Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

working with cluster annotations in fs-fast
by Abigail Noyce 31 May '16

31 May '16

Hi folks, I'm trying to split a cluster from mri_glmfit-sim into two separate regions. (Ginormous blob of activation across multiple structures of interest...) I've gotten to the point of generating a new annotation with the separate labels for my separate regions, but am stuck getting a "cluster size" for the new labels. It looks like one can't use mris_anatomical_stats on fsaverage... but something like that must be happening inside of mri_glmfit-sim to get cluster sizes? What's the best way to get these values for my new annotation? (Or is this a terrible idea for some reason I haven't yet considered?) Thanks! Abby Noyce -- Abigail Noyce, Ph.D. Department of Psychological & Brain Sciences Boston University anoyce(a)bu.edu

2 1

recon-all with input T1s at different resolutions
by Satrajit Ghosh 31 May '16

31 May '16

hi folks, does recon-all work if the input T1s for the same participant have different resolutions? (i don't have a dataset to test, but trying to debug some issues another group has been having). cheers, satra

4 7

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

1 0

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

31 May '16

1 0

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>

2 2

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

1 0

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

2 1

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!

2 1

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

2 2

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>

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer