Freesurfer

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30132 discussions

last index missing when using mri_label2vol
by David Grayson 27 Feb '12

27 Feb '12

Hi, I am noticing that when I use ‘mri_label2vol --annot’ it is not creating the final label from the color table file. I tried using the --thresh 1 option, but that didn't work either. i.e... mri_label2vol --annot lh.custom.annot --temp ../mri/orig.mgz --o custom_lh.nii.gz --subject FREESURFER --hemi lh --identity The last index is no where to be found in the custom_lh.nii.gz. But the other indices look OK. Has anyone encountered this before, and know what to do? Thanks very much! David

2 1

?h.dpial.ribbon.mgz not found
by octavian lie 27 Feb '12

27 Feb '12

Dear Bruce & FreeSurfers, I ran freesurfer (86x64_64 centos version 5.1.0) on my new linux box (Ubuntu 11.10 64 bit, NVIDIA GEforce GTX 580, no CUDA for now) using recon-all -all; it went on for 8 hours, I got the message (Recon complete without errors) in the log.txt file in my subject directory. However, when trying to use mri_convert or tkmedit to see the lh.dpial.ribbon.mgz, there was an error (could not open file). I searched for the file in all the /mri folder and the whole file system on my box, could not find it. I found lh.ribbon.mgz, rh.ribbon.mgz, and ribbon.mgz, but not the dpial.ribbon.mgz file or any other ?.ribbon.mgz variety. I appreciate your suggestions. Octavian.

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FSL_niftii
by Gabor Perlaki 27 Feb '12

27 Feb '12

Dear all, I've some fsl niftii MPRAGE images converted by MRIConverter. They look fine in fslview and I can open them by freesurfer as well (tkmedit -f *.nii.gz) , but when I compare the images between fslview and tkmedit they look slightly different. It seems that the orientation is the same in both viewer, but the rotation is slightly different. Why are the images slightly rotated (reoriented) viewing by tkmedit? Is it affect any statistics by freesurfer? Thanks, Gabor

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Re: [Freesurfer] Choosing a Contrast
by Douglas N Greve 27 Feb '12

27 Feb '12

what do you want to test? doug Allie Rosen wrote: > Hi Doug, > > I have. I think that I have two groups (patients/controls) with one > covariate (age), so the following is my situation: > > http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V > > Thank you again, > Allison > > > > On Mon, Feb 27, 2012 at 10:31 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Allison, have you looked at > http://www.freesurfer.net/fswiki/PairedAnalysis ? > doug > > Allie Rosen wrote: > > Hi All, > > I am trying to figure out the contrasts to use for a study. I > am comparing age matched patients and controls (all female). > The FSGD file has 4 columns, but I'm not sure how to make an > appropriate contrast matrix. I can't seem to find an > applicable example on the wiki. > > Any guidance would be appreciated. > Thank you, > Allison > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

How to change the work path of freesurfer
by bowang21＠mail.ustc.edu.cn 27 Feb '12

27 Feb '12

Dear Nick Schmansky I am a beginner of freesurfer,and now I'm in trouble. I have install the VirtualBox to run freesurfer,but the disk space is not enough (11.0G).So I need to mount a disk to the system. And now I want to know how to change the working path of freesurfer such as SUBJECT_DIR. If you have some better idea to solve the problem,please tell me. Thanks in advance. Yours BoBO

3 2

Choosing a Contrast
by Allie Rosen 27 Feb '12

27 Feb '12

Hi All, I am trying to figure out the contrasts to use for a study. I am comparing age matched patients and controls (all female). The FSGD file has 4 columns, but I'm not sure how to make an appropriate contrast matrix. I can't seem to find an applicable example on the wiki. Any guidance would be appreciated. Thank you, Allison

2 1

Question about contrast matrix
by 林鄞 27 Feb '12

27 Feb '12

Dear all I have a question about the design of matrix. I have one group of two levels ( patient and control) and two continous variables (age and weight). And I want to know the difference of correlation of cortical thickness and the weight while controlling age between patient and control. My fsgd file is mainly like this: Class patient Class control Variables age weight I design the 1.mtx file as: 0 0 0.5 0.5 1 -1. I can not find the same sample in wiki. And I want to confirm whether my mtx file is right or wrong. If it makes mistakes, how to correct it? I really hope somebody can help me. Thanks for all! All the best, Lin

2 1

How to only do spatial normalization in FreeSurfer.
by Long 26 Feb '12

26 Feb '12

Dear all, I had EPI images and T1 image and the EPI images are already co-registered to T1 image in their native space. I also run 'recon' on T1 image. I'd like to try surface-based spatial normalization in FreeSurfer, so how can I only do the spatial normalization of EPI images in FreeSurfer, i.e., transform EPI images from native space to mni152 space, then I could have surface-based normalized EPI images. Best, Xiangyu

2 3

volume size
by Colin Reveley 25 Feb '12

25 Feb '12

Hi - I would really like to use a volume size greater than 256^3. I know of all the options and reasons. what I want is a white matter surface than has fairly evenly spaced nodes that are in approximate match to the voxels they enclose. the reason is to seed, track and target using FSL surface tractography. the brain is a 250um macaque, and it's 320 voxels long unfortunately. the structural and DWI are the same resolution and in register and acpc aligned. such a shame to waste. the freesurfer surfaces are imported into CARET and cross-registered to F99. but they keep their mesh if I want. work with another sample showed that node numbers and even coverage over the WM/GM boundary had a signifiant effect on the FSL metrics, with the original FS WM surface and derivatives yielding the best results over other meshes like F99's or anything made with surefit directly from a downsampled version of the data. that data I could fit into 256^3. I doubt that the nodes and voxels need to match perfectly, just ballpark and fairly even spacing. if I used a downsampled volume at 500um to make surfaces in freesurfer, maybe I could upsmaple the surfaces afterwards? but then the pial and white would have to be resampled independently and that's probably no good. If I have to resample the volume or apply a scaling transform the world won't end. In fact it will take less time to do probably. But it would be nice to use a larger size than 256^3 to take advantage of what I've got. best, Colin, Sussex

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Frontal signal drop out
by Mahinda Yogarajah 24 Feb '12

24 Feb '12

Dear Experts, Sorry if this is a repost, but I was not sure it got posted. I have a few subjects that I want to salvage and use where there appears to be significant signal inhomogeniety in the last few frontal slices (see T1.mgz in attached figure 1). Despite the use of control points (placed with careful adjustments of windowing parameters), I still can't encompass all of the the gyri right at the front (see brainmask.mgz coronal slice in figure 2). I would really appreciate some advice on how to proceed from here. Is placing white matter voxels in wm.mgz a possible solution ? Or is there another solution ? Thanks. M

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