recon-all, output: orig.nii subject in Native space to other Freesurfer space using dt_recon, output: lowb.nii and register.dat >From the other Freesufer space to Freesurfer conformed space using register.dat, output: lowb2orig.nii attempting to convert from Freesurfer conformed space to Native space: using mri_vol2vol and --regheader --> poor registration using tkregister2 to make register.native.dat, then mri_vol2vol and register.native.dat --> poor registration I am running Freesurfer version 6 on Windows. Thanks in advance! -Hedyeh Javaheri

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