Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

Error using LGI script despite making suggested chages to Matlab script.
by prasser 03 Oct '16

03 Oct '16

Hi, I'm looking to please get some help with -lgi. I'm using matlab R2015b and FS5.3 with recon-all -s subj_id -lgi on os x 10.11. Looking at the output, the first error occurs about here: preparing pial mesh structure ... ...searching for mesh edges...done (206.94 sec). ... creating path file for vertex 1 / 65274 area file for outer ROIs saved at 1 In an assignment A(:) = B, the number of elements in A and B must be the same. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); I have changed the script SearchProjectionOnPial.m as suggested on the ReleaseNotes page. Any help would be much appreciated. Thanks.

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Output uncorrected p-values using mri_surfcluster
by Corinna Bauer 03 Oct '16

03 Oct '16

Hello all, I would like to get a table of the uncorrected p-values to compare with the corrected ones obtained using mri_glmfit-sim. I tried the following, which outputs a table of clusters and their vertices, but it does not include p-values. Is there a flag that I shoudl include to output the p-values? mri_surfcluster --in sig.mgh --sign abs --subject fsaverage --hemi lh --surf white --annot aparc --no-adjust --bonferroni 2 --no-fixmni --ocn cache.uncorr.abs.sig.ocn.mgh --oannot cache.uncorr.abs.sig.ocn.annot --cwsig cache.uncorr.abs.sig.cluster.mgh --thmin 2.3 --sum cache.uncorr.abs.sig.ocn.dat Thanks corinna

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Best way to run GLM on a single subject across multiple sessions?
by Taylor, Johnmark 03 Oct '16

03 Oct '16

Hello, I am looking to run a GLM on a single subject, where data was collected across several different sessions. What is the best way to go about doing this in the FSFAST pipeline? I was thinking that I should just 1) drop the data for all the runs into a single BOLD directory as though they were from a single session, and 2) let the registration and motion correction do as well as they can. Is this a reasonable approach, and if so, are there any settings in the preprocessing or GLM that would advisable (for instance, in terms of running the GLM on the surface versus the volume, or doing the registration per-run versus per-session)? Thank you very much, JohnMark

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mri_glmfit: Hierarchical Regression?
by Elizabeth Bartlett 03 Oct '16

03 Oct '16

Hello all, I am using mri_glmfit (DODS method) to run a CT analysis with 2 groups and 4 covariates and have a couple of questions regarding the statistical tests performed within the group analyses: 1. Can Freesurfer test the change in model fit or delta R-squared in a hierarchical regression? As far as I can tell, there is only simultaneous regression. Alternatively, can I change the Sum of Squares Type to Type 1 (I think default is Type 3) to simulate a hierarchical regression? 2. I think the default model in FreeSurfer accounts for all other main effects. But, does it also account for all 2 and 3 way interactions, whether or not I specify any? In other words, is the default a fully factorial model? Thank you very much for your time! -Elizabeth

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Gaussian curvature or Mean curvature
by Hanbyul Cho 03 Oct '16

03 Oct '16

Dear FreeSurfer Team, I heard that FreeSurfer could calculate the Gaussian curvature and Mean curvature by vertex level. Do the computed curvature values be saved as the subject/surf/lh.curv or rh.curv files? When I prepared the generated mass-univariate data, I used the mris_preproc with [--meas curv] option, not [--meas thickness]. *mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas curv--out lh.curv.mgh* I wonder this option is right usage to analyze the cortical curvature. And I wonder the 'curv' is what specific value is meaning. If I want to designate the specific curvature values(Gaussian or Mean curvature ) to analyze by vertex level, how can I use the [--meas] option? Thank you, Best wishes, Han.

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Brainhack: Anatomy edition in Paris, 24-26 October 2016
by Anastasia Osoianu 03 Oct '16

03 Oct '16

Registration is now open for Brain-anatomy-hack in Paris. Brain-anatomy-hack aims at promoting the interaction between scientists on questions concerning (1) the investigation of brain anatomy based on magnetic resonance imaging or post mortem dissection; (2) the evolution of nervous systems across species; (3) the variability of brain features across healthy participants; (4) the insurgence of brain pathologies. Program Each of the three days will begin with an “Ignite Session” in which speakers will give 15-30 minute talks that will address wide questions in neuroanatomy that would benefit from open, interdisciplinary collaborations. The “Ignite Session” will be followed by a “hack session” and a dynamic set of talks organized by attendees. During the “hack sessions”, participants will be encouraged to work together in small groups on relevant projects. The workshop will culminate on the last day, when participants will have the opportunity to present a brief overview of their project. Participants can bring their own dataset, discuss a project and recruit a team of collaborators on site. Access to free big online databases of MRI images will be also available during the three days, for new creative ideas to be tested. This workshop is also an opportunity to learn methods, develop skills and collaborate with other participants. Participants will be supervised and receive advice on methods from a team of very capable nerds including Roberto Toro, Michel Thiebaut de Schotten, Alexandros Goulas, Julien Lefèvre, Daniel Margulies and Leonardo Cerliani throughout the three days. A constant flow of food and drinks (especially coffee…) will be provided during the conference breaks. We kindly request an online preregistration (70€) in order to cover the expenses for the venue, the equipment and the food/drinks. Deadline is 16th of October 2016. For more information and preliminary schedule visit: http://neuroanatomy.github.io/events/brainhack/ To learn more about Brainhack and previous events: http://brainhack.org/

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Regarding: freesurfer vs. Neuroquant
by Dr Sampada Sinha 02 Oct '16

02 Oct '16

Hello freesurfer experts, Is there any paper comparing the volumetric analysis done by freesurfer and that done by Neuroquant? So far, I have found only one link on Neuroquant topic on freesurfer forum (that says Neuroquant uses only one part of freesurfer). Will appreciate if I can be given more information on this. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16800.html Thanks and regards, Yours, Sampada -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India

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[Repost] question about mris_anatomical_stat
by Ali-Reza Mohammadi-Nejad 30 Sep '16

30 Sep '16

Dear Freesurfer experts Based on the FS wiki, I calculated the cortical thickness difference between the LH and RH of a subject in subject's native surface.Now, I want to use FS commands to extract the information such as "?h.aparc.stats" for this difference map (LH - RH).Now this difference map is saved in a .mgh file.I think, I can use "mris_anatomical_stats" command for this propose.But, based on the help of this command, I did not find any .mgh file as an input.Therefore, would you please help me to create such stats file?Thank you very much for your help Best regards,Alireza

2 1

Longitudinal surface analysis of PET data
by Matthieu Vanhoutte 30 Sep '16

30 Sep '16

Dear Freesurfer’s experts, I would like to use the longitudinal mixed-effects model for surface PET analysis. Although I could find all the process to follow the longitudinal analysis of cortical thickness, I couldn’t resolve the steps/commands to apply successively to coregistered PET data on T1 MRI. Could you precise me the process and commands to use for PET longitudinal analysis ? Many thanks in advance ! Best regards, Matthieu

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get non-cortex vertices
by Dorothy Sincasto 30 Sep '16

30 Sep '16

Hi freesurfers, I am doing a connectivity analysis on cortical areas. I load the 2d fmri surface file in fsaverage5 space into matlab and I get 20484 vertices for both hemispheres. Some of which are zero because I previously specified to get only the cortex vertices. However, the number of non-cortex vertices changes across subjects. Is it possible to get from fsaverage5 any overlay mask that specifies if it is cortical or not, so when I load it into matlab i can get a logical vector of 20484 elements? Thanks Dorothy

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