Freesurfer November 2013

freesurfer@nmr.mgh.harvard.edu

120 participants
198 discussions

glm_fit --pvr
by celine＠nmr.mgh.harvard.edu 06 Nov '13

06 Nov '13

Dear Freesurfer team I am still trying to run a glm analysis between 2 surfaces but I am having weird results so I guess I missed something. So I sampled a DTI surface 2mm below the WM surface, and another intracortical surface (T2* actually) at 75% depth from the pial surface. The question I'd like to investigate is: is there a spatial relationship between DTI metrics below the WM surface and intracortical metrics here DTI in a patient population. So I run glm_fit with -pvr option. My design matrix has 2 classes (male and female) and 1 variable (age) that I entered as covariates. Here is the command: mri_glmfit --y lh.t2star_corr_disco_fsaverage__r0.9_depth0.75_fwhm3.mgh --pvr lh.L1_fsaverage_depth-2_fwhm5.mgh --fsgd ms_age_gender.fsgd --C lh_age_gender_pvr.mtx --surf fsaverage lh --glmdir t20.75_L1-2 --y input is the T2* surfaces for each subject concatenated -- pvr input is the DTI surface below the WM for each subject concatenated I wasn't so sure about the contrast, as I have 2 class, 1 variable + the pvr regressor I thought I would need 6 values (0 0 0 0 0 1) but I got an error about the contrast saying I should put 5 factors so my contrast is 0 0 0 0 1, to test the slope between T2* and DTI at each vertex, after taking into account gender and age. The output sig.mgh doesn't give me any significant result, even at the lowest possible threshold. So my first question would be: is it fine to correlate different surfaces that were not build at the same depth? And the 2nd question would be: is the contrast correct to test the correlation between the 2 surfaces at each vertex? Thanks a lot for your help Celine PS: here is the terminal output: gdfReadHeader: reading ms_age_gender.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 43.1176 9.02534 Class Means of each Continuous Variable 1 F 43.0435 2 M 43.2727 INFO: gd2mtx_method is dods Reading source surface /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.3/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /autofs/cluster/mscat/users/sindhuja/data/3T/results_2013-11-06_t2star_dti cmdline mri_glmfit --y lh.t2star_corr_disco_fsaverage__r0.9_depth0.75_fwhm3.mgh --pvr lh.L1_fsaverage_depth-2_fwhm5.mgh --fsgd ms_age_gender.fsgd --C lh_age_gender_pvr.mtx --surf fsaverage lh --glmdir t20.75_L1-2 sysname Linux hostname panarea machine x86_64 user celine FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/cluster/mscat/users/sindhuja/data/3T/results_2013-11-06_t2star_dti/lh.t2star_corr_disco_fsaverage__r0.9_depth0.75_fwhm3.mgh logyflag 0 usedti 0 FSGD ms_age_gender.fsgd labelmask /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.3/fsaverage/label/lh.cortex.label maskinv 0 glmdir t20.75_L1-2 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory t20.75_L1-2 Loading y from /autofs/cluster/mscat/users/sindhuja/data/3T/results_2013-11-06_t2star_dti/lh.t2star_corr_disco_fsaverage__r0.9_depth0.75_fwhm3.mgh INFO: gd2mtx_method is dods Saving design matrix to t20.75_L1-2/Xg.dat Normalized matrix condition is 117.356 Matrix condition is 121295 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 2487 voxels in mask Saving mask to t20.75_L1-2/mask.mgh Reshaping mriglm->mask... search space = 1064.228206 DOF = 29 Starting fit and test Fit completed in 0.0014 minutes Computing spatial AR1 on surface Residual: ar1mn=0.602743, ar1std=0.415130, gstd=0.568767, fwhm=1.339345 Writing results lh_age_gender_pvr maxvox sig=4.08 F=20.9043 at index 63635 0 0 seed=1384618381 mri_glmfit done

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LME Mass Univariate analysis and .long directories
by Jonathan Holt 06 Nov '13

06 Nov '13

FS experts, I have two questions, when running mris_preproc and mri_surf2surf should I be passing these any of the .long directories created with recon-all -long? As I read through the tutorial I’m missing their significance in the analysis section of the longitudinal stream. It seems like fsaverage is being used (I’m not sure when that was even generated) Secondly, I see that mris_preproc outputs a thickness.mgh file, but I’m wondering where, in your tutorial examples lh.thickness_sm10.mgh comes from/is located. Found in mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex —noreshape best, jon

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longitudinal measures
by Qi Wu 06 Nov '13

06 Nov '13

Hi Freesurfer users, For the longitudinal stream in FS5.1, there are only 4 options of measures (do-avg, do-rate, do-pc1 and do-spc). However, if I need other measures, such as the difference between two time points (thick2-thick1), how should I do to get the values and still be able to do the voxel-wise analysis for regional difference in cortical thickness (with glmfit)? Many thanks Keith Postdoc research fellow Toronto Western Hospital 1. The temporal average is simply the average thickness: *avg = 0.5 * (thick1 + thick2)* 2. The rate of change is the difference per time unit, so *rate = ( thick2 - thick1 ) / (time2 - time1)*. 3. The percent change (pc1) is the rate with respect to the thickness at the first time point: *pc1 = rate / thick1*. 4. The symmetrized percent change (spc) is the rate with respect to the average thickness: *spc = rate / avg*.

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longitudinal hippocampal subfields
by Joana Braga Pereira 06 Nov '13

06 Nov '13

Dear all, I'm interested in assessing the changes in the volumes of hippocampal subfields between 2 time points. Can I use the longitudinal pipeline of Freesurfer and add the -hippo-subfields flag to the longitudinal runs of the 2 time points? Thanks!

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Re: [Freesurfer] feat to qdec
by Douglas N Greve 06 Nov '13

06 Nov '13

That should also be in $FREESURFER_HOME/bin. If not, just copy or symlink your flirt program to it. doug ps. Please remember to post to the FS list and not to me personally. thanks! On 11/06/2013 05:11 AM, Christophe de Bezenac wrote: > Thanks for responding Doug, > > <reg-feat2anat> is in my path. I've actually now managed to run <reg-feat2anat> till the <flirt.fsl> command which produces the error (Command not found). > > /Users/chdebezenac > flirt.fsl -ref /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/exf2anat.init.fsl.mat > flirt.fsl: Command not found. > ERROR: flirt > > Do you know why this might be? > > Thanks again, > Christophe > > > > On 5 Nov 2013, at 23:18, Douglas N Greve wrote: > >> Is reg-feat2anat in your path? It should be in >> $FREESURFER_HOME/bin/reg-feat2anat >> doug >> On 11/05/2013 12:15 PM, Christophe de Bezenac wrote: >>> Hi everyone, >>> >>> I am very new to freesurfer/qdec. What I would like to do is examine the results of a feat analysis in qdec and then perform further between-subject analyses with behavioural data (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer) I've run against problems at the first stage (registration) (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomi…) I imagine something is not set up right? >>> >>> Christophe-de-Bezenacs-MacBook-Pro:~ chdebezenac$ tcsh >>> setenv FREESURFER_HOME freesurfer >>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv FREESURFER_HOME freesurfer >>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% source freesurfer/SetUpFreeSurfer.csh >>> -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- >>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> FREESURFER_HOME freesurfer >>> FSFAST_HOME freesurfer/fsfast >>> FSF_OUTPUT_FORMAT nii.gz >>> SUBJECTS_DIR freesurfer/subjects >>> MNI_DIR freesurfer/mni >>> FSL_DIR /usr/local/fsl >>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv SUBJECTS_DIR freesurferX/subjects >>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR >>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% cd scan1Cor.feat >>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] chdebezenac% ln -s $SUBJECTS_DIR/fsaverage >>> ln: ./fsaverage: File exists >>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] chdebezenac% ln -s $SUBJECTS_DIR/S1 >>> ln: ./S1: File exists >>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] chdebezenac% reg-feat2anat --feat scan1Cor.feat --subject S1 >>> reg-feat2anat: Command not found. >>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] chdebezenac% cd >>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR >>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% ls >>> S1 S4 fbert lh.EC_average scan1Cor.feat >>> S2 S5 fbert2.feat qdec >>> S3 bert fsaverage rh.EC_average >>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% reg-feat2anat --feat scan1Cor.feat --subject S1 >>> reg-feat2anat: Command not found. >>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% >>> >>> Any help would be greatly appreciated, >>> >>> Christophe >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and properly >> dispose of the e-mail. >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] glmfit for paired-diff on 2 groups
by Vivian R. Steiger 06 Nov '13

06 Nov '13

Hi Doug Thanks for your answer on my issue "glmfit for paired-diff on 2 groups" in the mailinglist Commands: mris_preproc --target 1_average_30VPs --fsgd responder.txt --hemi lh --meas thickness --out respnon_lh_thickness.mgh —paired-diff-norm mri_surf2surf --hemi lh --s 1_average_30VPs --fwhm 25 --sval respnon_lh_thickness.mgh --cortex --tval respnon_lh_thickness.sm25.mgh mri_glmfit --y respnon_lh_thickness.sm25.mgh --fsgd responder_paired.txt doss --C sad_groups.txt --surf 1_average_30VPs lh --cortex --glmdir respnon_lh_thickness FSGD 1: (responder.txt) GroupDescriptorFile 1 Title Resonder_NonResponder Class resp Class nonresp Input 1Pre_VP02.long.VP02_Base resp Input 2Post_VP02.long.VP02_Base resp Input 1Pre_VP03.long.VP03_Base nonresp Input 2Post_VP03.long.VP03_Base nonresp Input 1Pre_VP04.long.VP04_Base resp Input 2Post_VP04.long.VP04_Base resp Input 1Pre_VP05.long.VP05_Base nonresp Input 2Post_VP05.long.VP05_Base nonresp Input 1Pre_VP06.long.VP06_Base resp Input 2Post_VP06.long.VP06_Base resp Input 1Pre_VP07.long.VP07_Base resp Input 2Post_VP07.long.VP07_Base resp Input 1Pre_VP08.long.VP08_Base resp Input 2Post_VP08.long.VP08_Base resp Input 1Pre_VP09.long.VP09_Base resp Input 2Post_VP09.long.VP09_Base resp Input 1Pre_VP10.long.VP10_Base nonresp Input 2Post_VP10.long.VP10_Base nonresp . . . FSGD 2: (responder_paired.txt) GroupDescriptorFile 1 Class resp Class nonresp Input VP02pair resp Input VP03pair nonresp Input VP04pair resp Input VP05pair nonresp Input VP06pair resp Input VP07pair resp Input VP08pair resp Input VP09pair resp Input VP10pair nonresp . . . Best, Vivian _____________________________________________________________ On 11/04/2013 03:34 PM, Douglas N Greve wrote: >Yes, that looks correct, though I could be more confident if you send >the command lines used and your fsgd file(s). >doug _____________________________________________________________ On 10/31/2013 07:32 AM, Vivian R. Steiger wrote: > Dear FS-Experts, > > I would like to compare 2 Groups (Responder (N=19) vs. Non-Responder (N=11)) > with longitudinal data. > Participants from both groups had only 2 scan sessions in each case 10 weeks > apart. > > So far is used the glmfit-variant with --paired-diff option in the first > place. (based on http://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis ) > > The paired-fsgd contained then 2 classes (Responder, Non-Responder) which is > used in glm-fit for comparison with the contrast (1 -1) for group diffs. > > This approach confirmed our hypothesized effects but I'm not sure whether I > used the right strategy. > > Could you might help me with this issue? > > Thank in advance > > > Best, > > Vivian > >

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Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem
by Douglas N Greve 06 Nov '13

06 Nov '13

Can you send your command lines for both aparc+aseg and aseg? doug ps. Please remember to post to the list and not to me personally. Thanks! On 11/05/2013 12:45 PM, Roderick McColl wrote: > Actually does not display properly at least not in freeview. > Slices are also upside down. > Also the output dims are 256x256x256 and I was expecting 182x218x182 which are the dims > For $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz. > But I agree that I should get in contact which the FSL people also. > Thanks > -roddy > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Monday, November 04, 2013 5:22 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem > > > Hi Roddy, aparc+aseg.mgz and aseg.mgz are in the exact same space and the same command line should generate the same result. Does it display properly in tkmedit? If so and if you're having problems visualizing with fslview, contact the FSL crew. > doug > > > > > On 11/04/2013 05:52 PM, Roderick McColl wrote: >> Hmmm, >> >> Actually using aseg.mgz works just fine (just tried this now), >> displays correctly on fslview. >> What I was really trying to do was convert aparc+aseg.mgz which does >> not provide the expected orientation in fslview. >> Does this mean aparc+aseg.mgz and aseg.mgz are in different spaces somehow? >> >> For the aparc_aseg_mni152.nii.gz output, >> 1) the coronal image in fslview (top left) >> has the S/I labels upside down compared to the coronal slice, >> (or the coronal slice upside down compared to the S/I labels) >> 2) the sagittal image (top right) has the same S/I issue >> 3) the axial image (bottom left) has the A/P labels the >> opposite of the image slice. >> >> Thanks for any advice >> >> -roddy >> >> ________________________________________ >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Roderick McColl >> [Roderick.McColl(a)utsouthwestern.edu] >> Sent: Monday, November 04, 2013 3:37 PM >> To: freesurfer(a)nmr.mgh.harvard.edu >> Subject: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into >> $FSLDIR Nifti with MNI152_T1_1mm target >> >> I am obviously using mri_vol2vol incorrectly but I'm stumped. >> >> Goal is to get the $SUBJECTS/fsaverage/mri/aseg.mgz file into the FSL MNI152 space to do some fslmaths. >> >> >From looking around it seemed the command to accomplish this is >>> (inside $SUBJECTS/fsaverage/mri) >> mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz \ >> --mov aseg.mgz --reg transforms/reg.mni152.1mm.dat --o >> asegmni152.nii.gz >> >> which does execute but if I load asegmni152.nii.gz into fslview all of the orthogonal views are upside down. >> >> There is something missing regarding the co-ordinate system but I'm not sure what. >> >> Can anyone point me in the right direction? >> >> Thanks >> >> -roddy >> >> ________________________________ >> >> UT Southwestern Medical Center >> The future of medicine, today. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom >> it is addressed. If you believe this e-mail was sent to you in error >> and the e-mail contains patient information, please contact the >> Partners Compliance HelpLine at http://www.partners.org/complianceline >> . If the e-mail was sent to you in error but does not contain patient >> information, please contact the sender and properly dispose of the e-mail. >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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mri_label2vol not working
by Zhao Jingjing 06 Nov '13

06 Nov '13

Hi Doug, I have tried the command that you suggested below. Still not working. System gave the same error message again "segment fault". Any other ideas? Best wishes, Jingjing * try running this command mri_label2vol --label lh.words10_10.label --temp rawavg.mgz --reg rawreg.dat --fillthresh .5 --o lh.words10_10.nii * On 11/04/2013 07:55 AM, Zhao Jingjing wrote: > Hi Doug, > > I asked a question a couple days ago for how to convert .label files > into .nii files in freesurfer. At the end of this email, you can see > the original email from me and your response. > > I tried to run the function mri_label2vol by myself. However, it seems > not working quite well. > > In order to run mri_label2vol, it seems that I have to have a > registration.dat file. I search online for how to generate it and get > an answer from maillinglist posted by you several years ago. That is, > I need to run the function of tkregister2. Then I tried to find out > how to run tkregister2 and I found out an example suggested by you, > although I don't know how it works because there is no information > online for this function. > > Your example is like this: > > *tkregister2 --mov rawavg.mgz --targ aseg.mgz --regheader > --regrawreg.dat --noedit* > > > I ran it and it successfully generated a rawreg.dat file, but I don't > know if it is a correct file that I should use. Below is the results > that I got from the command window: > > *tkregister_tcl /opt/freesurfer/lib/tcl/ tkregister2.tcl > target volume aseg.mgz > movable volume rawavg.mgz > reg file rawreg.dat > LoadVol 0 > ZeroCRAS 0 > $Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $ > Diagnostic Level -1 > INFO: loading target aseg.mgz > Ttarg: -------------------- > -1.000 0.000 0.000 128.000; > 0.000 0.000 1.000 -128.000; > 0.000 -1.000 0.000 128.000; > 0.000 0.000 0.000 1.000; > INFO: loading movable rawavg.mgz > Tmov: -------------------- > -0.900 0.000 0.000 100.799; > 0.000 0.000 0.898 -115.000; > 0.000 -0.898 0.000 115.000; > 0.000 0.000 0.000 1.000; > mkheaderreg = 1, float2int = 0 > Computing reg from header (and possibly input matrix) > ---- Input registration matrix (computed) -------- > -1.000 -0.012 -0.025 -0.000; > -0.025 0.069 0.997 0.000; > 0.010 -0.998 0.070 -0.000; > 0.000 0.000 0.000 1.000; > --------------------------------------- > ---- Input registration matrix -------- > -1.000 -0.012 -0.025 -0.000; > -0.025 0.069 0.997 0.000; > 0.010 -0.998 0.070 -0.000; > 0.000 0.000 0.000 1.000; > Determinant -1 > subject = subject-unknown > RegMat --------------------------- > -1.000 -0.012 -0.025 -0.000; > -0.025 0.069 0.997 0.000; > 0.010 -0.998 0.070 -0.000; > 0.000 0.000 0.000 1.000;* > > Then I tried to run the function of mri_label2vol. I specifically > referred to the example posted online in freesurfer website. It seems > to me that this is a popular function that a lot of people have used. > My command line is as below: > > *mri_label2vol --label lh.words10_10.label --temp T1.mgz --reg > rawreg.dat --fillthresh .5 --o lh.words10_10.nii* > > > However, my command line didn't run successfully to generate the nii > file that I want. The error message is "segmentation flaut". Here I > attached all the results from the command window after I run this > function. > > *Number of labels: 1 > lh.words10_10.label > Annot File: (null) > Template Volume: T1.mgz > Outut Volume: lh.words10_10.nii > Registration File: rawreg.dat > Fill Threshold: 0.5 > Label Vox Vol: 1 > ProjType: (null) > ProjTypeId: 0 > ProjStart: 0 > ProjStop: 0 > ProjDelta: 0.1 > Subject: (null) > Hemi: (null) > UseNewASeg2Vol: 1 > DoLabelStatVol 0 > $Id: mri_label2vol.c,v 1.32 2009/10/22 23:35:53 greve Exp $ > Template RAS-to-Vox: -------- > -1.000 0.000 0.000 128.000; > -0.000 -0.000 -1.000 128.000; > -0.000 1.000 -0.000 128.000; > 0.000 0.000 0.000 1.000; > Template Voxel Volume: 1 > nHits Thresh: 0.5 > Loading registration from rawreg.dat > RegMat: -------- > -1.000 -0.012 -0.025 -0.000; > -0.025 0.069 0.997 0.000; > 0.010 -0.998 0.070 -0.000; > 0.000 0.000 0.000 1.000; > Label RAS-to-Vox: -------- > 1.000 0.012 0.025 128.000; > -0.010 0.998 -0.070 128.000; > -0.025 0.069 0.997 128.000; > 0.000 0.000 0.000 1.000; > Allocating Hit Volume (16777216) voxels > nlabels = 1 > Loading lh.words10_10.label > > Thesholding hit volume. > Segmentation fault* > > > I was surprised by this result, because it tells me that "the template > voxel volume is 1". How strange! And finally, no nii file was generated. > > Can you help check whether I did something wrong? Attachment I put the > files that might be used for running these two functions (I didn't put > T1.mgz and rawavg.mgz in this email since it makes the file bigger > than 500K, but if you need it please let me know and I will send you > the link from my dropbox). I might need to specify more parameters in > the functions, which I didn't how to either. If you can supervise me > for how to write the functions correctly, that would be really > appreciated. > > And after I generate nii file, how can I visualize it and see how it > matches the ROI from the .label file? I tried tksurfer "subject name" > lh inflated, but it doesn't work. If I can get some instructions for > this command, that would be also helpful. > > Thanks. > > Best, > Jingjing > > > > Date: Tue, 29 Oct 2013 10:21:59 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] how to transfer .label file to .nii file > To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <526FC487.6020601(a)nmr.mgh.harvard.edu > <mailto:526FC487.6020601@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > You can use mri_label2vol to create a nii mask from the label. To map > the label to the DTI space, register your DTI (b=0) to the anatomical > using bbregsiter. You can then use mri_label2vol to transfer the label. > > doug > > > On 10/28/2013 06:14 AM, Zhao Jingjing wrote: > > Hi, > > > > Our lab have managed to generate ROIs in T1 images using Freesurfer, > > which led to .label files. We succesfully measured the cortical > > thickness in these ROIs for each subject in Freesurfer. Now we are > > aiming to track white matter fibers from these ROIs in a tractography > > software Trackvis. However, .lable files seem not be readable in > > Trackvis. Thus, we are wondering if .label files can be tranferred to > > .nii files easily in Freesurfer so that we can use the converted .nii > > ROI files to track fibers in Trackvis. Another related question is how > > can we coregister the ROIs drawn in T1 images with DTI images and make > > sure that those ROIs converted from T1 images are the still in the > > same regions in the DTI images? > > > > Thanks. > > Jingjing Zhao

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Re: [Freesurfer] How do you create labels from binary masks?
by Douglas N Greve 06 Nov '13

06 Nov '13

areyou loading the label (output of mri_cor2label) or did you create an annotation? Try loading the label. Then try loading LeftHippoBody_surf.mgh. If that does not look ok, check the registration between binLeftHippoBody.mgz and subj1 with --regheader doug On 10/24/2013 06:40 PM, Marcos Martins da Silva wrote: > Hi, Doug > Thanks again for your help. > Using the command tksurfer suj1 lh surfHippo, I get the surface loaded > in tksurfer in the same way that I get in freeview. The only > difference is that the terminal window output is more verbose and that > is valuable when investigating this kind of situation. I am attaching > a screenshot. I got this just after I used tksurfer to import an > annotation (lh.surfHippo + hippo.annot.png). > The screenshot show just a few vertices with color. Indeed this is > similar to what we see in freeview, except that in this last tool all > vertices not in label appears in black and tksurfer preserves the gray > color. > At terminal output we can see tksurfer expects the surface refers to > lh.white. That is not the case, I guess. I think it helps explain the > terminal window output we see in freeview and also in tksurfer when I > try to load the annot file. It seems we have lots of vertices in annot > file that both tools cannot find in surface file and at the same time > we have lots of vertices in my surface file not described in the annot > files. At least now I can understand the situation. It puzzles me > because the surface, binary masks, labels and annotations were created > from the same source: the posterior*.mgz files created by recon-all > --hippo-subfields. But, well, I probably misunderstood something in > documentation and lost my way in some point. I hope you can help me > with the correct steps to be followed. I still dream of showing the > hippocampus in a similar way we do with cortex when we load lh.pial > and lh.aparc.annot. > Thank you for your help and attention. > Cheers, > Marcos. > Em Qui, 2013-10-24 às 12:40 -0400, Douglas N Greve escreveu: >> Can you load it properly in tksurfer? >> >> >> On 10/23/2013 12:44 AM, Marcos Martins da Silva wrote: >> > >> > Hi, Doug >> > Sorry for this late feedback. >> > Just so you can understand what is binLeftHippoBody.mgz I will explain >> > its origin. >> > 1) recon-all --hippo-subfields >> > 2) mri_concat the posterior*.mgz to get the whole hippocampus >> > 3) a custom octave routine to segment the whole hippocampus into head, >> > body and tail. This routine preserves the probability values of the >> > original posterior*.mgz >> > 4) mri_binarize the whole hippocampus and its segments. So >> > binLeftHippoBody.mgz is the binary mask of left hippocampal body. >> > 5) mri-tesselate and mris_smooth the whole hippocampus binary mask to >> > create a surface (lh.surfHippo) >> > >> > Now that is the reason I would like to get the surface labels for >> > head, body and tail. I would like to build a annot in order to display >> > the colored segments over the whole hippocampus surface. >> > Your last tip was great and now I have vertex numbers at the labels >> > files and mris_label2annot works. It follows the commands I used to >> > process the hippocampal body: >> > mri_vol2surf --src binLeftHippoBody.mgz --out LeftHippoBody_surf.mgh >> > --out_type mgh --hemi lh --regheader suj1 --surf surfHippo >> > mri_cor2label --i LeftHippoBody_surf.mgh --surf suj1 lh surfHippo --id >> > 1 --l lh.HippoBody.label >> > >> > I put the --surf parameter pointing to lh.surfHippo because, if not, >> > it would use lh.white (default). As I said it works but the results >> > are not visually correct (see attached file). The surface loads on >> > freeview with no problem but if I try to load the label representing >> > the body or the annot with the 3 segments they do not appear. It seems >> > only a small part of the vertices appears in blue. I also get the >> > following output at the terminal window I used to start freeview: >> > >> > MRISreadAnnotationIntoArray: vertex index out of range: 122882 >> > i=00000000, in_array_size=11627 >> > annot file: ../label/lh.Hippo.annot >> > MRISreadAnnotationIntoArray: vertex index out of range: 122883 >> > i=00000000, in_array_size=11627 >> > annot file: ../label/lh.Hippo.annot >> > MRISreadAnnotationIntoArray: vertex index out of range: 122884 >> > i=00000000, in_array_size=11627 >> > annot file: ../label/lh.Hippo.annot >> > MRISreadAnnotationIntoArray: vertex index out of range: 122885 >> > i=00000000, in_array_size=11627 >> > annot file: ../label/lh.Hippo.annot >> > reading colortable from annotation file... >> > colortable with 4 entries read (originally ../label/Hippo.ctab) >> > colortable with 4 entries read (originally ../label/Hippo.ctab) >> > =00000000, in_array_size=11627 >> > >> > Since the posterior*.mgz files are 0.5 x 0.5 x 0.5 mm I also tried to >> > use mri_convert --vs 1 1 1, but it did not worked too. >> > I guess, or at least, I hope I am closer the image I want but I guess >> > some more steps are necessary. >> > Thank you for any help. >> > Marcos >> > >> > >> > >> > Em Qui, 2013-10-17 às 22:19 -0400, Douglas Greve escreveu: >> >> >> >> Is *binLeftHippoBody.mgz a volume label or a surface label? If a >> >> volume label, map it onto the surface with mri_vol2surf, the run >> >> mri_cor2label *specifying --surf >> >> >> >> doug >> >> >> >> >> >> >> >> >> >> On 10/17/13 5:00 PM, Marcos Martins da Silva wrote: >> >> >> >>> Hi, Doug >> >>> Thank you for your answer. >> >>> >> >>> I am trying cor2label as you suggested. First of all I am afraid to >> >>> say that website documentation and help from the own command are a >> >>> bit different so I got a little confused. But the following command >> >>> worked: *mri_cor2label --i binLeftHippoBody.mgz --id 1 --l 2.leftBody* >> >>> >> >>> Using freeview I could load the hippocampus volume and 2.leftBody as >> >>> a ROI. I attached a screenshot that also included 1.leftHead and >> >>> 3.leftTail, generated in the same way. >> >>> When I tried to concatenate the 3 labels into an annot file I got an >> >>> error: >> >>> >> >>> *mris_label2annot --s bert --h lh --ctab HippoColorLUT.txt --l >> >>> 1.leftHead.label --l 2.leftBody.label --l 3.leftTail.label --a >> >>> lefthippo* >> >>> *Loading /home/marcos/freesurfer/subjects/bert/surf/lh.orig* >> >>> *1 16711680 leftHead* >> >>> *ERROR: 1.leftHead.label, n=0, vertex -1 out of range* >> >>> >> >>> When I checked label file generated by mri_cor2label the first >> >>> collumn (vertex number) contains only *-1* as value. >> >>> It seems that when you use mri_cor2label it does not preserve or >> >>> even recover the vertex number. It also seems I need the correct >> >>> vertex number in label file to use mris_label2annot >> >>> Just to rule out a problem with the hippocampal subfield files I >> >>> tried the example command (extracted from command help): >> >>> mri_cor2label --i aseg.mgz --id 12 --l left-putamen.label >> >>> This label also shows only -1 as vertex number. >> >>> >> >>> Could you please explain me what do I need to do to get the vertex >> >>> numbers in the label file as output of mri_cor2label? >> >>> >> >>> Cheers, >> >>> Marcos >> >>> >> >>> >> >>> >> >>> Em Qua, 2013-10-16 às 20:34 -0400, Douglas Greve escreveu: >> >>>> I think you need to use mri_cor2label (not very well named:) >> >>>> doug >> >>>> >> >>>> >> >>>> On 10/16/13 4:24 PM, Marcos Martins da Silva wrote: >> >>>> >> >>>>> Hi, Freesurfers. >> >>>>> I need to create some labels from binary masks. Sometime ago I >> >>>>> read a post >> >>>>> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-October/033783.… >> >>>>> ) and, unless I am wrong, it seemed to me that mri_label2vol could >> >>>>> be the tool to get it. If so, could you please explain how? I >> >>>>> read documentation on wiki and help from the command itself and >> >>>>> could not see how to accomplish that. I could only find how to >> >>>>> create a volume from a label. What I need to do is to get a mask >> >>>>> like the binLeftHippoHead.mgz (attached) and create a label. >> >>>>> Assuming it is possible, I could also make labels for Hippocampal >> >>>>> body and head, merge the 3 labels into an annot file. This way i >> >>>>> can use Freeview to load the whole hippocampal surface and >> >>>>> discriminate the 3 segments by colors with the annot file. >> >>>>> Thanks in advance for any help. >> >>>>> Cheers, >> >>>>> Marcos. >> >>>>> >> >>>>> _______________________________________________ >> >>>>> Freesurfer mailing list >> >>>>>Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >>>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>>> >> >>>> _______________________________________________ >> >>>> Freesurfer mailing list >> >>>>Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>>> >> >>>> >> >>>> The information in this e-mail is intended only for the person to whom it is >> >>>> addressed. If you believe this e-mail was sent to you in error and the e-mail >> >>>> contains patient information, please contact the Partners Compliance HelpLine at >> >>>>http://www.partners.org/complianceline . If the e-mail was sent to you in error >> >>>> but does not contain patient information, please contact the sender and properly >> >>>> dispose of the e-mail. >> >>> >> >> >> > >> > >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

3 8

feat to qdec
by Christophe de Bezenac 06 Nov '13

06 Nov '13

Hi everyone, I am very new to freesurfer/qdec. What I would like to do is examine the results of a feat analysis in qdec and then perform further between-subject analyses with behavioural data (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer) I've run against problems at the first stage (registration) (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomi…) I imagine something is not set up right? Christophe-de-Bezenacs-MacBook-Pro:~ chdebezenac$ tcsh setenv FREESURFER_HOME freesurfer [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv FREESURFER_HOME freesurfer [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% source freesurfer/SetUpFreeSurfer.csh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME freesurfer FSFAST_HOME freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR freesurfer/subjects MNI_DIR freesurfer/mni FSL_DIR /usr/local/fsl [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv SUBJECTS_DIR freesurferX/subjects [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% cd scan1Cor.feat [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] chdebezenac% ln -s $SUBJECTS_DIR/fsaverage ln: ./fsaverage: File exists [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] chdebezenac% ln -s $SUBJECTS_DIR/S1 ln: ./S1: File exists [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] chdebezenac% reg-feat2anat --feat scan1Cor.feat --subject S1 reg-feat2anat: Command not found. [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] chdebezenac% cd [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% ls S1 S4 fbert lh.EC_average scan1Cor.feat S2 S5 fbert2.feat qdec S3 bert fsaverage rh.EC_average [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% reg-feat2anat --feat scan1Cor.feat --subject S1 reg-feat2anat: Command not found. [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% Any help would be greatly appreciated, Christophe

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Freesurfer November 2013