Freesurfer

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30132 discussions

Entorhinal Labels and labels generally
by Joshua Lee 24 Jan '12

24 Jan '12

I'm relatively new to Freesurfer, and have mostly focused of the aseg.mgz segmentation. However, I am also interested in entorhinal cortex and loaded the label up in tkmedit. What I noticed was that it seemed each label essentially noted the border between white and gray matter, but didn't really cover all the gray matter...this seems to be true in all the labels I load in tkmedit. In sum, I don't really know what labels are for, or how they differ from segmentations (is a segmentation a collection of labels?). How do I use the entorhinal label, and do the entorhinal-stats actually give the gray matter thickness despite appearing only as a border in tkmedit. I'm afraid I'm quite ignorant, and I can't seem to find a direct answer to them in the wiki. Thanks, Joshua

2 1

generate binary mask from GLM output
by Miranka Wirth 24 Jan '12

24 Jan '12

Dear Freesurfers, I would to like to generate a binary surface-based mask from the GLM output file (e.g., sig.mgh) the way that vertices above a certain p threshold are set to 1 and below this threshold to 0. I believe I can use this mask in the mri_glmfit procedure? Thank you for helpful information Miranka

2 1

Extracting Cortical Thickness for Parcellated Data
by Jeff Stout 24 Jan '12

24 Jan '12

Hi All,I am relatively new to freesurfer. I am trying to extract cortical thickness information from the freesurfer data. What is the difference (with thickness options as outputs) between asegstats2table and mris_anatomical_stats. I see that asegstats2table gives the option for multiple Subject input which is very convenient for tabulating multisubject data. In freesurfer there is the option to perform surface based thickness filtering using qcache with varying fwhm. If I am trying to output parcellation based thickness estimates, is it important to use surface filtered metrics as the thickness is averaged over the region versus nodewise thickness estimates in qdec? I am assuming that averaging over the area would have a similar low pass effect as the surface filter. Thank you,Jeff Stout

2 1

recon-all -use-gpu issue
by aurelien monnet 24 Jan '12

24 Jan '12

Hi everybody, I am trying to use recon-all with gpu. So I installed the CUDA librairies successfully (it seems). I am using freesurfer 5.0, cuda driver 3.2. Here is the cudadetect output : Detecting CUDA... There is 1 device supporting CUDA: Device 0: "D13U" CUDA Driver Version: 3.20 CUDA Runtime Version: 3.20 CUDA Capability Major revision number: 2 CUDA Capability Minor revision number: 0 Total amount of global memory: 1341325312 bytes Number of multiprocessors: 15 Number of cores: 480 Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 49152 bytes Total number of registers available per block: 32768 Warp size: 32 Maximum number of threads per block: 1024 Maximum sizes of each dimension of a block: 1024 x 1024 x 64 Maximum sizes of each dimension of a grid: 65535 x 65535 x 1 Maximum memory pitch: 2147483647 bytes Texture alignment: 512 bytes Clock rate: 1.46 GHz Concurrent copy and execution: Yes Run time limit on kernels: Yes Integrated: No Support host page-locked memory mapping: Yes Compute mode: Default (multiple host threads can use this device simultaneously) But I get the already known error message with recon-all : mri_em_register_cuda -skull nu.mgz /home/global//freesurfer//average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta Acquiring CUDA device Using default device CUDA Error in file 'devicemanagement.cu' on line 46 : all CUDA-capable devices are busy or unavailable. I rebooted my station but still get the same error. I'd like to know if there's something new about this issue ? Kind regards, -- Aurélien Monnet

1 0

Study-average brain and Talaraich
by Adam David Felton 23 Jan '12

23 Jan '12

Hello. Instead of using Freesurfer's averaged brain in qdec, I ran the following command to create an average of our participants: recon-all -s [subject] -qcache target avgsub While running, it reported the following for every subject: Error: could not open file "/Users/Tiana/ucr_freesurfer_data/subjects_10/avgucr/mri/transforms/talairach.xfm". System message: No such file or directory mri_surf2surf: could not load transform file '/Users/Tiana/ucr_freesurfer_data/subjects_10/avgucr/mri/transforms/talairach.xfm' and Reading smoothing mask label lh.cortex.label No such file or directory NN smoothing output with n = 68 Saving target data Saving to lh.thickness.fwhm10.avgucr.mgh rm: No match. (It couldn't find the Talairach file, which becomes another problem...) After finishing the command for all of the participants, I ran a simple analysis in qdec and no brain displayed for the results. However, it did say that there were significant clusters. When I clicked on "find significant clusters" (of course) the Talairach coordinates were missing. Does anyone know what I might've done incorrectly? Specifically, 1) how can I get the study-average brain to display in qdec and 2) how can I get the Talairach coordinates to display? Thank you for your help, Adam PS: Candy at the CNS conference for anyone who helps me.

1 0

mri_glmfit-sim --grf? --cache?
by yukoyy 23 Jan '12

23 Jan '12

Dear all, I'm conducting volume based group analysis and corrections for multiple comparisons. My environment :Mac OS 10.6.8, Freesurfer 5.0.0 I followed the instruction I found here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel When I first successfully ran: mri_glmfit --y ces.005.nii --wls cesvar.005.nii --osgm --glmdir F2glm.wls --nii.gz tkmedit fsaverage orig.mgz -aparc+aseg -overlay F2glm.wls/osgm/sig.nii.gz -fminmax 3 7 Then, I wanted to do corrections for multiple comparison. mri_glmfit-sim --glmdir F2glm.wls --grf 3.0 pos --cwpvalthresh .0166 However, FreeSurfer does not seem to recognize --grf, and I don't understand what does grf do. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ERROR: Flag --grf unrecognized. --glmdir F2glm.wls --grf 3.0 pos --cwpvalthresh .0166 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I chose to use --grf because it was suggested in the tutorial, and in FreeSurfer mailing list archive. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20573.html I am guessing that I cannot use --cache for volume analysis because I don't have /Applications/freesurfer/average/mult-comp-cor/fsaverage/volume/cortex/fwhm12/pos/th30/mc-z.csd I also tried monte-carlo simulation, and it worked okay. So, here is my question. What does --grf do? and Is there any documentation? Thank you! Yuko Yotsumoto yukoyy(a)a7.keio.jp

2 1

Ubuntu 11.10 64 bit
by octavian lie 23 Jan '12

23 Jan '12

Dear All, I am in the process of getting a powerful linux laptop to run Freesurfer. Can I run Freesurfer on a 11.10 version of Ubuntu 64 bit ? Are there any incompatibilities between the latest Freesurfer version and Ubuntu? Is there any configuration issues and solution particular to my situation that you can comment on? Thank you, Octavian.<mhtml:{57E897FE-D0ED-4693-ACA6-A3EF0E2D03DA}mid://00000000/!x-usc:mailto:Octavian.octavian.lie@gmail.com>

4 5

qdec and scatterplots
by Cat Chong 22 Jan '12

22 Jan '12

Hello Experts, I apologize for the basic question. I am currently examining the cortical thickness differences between two groups, contolling for age. On the scatterplot, I thought there was a way to view slopes and intercepts (between groups)? I can't however, figure out a way to get these trendlines to show up. best regards, and Happy Chinese New Year Catherine

1 0

problems with license
by pietro de rossi 22 Jan '12

22 Jan '12

Dear Experts, I'm sorry to bother you with a very silly question but...I'm trying to setup free surfer on my Mac and I'm having problems due to the fact that it keeps giving me errors saying that I don't have a valid license.... I've received the email with the three line license after the download...I've created a .txt file and I moved it to .license in the free surfer directory. What else should I do to make it work?

1 0

Signal inhomogeneity
by Mahinda Yogarajah 22 Jan '12

22 Jan '12

Thanks for the advice on cerebellum and pia Bruce. I had one other question for freesurfer experts, 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. Thanks. Mahinda

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