Freesurfer

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30088 discussions

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

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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

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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 > > >

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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

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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

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"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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Functional ROI in whole brain
by Tomer Livne 12 Apr '12

12 Apr '12

Hi, I'll appreciate some help with the following issue. I need to define an ROI in a whole brain volume to be used as a mask in PyMVPA. That means having a whole brain .nii file with '1' within the ROI and '0' in every other voxel. Is there a way to define a functional ROI in a whole brain volume, in a similar way to what I get when running funcroi with an annotation from aparc for a specific hemi? Or alternatively, is there a way to convert the aparc based ROI for a single hemi surface into a whole brain volume? Best, Tomer

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Manual editing of segmentation
by Cynthia Elisabeth Krafft 12 Apr '12

12 Apr '12

Hello, Sorry for a newbie question. If we have to edit the segmentation (and all that we are interested in investigating is the volumetric data), what step should I run after that? Is it necessary to run "recon-all -autorecon2 -autorecon3" or is there some less time-consuming processing that will be sufficient? Thanks, Cindy

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Re: [Freesurfer] Resampling volumes from functional to anatomical space
by Lingqiang Kong 12 Apr '12

12 Apr '12

Thanks Bruce. I used mri_info to verify. And there seems to be a small mismatch. I have an original contrast overlay file 'sig.nii', then I used mri_vol2vol --mov sig.nii --targ $SUBJECTS_DIR/$subj/mri/T1.mgz --reg register.dat --o sig-aligned.nii to get a new overlay sig-aligned.nii which is aligned with T1.mgz. >From mri_info, 'sig.nii' is 64*64*42 'sig-aligned.nii' and 'T1.mgz' both 256*256*256 however, the voxel to ras transform for 'sig-aligned': -1 0 0 130.5 0 0 1 -111.6 0 -1 0 115.8 0 0 0 1.0 and voxel to ras transform for 'T1.mgz': -1 0 0 129.9 0 0 1 -105.6 0 -1 0 129.2 0 0 0 1.0 So the two matrices are different from one another. Is that OK? Lingqiang > you can use mri_info to verify that the geometry is the same > On Thu, 12 Apr > 2012, Lingqiang Kong wrote: > >> Hi Bruce, >> >> Yes that's what I wanted! The --fstarg flag uses the >> $SUBJECTS_DIR/$subj/mri/orig.mgz as the targ so in my case it would be >> the >> same as using --targ $SUBJECTS_DIR/$subj/mri/T1.mgz. >> >> So I guessed it had worked from the beginning but I had mistakenly >> thought >> that it didn't. It just looked different to my eyes because the >> functional >> contrast sig.nii looked one size bigger than the T1 structural and a lot >> of stuff seems to be outside the brain (now I take it that it's normal >> to >> look this way?). >> >> >> Thank you so much for your clarification. I was really confused about >> what >> mri_vol2vol was doing. >> >> Lingqiang >> >>> Hi Lingqiang >>> >>> do you mean in voxel register with the anatomy, with the same voxel >>> dimensions, etc...? If so I think you can specify --targ \ >>> $SUBJECTS_DIR/$subject/mri/T1.mgz >>> >>> or you mri_convert with -rl <path to T1.mgz> >>> >>> cheers >>> Bruce >>> >>> >>> On Thu, 12 Apr 2012, Lingqiang Kong wrote: >>> >>>> Hi Surfers, >>>> >>>> I am trying to resample a GLM analysis contrast overalay ('sig.nii') >>>> back >>>> to individual subject anatomical space (T1.mgz). The functional scans >>>> and >>>> the anatomical scans were acquired on two different days and were >>>> co-registered with register.dat. The T1.mgz has high resolution and >>>> the >>>> sig.nii has low resolution. >>>> >>>> I used >>>> mri_vol2vol --mov sig.nii --fstarg --reg register.dat --o sig_high.nii >>>> >>>> trying to generate a new overlay 'sig_high.nii' which is aligned with >>>> T1.mgz. >>>> >>>> However, this only generated the appropriate tranformation but did not >>>> really "MOVE" the sig_high.nii to align with the T1.mgz. (I checked >>>> using >>>> tkregister2 and also with loading all three files in Matlab using >>>> MRIread()). The sig_high.nii is aligned with sig.nii instead of >>>> T1.mgz. >>>> >>>> In the end, I want to load them in Matlab by MRIread and have the new >>>> sig_high.nii aligned with T1.mgz. How do I do that? >>>> >>>> >>>> Thank you. >>>> >>>> Lingqiang >>>> >>>> >>>> >>>> >>> >>> >>> >> >> >> > > > -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/

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Re: [Freesurfer] Clarification on centos version/updates/patches
by Watson, Christopher 12 Apr '12

12 Apr '12

Hi Nick, So would you recommend I install Centos 6 on the new workstation? In addition, I've run recon-all on a large study group (>100); I take it I'll have to re-run all of them? Thanks, Chris -------------------- Chris, yes, the centos5 build freesurfer 5.1 will work on centos6 (we use it in-house). when the v5.2 release of freesurfer is ready (hopefully at the end of may) you will want to use the centos6 build, as it will get a bit better performance because of the compiler and some openmp options. n. On Wed, 2012-04-11 at 10:48 -0400, Chris Watson wrote: > H i Nick, > Will the centos5 build of v5.1 work with centos6? I'm getting a new > workstation and want to know which version of centos is better to install. > > On 04/10/2012 10:08 AM, Nick Schmansky wrote: > > Wil, > > > > Hi, the contents of that 'misc' directory is just a filedrop of sorts to > > supply fixes to individuals who need particular updates. We dont supply > > formal patches, as it gets too unwieldy to track versions. Rather bug > > fixes are documented (mostly!) on the ReleaseNotes page with links to > > fixes. > > > > We have a centos6 build, but dont release it. We will for the next > > release, v5.2, hopefully by the end of May, as the centos6 build runs a > > little faster than the centos4/5 build because it uses a newer gcc, but > > this will mean it wont be possible to mix versions, and a centos6 platform > > (or kernel 2.6.32-220.7.1.el6.x86_6) will be needed. > > > > mri_info versioning wont affect the stream. i dont think it has any bug > > fixes outstanding. > > > > i think the trac-all script is the same, the versioning is different > > because our 'dev' tree version was committed to our 'stable' branch, and > > the two have different versions (but the file is the same). > > > > n. > > > > > > > >> Hi- > >> > >> It would appear the stable release for centos6 is ready for primetime > >> 'stable5.1-bin.tgz'; Is this correct? There is an updated version of > >> 'mri_info' based on file size > >> (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86…) > >> > >> > >> mri_info in 'stable5.1-bin.tgz': 9787048 04-Oct-2011 13:45 > >> mri_info outside of 'stable5.1-bin.tgz': 9866032 04-Oct-2011 11:32 > >> > >> Which version is the most current? > >> > >> Can the contents of 'stable5.1-bin.tgz' be extracted into /freesurfer/bin > >> to overwrite the extant files? > >> > >> Additionally, there is a versioning discrepancy between 'trac-all' located > >> in > >> (http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/) > >> > >> '$Id: trac-all,v 1.35 2011/09/02 19:19:22 ayendiki Exp $'a > >> > >> and the version packaged with the cenos6_x86_65 'stable5.1-bin.tgz' > >> > >> '$Id: trac-all,v 1.22.2.9 2011/09/02 19:21:03 ayendiki Exp $' > >> > >> I did not comprehensively look for any other discrepancies-these just > >> happened to stand out based on the work I was doing today. > >> > >> Thanks much, > >> Wil > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > > 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

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