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30084 discussions

about label to surface
by 于倩倩 05 Dec '19

05 Dec '19

External Email - Use Caution Dear Freesurfer Expert: First, I got the lh.parsorbitalis.label according to the command:mri_annotation2label --subject fsaverage --hemi lh --outdir /Users/qianqianyu/Desktop/fsl_bold/label_fsaverageNow, I want to make the lh.parsorbitalis.label to fsaverage surface file (nii.gz). How? I did the conversion myself using the following method, but an error occurred. The structure of lh.parsorbitalis.label is as follows： I think the first column is coordinate information. So, I use the following commands to convert in Matlab. a=[116,255,256,735,...3806,...];%All values in the first column are assigned to the matrix, a. n=1:163842; %cause the vol matrix of fsaverage lh is1*163842 t=zeros(1,length(n)); t(1,a)=1;%value of lh.parsorbitalis area were 1 MRIread('/Users/qianqianyu/Desktop/Project/Sess06/bold/my-syn.sm04.lh/sem-v-fj/sig.nii');%read a fsaverage image ans.vol=t; err = MRIwrite(ans,'lh.parsorbitalis.mask.nii.gz') But, when I check the lh.parsorbitalis.mask.nii.gz in Freeview, I find it is not consistent with the lh.parsorbitalis.label I am now very very anxious to know how to get the right lh.parsorbitalis.mask.nii.gz！Looking forward to your reply！ Best wishes! Qianqian Yu

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DWI to T1 registration accuracy with bbregister
by VictorM - Gmail 05 Dec '19

05 Dec '19

External Email - Use Caution Hi Freesurfer experts, I have been trying to run a registration between my DWi data and the T1. I am struggling to obtain a good cortical matching, despite I have previously run it withour problems in other datasets. The mincost for most of the individuals is >0.8, which is pretty bad. My guess is that there is a problem with the initialization (mri_coreg not converging correctly?). I have tried different approaches to improve the results with no success: 1) Typical bbregister command: >> bbregister --s XX --mov XX_b0_brain.nii.gz --reg dwi2anat.reg.lta --dti 2) Initialize with fsl (using --init-fsl and using flirt independently with mutual information cost) 3) Playing around with mri_coreg different parameters (dof, non-mask, different smooth of target/mov, etc). 4) Use bbregister with the pial surface (since the contrast CSF/GM is higher than GM/WM) with the command: >> bbregister --s XX --mov 'XX_b0_brain.nii.gz' --reg reg.csf.gm.contrast.dat --surf pial --o dwi2anat.nii.gz --t1 --gm-proj-abs 1 --wm-proj-abs 1 Any insight on how to improve the results? Victor Montal PS: Please, see below the output of mri_coreg when initializing the bbregister with default parameters (method1): $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux testPC 4.15.0-64-generic #73~16.04.1-Ubuntu SMP Fri Sep 13 09:56:18 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert XX_b0_brain.nii.gz ./tmp.bbregister.28271/template.nii mri_convert.bin XX_b0_brain.nii.gz ./tmp.bbregister.28271/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from XX_b0_brain.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998604, 0.0523657, -0.00685515) j_ras = (0.0495749, 0.974205, 0.220152) k_ras = (-0.0182067, -0.219505, 0.975442) writing to ./tmp.bbregister.28271/template.nii... mri_coreg --s XX --mov ./tmp.bbregister.28271/template.nii --regdat ./tmp.bbregister.28271/reg.init.dat --reg ./tmp.bbregister.28271/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /home/testPC/Desktop/tmp/todel_max/test_subject/DTI/XX cmdline mri_coreg --s XX --mov ./tmp.bbregister.28271/template.nii --regdat ./tmp.bbregister.28271/reg.init.dat --reg ./tmp.bbregister.28271/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname testPC machine x86_64 user testPC dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Reading in mov ./tmp.bbregister.28271/template.nii Reading in ref /home/testPC/Desktop/tmp/todel_max/test_subject/FS/XX/mri/brainmask.mgz Reading in and applying refmask /home/testPC/Desktop/tmp/todel_max/test_subject/FS/XX/mri/aparc+aseg.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -0.1963 -2.6892 11.5267 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 1692.0000 mov gstd 1.6917 1.6917 1.6917 Smoothing mov refsat = 116.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0432535803 nhits = 124061 out of 16777216, Percent Overlap: 47.3 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -0.19633; 0.00000 1.00000 0.00000 -2.68918; 0.00000 0.00000 1.00000 11.52671; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.49930 0.00343 0.02618 -3.93636; -0.02479 -0.11008 0.48710 18.58949; 0.00910 -0.48772 -0.10975 106.51717; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -2.19633 7.31082 -4.47329 2.00000 0.00000 4.00000 -1.0498706 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0708609819 #@# 4 188 -2.19633 7.31082 -4.47329 2.00000 0.00000 4.00000 -1.0708610 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.070861 #@# 4 190 -1.19633 7.31082 -4.47329 2.00000 0.00000 4.00000 -1.0711184 #@# 4 195 -1.38650 7.31082 -4.47329 2.00000 0.00000 4.00000 -1.0711316 #@# 4 201 -1.38650 5.69279 -4.47329 2.00000 0.00000 4.00000 -1.0721272 #@# 4 202 -1.38650 4.18476 -4.47329 2.00000 0.00000 4.00000 -1.0723432 #@# 4 203 -1.38650 4.46454 -4.47329 2.00000 0.00000 4.00000 -1.0723693 #@# 4 206 -1.38650 4.64374 -4.47329 2.00000 0.00000 4.00000 -1.0723741 #@# 4 207 -1.38650 4.62484 -4.47329 2.00000 0.00000 4.00000 -1.0723747 #@# 4 216 -1.38650 4.62484 -4.34018 2.00000 0.00000 4.00000 -1.0723816 #@# 4 225 -1.38650 4.62484 -4.34018 1.38197 0.00000 4.00000 -1.0724094 #@# 4 237 -1.38650 4.62484 -4.34018 1.38197 -0.28207 4.00000 -1.0724264 #@# 4 238 -1.38650 4.62484 -4.34018 1.38197 -0.29894 4.00000 -1.0724277 #@# 4 251 -1.38650 4.62484 -4.34018 1.38197 -0.29894 3.98803 -1.0724281 powell nthiter 1: fret = -1.072428 #@# 4 283 -1.38650 4.62484 -4.37900 1.38197 -0.29894 3.98803 -1.0724293 #@# 4 292 -1.38650 4.62484 -4.39237 1.46777 -0.29894 3.98803 -1.0724353 #@# 4 303 -1.38650 4.62484 -4.39237 1.46777 -0.35779 3.98803 -1.0724378 Powell done niters total = 1 OptTimeSec 11.2 sec OptTimeMin 0.19 min nEvals 319 Final parameters -1.38650012 4.62484455 -4.39237213 1.46777403 -0.35779098 4.00846672 Final cost -1.072437818483776 --------------------------------- mri_coreg utimesec 72.570349 mri_coreg stimesec 0.163951 mri_coreg ru_maxrss 432564 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 128483 mri_coreg ru_majflt 31 mri_coreg ru_nswap 0 mri_coreg ru_inblock 11360 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 35 mri_coreg ru_nivcsw 3612 Final RefRAS-to-MovRAS 0.99753 0.06990 -0.00624 -1.38650; -0.06972 0.99724 0.02561 4.62484; 0.00802 -0.02512 0.99965 -4.39237; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.49992 -0.00036 -0.00871 1.07589; 0.00835 -0.12236 0.48473 17.73093; -0.00248 -0.48480 -0.12233 100.50899; 0.00000 0.00000 0.00000 1.00000; Final parameters -1.3865 4.6248 -4.3924 1.4678 -0.3578 4.0085 nhits = 123915 out of 16777216, Percent Overlap: 47.3 mri_coreg RunTimeSec 72.8 sec

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Re: [Freesurfer] Converting labels drew by freeview to volumeError: coordinate mismatch
by ZORO 04 Dec '19

04 Dec '19

External Email - Use Caution Thank you so much! It works.

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TRACULA QUESTION:CONFIGURATION FILE ISSUE
by Benxamin varela lópez 04 Dec '19

04 Dec '19

External Email - Use Caution Dear Freesurfers experts, I'm a beginner in the diffusion imaging preprocessing. I was following the freesurfer/dti tutorial with my own data when i get stuck in the trac-all step. I have created the configuration files trying to follow the tutorial instructions and when I tried to run the trac-all command I get the following error: pcpb3846:4220 lab1-rmn$ trac-all -prep -c $TUTORIAL_DATA/outputs/dmrirc.tutorial set: Variable name must contain alphanumeric characters. ERROR: must specify either one number of control points ERROR: or as many numbers as pathways You can find my configuration file in attached. Any help would be very appreciated. Thank in advance. Best regards,

2 1

hippocampal subfields as masks for mri_segstats
by Marcel Heers 04 Dec '19

04 Dec '19

External Email - Use Caution Dear all, (dear Eugenio), I would like to use hippocampal subfields as masks for mri_segstats to retrieve intensity values. I am having problems loading the subfields file although it works fine with aseg.mgz. Does anyone know the cause? Thank you in advance! Best regards Marcel mri_segstats --seg $SUBJECTS_DIR/test/mri/aseg.mgz --ctab-default --sum output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz mri_segstats --seg $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz --sum output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz ERROR: loading $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz

3 2

MRI label 2 label issue
by Rellick, Stephanie 04 Dec '19

04 Dec '19

External Email - Use Caution Hello, I am having an issue with the mri_label2label command. What I did was mri merge of the BA4 a and p labels for each hemisphere from the fsaverage files, ending up with a lh.BA4.label and a rh.BA4.label. I am wanting to now map the fsaverage lh.BA4.label and rh.BA4.label onto the individual subjects into my study, and was told that to do this, I needed to create those same labels using the BA4 a & p labels in the individual subject label file, and then run the command mri_label2label. This is the command that I am running: mri_label2label --srcsubject fsaverage --srclabel lh.BA4.label --trgsubject SRMC01_1.long.SRMC01 --trglabel lh.BA4.label --regmethod surface --hemi lh And it keeps giving me this error message: srclabel = lh.BA4.label srcsubject = fsaverage trgsubject = SRMC01_1.long.SRMC01 trglabel = lh.BA4.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR ./ FREESURFER_HOME /Applications/freesurfer Loading source label. Found 7403 points in source label. Starting surface-based mapping Reading source registration .//fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface .//SRMC01_1.long.SRMC01/surf/lh.white MRISread(.//SRMC01_1.long.SRMC01/surf/lh.white): could not open file No such file or directory ERROR: could not read .//SRMC01_1.long.SRMC01/surf/lh.white The lh.white file is definitely in the surface folder under that subject so I'm not sure why is says there is no such file or directory. Any help would be greatly appreciated!! Stephanie

2 1

3 positions at Barcelonabeta Brain Research Center
by Juan Domingo Gispert López 04 Dec '19

04 Dec '19

External Email - Use Caution The Neuroimaging Research Group of the Alzheimer's Prevention Program of the Barcelonabeta Brain Research center is seeking a Post-Doctoral researcher (open to Ph.D. students), a Neuroimaging Data Analyst and a Scientific Project Manager. For further information on the positions and instructions on how to apply, please visit the following links: Post-Doctoral or PhD position: https://www.barcelonabeta.org/sites/default/files/2019-11/Predoc_postdoc_AM… Neuroimaging Data Analyst: https://www.barcelonabeta.org/sites/default/files/2019-11/MRI%20Analyst-AD%… Scientific Project Manager: https://www.barcelonabeta.org/sites/default/files/2019-11/1906%20Scientific… -- *Juan Domingo Gispert*Group Leader - Neuroimaging *BarcelonaBeta* * Brain Research Center (BBRC) *jdgispert(a)barcelonabeta.org T. (+34) 93 326 31 67 C/ Wellington, 30 <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> 08005 Barcelona <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> www.barcelonabeta.org www.fpmaragall.org ------------------------------ Confidencialitat correu electrònic BBRC <https://www.barcelonabeta.org/ca/politica-privacitat-web>. Confidencialidad correo electrónico BBRC <https://www.barcelonabeta.org/es/politica-privacidad-web>. E-mail confidentiality BBRC <https://www.barcelonabeta.org/en/privacy-policy-web>. Gràcies per estalviar paper. *Gracias por ahorrar papel. *Thanks for saving paper.

1 0

Trouble running Freeview from Mac Terminal
by Stockmann, Jason 04 Dec '19

04 Dec '19

Hi, I have been having trouble running freeview from the Mac OS terminal via XQuartz on my laptop. I have seen the problem with both Mac OS 10.15.1 (Catalina) and the previous version of Mac OS. I get the error copied below. I am however able to run other GUIs such as fslview. The problem seems to be unique to freeview as best I can tell. Has anyone else ever experienced this error? --- Jason > [deepbrain:~] (nmr-stable60-env) freeview > X Error: BadValue (integer parameter out of range for operation) 2 > Extension: 149 (Uknown extension) > Minor opcode: 3 (Unknown request) > Resource id: 0x0 > Abort (core dumped) > [deepbrain:~] (nmr-stable60-env) > ---- Jason Stockmann Assistant Professor in Radiology A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown, MA 02129 jstockmann(a)mgh.harvard.edu<mailto:jstockmann@mgh.harvard.edu> +1 315 450 3309

2 1

Converting labels drew by freeview to volume Error: coordinate mismatch
by zorothustra 04 Dec '19

04 Dec '19

External Email - Use Caution Hello Freesurfer Developers, I'm trying to get superior colliculus' ROI mannually by freeview. I load "orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw the ROI and save it as a label file. After that I use "mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii --s SUB --regheader --noedit --reg register.dat", and it worked, but the coordinate mismatch, much different from the SC's position in the T1 space( Load T1.nii as volume and SC.label as ROI in freeview, and they are matched). Can anyone help me? Thank you! 1)FreeSurfer version: freesurfer-local-build-dev-20191104 2)platform: Ubuntu 18.04

5 6

LME Contrast Question
by Hua, Jessica 04 Dec '19

04 Dec '19

External Email - Use Caution Hi FreeSurfer Experts, I had a question regarding contrasts for univariate LME models. I am interested in looking at the interaction of alcohol with change in volume across two time-points. Included in my model are covariates Gender, ICV, and Previous Drinking History. My X matrix includes 7 columns: Column 1 = 1s Column 2 = time Column 3 = alcohol Column 4 = time*alcohol Column 5 = Gender Column 6 = ICV Column 7 = Previous Drinking History My contrast is C = [0 0 0 1 0 0 0 ]. I have 4 different previous drinking history variables. However, when I change column 7 with my different previous drinking history variables, the F and P values for the interaction are the same. Am I setting up my contrasts incorrectly? Best, Jessica Hua

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