Freesurfer October 2010

freesurfer@nmr.mgh.harvard.edu

100 participants
129 discussions

How to transform the thickness per vertex to another space?
by Mohammed el Morabit 25 Oct '10

25 Oct '10

Dear FS experts, I 've question concerning the thickness per vertex. Here is what I want to do: I have a data series which entered the FS pipeline. Afterwards, I transformed the aparc+aseg file to another space. Is it somehow possible to transform the thickness per vertex to this space using the same transformation matrix? Thanks, Mo

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Error with mri_segstats
by Ed Gronenschild 25 Oct '10

25 Oct '10

Hi, I'm trying to use mri_segstats and get the following error: ERROR: could not open stats/aseg1.stats for writing The full command I gave was: mri_segstats --seg mri/aseg.mgz --sum stats/aseg1.stats --pv mri/ norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent -- subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity- units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab / Applications/freesurfer/ASegStatsLUT.txt --subject C001 The SUBJECTS_DIR was set to the directory containing the subject C001. I have full privileges to read/write to all folders. If I try to write to just aseg1.stats (so using option --sum aseg1.stats) I get the error message that aseg.mgz could not be opened. I'm on a Mac using FreeSurfer v5.0.0. Ed

2 1

average p-value from an ROI
by Agnieszka Burzynska 25 Oct '10

25 Oct '10

Dear all, I have a follow-up question to the previous discussion ("correction for behavioral varialbles in qdec" Tue, 04 Aug 2009. Is there an option to extract the average p-value from a ROI? After a group analysis I specified ROIs at p < 0.001 and extracted the mean cortical thickness, the peak p-value, and mean ROI size. Now, I would like to report not the peak, but the average p-value of an ROI in the fsaverage space. Is there any flag to obtain this information? I did not use the mri_surfcluster command, but a matlab script to extract the information form the output of the mri_segstats command. Thanks for help! Cheers, Aga

3 2

mni coordinates to volume index
by Yigal Agam 25 Oct '10

25 Oct '10

Hi, Is it possible in matlab to get the volume index coordinates corresponding to specific MNI coordiates? Thanks, Yigal

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data not Surving FDR
by Mira Michelle Raman 25 Oct '10

25 Oct '10

Hi, I have a dataset that seems to have some very nice group differences (please see the graph and qdec image), but they never seem to survive FDR. I noticed when I run the "Set Using FDR", it generates a very high threshold above 5; where as, with some of my other datasets FDR is set much lower (often in the 2's and 3's). Can you please give me some insight into why the threshold is being set so high? Is it solely linked to the small sample size, or is there something additional we can do in the processing, so that regions with such large group differences will survive correction? Thank you, Mira

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new GPU binaries
by Nick Schmansky 25 Oct '10

25 Oct '10

Freesurfanados and GPU fans, We (namely Richard) have fixed some of the problems with the existing freesurfer gpu binaries, which were the result of building against cuda 3.0 on our build platforms, which seemed to be incompatible with 3.1. We've built against 3.1, although now i see nvidia has come out with 3.2, but i've tested against that and they seem to work. So you can get the binary tarball here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… and here for the 32b linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… copy the extracted contents of those tarball into your freesurfer/bin dir. The binaries are: mri_ca_register_cuda mri_em_register_cuda mris_fix_topology_cuda mris_flatten_cuda mris_inflate_cuda mris_sphere_cuda mri_vol2vol_cuda No doubt people will encounter problems, so let us know. But hopefully you will see a dramatic reduction in the runtime of the subcortical segmentation stage (mri_ca_register). Also, to remind people, Richard is targeting our gpu development for the Fermi class of gpu card, which has better memory management which leads to better performance of some algorithms, so if you're buying new hardware, be sure to spec that class of card (see nvidia site). Nick

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question about using lta file from mri_robust_register
by Mehul Sampat 23 Oct '10

23 Oct '10

Hi Folks, I am trying to troubleshoot an issue and I have not been able to find a solution yet. Here is what I am trying to do: 1. I used mri_robust_register to register a t1-weighted image to a t2-image. mri_robust_register works very well and i also got an lta file (t1-to-t2.lta) 2. now i also have the wm-mask from the freesurfer output. this was created using: mri_binarize --i aparc+aseg.mgz --wm --o t1-wm-mask-fs.mgz 3. Then I take the wm-mask to native space using: mri_convert -rl orig/001.mgz t1-wm-mask-fs.mgz t1-wm-mask-ns.nii 4. Finally, I want to apply the t1 white matter mask to the t2 image using the lta file generated in step 1. for this I use: mri_convert --apply_transform t1-to-t2.lta t1-wm-mask-ns.nii t1-to-t2.nii step 1-3 work fine. but when i try to apply the transform in the last step, the output is zeros. The output of mri_robust_register in step 1 is fine. Does mri_robust_register use mri_convert to apply the transform and create the output image ? Or am I making some error ? thanks Mehul

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Re: [Freesurfer] Nifti surface to FreeSurfer surface
by Nick Schmansky 22 Oct '10

22 Oct '10

use mri_binarize to set each brain voxel value to the same value (maybe bet does this), then use something like: mri_tesselate mybrainmask.nii.gz 127 mybrainmask.surf where '127' happens to be voxel value used in the binarization. n. On Fri, 2010-10-22 at 15:08 -0600, Alexander Hunold wrote: > Dear experts, > > > > I got BEM surfaces out of the BET tool from the FSL package. The > surface files are in nifti format (*.nii.gz). > Now I wonder if there is any opportunity to convert nifti surfaces to > FreeSurfer surface in surf format (*.surf)? > > I appreciate any hint. > > Thank you so much in advance. > > > > Sincerely, > > Alexander > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Nifti surface to FreeSurfer surface
by Alexander Hunold 22 Oct '10

22 Oct '10

Dear experts, I got BEM surfaces out of the BET tool from the FSL package. The surface files are in nifti format (*.nii.gz). Now I wonder if there is any opportunity to convert nifti surfaces to FreeSurfer surface in surf format (*.surf)? I appreciate any hint. Thank you so much in advance. Sincerely, Alexander

1 0

Talairach coordinates for Desikan gyral regions
by Robustelli, Briana (NIH/NIMH) [F] 22 Oct '10

22 Oct '10

Hi all, We are trying to depict spatial relations of each of the Desikan et. al (2006) gyral regions in a separate 3-D graph. To do this we need every regions' center Talairach coordinates in common space, not in relation to any particular group or subject. Is there a way to do this using Freesurfer? Thank you. Briana

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Freesurfer October 2010