Freesurfer

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30080 discussions

About TRACULA results
by Kang, XJ 31 Aug '16

31 Aug '16

Hi, I am trying to computer the changes of cortical parcellations and fiber pathways using FreeSurfer v5.3 and Tracula (2014/05/26 update) . I copied the anatomical and DWI images from the same scan session into five directories. Run recon-all and trac-all on the 5 same data sets, in order to check thereproducibility of the analysis. Here are what I got: the /Desikan/-Killiany parcellations in both GM and WM, and the subcortical structures, repeat well. No difference found in volume or size of those structures. However, the volume and averaged DTI parameters of the fiber pathways, which found in the file ~/sub/dpath/*_PP_avg33_mni_flt/pathstats.overall.txt, varies for the 5 sets. tracula.conf files were copied from ~/freesurfer/bin/dmrirc.example. The changes are calculated in percentage by (S1-S0)/((S1+S0)/2)*100%. For example, the changes of averaged FA between the 5 data sets are : S1-S0, S2-S0, S3-S0, S4-S0 Corpus Callosum - Forceps Major , -1.1 , 6.0 , 0.5 , 1.3 , Corpus Callosum - Forceps Minor , 0.1 , 0.0 , -1.6 , 0.0 , Right Anterior Thalamic Radiations , 0.1 , -1.0 , 0.5 , 0.9 , Right Cingulum - Angular Bundle , -4.8 , -2.0 , -1.5 , 3.8 , Right Cingulum - Cingulate Gyrus Endings , 0.5 , -0.9 , 0.4 , -2.3 , Right Corticospinal Tract , 1.9 , 0.6 , -2.2 , 1.4 , Right Inferior Longitudinal Fasciculus , -2.2 , -0.8 , -1.3 , 3.0 , Right Superior Longitudinal Fasciculus - Parietal Endings , 0.8 , -0.4 , -1.2 , 0.2 , Right Superior Longitudinal Fasciculus - Temporal Endings , -4.9 , -0.6 , -2.6 , -1.3 , Right Uncinate Fasciculus , 0.5 , 1.6 , -0.9 , 3.5 , Even larger changes for the volume of the pathways: S1-S0, S2-S0, S3-S0, S4-S0 Corpus Callosum - Forceps Major , 2.2 , -33.7 , -12.3 , 1.1 , Corpus Callosum - Forceps Minor , 11.9 , 4.8 , 0.6 , 7.2 , Right Anterior Thalamic Radiations , -8.9 , 2.2 , -12.5 , 7.5 , Right Cingulum - Angular Bundle , -38.1 , 41.6 , 34.8 , 8.6 , Right Cingulum - Cingulate Gyrus Endings , 24.4 , 33.1 , 21.3 , 17.5 , Right Corticospinal Tract , 9.8 , -3.0 , 2.2 , 19.5 , Right Inferior Longitudinal Fasciculus , 7.2 , 24.1 , -7.3 , 23.8 , Right Superior Longitudinal Fasciculus - Parietal Endings , 17.2 , 10.2 , 25.1 , 9.9 , Right Superior Longitudinal Fasciculus - Temporal Endings , 15.4 , 3.4 , -3.1 , -11.5 , Right Uncinate Fasciculus , 13.3 , -1.2 , 16.4 , -3.4 , Any expert has the experience on these? Thank you for your help. XJ Kang

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Satellite Symposia - Resting-State and Brain Connectivity Conference
by Anastasia Yendiki 31 Aug '16

31 Aug '16

Dear FreeSurfers - If you're attending the Resting-State and Brain Connectivity Conference in Vienna, you can now register for satellite symposia, including one on diffusion MRI. Hope to see you there! a.y ---------- We are pleased to inform you that registration for the six Satellite Symposia at the Resting-State and Brain Connectivity Conference is open! These specialised meetings will take place on Saturday, September 24th right after the Resting-State and Brain Connectivity Conference. So why not extend your stay in Vienna for the sake of maximizing knowledge gain, deepening the vivid scientific exchange and socializing with your community members? The Satellite Symposia will will cover diffusion MRI, optogenetics, PET/MRI, TMS/fMRI and predictive analyses of neuroimaging data. We made sure to provide a large selection of topics for our six Satellite Symposia, so that everyone gets to choose the most interesting on their behalf: * Symposium #1: Probing white-matter anatomy and microstructure with diffusion MRI * Symposium #2: Tackling connectivity using non-invasive brain stimulation (fMRI/TMS, tDCS, tACS) * Symposium #3: The Emerging Field of Predictive Analytics in Neuroimaging: Applications, Challenges and Perspectives * Symposium #4: Multi-modal fMRI from photons to protons * Symposium #5: Dynamic Functional Connectivity * Symposium #6: Network-Based Approaches for Neuroimaging: Graph Theory Techniques for Brain Connectivity Research http://www.restingstate.com/2016/satellite-symposia/ So don’t hesitate to register for a satellite symposium now! We look forward to welcoming you to Vienna in September 2016! On behalf of the local and international organizing committees Christian Windischberger Claus Lamm Rupert Lanzenberger Bharat Biswal Mark Lowe Christopher Pawela Martin Walter Susan Whitfield-Gabrieli

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LGI problem
by Alan Francis 31 Aug '16

31 Aug '16

Hi Marie: I am trying to run the LGI algorithm on 32 brains. As shown in the archives, I set the environment (on tcsh) and provided the MATLAB pathway. [afrancis-mac:~] afrancis% setenv MATLABPATH /Applications/MATLAB_R2015a.app/ [afrancis-mac:~] afrancis% setenv PATH ${MATLABPATH}/bin:${PATH} I also do have the Image processing toolbox. I got the following error: Current: /Applications/freesurfer Previous: /cm/shared/freesurfer /Applications/freesurfer/subjects/DM99/surf #-------------------------------------------- #@# Local Gyrification Index lh Wed Aug 31 13:37:51 EDT 2016 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf /Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2015 The MathWorks, Inc. R2015a (8.5.0.197613) 64-bit (maci64) February 12, 2015 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic License >> reading filled volume... closing volume... Undefined function 'fspecial' for input arguments of type 'char'. Error in make_outer_surface (line 31) Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file '/Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Darwin afrancis-mac.mclean.harvard.edu 14.5.0 Darwin Kernel Version 14.5.0: Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64 recon-all -s DM99 exited with ERRORS at Wed Aug 31 13:38:36 EDT 2016 For more details, see the log file /Applications/freesurfer/subjects/DM99/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting thanks so much, best regards, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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problem with Qdecrc file
by Clara Kühn 31 Aug '16

31 Aug '16

Dear FreeSurfer experts, I'm trying to run a 2stage Model in QDEC but I have troubles with incorporating the .Qdecrc file. Sadly the option of spc etc doesn't show up the Design tab when I want to chose a measure. the file is in the same directory the table.dat file is in. What might be the problem? Thank you for your help! Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Questions about surface coordanates
by Dongnandi 31 Aug '16

31 Aug '16

Dear Experts, I tried to extract vertex coordinates information from 'fsaverage/surf/lh.pial' file using matlab function 'read_surf', but I found that the coordinates returned by the function are different from what I saw in tksurfer, here are the screenshots: The vertex index starts from 0 in tksurfer, so I select the second elements in matlab. Why is the result different from what has been shown in tksurfer(also different in freeview)? Which one should I report? Is there any way to transform the surface coordinates to the MNI152 space? Thank you very much! Dong

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hippo sf segmentation 6.0 dev
by Vaz pandolfo, Renata 30 Aug '16

30 Aug '16

Dear Eugenio, I have a couple of questions regarding the hippocampus subfields segmentation on the dev FS 6.0 which I hope you could help me with. We are comparing the volumes of hippocampal subregions of patients and controls, and we would like to be as consistent as possible with the input so that the output reflects only the differences we expect to see. The problem is that we have a large number of controls but not all of them have the same sequences (T1, T2 or FLAIR) as the patients. So our questions are: If the T1s from some subjects have a 1x1x1 resolution and others have 0.8x0.8x0.8 isotropic resolution, do we have to create two groups of controls and patients for each sequence? In other words, does the resolution of the T1 affect the freesurfer segmentation in a way that we can't compare 1x1x1 with 0.8 x 0.8 x 0.8? Also, we would like to use T2s or FLAIRs as additional inputs to improve the results. Which sequence is preferably recommended? In our case, most controls and patients have the same FLAIR sequence, so to keep it consistent we would probably use FLAIR if that's worth it. Finally, we also have different T2s: some isotropic, some anisotropic and partial cooverage of the brain, and some anisotropic that are aligned to the hippocampus (resolution: 1x1x3, best resolution on coronal slices). Considering that they are just additional inputs, do they have to be consistent as well? In other words, should we *only* compare patients and controls that had the same T2 sequence as additional input and same T1 sequence as main input, or can we "mix and match" the additional inputs? Thank you in advance for your help, Renata

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Brainstem nucleus
by Alshikho, Mohamad J. 30 Aug '16

30 Aug '16

Hi Iglesias, Kindly, we would like to know if there are any methods in Freesurfer that can help to segment that brain stem nucleus. I mean output the nucleus automatically as a small masks, so these small masks can be used in other analyses (e.g. fMRI) I am thinking of creating masks for these nucleus depending on an atlas. I open the T1 image in Fslview and I create the mask for the nucleus of interest. But this is so hard, not accurate and time consuming. The reason for my question. We highly appreciate any suggestion! Best, Mohamad

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Re: [Freesurfer] rfMRI and T2w image
by Dev vasu 30 Aug '16

30 Aug '16

Dear sir, I was checking for your reply about my question in Freesurfer Forum but unfortunately i could not your answer although ":Freesurfer Digest, Vol 150, Issue 43 " Today's topics section indicates that you have replied to my question. Following is my question : In order to run my structural analysis pipeline , i require T2w images, but unfortunately we have not performed T2w scans , my colleague suggests we can use rfMRI instead T2w images Could you please let me know if i can use rfMRI image instead of T2w image?. Thanks Vasudev

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mri_glmfit-sim permutation testing running after 3 days!
by Ajay Kurani 30 Aug '16

30 Aug '16

Hi Freesurfer Experts, I am trying to use freesurfer's mri_glmfit-sim tool to run permutation testing on cortical thickness data (as recommended by Doug in my previous post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html ) Most of the tutorials I found were not related to permutation testing so the subsequent steps may be incorrect. Please let me know where I go wrong... 1) I first ran QDec to generate a folder for the analysis which would create the subsequent fsgd and y files needed my mri_glmfit-sim. I am running both left and right hemisphere cortical thickness analysis with 10mm smoothing. The following is for just the left hemisphere. Note I am doing a 3 group comparison, but for this 2 group ttest I manually centered the data based on the 3 group mean for age and education. 2) I ran the following command: /mri_glmfit-sim --glmdir ./HCvsPAT_lh_thickness_10mm/ --sim perm 10000 2 perm.abs.2 --sim-sign abs --bg 16 Prior to running the command above, from the y.fsdg file I deleted the fwhm estimate of 13mm since this was not correctly estimated (ACF with long tails). I assumed that by removing this estimate, it would force the permutation test to calculate based on the data but when looking at the log output I see the following which says fwhm 0: cmdline mri_glmfit.bin --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Avg-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-Male-Female-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-PD-MCI-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-X-Gender-Group-Intercept-thickness.mtx --sim perm 625 2 ./HCvsPAT_lh_thickness_10mm//csd/perm.abs.2.j013 --y /home/akurani/Documents/PPMI/FS_Final/qdec/HCvsPAT_lh_thickness_10mm/y.mgh --mask ./HCvsPAT_lh_thickness_10mm//mask.mgh --sim-sign abs --fwhm 0 --fsgd ./HCvsPAT_lh_thickness_10mm//y.fsgd dods --surf fsaverage lh white --sim-done ./HCvsPAT_lh_thickness_10mm//csd/poll/done.perm.abs.2.j013 3)I started this a few days ago on a 16 core machine and it is still running in the terminal. I have 150 subjects in the analysis and specified 10000 iterations. In the terminal I assumed when I reach Poll 10000 it would be complete but currently I am at : Poll 13341 job 1 Thu Aug 25 12:03:51 CDT 2016 Questions: a) I am curious, is this going to run 10,000 simulations X 150 patients or does the Poll number not have anything to do with the number of iterations it is on? b) Did I run this procedure correctly? Was I incorrect in deleting the fwhm estimate from y.fsgd file generated by Qdec even though we know the estimate is incorrect since smoothness assumed a gaussian distribution as opposed to gaussian with heavy tails c) I noticed in the logfile the following warning: INFO: gd2mtx_method is dods Computing normalized matrix Normalized matrix condition is 5.65727 Matrix condition is 935.597 Found 136777 voxels in mask Reshaping mriglm->mask... search space = 89675.729228 ERROR: design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with --perm-force Poll 2 job 1 Tue Aug 23 22:58:18 CDT 2016 I am not sure if this means my simulation is incorrect? Thanks, Ajay

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Re: [Freesurfer] Questions about surface coordanates
by Islem Rekik 30 Aug '16

30 Aug '16

It is a software that visualizes VTK files and also "mha" images: http://www.paraview.org/ [image: Inline image 1] Thanks! I really appreciate your help! Islem On Tue, Aug 30, 2016 at 10:28 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu> wrote: > What is paraview? I would contact the developers. > > On 8/30/16 10:24 AM, Islem Rekik wrote: > > Hi all, > > I have a similar problem using Paraview: > When I visualize the surface lh.pial and the anatomical image > brainmask.mgz using FreeView they nicely overlap; however, after I convert > lh.pial to lh.pial.vtk and brainmask*.mgz* to brainmask*.mha* and > visualize them using Paraview, they are in different spaces. > > Do I need to apply a transformation matrix to lh.pial using the command > line mri_surf2surf so the VTK surface will overlap with the image when > using Paraview? > > I find this quite confusing. > > Thanks! > Kindly, > Islem > > > On Tue, Aug 30, 2016 at 9:21 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu> > wrote: > >> tksurfer always uses the ?h.orig coordinates. Also keep in mind that the >> vertex index is 0-based whereas matlab is 1-based. When you click on a >> point, you should see something like the following print out >> selected vertex 123491 out of 163842 >> current -39.11 15.65 11.26 >> orig -55.67 -10.37 19.95 >> pial 0.00 0.00 0.00 >> white -55.76 -10.29 19.93 >> >> >> >> >> On 8/30/16 5:12 AM, Dongnandi wrote: >> >> Dear Experts, >> >> I tried to extract vertex coordinates information from >> ‘fsaverage/surf/lh.pial’ file using matlab function ‘read_surf’, but I >> found that the coordinates returned by the function are different from what >> I saw in tksurfer, here are the screenshots: >> >> The vertex index starts from 0 in tksurfer, so I select the second >> elements in matlab. Why is the result different from what has been shown in >> tksurfer(also different in freeview)? Which one should I report? >> >> Is there any way to transform the surface coordinates to the MNI152 space? >> >> >> >> Thank you very much! >> >> Dong >> >> >> >> >> _______________________________________________ >> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e >> du/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. > > -- > Dr. Islem Rekik; MSc, PhD > IDEA Lab, UNC-Chapel Hill > Biomedical Research Imaging Center > Chapel Hill, NC 27599 > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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. > > -- Dr. Islem Rekik; MSc, PhD IDEA Lab, UNC-Chapel Hill Biomedical Research Imaging Center Chapel Hill, NC 27599

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