Freesurfer

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30132 discussions

pathstats.byvoxel.txt
by Susan Kuo 15 Jul '13

15 Jul '13

Hi Anastasia, I believe the issue I had with the pathstats.byvoxel.txt not displaying the last four values (AD_Avg RD_Avg MD_Avg FA_Avg ) is owing to the fact that trac-all was run with FREESURFER 5.1. I believe that FREESURFER 5.2 may be needed to generate path.pd.trk, and from that, the above values are derived. Is this correct? Thank you again, and have a good day! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear*

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Freesurfer for animal data
by Qasim Bukhari 15 Jul '13

15 Jul '13

Dear all, I attended the Seattle course a couple of weeks ago. Actually I m using mice data in my analysis, and I was wondering if I can use freesurfer for that as well ?I understand there is not so much sulci and gyria problem in mice data as in human, however a flattened surface registration and analysis might still be interesting to see. Is it possible at all to do that ? Thanks a lot and best,Qasim Qasim BukhariResearch Assistant and Doctoral CandidateInstitute for Biomedical EngineeringETH and University ZurichWolfgang-Pauli-Strasse 27, HIT E22webpages: MR-pagehttp://www.biomed.ee.ethz.ch/people/sybukhar

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Re: [Freesurfer] FreeSurfer: plot activation foci
by Frédéric Briend 15 Jul '13

15 Jul '13

Dear FreeSurfer team, Firstall, thanks a lot to your great contribution in the neuroscientific and the free software world. I would like to know if is it possible to make a plot activation foci (i.e. example by PySurfer: http://pysurfer.github.io/auto_examples/plot_foci.html) by FreeSurfer directly, and how can it be done? Sincerly, Frédéric Briend CNRS, Archives Husserl Ecole Normale Supérieure, Paris, France

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Generating a fsgd file for regression analyses
by Avram Holmes 15 Jul '13

15 Jul '13

Freesurfer et al., I'd like to try out some simple cortical thickness regression analysis in mri_glmfit. These would be analyses of one continuous score (e.g., Temperament) and several continuous nuisance variables (e.g., Age, IQ, Site, etc). However, before getting started I wanted to run my fsgd and contrast files by the mailing list to make sure I am entering things correctly. If any freesurfer pros have a free moment I've love to hear if I am on the right track. My fsgd file looks like the following: GroupDescriptorFile 1 Title Temp MeasurementName thickness Class Main Variables Temperament Age Scanner Console IQ Input Subj1 Main -2.65 22 3.00 4.00 103.0 Input Subj 2 Main -2.24 24 3.00 3.00 109.0 Input Subj 3 Main -1.82 20 1.00 4.00 121.0 Input Subj 4 Main -1.79 19 3.00 3.00 113.5 Input Subj 5 Main -1.77 19 1.00 3.00 101. 6 .... My contrast1.mat file is: 0 1 0 0 0 0 It is my hope that when I call: mri_glmfit --fsgd GLMFIT/fsgd.txt --y GLMFIT/lh.TEMP.mgh --C GLMFIT/c.txt --surf fsaverage lh --cortex --glmdir GLMFIT/lh.TEMP.output I am prepping to run a regression looking at the relationship between Temperament and cortical thickness, partialing out age, scanner, console, and IQ. Thanks in advance for any help you can offer, Avram -- Avram Holmes PhD Instructor in Psychiatry, Harvard Medical School Assistant in Research, Massachusetts General Hospital

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talairach and MNI305 Atlas
by Mark Plantz 15 Jul '13

15 Jul '13

Hello freesurfers, I am currently attempting to create a normalized .mgz file from an input brain using mri_ca_normalize. Ultimately, I will use the norm.mgz file to create a .gca atlas for infant MRI's. Currently, I have three of the four required arguments. I am lacking the talairach.lta file. In order to obtain this file, I must run recon-all. However, I do not wish to run recon-all until I have obtained the necessary .gca atlas described above. Is there possibly some sort of alternative iterative method to create the talairach transform? If so, does it require a different atlas than the MNI305 atlas? Thanks for the help! -Mark

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Confused results from Qdec
by Wayne Su 15 Jul '13

15 Jul '13

Dear Freesurfers, I used Qdec to do two-group comparison on cortical thickness. Demeaned age was used as the covariate. The question I¹m looking at is that ³Does the thickness-age correlation differ between C1 and C3?² When FWHM=15mm was chosen, I got confused results: When I used threshold 1.3(0.05) in Monte Carol Null-Z Simulation, I didn¹t get any significant cluster. However when I used threshold 2(0.01), I did get one significant cluster. However I expected I at least got same significant area when I used lower threshold. If I chose FWHM=10mm, I got another significant cluster when the threshold 1.3 was used, and got nothing when the threshold 2 was used. However this cluster is not the same area I got when FWHM=15mm was used. At this point, I¹m totally confused, and don¹t know which one should be trusted. Should I used FWHM=10 or 15? Should I used threshold 1.3 or 2.0? My group one have 49 subjects and group two have 46 subject. All subjects are males. Hope someone can point the right direction for me. Thank you very much. Wayne

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using mcextreg.bhdr in version 5.x?
by Caspar M. Schwiedrzik 15 Jul '13

15 Jul '13

Hi! I am doing motion correction outside Freesurfer and would like to use motion nuisance regressors in my GLM, which I run in FSFAST. I am externally creating mcextreg.bhdr, mcextreg_000.blfoat and mcextreg_000.hdr for analyses in Freesurfer v4.5, but I was wondering whether I can use the same files for analysis in Freesurfer v5.x. Or should I convert them to something else? The documentation is slightly ambiguous about this. Thanks! Caspar

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Editing the endpoint ROIs, and re-running trac-all -path
by Susan Kuo 15 Jul '13

15 Jul '13

Hi Anastasia, For one of my subjects, I am noticing that the right uncinate fasciculus is very diffuse and more importantly, erroneously crosses from the frontal to the temporal lobe. I looked at the original endpoint ROI generated by trac-all -prior (rh.unc_AS_avg33_mni_bbr_end1.nii.gz) and the dilated endpoint ROI in the temporal lobe (rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz) and noticed that the endpoints appeared to cross over into the frontal lobe. Attached is a snapshot for your perusal. On the left side is a display of the <subject>/dmri/dtifit_FA.nii with the <subject>/dpath/rh.unc_AS_avg33_mni_bbr/path.pd.nii.gz tract superimposed over. As you can see, the right unc tract crosses from the frontal to the temporal lobe. On the right side is a display of the <subject>/dmri/brain_anat_mni.nii.gz with the endpoints <subject>/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2.nii.gz in green and <subject>/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1.nii.gz in blue (the red dots are control points). As you can see, the blue endpoints bleed over from the temporal to the frontal lobe. I tried to eliminate these blue points with fslview and then writing over rh.unc_AS_avg33_mni_bbr_end1.nii.gz. I performed a similar function manually editing rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz to better reflect the boundaries . I subsequently tried to re-run trac-all -path, and unfortunately, all my tracts looked much worse. Do you know if incorrectly placed endpoints impair the path reconstruction? Do you think you can help me? Any advice you can give would be much appreciated. -- Susie Kuo NIH Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear*

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lh.curv VS lh.inflated.h
by 宋银南 15 Jul '13

15 Jul '13

Dear Sir， I have found two files in the surf folder.One is 'lh.curv',the other is 'lh.inflated.h'.I have found some one said that the 'lh.curv' can be used to quantify the curvature. but int the wiki, the command 'mris_curvature' can ouput the file 'lh.inflated.h' which is MeanCurvature. So I want to know which should I use. I also want to know what the 'lh.curv' is ? MeanCurvatur or GaussCurvatur,or some other? Thank you very much! Thank you for the freesurfer, it is really very good! Best Wish! YinNan Song

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pathstats.byvoxel.txt
by Susan Kuo 15 Jul '13

15 Jul '13

Hi Anastasia, I noticed that my pathstats.byvoxel.txt files are missing the last four values (AD_Avg RD_Avg MD_Avg FA_Avg) even though I'm certain I ran trac-all -path -c <dmrircFile> correctly. Do you have any idea why this might be? e.g. a configuration file change? Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear*

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