Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Problems with autorecon2-cp
by Annemarie Brandhofe 07 Nov '13

07 Nov '13

Dear freesurfer community, we are conducting cortical-thickness analysis using freesurfer-5.3.0 and have been experiencing a problem with the automatic recognition of the control points. After setting the control points and running autorecon2-cp white matter segmentation is faulty in almost every slice. I attached screenshot of two slices. Can you recommend us a procedure to improve the automatic recognition of control points? Below, we provide the details of our setup. Feel free to ask for more information. Thank you very much for your help! Yours sincerely, Annemarie $ bugr FREESURFER_HOME: /apps/prod/i486/freesurfer-5.3.0 Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Debian version: 5.0.6 Kernel info: Linux 2.6.27.39-1-ql-beowulf i686 $ which freesurfer -> /apps/prod/i486/freesurfer -5.3.0/bin/freesurfer Used command: recon-all –autorecon2-cp –subjid ET39_mdeft.

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Literature values of cortical thickness
by Emma Biondetti 07 Nov '13

07 Nov '13

Dear Freesurfer experts, I need to compare the cortical thickness values, obtained from a data set of 32 healthy subjects, with some reference literature values of cortical thickness. I'd like to check the values of mean and standard deviation for each one of the 32 cortical parcellations automatically generated by Freesurfer. This is to decide if the data set can be used for the following steps of my work or not. On the mailing list, I read an old thread that talks about the existence of a set of literature reference values, obtained by Rauhl Desikan. Would it be possible to access those data? Thank you Emma Biondettu

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Re: [Freesurfer] MRISread error
by Anita van Loenhoud 07 Nov '13

07 Nov '13

It finally worked! Thank you so much Louis. My SUBJECTS_DIR was pointing to a folder within my TUTORIAL_DATA directory (I thought it was supposed to be like that when I read the instructions), but now they point to the same folder and it works. Thanks again! Anita

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A question as to subcortical volumetric measurement
by jh kim 07 Nov '13

07 Nov '13

Dear Doug and experts I've analyzed structural changes of the subcortical GM by using both VBM (DARTEL in SPM8) and subcortical volumemetric measurement using FreeSurfer 5.1. While there is no significant volumetric difference between the groups in VBM (corrected p<0.05), FS results showed that some subcortical GM had significant volume reductions in patients relative to controls (MANCOVA controlling for the effect of ICV, age, gender, followed by Bonferroni correction). One of the referees raised the question regarding this discrepancy between the VBM and FS findings. How can I cope with it? Thank you in advance for your help. Kim

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unilateral hippocampus segmentation fail
by Andreas Berger 07 Nov '13

07 Nov '13

Hi FreeSurfers, i came across a few subjects in which FreeSurfer 5.3 failed to properly label most of the hippocampus in one hemisphere. Specifically, it is the left hippocampus in all of the 5 cases in which this occured. The subjects are young, healthy, and without any anatomical peculiarities. Segmentation was fine in these subjects with FreeSurfer 5.1. Screenshots of one of these subjects are attached. EDIT: that didn't seem to work, i uploaded them here: http://www.students.meduniwien.ac.at/~n0642496/files/freesurfer/freeview_hi… http://www.students.meduniwien.ac.at/~n0642496/files/freesurfer/freeview_hi… regards, Andreas

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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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