Freesurfer October 2014

freesurfer@nmr.mgh.harvard.edu

129 participants
187 discussions

Bus error when trying to launch tksurfer
by Claire Morley 20 Oct '14

20 Oct '14

Good Morning, I have now been able to get the testing command: tksurfer bert rh pial to run, but it stops midway and issues a bus error. Please see the following script: DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial subject is bert hemi is rh surface is pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/dbmuser checking for nofix files in 'pial' Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=133299, faces=266594 surfer: single buffered window surfer: tkoInitWindow(bert) Bus error Any idea what might be going wrong? I really need to use tksurfer to look at cortical thickness in gyrification in ROIs. (Oh and before I did this, I did set the environment as normal). Thanks so much for your help! Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot*

3 2

pial vs. aseg
by Wegbreit, Ezra 17 Oct '14

17 Oct '14

Dear Freesurfer community, 1. Does the cortical segmentation (tinted red in the attached aseg_vs_pial.png) need to follow the pial surface (red line) precisely? Does the region under the cursor that is marked as cortex but is outside the pial surface count in the aparc results? In general, should I fix pial surfaces so that aseg and pial match precisely? For this participant, the skull strip and white matter segmentation both looked really good, especially in this region. 2. What about small pieces of remaining dura (or other outside brain material) labeled red as cortex in the aseg? Do they count in cortical thickness values, even though there's a clear gap between them and the cortex proper? (see cortex_outside_brain.png) I did find this old post on the mailing list but I was unsure if it answers my question: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg03807.html >From what I gather from this post and some others*, the aparc results are based on the surface and the aseg values are only relevant to subcortical structures, but I am still unsure if this is the correct interpretation. The original question in the mailing list concerns the hippocampus, but my questions are about the top of the cortex. Many thanks for answers! Ezra * e.g., http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg07810.html *___________________________________________________________* *Ezra Wegbreit, PhD* NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Warren Alpert Medical School (401) 432-1615 ezra_wegbreit(a)brown.edu *___________________________________________________________*

2 1

watershed error again
by Janosch Linkersdörfer 17 Oct '14

17 Oct '14

Hi all, I posted this problem earlier, but did not get an answer, so I am posting it again, sorry! --- recon-all runs smoothly for all my subjects but one. It throws the error "mri_watershed Error: indices out of bounds" and finishes (see https://www.dropbox.com/s/4del0uy8g1qw5az/recon-all.log ). The image quality does not seem to be different... The error has been discussed on the list ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021896.… ), but I don't know where in the brain and in which image space I should add control points or what else I can do to prevent this from happening. --- Thanks for your help, Janosch

1 0

bbregister / mri_vol2vol with nifti file header
by Ajay Kurani 17 Oct '14

17 Oct '14

Dear Freesurfer users, I wanted to see if anyone knows what part of the file NIFIT header mri_vol2vol or mri_convert uses to write transform information from register.dat acquired from bbregister? I used the following commands to register the anatiomcal brain.mgz to the last time point of my EPI scan: bbregister --s ${sub}_FS --mov $bbrest_file --reg ${sub}_RS_register.dat --init-header --bold --frame $NP_last --nearest --template-out ${sub}.RS.template.nii mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ $SUBJECTS_DIR/${sub}_FS/mri/ brain.mgz --o $out_dir/brain_aligned.nii --inv --no-save-reg --reg $out_dir/${sub}_RS_register.dat When i view the images in Afni they look misaligned, but display perfectly in freesurfer (tkregister2 --mov EP_001.RS.template.nii --reg EP_001_RS_register.dat --surf) so I am assuming each program looks at a different field in the nifti file header. I used mri_vol2vol to apply the inverse transform of register.dat to brain.mgz so that it aligns with the EPI but for some reason it is not showing up correctly in afni so I wanted to get a better understanding of how freesurfer files write transformation information in nifti format (sform, qform, another part of the header) and if there is an easy way to get this into a format that afni reads correctly? Thanks, Ajay

1 0

problem with gyrification index extraction
by elisa veronese 17 Oct '14

17 Oct '14

Dear FreeSurfers, I'm facing a problem with the estimation of local gyrification index. I've already performed the analysis with QDEC and the insertion of the MEASURE1 = pial_lgi line in the .Qdecrc file, but I'd like to see if it is possible to use the *aparcstats2table *command in order to have more concise and easy-to-read results. >From the QDEC GUI I've drawn a label in the temporal pole, and applied it to all my subjects (*mris_anatomical_stats -l rh.MR_TmpPole.label -t rh.pial_lgi -b -f s1/stats/rh.MR_TmpPole.stats s1 rh*) The problem is that when I call the *aparcstats2table --hemi rh --subjects s1 s2 ... --parc MR_TmpPole -t GI_MR_TmpPole.txt* I get a .txt file like this: rh.MR_TmpPole.area rh_rh.MR_TmpPole.label_area rh_WhiteSurfArea_area s1 6623.0 96171.8 s2 6257.0 85247.3 ... but I'm not sure what those numbers stand for. I'm afraid they have nothing to do with the gyrification index. Thank you, best elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php <http://icbn.uniud.it/tiki-index.php>*

3 5

mkcontrast-sess errors no-octave
by elahe' yargholi 16 Oct '14

16 Oct '14

Dear Freesurfer experts, As I run mkcontrast-sess, I receive no octave error: fsl@fslvm6 MT_Localizer]$ mkcontrast-sess -analysis MT.lh -contrast MS -a 1 -c 2 INFO: Found 2 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 -1.00000000000000000000 mkcontrast -anadir MT.lh -wcond 1.00000000000000000000 -1.00000000000000000000 -sumconds -o MT.lh/MS.mat -wdelay 1 -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile MT.lh/MS.mat nconds 2, wcond 1.00000000000000000000 -1.00000000000000000000 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir MT.lh -wcond 1.00000000000000000000 -1.00000000000000000000 -sumconds -o MT.lh/MS.mat -wdelay 1 -no-octave Fri Oct 17 06:39:59 BST 2014 I have installed matlab and added path /home/fsl/Desktop/freesurfer/matlab /home/fsl/Desktop/freesurfer/fsfast/toolbox I will appreciate in advance if you possibly could help me to solve the problem. Best Regards, Elahe' Windows 7 and vmware10 Linux version: ------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/fsl/Desktop/freesurfer FSFAST_HOME /home/fsl/Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/fsl/Desktop/freesurfer/subjects MNI_DIR /home/fsl/Desktop/freesurfer/mni FSL_DIR /usr/local/fsl Current working directory: *pwd* */home/fsl* *which freesurfer* */home/fsl/Desktop/freesurfer/**bin/freesurfer* *which mkanalysis-sess* */home/fsl/Desktop/freesurfer/fsfast/bin/mkanalysis-sess* *which mkcontrast-sess* */home/fsl/Desktop/freesurfer/fsfast/bin/mkcontrast-sess* Command lines: *mkdir FIVA* *cd FIVA* *mkdir MT_Localizer* *cd MT_Localizer* *mkdir subj1sess1 * *cd subj1sess1* *unpacksdcmdir -src /home/fsl/Desktop/MTLocalizer/IMAGES -targ . -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii -run 11 bold nii f.nii* Within subj1sess1, made a text file named subjectname, and wrote subj001 (the name of my anatomical subject). *cd ..* *preproc-sess -s subj1sess1 -fsd bold -surface self lhrh -mni305 -fwhm 5 -per-run* For each run, a paradigm file (paradigm.par) is included. *mkanalysis-sess -a MT.lh -surface self lh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg* *mkanalysis-sess -a MT.rh -surface self rh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg * *mkcontrast-sess -analysis MT.lh -contrast M_S -a 2 -c 1 *

1 0

FreeSurfer graphics requirement
by velocci＠physics.utexas.edu 16 Oct '14

16 Oct '14

Dear FreeSurfer users, I'm interested in using FreeSurfer on my Thinkpad X230 (Ivy Bridge) laptop with 8GB of RAM. My laptop does not have a dedicated graphics card, but rather an Intel HD Graphics 4000. Do you think I would still be able to run FreeSurfer, or should I really opt for a more capable machine? Thanks very much. I appreciate your time! Vince Velocci

4 3

Freesurfer volume-based segmentation
by Gabor Perlaki 16 Oct '14

16 Oct '14

Dear all, I'd like to ask which steps are essential to check if I'm interested only in the volume based (aseg) results. I think Skull strip and Talairach transformation are essential. Any other steps I need to check? Thanks, Gabor

2 1

Convert "curv" into volume
by Roberta Santoro 16 Oct '14

16 Oct '14

Dear all, I am trying to convert the curv surface into a volume by using the following command: mri_surf2vol –surf curv –hemi lh –template $subj/mri/T1.mgz –surfval $subj/surf/lh.curv –projfrac 0 –volregidentity $subj –o CurvatureVolume.nii I get the following error: the lh.curv has many more faces than vertices! If the curv file is not a surface, is it possible at all to convert it into a volume? Thanks a lot for your help. Best, Roberta

3 7

Re: [Freesurfer] Centos 7
by will brown 16 Oct '14

16 Oct '14

Hi Zeke, I have completed a recon on CentOS 7. As far as I can see, the output matches the results from my previous recon of this subject using Freesurfer on CentOs 6. Is there any particular log that you would like to see? Will

2 1

← Newer
1
...
7
8
9
10
11
12
13
...
19
Older →

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 October 2014