Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

High Intensity Spots causing surface issues
by Jonathan Holt 20 May '14

20 May '14

Hi all, this is a recurring issue that I'm hoping I can find a solution to. Pictured is a brain with a particularly high intensity area that seems to defy surfacing. Is there a way to work around this? See attached image

1 0

registering MRI structural data with MEG volume converted data
by Franklin Lovell Orndorff-Plunkett 20 May '14

20 May '14

Hello Freesurfer Experts, We've used the following tcsh script to convert MEG surface data, morphed to fsaverage .w paint (every timestep) format, to volume data in NIFTI format: # Convert to .nii format (volume from surface data of dSPM) placing .nii files in NII_DIR # FREESURFER_HOME is the base directory for FreeSurfer; sourcing from SetUpFreesurfer.sh setenv FREESURFER_HOME /apps/freesurfer/ && source ${FREESURFER_HOME}SetUpFreeSurfer.csh # set file numbers denoting each time step set Tmin = -0200 && set Tstep = 10 && set Tmax = 1000 # foreach FileNum (` seq -w $Tmin $Tstep $Tmax ` ) # CONVERT SURFACE DATA TO VOLUME DATA FROM PAINT TO MGZ to NII mri_surf2vol --surfval ${STC_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.w paint --hemi lh --volreg ${SUBJECTS_DIR}/fsaverage/mri/transforms/reg.mni152.2mm.dat --template ${SUBJECTS_DIR}/fsaverage/mri/T1.mgz --outvol ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.mgz mri_convert ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.mgz ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.nii mri_surf2vol --surfval ${STC_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.w paint --hemi rh --volreg ${SUBJECTS_DIR}/fsaverage/mri/transforms/reg.mni152.2mm.dat --template ${SUBJECTS_DIR}/fsaverage/mri/T1.mgz --outvol ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.mgz mri_convert ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.mgz ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.nii # mri_concat does temporal concatenation. Done this way, each image will include the left # hemisphere solution, and then the right hemisphere solution. You have to do this separately #for each hemisphere, and then add the two hemispheres together using something like #fslmaths or 3dcalc. # Have to convert mgz to nii first using e.g.: mri_convert input.mgz output.nii # e.g., 3dcalc -a left.nii -b right.nii -expr 'a+b' -prefix test_combined.nii # MERGING OF HEMISPHERES (.nii) AT EACH TIMESTEP ${AFNI_DIR}/3dcalc -a ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.nii -b ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.nii -expr 'a+b' -prefix ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0.nii set ExecString = 'mri_concat ' foreach FileNum (` seq -w $Tmin $Tstep $Tmax ` ) set ExecString = "${ExecString} ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0.nii " end The .nii files come out uniform size and a colleague suggested that I add a baseline to the original data. It seems like the issue is happening at the mri_convert step and the T1.mgz fsaverage template seems to not register properly. Is there some syntax I should be adding to the --template option in mri_surf2vol? Perhaps it's something else. -Franklin

2 1

A newbie to fMRI analysis
by Dr Sampada Sinha 20 May '14

20 May '14

Hello I have only recently started the fmri data analysis and I downloaded freesurfer point by point from martinos site and incorporated the license file as well into the Applications/freesurfer directory. I have run into the first problem and that is of data conversion. My file is in dcm format and I have 11,000 dcm files to convert. However, before I was using Jamaan Alghamadi created gui and it is not able to convert the mri dcm files. Then I shifted to UNIX and again it is saying error. My file is on the desktop and I have given it subject id as Grace. My directory to the dcm file is '/Users/sampada/desktop/Grace. My terminal look like this before I proceed with the file conversion Last login: Mon Apr 28 15:10:13 on ttys001 dhcp020-223-179:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Will anyone please let me know what I am doing wrong? I will be very grateful for any input. Thanks and regards, Sampada Senior research support specialist Molecular and neuroimaging department Department of Psychiatry 451, biomedical research building University at Buffalo (south campus) Buffalo, NY-14216

5 19

ASL Image Exception: # 22 ERRORS
by Athanasia Monika Mowinckel 20 May '14

20 May '14

Hi. I'm trying to run an ASL analysis on my data. I have pcASL control-tag data that for the most part are getting run through the analysis without problems. However, there seems to be some difficulties with the calibration. I'm running the command as root in csh: oxford_asl -i $INPUT/analysis/diffdata -o $INPUT/analysis/KMI_data --tis 3.6 --bolus 1.8 --bat 1.8 --casl \ --t1b 1.6 --alpha 0.98 --artoff --fixbolus \ --infert1 -s $ANATFOLDER/anat_roi_brain --report \ --regfrom $INPUT/PCASLmean_brain --spatial \ -c $INPUT/M0.nii.gz --tr 12 the error is such: Number of voxels is:81920 Number of repeats in data is:70 Outputting ASL data mean at each TI Done. OXFORD_ASL - running Creating output directory Saving results in natve (ASL aquisition) space to ASL/analysis/KMI_data/native_space Saving results in structural space to ASL/analysis/KMI_data/struct_space Pre-processing Creating mask Performing registration ASL_REG Input file is: /ASL/PCASLmean_brain Running FLIRT Tidying up ASL_REG - Done. Segmenting the structural image Calculating M0a - calling ASL_CALIB ASL_CALIB Tissue reference is: csf *Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_SsEGkZ_asl_calib/seg_bias* *libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException* */usr/local/fsl/bin/asl_calib: line 568: 58142 Abort trap: 6 ${FSLDIR}/bin/applywarp --ref=$calib --in=$temp_calib/seg_bias --out=$temp_calib/biasfield --premat=$temp_calib/high2low.mat --super --interp=spline --superlevel=4* *Cannot open volume /tmp/fsl_SsEGkZ_asl_calib/biasfield for reading!* *Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_SsEGkZ_asl_calib/sens* *libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException* */usr/local/fsl/bin/asl_calib: line 689: 58150 Abort trap: 6 fslmaths $temp_calib/calib -div $temp_calib/sens $temp_calib/calib* M0:874.58000000000000000000 ASL_calib - DONE. Best regards, Athanasia Mowinckel

2 1

mris_anatomical_stats lgi error
by _andreia_＠sapo.pt 20 May '14

20 May '14

Hello all, I generated the lgi.stats file for all my subjects and in one of them I got this warning: mris_anatomical_stats -a aparc.annot -t pial_lgi -f SUBJ/stats/lh.aparc_lgi.stats SUBJ lh computing statistics for each annotation in aparc.annot. using thickness file pial_lgi. reading volume /home/user/visao/Freesurfer//SUBJ/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//SUBJ/surf/lh.white... reading input pial surface /home/user/visao/Freesurfer//SUBJ/surf/lh.pial... reading input white surface /home/user/visao/Freesurfer//SUBJ/surf/lh.white... MRISREADANNOTATIONINTOARRAY: VERTEX INDEX OUT OF RANGE: 150843 I=007D324B, IN_ARRAY_SIZE=150843 ANNOT FILE: /HOME/USER/VISAO/FREESURFER//SUBJ/SURF/../LABEL/LH.APARC.ANNOT MRISreadAnnotationIntoArray: vertex index out of range: 150844 i=007D324B, in_array_size=150843 annot file: /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 150845 i=007D324B, in_array_size=150843 annot file: /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot (...) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) structure is "bankssts" number of vertices = 1139 total surface area = 795 mm^2 total gray matter volume = 2868 mm^3 average cortical thickness = 3.820 mm +- 0.158 mm average integrated rectified mean curvature = 0.117 average integrated rectified Gaussian curvature = 0.031 folding index = 10 intrinsic curvature index = 1.3 structure is "caudalanteriorcingulate" number of vertices = 812 (...) Even thought there was the warning, everything seems to be fine with the lgi values, should I be concerned about this or I may just ignore it? Thank you! Andreia

4 21

Referencing
by WaliD YassiN 20 May '14

20 May '14

Hello, We would like to cite Freesurfer for using its subcortical segmentation, but we are limited in the number of references for a case study.we can assign 1 reference to that, can you please let us know which of these 2 should we use. Fischl et al., 2002; Fischl et al., 2004a?Thanks W. Please consider your environmental responsibility. Before printing this e-mail message, ask yourself whether you really need a hard copy.

2 1

Mean Thickness for each hemisphere from ?.aparc.stats
by amirhossein manzouri 20 May '14

20 May '14

Dear Doug, I have read this post( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html) regarding extracting Mean Cth of each hemisphere and I just get insula as the last and totally 34 numbers, I use aparcstats2table --hemi lh --subjects bert -m thickness --tablefile lh.Cth.bert.txt Best regards, Amirhossein Manzouri

2 7

Registration and Surface flatten
by Caka 19 May '14

19 May '14

Hi Doug, Thanks for your suggestion on tksurfer, it works. I would like to map all the subjects into a flat map because I am curious about the 2-D thickness patterns between different groups. I think there will be some distinctions. But if I flatten fsaverage, how can I map everyone?s 3D surface onto the fsaverage?s 2D map? Is there a command? Best, Qiongmin On 05/13/2014 11:19 PM, Caka wrote: > Dear Doug and all, I have already done two things: (1) 'recon-all? to > the segmentation for 140 subjects; (2) surface registration to > fsaverage template for 1 subject using: mri_surf2surf --hemi lh > --srcsubject sub001 --srcsurfval thickness --src_type curv > --trgsubject fsaverage --trgsurfval ./sub001-thickness-lh.mgz Now I > have got the 'sub001-thickness-lh.mgz' file. I have two questions: (1) > Is this 'sub001-thickness-lh.mgz? a surface file or a volume file? How > can I read it? I used ?freeview sub001-thickness-lh.mgz? to read it, > but a dark scene was shown, nothing can be found. I also used > ?mris_convert -c $SUBJECTS_DIR/sub001/sub001-thickness-lh.mgz > $SUBJECTS_DIR/sub001/surf/lh.orig lh.thickness.asc?, an error occurred > like ?ERROR: number of vertices in > /disk250/data_analysis/sub001/sub001-thickness-lh.mgz does not match > surface (163842, 132230)?. Try tksurfer fsaverage lh inflated -aparc -overlay sub001-thickness-lh.mgz -fminmax .01 4 > (2) After the registration, I want to flatten the surface of curvature > or thickness into a full plane. The wiki says we should first specify > 5 vertices and cut the whole area without the midline region, then > ?kris_flatten? can be used. Indeed, this procedure requires quite a > lot manually operation. I am wondering if there are some automatically > commands that can do this flatten projects for 140 subject? Any reply > would be really appreciated! Qiongmin > _______________________________________________ Freesurfer mailing > list Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer I don't think so, though I think bruce was working on something. You could just flatten fsaverage and then map everyone to fsaverage (as you have already done). Why do you want to map everyone to a flat map? doug

2 1

LGI qdec analysis on longitiudinal data
by Jon Wieser 19 May '14

19 May '14

Hi freesurfer experts I am trying to analyze the longitudinal effects on LGI. I've run all my subject's through the longitudinal processing stream. I set-up my qdec dat file: fsid fsid-base years 100674-0107 100674_base 1.6 100674-0408 100674_base 2.8 100674-0605 100674_base 0 100712-0505 100712_base 0 100712-0708 100712_base 3.2 100712-1006 100712_base 1.4 100724-0605 100724_base 0 100724-0808 100724_base 3.2 100724-1206 100724_base 1.5 100733-0106 100733_base 0 100733-0507 100733_base 1.3 100733-1008 100733_base 2.8 I ran long_mris_slopse for both hemispheres: long_mris_slopes --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --meas pial_lgi --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Studies/UCSDsubjects-NIDA/Cluster_Proc long_mris_slopes --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --meas pial_lgi --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Studies/UCSDsubjects-NIDA/Cluster_Proc i also ran long_qdec_table long_qdec_table --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --cross --out ./qdec/cross.qdec.table.dat then I ran qdec: qdec --table ./qdec/cross.qdec.table.dat I specified pial_lgi as the Measure, and selected years as the covariate when I press Analyze, I get the following error: Error in Analyze: Couldn't open 100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgz or mgh file when looking in the directories, I have lh.pial_lgi.fwhm10.fsaverage.mgh files in the 100674-0107.long.100674_base directories: \100674-0107.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-0605.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0107.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-0605.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100674-0408.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-0808.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0408.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-0808.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100674-0605.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-1206.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0605.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-1206.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-0505.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-0106.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-0505.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-0106.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-0708.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-0507.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-0708.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-0507.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-1006.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-1008.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-1006.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-1008.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh but not in the following directories 100674_base/surf 100712_base/surf 100724_base/surf 100733_base/surf How can I fix this? Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

2 4

bbregister to convert .labels to MNI space
by Nathan Hutcheson 19 May '14

19 May '14

Hello, I am trying to use bbregister to take an .annot file of a particular structure and register it to MNI space. I want to be able to use one of the FreeSurfer parcellations of the ACC (lh.caudalanteriorcingulate.label) and do a fMRI BOLD extraction in FSL in MNI space. Below is the command I used and the error message I am getting. Please let me know if what I am doing makes any sense or if I am way off base. Input > bbregister --s fsaverage --mov > /u/home/n/nhutche/temp/labels/lh.caudalanteriorcingulate.label --t1 > --init-fsl --reg register.dat > > Output > mkdir: cannot create directory `./tmp.bbregister.6489': Permission denied > > Log file is register.dat.log > > register.dat.log: Permission denied. > Take care, Dr. Nathan Hutcheson Postdoctoral Researcher University of California Los Angeles Semel Institute 760 Westwood Plaza C8-202 Los Angeles, CA 90024 T: 770.841.1694 nathanhutcheson.com <http://www.linkedin.com/pub/nathan-hutcheson/3a/7a8/a46>

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