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30088 discussions

GLM question
by Govindarajan, Koushik Athreya 23 Dec '11

23 Dec '11

Hello group, I am a new user of Freesurfer and just learning to process data through the pipeline. Sorry if this is an amateur question. I was just trying to look at cortical thickness differences between a patient group and a control group. So, my fsgd file would just list the input files and the corresponding diagnosis. Now, if I were to design a contrast matrix to look at cortical thickness differences between the 2 groups, I understand that I would have only 2 regressors . So, my contrast matrix would just be [-1 1]? I tried doing that and I got a matrix read error for the contrast file. Thanks in advance for your help. Regards Koushik

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about labels
by LAOUCHEDI MAKHLOUF 23 Dec '11

23 Dec '11

hi eveyone i am quite new in freesurfer, is it possible to generate aparc.a2009s+aseg.mgz from aparc.a2005s+aseg.mgz without re running recon-all thanks

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Surface-based cortical volume calculation
by _andreia_＠sapo.pt 23 Dec '11

23 Dec '11

Hello, Recalling these emails: "The methods are somewhat different. For the value in the aseg.stats table, the method is to compute the total volume inside the pial surface and subtract the total volume inside the white surface. For mris_anatomical_stats, the method is to compute the thickness times area of each vertex. This method will probably underestimate the total volume because it uses the area of the white surface when it should use the area of the surface in the middle between the white and pial surfaces. I've added this to the list of known issues on our release page. doug Alexopoulos, Dimitrios wrote: > I have generated surfaces using the the centos4 build (version 5.0) > and want to confirm that my surface-based GM and WM volumes are correct. > For the surface-based GM calculation I originally used > 'mris_anatomical_stats -l lh.cortex.label subjectID hemi' > (run from within the 'label' subdirectory) and for WM i used > 'mris_wm_volume subjectID hemi' (run from within > the 'surf' subdirectory). > When I add the calculated left/right cortical volumes, I get a total > that is different from what is output in > the 'aseg.stats' file, which in version 5.0 is noted to contain > total surface-based GM volume > (Cortex, CortexVol: Total cortical gray matter volume (based on > surface-stream). > What are the correct GM and WM surface-based volumes? > Thanks. Jim" I question came up to me: The surfaces in the hippocampus/amygdala are inaccurate and should be ignored. However, in version 5.0 the cortical volume is surface-based, thus it takes into account the surfaces in the hippocampus/amygdala, is this correct? If so, it is expected that an error is introduced in the surface-based calculation of cortical volume. Has anyone checked the influence of this error? Or FS compensates for the inaccuracy of the surface estimation of these regions somehow? Thanks! Andreia

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FsFast Functional Connectivity with subject-specific surface seeds
by konglq＠nmr.mgh.harvard.edu 22 Dec '11

22 Dec '11

Hi Freesurfers, We are trying to do a resting-state functional connectivity analysis using freesurfer. Instead of using the aparc+aseg segmentations as seeds, we would like to use a subject-specific surface labels that we have defined apriori. In the fcseed-config step, we then don't have a "segid" as in the anatomical seeds case. What should we specify as the -segid and -seg (segmentation)? We also looked into the ROI-based options using "-roi" but this takes seeds from output of "funcroi-config" and requires that we specify a contrast and an analysis. How should we just specify a surface label without generating a new analysis and contrast? Any help or suggestions are appreciated. Lingqiang

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mri_matrix_multiply to move functional images to common space
by Andrew Dumas 22 Dec '11

22 Dec '11

Hi, I'm trying to move a bunch of partial FOV functional images (occipital cortex only with oblique coronal slices) into common space. For each subject, I have a registration file (register.dat) to register functional images to anatomicals, and I'd like to incorporate the talairach.xfm registration so that I have a matrix that registers the functional images to the mni305 volume. I've been using the following, but registrations aren't coming out properly: mri_matrix_multiply -im register.dat -iim <subject>/mri/transforms/talairach.xfm -om reg_to_common.dat I'm checking them using tkregister2, but the results don't look great. Is there a better/easier way to do this? Thanks! Andrew

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Re: [Freesurfer] mri_matrix_multiply to move functional images to common space
by Douglas N Greve 22 Dec '11

22 Dec '11

Yea, you need to do it in the two steps you mention. You can do that from one command line with something like bbregister --s subject --mov epi.nii --init-{fsl,header} --bold --int aascout.nii --o register.dat The --int is an "intermediate" volume. doug Andrew Dumas wrote: > That did the trick, thank you! As for using bbregister, I haven't had > any luck using bbregister for the partial volume EPIs... they're always > off. We have a strange protocol where only the functionals get the > 32-channel coil, so right before the EPIs get done I have an AAscout > image. I've been using bbregister to align the FS MPRAGE scans with the > AAscout (first frame), then using that registration on the EPIs. It > seems to come out a LOT better than using bbregister on EPIs directly. > > Andrew > > > On Tue, 2011-12-20 at 14:58 -0500, Douglas N Greve wrote: > >> Hi Andrew, use mri_vol2vol with the --tal --talres 2 or 2mm option (or >> --talres 1 for 1mm isotropic) option. This will put it into an MNI305 >> space. So something like >> >> mri_vol2vol --reg register.dat --mov yourvolume.nii --tal --talres 2 --o >> yourvolume.mni305.nii >> >> If you did not create the register.dat with bbregister, I would strongly >> suggest it. It works really well on the partial volume files. If you do, >> you should specify your current register.dat as the init registration. >> >> doug >> >> Andrew Dumas wrote: >> >>> Hi, >>> >>> I'm trying to move a bunch of partial FOV functional images (occipital >>> cortex only with oblique coronal slices) into common space. For each >>> subject, I have a registration file (register.dat) to register >>> functional images to anatomicals, and I'd like to incorporate the >>> talairach.xfm registration so that I have a matrix that registers the >>> functional images to the mni305 volume. I've been using the following, >>> but registrations aren't coming out properly: >>> >>> mri_matrix_multiply -im register.dat -iim >>> <subject>/mri/transforms/talairach.xfm -om reg_to_common.dat >>> >>> I'm checking them using tkregister2, but the results don't look great. >>> Is there a better/easier way to do this? Thanks! >>> >>> Andrew >>> >>> _______________________________________________ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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labels broblem
by LAOUCHEDI MAKHLOUF 22 Dec '11

22 Dec '11

hi everyone i run recon-all -all on some subjects using the 5.1 version of freesurfer and instead of getting aparc.a2009s+aseg.mgz i got aparc.a2005s+aseg.mgz. the components of the cingulate cortex are quite different in both files a2005s and a2009s : in a2009s i used in my work: 11108 ctx_lh_G_and_S_cingul-Mid-Post 11109 ctx_lh_G_cingul-Post-dorsal 11110 ctx_lh_G_cingul-Post-ventral and in a2005s the whole labals of the cingulate cortex are : 1103 ctx-lh-G_cingulate-Isthmus 1104 ctx-lh-G_cingulate-Main_part 1200 ctx-lh-G_cingulate-caudal_ACC 1201 ctx-lh-G_cingulate-rostral_ACC 1205 ctx-lh-S_cingulate-caudal_ACC 1206 ctx-lh-S_cingulate-rostral_ACC 1207 ctx-lh-S_cingulate-posterior 1002 ctx-lh-caudalanteriorcingulate 1147 ctx-lh-S_cingulate-Main_part_and_Intracingulate 1148 ctx-lh-S_cingulate-Marginalis_part is there any way to get the a2009s cingulate components labels using the a2005s labels in the aparc.a2005s+aseg.mgz. thanks

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mri_glmfit-sim error
by j janssen 22 Dec '11

22 Dec '11

Hi, - FS version: 5.1 - system: Linux neuro3 2.6.27.41-170.2.117.fc10.x86_64 #1 SMP Thu Dec 10 10:36:29 EST 2009 x86_64 x86_64 x86_64 GNU/Linux - on-screen error output: cmdline mri_glmfit --glmdir rh_thickness_men_20fwhm_asp_vs_con_controlling_for_IQ_AGE --y rh.thickness.fwhm20.men.age.iq.mgh --fsgd FSGD_1F3L_2C.txt dods --C asp_vs_con_controlling_for_IQ_AGE.txt --surface fsaverage rh SURFACE: fsaverage rh log file is rh_thickness_men_20fwhm_asp_vs_con_controlling_for_IQ_AGE/cache.mri_glmfit-sim.log cd /home/neuro/asperger_psychosis_study/freesurfer51/qdec/3groups/DIAGNOSE_CI_AGE /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir rh_thickness_men_20fwhm_asp_vs_con_controlling_for_IQ_AGE --cache 1.3 abs $Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Wed Dec 21 15:58:23 CET 2011 Linux neuro3 2.6.27.41-170.2.117.fc10.x86_64 #1 SMP Thu Dec 10 10:36:29 EST 2009 x86_64 x86_64 x86_64 GNU/Linux neuro setenv SUBJECTS_DIR /home/neuro/asperger_psychosis_study/freesurfer51 FREESURFER_HOME /usr/local/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --glmdir rh_thickness_men_20fwhm_asp_vs_con_controlling_for_IQ_AGE --y rh.thickness.fwhm20.men.age.iq.mgh --fsgd FSGD_1F3L_2C.txt dods --C asp_vs_con_controlling_for_IQ_AGE.txt --surface fsaverage rh DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 31.421003 ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm31/abs/th13/mc-z.csd rh.thickness.fwhm20.men.age.iq.mgh was created by (i've attached the pertaining preproc log file): /usr/local/freesurfer/bin/mris_preproc --out rh.thickness.fwhm20.men.age.iq.mgh --target fsaverage --hemi rh --meas thickness --fsgd FSGD_1F3L_2C.txt --fwhm 20 when i create rh.thickness.fwhm25.men.age.iq.mgh (i've attached the pertaining preproc log file) the following command: mri_glmfit-sim --glmdir rh_thickness_men_25fwhm_asp_vs_con_controlling_for_IQ_AGE --cache 1.3 abs *does* work with output fwhm = 3.015979 what am i doing wrong? thanks, -joost

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Error with mri_cvs_register
by Antonella Kis 22 Dec '11

22 Dec '11

Dear experts, I was running the mri_cvs_register for a few times for a subject and I am getting an error. The registration will not bwe completed but I got most of the files so I wonder if I need to re-run the whole registration steps or there is a way to just re-run the registration from the step where it stopped. If yes, how I can continue the registration? Many thanks and Happy Holidays! Antonella

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Reading annotation file in Matlab
by Martijn Steenwijk 22 Dec '11

22 Dec '11

Dear all, I'm trying to read aparc.annot into Matlab using the matlab/read_annotation.m function. Is it correct that the *labels* read by this function do not correspond with for example the FreeSurferColorLUT? Are the labels stored as 16 bit (unsigned)integers, or in another way? Best, Martijn

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