Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Error saving a tiff file using tksurfer with NoMachine
by Evans, Jennifer (NIH/NIMH) [F] 26 Mar '18

26 Mar '18

Hi, I’m getting an error when trying to save a tiff file using tksurfer using NoMachine v5.0.47. I’m running the ENIGMA QA pipeline which has a call similar to: tkfsurfer bert lh inflated. Then, trying to save the tiff either from the GUI or using their script doesn’t work and causes the error: pixel read error/resource temporarily unavailable. Is there a way to get this to work? Thanks, Jen

1 0

Tessellation of hippocampus
by pooja prabhu 26 Mar '18

26 Mar '18

Hi list, I was segmented the hippocampus using "recon-all -all -s -hippocampal-subfields-T1" using Freesurfer. Now i want to tessellate the segmented volume. I tried using "mri_tessellate"(Freesurfer) it is not working?? How can i tessellate the hippocampus alone? Please help me Thank You -- Thank You Pooja Prabhu

2 1

lGI values below 1
by Kai Ohmstedt 24 Mar '18

24 Mar '18

Dear all, I am conducting an analysis using the lGI to quantify cortical folding. As advised in the tutorial I checked all reconstructed subjects for errors in reconstruction and lGI-computation. To do I used the pial_lgi-file as an overlay in tksurfer and set the minimal threshold to 1. Using those settings no gray areas showed on the cortex, so I assumed all values had been computed correctly and no values below 1 are present. After the analysis I wanted to create scatter plots for the maximum vertices of the clusters that were found. When I displayed the scatter plots in tksurfer, lGI values below 1 were present in many of my subjects. This only seems to be a problem in vertices that are close to the corpus callosum, vertices that are further away show values well above 1 for all subjects. Have any of you already encountered this problem? If so, do you know if the values are in any way reliable? Could this be caused by the split of the hemispheres during the reconstruction process? Thank you for your help! Best regards, Kai Ohmstedt

1 0

Hippocampal Subfields Module, output error
by Hurtado, Aura Maria 23 Mar '18

23 Mar '18

Hi, I am attempting to use the longitudinal pipeline of the "hippocampal subfields and nuclei of amygdala”, but keep getting a flawed output. My dataset consists of images from a longitudinal study with some dropouts. First, I ran the reconall longitudinal pipeline in fs60 for all subjects. I got no errors. Then, I tried 1. Running the longitudinal pipeline of the hippocampal module, loading Matlab 8.2 to run segmentHA_T1_long.sh SUBJ1_basetemplate segmentHA_T1_long.sh SUBJ2_basetemplate etc I got an error in most of these jobs (mostly for templates of subjects with multiple visits) that read "ERROR: MatlabObjectArray(0x7fd7ce84cea0): Trying to access non-existing object (25) Error in kvlGetOptimizer (line 11) Error in SegmentSubfieldsT1Longitudinal (line 1155)” 2. I then tried running the cross sectional pipeline for each one of the timepoints in subjects already processed by the reconall longitudinal pipeline (i. e. segmentations in the .long. directories) segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_basetemplate segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_basetemplate segmentHA_T1.sh SUBJ2_timepoint1.long.SUBJ2_basetemplate segmentHA_T1.sh SUBJ3_timepoint1.long.SUBJ3_basetemplate etc Most of them ran without errors, but some still did. 3. I then tried to run the cross sectional hippocampal module for all subjects/timepoints without using the reconall longitudinal pipeline segmentHA_T1.sh SUBJ1_timepoint1 segmentHA_T1.sh SUBJ1_timepoint2 segmentHA_T1.sh SUBJ2_timepoint1 segmentHA_T1.sh SUBJ3_timepoint1 etc They were processed without errors. But when inspecting the processing log, there was a message that appeared 4 times in the file "WARNING: Registration did not converge in 5 steps! * Problem might be ill posed. * Please inspect output manually! ……… …….. …... Everything done! It took 766.0135 seconds “ With manual inspection, subfield segmentations output by fs60 seemed fine in all the directories of the reconall cross sectional and longitudinal outputs (hippoSfLabels-T1). For the Hippocampal Module outputs (hippoAmygLabels-T1), the hippocampus was abbruptly cut, sometimes laterally, sometimes dorsally. This was the case for all three analyses. I wonder what is the problem and what I can do to fix it so I can successfully run the longitudinal pipeline of the "hippocampal subfields and nuclei of amygdala” Thanks for your help! Aura M.

2 5

Functional Overlap Map
by nm644 23 Mar '18

23 Mar '18

Hello Freesurfer experts, My question may have already been solved in a previous thread. I have three runs of block-design bold scans. All three are quite similar. They all have only 2 blocks, one for rest and one for task. I’m trying to create a functional map that displays where the functional activation of these three runs overlap. I used the code below with no errors: preproc-sess -s subj01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run mkanalysis-sess \ -fsd bold -stc up -surface fsaverage lh -fwhm 5 \ -event-related -paradigm para.tsv -nconditions 1 \ -spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \ -analysis TaskOverlap.lh -per-run -force mkcontrast-sess -analysis TaskOverlap.lh -contrast con1 -a 1 selxavg3-sess -s subj01 -analysis TaskOverlap.lh And to display: tksurfer-sess -s subj01 \ -analysis TaskOverlap.lh \ -c con1 Or tksurfer-sess -s subj01 \ -analysis TaskOverlap.lh \ -c con1 -map fsig The problem is that when I view the output it seems that there’s far more activation than there should be when trying to find mutual overlap between the three tasks. If anyone has any suggestions it would be much appreciated. Have a great day!

3 4

Re: [Freesurfer] Different DWI protocols
by Yendiki, Anastasia 23 Mar '18

23 Mar '18

Probably not a good idea, depending on how the data are balanced across acquisition protocols. If you find differences between time points of subjects or between subjects, you want to be ensure that those differences are not because of acquisition differences. If, for example time point is always collected with one protocol and time point 2 is always collected with another, you won’t be able to tell. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Cano Catala, Marta" <MCANOCATALA(a)mgh.harvard.edu<mailto:MCANOCATALA@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, March 19, 2018 at 11:20 AM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Different DWI protocols Dear TRACULA experts, I'm running a longitudinal trac-all analysis and I'm wondering whether or not I could include different DWI acquisition protocols both between subjects and within subjects in the same analysis. Thank you, M. Cano

2 3

using T2 for hippo subfields
by Alexopoulos, Dimitrios 23 Mar '18

23 Mar '18

Hi. We are acquiring sequences on a pediatric cohort that include a T1-mprage (0.8mm isotropic) and a T2-space (1mm isotropic), and I'd like to run the hippocampal subfields module on the subjects using FS 6.0. Is it recommended/useful to run the multispectral segmentation mode with the additional lower resolution T2 sequence? I read that you really only benefit if the T2 is of similar or better resolution than the T1. If that's the case, would it be best to just run with the single T1 but with the hi-res flag in the recon-all command? Thanks. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

1 0

Volume are different in asegstats vs matlab
by Lee Subin Kristine 23 Mar '18

23 Mar '18

Hi, I have a question about volume info from freesurfer vs matlab. I am looking at, say, the left hippocampus volume from asegstats, which was 3778.2 mm^3. When I try to get the same volume by loading aseg.nii on matlab, however, I get a different number, 3945. For matlab, I used the following command, which counts the number of voxels equal to the left hippocampus segment id: length(find(aseg.img==17)) This was done after I converted the original aseg.mgz file into native space, using 2 different methods: (1) mri_convert -rl rawavg.mgz -rt nearest -i aseg.mgz -o bert_aseg.nii (2) mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o bert_aseg.nii --regheader aseg.mgz In both cases, the output was 3945. The rawavg.mgz used here is also 1mm isovoxel, so I don't think it is due to the difference in voxel dimensions. What could be the cause of the difference in volume? Thanks, Kristine Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

2 1

Positions available in Dr. Zeynep Saygin's lab at OSU
by Saygin, Zeynep M. 23 Mar '18

23 Mar '18

TECHNICAL ASSISTANT, The Ohio State University, Dept. of Psychology – Dr. Zeynep Saygin’s Lab, to assist with neuroscience research on the functional and structural architecture of the human brain in adults and children. The Z-lab studies the functional differentiation of the human brain across early development and adulthood, and the plasticity of the brain in response to disorders and injury (see zeynepsaygin.com<http://zeynepsaygin.com/> for recent publications). The primary responsibilities will include programming, running, and analyzing behavioral and brain-imaging experiments using functional magnetic resonance imaging (fMRI), diffusion weighted imaging (DWI), functional connectivity, and behavioral evaluations of infants, children, and adults. This position is an excellent opportunity for individuals considering future graduate studies. We are seeking an aspiring, self-motivated researcher with strong coding/programming skills who is excited about the developing brain, cognitive neuroscience, and/or clinical disorders and demonstrates evidence of a serious interest in a career in the field. Required: strong mathematical, statistical, and coding skills (e.g., MATLAB, Python, shell scripting); strong interpersonal skills for interacting with a diverse group of people including children and parents; a bachelor's degree in psychology, neuroscience, cognitive science, computer science, data science, engineering, physics, or math; and strong organizational skills. Interested individuals should contact saygin.3(a)osu.edu<mailto:zsaygin@mit.edu> with a CV and names of 2-3 references. POSTDOCTORAL FELLOW, The Ohio State University, Dept. of Psychology – Dr. Zeynep Saygin’s Lab. We seek an outstanding scientist with a recent Ph.D. in cognitive neuroscience, developmental psychology, or related area, who has experience with neuroimaging methods (MRI, fMRI, DWI, and/or functional connectivity) and who is interested in any or all of the following: understanding the functional and structural architecture of the brain, how it develops in healthy individuals, and how it changes with disorders and brain injury in both adults and children. See zeynepsaygin.com<http://zeynepsaygin.com/> for recent publications. The fellow will be involved in conducting and planning behavioral and neuroimaging research studies in neonates, infants, children, and adults. Proficiency in programming is necessary. This position is fully funded. Initial hire is for one year with additional years contingent on fit and progress. OSU is located in Columbus, Ohio and is home to a vibrant community of cognitive neuroscientists, computational modelers, and vision scientists in the Psychology Department and Center for Cognitive and Brain Sciences. Fellows will have access to state-of-the-art MRI and EEG facilities located inside the Psychology building. Interested individuals should contact saygin.3(a)osu.edu<mailto:zsaygin@mit.edu> with a CV, names of 3 references, and a statement of research interests. --- Zeynep M. Saygin, Ph.D. Assistant Professor of Psychology The Ohio State University 205 Psychology Bldg. 1835 Neil Ave Columbus, OH 43210 614-292-3059 zlab<http://zeynepsaygin.com>

1 0

Problem running mri_convert
by Jay Edelman 23 Mar '18

23 Mar '18

Dear Freesurfers, I am running the program "mri_convert" within the AFNI script, @SUMA_Make_Spec_FS, and am receiving the error below. I just installed freesurfer from your website and am running this on a Mac running Yosemite. I've looked at the online forums and see this addressed in other contexts, but unfortunately I can't find any fix. Thanks So Much! Jay Edelman Dept. of Biology, The City College of New York mri_convert.bin -ot nii mri/wm.seg.mgz /Users/jedelman/Dropbox/freesurfer/asim/./SUMA/wm.seg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/wm.seg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Users/jedelman/Dropbox/freesurfer/asim/./SUMA/wm.seg.nii... -- running 'mris_convert lh.smoothwm lh.smoothwm.asc' Trace/BPT trap dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib ?

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