Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

FDR question
by pfotiad＠nmr.mgh.harvard.edu 14 Feb '14

14 Feb '14

Hi FS community, I am doing a cortical thickness comparison between a diseased and a healthy group. After running the mri_glmfit command for both hemispheres, I project the uncorrected significance map and there are a number of significant clusters showing (if you consider the p value to be at most 0.05). However, instead of using the clusterwise Correction for Multiple Comparisons, I wanted to use FDR to see what the results would look like, and I had a few questions regarding the whole process: 1) Is Tksurfer the only tool in FS that I can apply the FDR correction with, or are there any other ways? 2) In Tksurfer, I tried using the "Set Threshold Using FDR" tool, and when I set the rate from 0.88 to 0.87 it bumps down the minimum threshold from 1.37 to 3.24 hence resulting in no significant clusters for rates less than 0.88. Does that sound normal? Thanks in advance! Panos

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Fwd: Tracula Error: bvecs and bvals don't have the same number of entries
by Francesco Baldacchini 14 Feb '14

14 Feb '14

Hi, Sorry Anastasia, I'm seeing that my question was not so clear. The files I sent you in the first mail are the bvecs and bvals saved by trac-all -prep in the dmri directory. The original files are in attachment in this mail, Francesco Baldacchini 2014/1/13 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Hi Francesco - The bvecs file that you're attaching has only 3 vectors, > while the bvals file has 65 b-values. Are these your original files, or the > ones saved by trac-all in the dmri/ directory? > > a.y > > > On Mon, 13 Jan 2014, Francesco Baldacchini wrote: > > Hi everybody, >> I'm trying to run the trac all -prep command but after some times I get >> this >> error "bvecs and bvals don't have the same number of entries". I've >> checked >> my bvals and bvecs, which are in attach, but they seems to be formatted in >> the right way. What can I do? Thanks, >> >> Francesco Baldacchini >> >> >> > > 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. > >

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Other things to consider when setting -min_border_white -min_gray_at_white_border?
by Erik Lindberg 14 Feb '14

14 Feb '14

Dear Bruce and Freesufers, Adding to our previous discussion. You managed to fix a very bad segmentation by setting some expert options (mri_normalize -gentle and setting a fixed level for -min_border_white -min_gray_at_white_border). It was a very nice recovery of, what I thought to be, a hopeless image. As I in my project have around 800 images I was also testing these options on 10 more images that you used to "recover" the bad image. The test on the 10 other images (that also worked well without expert options) was quite good. The segmentation looked ok. What I am wondering now is if there is other aspects to consider when setting fixed levels in mris_make_sufaces? As I told you I looked into the recon-all log file and found that when FS is running normally in creates different levels of -min_border_white -min_gray_at_white_border for each image. As this is the Normal way for FS to run I suppose that this is the optimal way to run. So what is the disadvantages of setting fixed levels for -min_border_white -min_gray_at_white_border? Thanks! Erik

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Number of pixel count
by Saurabh Thakur 14 Feb '14

14 Feb '14

Hello Free surfer Expert , I am kooking for the exact value of voxel / pixel which represent White ,Grey and CSF fluid matter in brain. I am trying to draw contour, and to measure the count...or How to count the pixel for particular region...? Thanks in advance for your timely advise. cheers Saurabh Thakur,

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Re: [Freesurfer] distribute dots on the surface
by Douglas N Greve 14 Feb '14

14 Feb '14

Please remember to post the list and not to us personally. Thanks! Actually, I don't know of a good way to do what you want to do (I thought I had an idea, but it won't work). One way to do this would be to select a random set of vertices. This would be approximately uniform. Alternatively, you can use mris_make_face_parcellation but you will be limited by the icosahedral series. If you want to go with the first option, you can run mri_volsynth --temp subject/surf/lh.thickness --pdf uniform --o junk.mgh mri_binarize --i junk.mgh --min .9 --o mask.mgh The first command synthesizes a surface overlay with uniformly distributed random numbers between 0 and 1. The second command thresholds at .9, so you'd get about 10% of the vertices doug On 02/13/2014 02:20 AM, peng wrote: > Hi Douglas, > > Thanks for your reply. Yes, I mean "a mask surface overlay with 1s > in some vertices and 0s in others". And I also wish to convert there > coordinates back to the volume coordinates later (e.g. RAS etc.), > which I think is possible. > > > On Wed, Feb 12, 2014 at 4:15 PM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > what do you mean by "dots"? Eg, a mask surface overlay with 1s in > some vertices and 0s in others? Or a label? > doug > > > > > On 2/12/14 9:52 AM, peng wrote: >> Dear Freesurfers, >> >> I have run recon-all and got a set of surfaces for the >> subjects. I wish to distribute N dots about evenly on the surface >> to cover most gyri and sulci , but I don't how to implement that. >> One way is to manually put them in the GUI of freeview, but it is >> not so convenient if N is relative large (say, 200). Can anyone >> give me a hint which function shall I use? >> >> >> best >> Peng >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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> > 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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Resample a mask on diffusion images using bbregister registration matrix
by Celine Louapre 13 Feb '14

13 Feb '14

Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images to further exclude the lesion voxels on the DTI maps (and to calculate DTI metrics within the lesions too). Using mri_vol2vol command I think I am missing something because I tried with the registration file produced by bbregister (through tracula) but the result does not look correct. I have the lesion mask in the freesurfer space that I can overlay on brainmask or dtifit_FA.nii on freeview and it seems correctly registered on both. The command I am running is: mri_vol2vol --mov recons_dir/subj1/dmri/lowb.nii.gz --targ /lesion_mask/subj1/lesion_WM.nii.gz --interp nearest --o /lesion_mask/subj1/lesion_WM_vol2vol.nii.gz --reg recons_dir/subj1/dmri/xfms/anatorig2diff.bbr.dat --no-save-reg --inv And then when I open lesion_WM_vol2vol.nii.gz in freeview, the voxel size is the same as the DTI images, but the lesions are not at the same place. On the mailing list I have also seen other options but I am not sure if they would be appropriate? I have seen mri_label2vol command where I could set the fill threshold parameter but it does not solve the problem of the registration file? also mri_convert And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension as the diffusion space? Thanks a lot Best Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

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resample lesion mask on diffusion images processed with tracula
by Celine Louapre 13 Feb '14

13 Feb '14

Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images (that have been processed with tracula) to further exclude the lesion voxels on the DTI maps. To do so I have found several possibilities on the mailing list but I am not sure about which one is appropriate. I have tried: mri_convert but I am not sure about which resampling method to use. The nearest voxel miss quite a few lesions. I have also seen the command mri_vol2vol: mri_vol2vol --mov /subject/dmri/lowb.nii.gz --targ lesion_mask.nii.gz --inv --interp nearest --o lesion_mask_resampled.nii.gz --reg /dmri/xfms/? --no-save-reg I don't know what registration file to use in that case? I have also seen mri_label2vol command where I could set the fill threshold parameter but I am not sure again about the registration file to use. And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension than the diffusion space? Thanks a lot in advance for your help Best Celine

2 2

bbregister and fnirt
by qtnguyen＠nmr.mgh.harvard.edu 13 Feb '14

13 Feb '14

Hi all, We're conducting the registration using bbregister that gives us a registration matrix (a .dat file) BUT the original structural file remains intact, i.e. the registered output can be viewed but not stored. Can we store the co-registered structural image as a .nii file? And if so, how? We are using the Connectivity Toolbox that requires structural data to be coregistered with functional data, and there is no way we can feed in the .dat file. Also, what are your thoughts on first using bbregister for linear coregistration, and then use fnirt on the output to get nonlinear coregistration? We ask this because we are working on a younger population (ages 8-25) with autism spectrum disorder and the data is affected by motion. Should we also be using --init-fsl instead of --init-spm if we want to use fnirt? Thank you for your help, Trang

3 2

wmparc
by sujith vijayan 13 Feb '14

13 Feb '14

Hi All, I have a couple of question about wmparc: What rule is used to determine what grey matter structure is reported for a point in the white matter? What exactly has to be the case when UnsegmentedWhiteMatter is reported? Is there a reference you could point me to? Thanks, Sujith

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Filipping issue
by Paola Valsasina 13 Feb '14

13 Feb '14

Dear List, we are starting the analysis of cortical thickness for a group of patients who have only one side affected. The majority of patients have the left hemisphere affected, but some patients have the right hemisphere affected. In order to do a group analysis, we would like to flip the images of some patients, so that the affected side is left for all subjects. Which is the best way to do this: 1) flip the 001.mgz volume and perform the entire recon-all pipeline with flipped images; or 2) perform the recon-all pipeline with the non-flipped volumes and flip only the final surfaces for statistical purposes? Thank you for any suggestion Kind regards Paola

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