Freesurfer

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3 participants
30135 discussions

WM & GM Parcellation Edit
by Limachia, Gaurang (NIH/NINDS) [F] 31 May '16

31 May '16

Hi freesurfer community, We are checking to see the accuracy of our subjects’ white and gray matter parcellation. We have found that for some subjects the contour lines for white matter surface and pial surface are somewhat inaccurate, and have been making modifications using the tutorials. Specifically, we made changes to the white matter wm.mgz file; this however did not alter the contour lines. We also used control points, and were able to see changes to the white matter surface contour lines using this approach. How do you recommend that we proceed to obtain the most accurate results? Should we continue making changes to the wm.mgz file as well as adding control points, or is it sufficient just to add control points? I am attaching a screen shot which shows changes to the contour lines after we added control points. Best Regards, Shyam

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WM & Gray Matter Parcellation Edit
by Limachia, Gaurang (NIH/NINDS) [F] 31 May '16

31 May '16

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Algebraic operations with scalars
by Francesco Cardinale 31 May '16

31 May '16

Dear Freesurfer experts, I would like to make some algebraic operations with scalars, such as ?h.thickness or sig.mgh. They are referred to the same surface, of course. How can I export the thickness values to a spreadsheet? (?h.thickness 2 table) How can I export the significance values to a spreadsheet? (sig.mgh 2 table) All my best Cico Francesco Cardinale, MD Neurosurgeon "Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda "Ca' Granda" Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia <x-apple-data-detectors://0/0> phone 0039 02 64442917 <tel:0039%2002%2064442917> fax 0039 02 64442868 <tel:0039%2002%2064442868> e-mail francesco.cardinale(a)ospedaleniguarda.it <mailto:francesco.cardinale@ospedaleniguarda.it>

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Re: [Freesurfer] Manual segmentation issues
by maryam_koochaki 31 May '16

31 May '16

Hi Antoine,Have you tried control points seeding, I usually place the control points right behind the surface in trouble areas so seeded points would push the surfaces forward.Maryam Sent from my Samsung Galaxy smartphone. -------- Original message --------From: Saturne Fox <saturne.fox(a)gmail.com> Date: 2016-05-31 1:20 AM (GMT-08:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Manual segmentation issues Dear freesurfer community, These days I am manually editing some data and this subject is giving me such a hard time. In fact I would like the near-to-cortexartefacts at the top right hand corner to be excluded from the surface but even after changing the intensity of the wanted part to 255 and the one of the excluded parts to 1 (which is nevertheless not visible on these images) the surface is still not what I would like it to become. In adition to editing the wm.mgz file, I also modified the aseg.presurf file to exclude these parts and I re-runned the -normalization2 and -maskbfs flags to generate new brain.mgz and brain.finalsurfs.mgz files. Any idea why these modifications are not affecting the surface ? Best regards, Antoine

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Retinotopy - Error in fast_selxavg3 (line 279)
by Steinmann, Iris 31 May '16

31 May '16

Dear freesurfers, I try to run a retinotopy analysis following the instruction on https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis (using Ubuntu 14.4 and freesurfer 5.3) My subject folder contains 4 runs (all 'positive polar'). After preprocessing I performed the following steps: mkanalysis-sess -a retinotopy_polar_pos_rh -TR 2 -paradigm polar_pos.par -retinotopy 30 -surface self rh -per-run -fsd bold -fwhm 5 -nskip 4 selxavg3-sess -s EP_polar -a retinotopy_polar_pos_rh The polar_pos.par file contains only the two following lines: stimtype polar direction pos selxavg3-sess stops with the following error: ... Saving X matrix to ~/PROJECTS/Retinotopy/subjects/EP_polar/bold/retinotopy_polar_pos_rh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 35) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n I found a lot of similar error reports in the mailing list, but unfortunately no explanation that fix my problem. Is it maybe a problem when I only process 'polar positve' measurements? I also attached the Xtmp.mat file that contains a lot of NaN. Does someone has an idea what's going wrong here? Thanks in advance! Iris

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Group_analysis_FSGD_contrast_matrix
by Hao wen 31 May '16

31 May '16

Hello, FS experts: I am now doing the group analysis with covariates(age, gender), I am using command line, not QDEC, so my Null hypothesis is: there is no significant difference for the thickness between my two groups( 'AD' and 'CN'), my covariates are age and gender, so if I define the classes like in the tutorial, is there an interaction between the group laber and gender, no? My question is that: If I define the FSGD file like the example here(we have two factors, 1 variable):https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V [https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]<https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V> Fsgdf4G1V - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V> surfer.nmr.mgh.harvard.edu FSGD File (g4v1.fsgd) GroupDescriptorFile 1 Title OSGM Class MaleRight Class MaleLeft Class FemaleRight Class FemaleLeft Variables Age Input subject1 MaleRight 30 ... Follow the tutorial, I think my contrast matrix should be like this: 0.5 -0.5 0.5 -0.5 0 0 0 0 So I know that if you have just one factor, for example, the gender, we should have four columns, like: 1. Intercept for Females 2. Intercept for Males 3. Slope for Females 4. Slope for Males But for my data, I also have the group lable(AD, CN), so anyone can explain this to me a little? Thanks in advance!

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Question about selxavg3-sess -no-con-ok
by Leila Reddy 31 May '16

31 May '16

Hi,I was just wondering what exactly the -no-con-ok option does in selxavg3-sess. Is it the same as setting the weights for all conditions to 1 and give the baseline/fixation (i.e., 0s in the para files) a weight of 0? Thanks, Leila

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Segmentation fault: Core dumped
by Sahil Bajaj 31 May '16

31 May '16

Hello FS experts, I am running a command "fcseed-sess -s S01 -cfg abc.config" to get *.dat file for further analysis. I used the same steps to calculate FC for 40 subjects, all steps run fine with 38 subjects but for 2 subjects I am getting an error: Segmentation fault: Core dumped. I checked the segmentation of anatomical data (generated using recon-all), and it looks fine to me. Here I am also attaching the log file created when I run this command. Any help would be really appreciated. Thanks, Sahil -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

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Freesurfer V6 beta
by Francis Tyson Thomas 31 May '16

31 May '16

Hello Fresurfer admin! I was looking for the v6 beta and it looks like it still hasn't been released after it was pulled down the last time. I would like to know what is the expected ETA for the beta. Last I remember it was mentioned it was on the verge of release about two weeks ago.I'm looking forward to get my hands on the beta! Thanks, Tyson

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Postdoctoral position available
by Olivier Coulon 31 May '16

31 May '16

Dear list members, please find below a link to a postdoc position annoucement that might be of interest, in the field of cortical morphometry for developmental studies and autism. http://www.meca-brain.org/2016/05/31/we-are-looking-for-a-post-doc/ O. Coulon -- Olivier Coulon, Aix-Marseille University, LSIS Laboratory CNRS Director of Research, olivier.coulon(a)univ-amu.fr <mailto:olivier.coulon@univ-amu.fr> http://olivier.meca-brain.org MeCA Research Group http://www.meca-brain.org Institut des Neurosciences de La Timone Faculté de Médecine, 27 Bd Jean Moulin, 13005 - Marseille, France Tél: +33 (0)4 91 32 40 59

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