Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

mri_glmfit --no-prune
by Nasiriavanaki, Zahra 19 Feb '20

19 Feb '20

Hi Freesurferers I am running mri_glmfit on a group data using --no-prune flag. i 'm getting the below error. I appreciate if you could let me know what the issue is. Loading y from /autofs/space/oprah_001/users/zn025/looming_3T/group_levels/patients_20/loom.lh/aw/ces.nii.gz ... done reading. Saving design matrix to main2.wls/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 Found 149955 points in label. Found 149955 voxels in mask Saving mask to main2.wls/mask.nii.gz Reshaping mriglm->mask... search space = 74612.583051 ERROR: MRInormWeights: value less than or eq to 0. c=336, r=0, s=0, v=0 Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

2 3

Problem running recon-all example from installation guide
by Andreas Vitikan 19 Feb '20

19 Feb '20

External Email - Use Caution Hello, I am trying to get the examples running as per the FreeSurfer installation guide. I initially got a recon-all not found error which turned out to be due to the lack of tcsh/csh, which I installed (I found this fix in the mailing list) and now get a different error. mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c /usr/local/freesurfer/subjects/bert/scripts/patchdir.txt: No such file or directory. I thought it might be related to permissions but running under sudo gives a different error. How do I fix this? - Andreas V.

2 1

tktools: Bad CPU type on Mac OSX 10.15. Any workarounds or fixes?
by Chris Klink 19 Feb '20

19 Feb '20

External Email - Use Caution Hi Everyone, The 'Bad CPU type in executable' error for tktools like tksurfer has been a problem for me since Mac OSX 10.15 (Catalina). I know this is a 64/32 bit problem, but I'm wondering if there's a fix or workaround (other then 'use a different OS'). I tried the development version of Freesurfer (7.0.0b0) and noticed the tktools were gone there. Does this mean there's not a solution yet? Will tksurfer functionality be moved to Freeview? Very much related: is there another way to make cuts in surfaces for flatmap generation that doesn't require tksurfer and will work on Catalina? (It's not super urgent as I do have a different system available where things do work, but if there's a way this can work I'd like to know about it..) Thanks, -- Chris Klink

1 0

Apply transformation
by Adam Rytina 19 Feb '20

19 Feb '20

External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxels size). It means to apply the same command as the command ApplyXFM in FSL FLIRT. Does this option exist also in Freesurfer? Thanks a lot Regards Adam

2 3

surface analysis with RBV PET images
by Marina Fernández 18 Feb '20

18 Feb '20

External Email - Use Caution Hi experts, I would like to know how to work correctly on the surface with PET images to which the RBV method was applied. I have tried to do it using the mri_coreg and mri_gtmpvc function (applying as RBV method) to obtain the rbv.nii.gz volume. Then I have masked this volume with a GM cortical mask, and I have taken the output to the surface of the average subject of my dataset (which is in ico7) with the mri_vol2surf command. I have loaded the surface in the file inflated with tksurfer and there were too many holes (see attached image). Are these steps correct? What can I do so that there are not so many holes in the surface? *In each step I have been checking that the registration was correct. Thanks for your attention! Marina.

2 1

help
by Parks, Sean 18 Feb '20

18 Feb '20

Hello, I am working through the tutorial fro FSFAST, and am up to the Preprocessing step. I followed the instructions as indicated and was not receiving errors up until the following command: preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run With this command I receive the error after the code runs for a while: MRISread(/home/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg): could not open file Reading target registration /home/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg No such file or directory ERROR: could not read /home/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg Checking the fsaverage/surf folder I do not see lh.sphere.reg or rh.sphere.reg. In the fsaverage/surf folder of my freesurfer home subjects, lh.sphere.reg and rh.sphere.reg are present. My question is: is rh.sphere.reg and lh.sphere.reg something that is created during the tutorial (ie is something wrong with my freesurfer installation that it cannot create these files), or are they simply missing from the tutorial subjects folder? I downloaded the tutorial package this week, and am using ubuntu 16.04 and freesurfer version 6. Any help would be greatly appreciated. Thank you.??

2 1

Support with CVS/BBR Issue
by Austin Patrick 18 Feb '20

18 Feb '20

External Email - Use Caution Dear FreeSurfer Community, I have used the CVS and BBR registration methods to spatially align T1 and diffusion images to an ideal subject’s T1. I have noticed some discrepancies when viewing the aligned images in FSLview. If I toggle between subjects in FSLview the alignment looks quite good; however, when all subjects’ diffusion images are merged into a single 4D volume, the alignment is quite poor and variable. The same is true for subjects’ T1s. Is this a known issue and, if so, is it a problem with FSLview or my implementation of FreeSurfer? Thanks, -Austin -- Austin M. Bazydlo, MS PhD Candidate Dept. of Medical Physics University of Wisconsin-Madison

2 1

hippocampal subfield segmentation - values for whole subfields
by Teresa Esteban 18 Feb '20

18 Feb '20

External Email - Use Caution Hello FreeSurfer Developers, I am trying to use the Hippocampal subfields tool (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) to extract the stats of each subfield. On version v21 I obtain the stats for the subdivisions head, body and tail of different structures (i.e. CA1-body, CA1-head), but not of the undivided subfield (i.e. CA1). Would this undivided subfield be just the sum of the divisions? This is, would adding CA1-body and CA1-head give me the volume of CA1, or is there other way of obtaining it? I have searched the wiki and the list and I have not been able to find an answer. I would appreciate any insight! Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Thanks in advance, Teresa Teresa Esteban Predoctoral Researcher BCBL www.bcbl.eu t.esteban(a)bcbl.eu Tel: +34 943 309 300 Ext #215 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

2 1

Difference bewteen beta and ces in FS-FAST
by Star Xi 18 Feb '20

18 Feb '20

2 1

Re: [Freesurfer] Volume to 5th order icosahedron tesselation Surface (with PET images)
by Marina Fernández 18 Feb '20

18 Feb '20

External Email - Use Caution Hi Doug, We thought it would be better to use 5th order icosahedron tesselation for PET because the resolution of the volume is lower: If, for thickness analysis, we carry the structural volumes with a resolution of 1x1x1 to ico7 on the surface, with PET-volumes or connectivity maps (resolution of 2x2x2 or 3x3x3) we thought it would be more appropriate to use ico5 on the surface because in the surface transformation the interpolation of the data is lower. In addition the number of statistical comparisons is greatly reduced. Regards, Marina. Marina. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi experts, This is a question related to PetSurfer steps. I would like to know if it is correct to sample the mgx volume onto the surface of the average subject of my dataset (created with 5th order icosahedron tesselation) instead of the fsaverage (created with 7th order icosahedron tesselation) or if there is any problem in the next steps following this procedure. We would like to do that because the volume PET resolution is more proportional to this number of vertex (10242). Do you think it is correct? Best wishes, Marina. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You could do it, but I would just use fsaverage. I don't understand what the relationship would be between the number of vertices on the surface and the number of voxels in the PET volume or the rational for using the 5th order ico

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