Freesurfer

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30132 discussions

mri_compute_volume_fractions
by Adrian Garcia 14 Apr '12

14 Apr '12

I would like to have Freesurfer calculate the percentage of wm/gm/csf from an MRI volume (produced with mri_volsynth). I have run recon-all to completion and have a registration matrix from the MRI to the Freesurfer anatomical (tkregister2). It looks like mri_compute_volume_fractions will do what I want, but I am not sure what parameters to supply, particularly the <output stem>. Would somebody be able to point me to some documentation for this function or an example of the command line to output the segmentation information? Best wishes Adrian

2 1

long.qdec.table.dat question
by Sabin Khadka 13 Apr '12

13 Apr '12

Hi all, I am trying to use qdec to perform comparison of cortical thickness in two different time periods. So I ran recon-all base and recon-all -long. then defined long.qdec.table.dat as fsid fsid-base years MRI_001_T1 MRI_001 0 MRI_001_T2 MRI_001 2 When I tried to run qdec it says it "cant find MRI_001_T1/surf/lh.thichkeness.fwhm10.fsaverage.mgh" which I think makes sense because I did not run qcache to smooth the surface. So my question is Is the way I am writing my lon.qdec.table.dat correct or should it be fsid fsid-base years MRI_001_T1.long.MRI_001 MRI_001 0 MRI_001_T2 .long.MRI_001 MRI_001 2 Also, if I need to run qcache should I run in MRI_001_T1 or MRI_001_T1.long.MRI_001. Thanks. Sabin

2 1

created a new subcortical atlas; what's next?
by Anthony Dick 13 Apr '12

13 Apr '12

Hello, I successfully created a new subcortical atlas for the cerebellum (at least I think I did--not sure how to check it without running a new segmentation). If I want to apply this to many brains, I think I want to run: recon-all -subcortseg -subjid <subject name> How do I tell it to call, e.g., RB_all_withskull_2012-04-13.gca instead of e.g., RB_all_withskull_2008-03-26.gca. Basically, I want to apply the new cerebellar parcellation to existing freesurfed brains. Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://www.fiu.edu/~adick Lab Webpage: http://dcn.fiu.edu

3 2

bbregister for fmri FEAT data
by Erlend Hodneland 13 Apr '12

13 Apr '12

Hi, we are trying to register fmri FEAT data (example_func.nii) to the anatomical scan (processed in Freesurfer) using bbregister to opt. the affine registration before running FNIRT. However, the orientation of the registered image is flipped around and is incorrect after applying bbregister. We have tried: 1) bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-header --bold --o example_func2highres-fs.nii 2) bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-fsl --bold --o example_func2highres-fs.nii 3) bbregister --s subj_501 --o example_func2highres-fs.nii --feat "myfeatdirectory" 4) tkregister2 --mov example_func.nii --regheader --reg tkreg.dat (this one looks correct) followed by bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-reg tkreg.dat --bold --o example_func2highres-fs.nii 5) reorienting to match the highres: fslorient -swaporient example_func fslswapdim example_func x -y z example_func_swap (correct orientation) followed by bbregister --s subj_501 --mov example_func_swap.nii.gz --reg register.dat --init-fsl --bold --o example_func_swap2highres-fs.nii with the output being flipped in wrong orientation for all options. We would greatly appreciate if you have any suggestions for how to overcome this problem! Cheers/Sincerly/All best Erlend Hodneland

2 1

qdec, monte-carlo clusterwise simulation, mutiple comparisons correction
by Mahinda Yogarajah 13 Apr '12

13 Apr '12

Dear Experts, I wonder whether someone could explain to me how the monte-carlo correction in qdec manages to be instantaneous. I appreciate it uses pre-computed data, but I am a little confused. I thought that this sort of permutation based method is based on relabelling of one's own specific dataset, and therefore do not understand how precomputed data is used. Thanks for the help. Mahinda

2 1

Freeview problem
by carlo cotugno 13 Apr '12

13 Apr '12

I'm a newbie with FreSurfer and Linux. I'm following Longitudinal Processing-Tutorial. now I have only files of tutorial data set and I don't have any other file to test. I can run Freeview and I can load volume from terminal and from interface, but when I try to load surfaces (from terminal with correct command -f OAS2.... or from interface of Freeview) I have the same result: Freeview interface crashes and in the terminal I find: MatrixMultiply: m2 is null! No such file or directory. I tried also with other surfaces and I had the same result. F <http://www.wordreference.com/enit/furthermore>urthermore when I installed long-tutorial in $FREESURFER_HOME/subjects directory the directory long-tutorial was with another owner and I had to change owner with command "chown -R", or I couldn't use it. I tried also to remove the directory and reinstall long-tutorial but the problem of owner still remains and I had to run "chown -R" in order to have access to the directory and its files. I followed instructions to the letter but now I don't really know how to fix it. sorry for my english thanks

1 0

Freeview problem I can't see volumes
by carlo cotugno 13 Apr '12

13 Apr '12

Dear FreeSurfer experts, > I'm sorry but I have another problem..now when I load a surface (freeview -v OAS2_0001_MR1.long.OAS2_0001/mri/norm.mgz)Freeview starts but i can't see the image and only when I change for example values in opacity or window, the image appears but immediately disappears. I forgot to say that i'm using ubuntu 11.10 64 bit. (FreeSurfer v5.1.0 on ubuntu 11.10 > > on a notebook ASUS i3-350M, 4GB RAM and ATI Mobility RadeonHD 5470 1GB RAM DDR3) > > Thanks Best regards Carlo Cotugno > > >

3 4

longitudinal analysis subcortical volumes
by Sabin Khadka 13 Apr '12

13 Apr '12

Hi all, Just to be sure, if I want to compare ICV or hippocampus volume between two time points I extract the values from aseg.stats of MRI_001.long.template and MRI_002.long.template right. Also, if thats the case is it okay if I rerun autorecon with -hippo-subfields flags for those MRI_001.long.template and MRI_002.long.template. Thanks, Sabin

1 0

freeview
by Adil Javed 13 Apr '12

13 Apr '12

Hi, is there any way to overlay only certain regions of interest from the LUT table and not all of them in freeview or tkmedit over a T1 image? I want to just display certain areas or ROIs. thanks, AJ

2 1

"MatrixMultiply: m2 is null! "
by carlo cotugno 13 Apr '12

13 Apr '12

Dear FreeSurfer experts, I have a problem using FreeView: it can load volume without problems, but when I try to load surface it crash.I'm following Longitudinal-Processing tutorial and when I run the command described in "inspecting Longitudinal Data" Freeview crashes.... The error is: MatrixMultiply: m2 is null! No such file or directory I'm using FreeSurfer v5.1.0 on ubuntu 11.10 on a notebook ASUS i3-350M, 4GB RAM and ATI Mobility RadeonHD 5470 1GB RAM DDR3. thanks everyone Carlo Cotugno carlo.cotugno(a)gmail.com

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