Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Surface and Volume do not align in Slicer3
by Steffen Bollmann 18 Jul '10

18 Jul '10

Dear freesurfer-mailinglist, I'm struggling since a few days with a problem I can't resolve: I ran recon-all without errors on my data and got the surfaces. Now I want to display surf/l(r)h.pial and mri/T1.mgz (or /orig/001.mgz) together to check the result in slicer3 (3.61.0). The problem occurring is, that any surface and the original volumes do not fit together - there is a small shift of the surfaces to the front. I already tried to apply transforms from mri/transform to the T1.mgz but nothing solved that issue. here is a screen shot of my problem: http://dl.dropbox.com/u/1263357/problem.png What am I doing wrong? Thank you for any hint in advance Best Regards Steffen

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OASIS Brains data...
by Gonzalo Rojas Costa 18 Jul '10

18 Jul '10

Hi: I used the command: "recon-all -subject OAS1_0153_MR1 -all -legacy" but I got the error: "ERROR: you have specified -legacy, but this does not look like a legacy analysis." Sincerely, Gonzalo Rojas Costa

2 4

OASIS Brains data...
by Gonzalo Rojas Costa 17 Jul '10

17 Jul '10

Hi: I want to reprocess some OASIS-Brains data with the newest version of freesurfer... Which are the freesurfer command line that I must use (with "legacy" option) ?... And, I must do the complete processing or only some of the stages (autorecon1, autorecon2 autorecon3) ?... Sincerely, Gonzalo Rojas Costa

2 1

mri_watershed error
by Toh Hock Wong 17 Jul '10

17 Jul '10

Dear freesurfer experts, I need your help on recon. I tried to perform recon-all on my anonymized control subjects (chunk of face/eyes removed on T1.mgz) and run autorecon1. It ran smoothly till the end of workflow of autorecon1 and came up with the following: mri_watershed Error: GLOBAL region of the brain empty! It then exited without compiling brainmask.mgz file. What should i try from here! Thanks for your help! Toh Wong Sydney, Australia

2 1

Total Grey Matter Volume Mismatch
by Matthew Ku 16 Jul '10

16 Jul '10

Dear Freesurfer Experts, I have been analyzing the data output from Freesurfer for grey matter volumes and have been manually tabulating the total grey matter from the lh.aparc.stats and rh.aparc.stats files. Upon totaling the grey matter values in these .stats files, I have found that the totals do not match with the total grey matter volume found in the mris_anatmoical_stats file. Does anyone know why the total grey matter from the lh.aparc.stats and rh.aparc.stats files does not match with the total found in the mris_anatomical_stats file? Thanks, Matt _________________________________________ Matthew Ku University of Pennsylvania School of Engineering Class of 2013 (845) 596-3840 mattku(a)seas.upenn.edu

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Questions about mcparams2extreg
by Gabriel A. Tobon 16 Jul '10

16 Jul '10

Hi, I noticed that mc-sess produces a file for external mc regressors that can be used for analysis with "mcparams2extreg". I can see the added regressors in my design matrix if I decide to include them. How are these external regressors actually calculated? Are the same set of motion parameters used at every voxel? The design matrix looks different than the design matrix produced by FSL's FEAT process when motion parameters are added there: http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html#stats FSL documentation says that adding these parameters is not really recommended. Is this the case for mcextreg in FsFast analysis? Thank you! Gabe

2 1

question: gray matter segmentation
by Yunjo Lee 16 Jul '10

16 Jul '10

Hi, I am a new user of FreeSurfer and trying to figure out gray matter segmentation. A volume that I extracted from aparc+aseg.mgz using mri_segstats did not match the volume reported in /stats/ text files (for example, aseg.stats, rh.aparc.stats). Even without specifying a mask in mri_segstats, there's always a discrepancy of 100 voxels or something. Where do the numbers in /stats/ files come from? Aren't they from aparc+aseg.mgz? Thanks! Yunjo

3 5

Spatial Smoothing in the processing stream for fMRI-freesurfer integration
by Joonkoo Park 16 Jul '10

16 Jul '10

Dear freesurfers, How is spatial smoothing performed during a conventional fmri processing stream? I used SPM to (1) run the 1st level analysis on each subject, (2) transformed the resulting volumetric statistical parametric map to the surface space, (3) normalized each individual's surface map onto fsaverage (which involves surface-based smoothing), and then (4) ran 2nd level analysis on these data. The question is: 3D-spatial smoothing is normally done (and I believe recommended) at step (1) above when estimating the GLM at the 1st level. However, performing 3D smoothing on raw functional images seems to be detrimental if the data will eventually be projected on to a surface space. I then thought about NOT 3D-smoothing at step (1), that is, estimating GLM on unsmoothed data, and then using 2D smoothing after step (2) when statistical parametric maps are projected onto the surface space. However, this sounds problematic since smoothing followed by model estimation might give different results from model estimation followed by smoothing. The third approach is to convert all the volumetric functional images into surface space, and then start model estimation in the surface space using FreeSurfer. But this means that I won't be able to use SPM or other packages to run model estimation (that might have superior functionality when it comes to fmri data analysis). Is this what's usually done to integrate fmri data with freesurfer procedures? Or, alternatively, is there a better integration protocol between FSL and FS (I don't know much about FSL) to address this issue? I'd be grateful to know how other people are doing this. Thank you! Joon

2 1

overlay registration
by Arslan, Ali 16 Jul '10

16 Jul '10

Hi, I'm trying to use a registration file while overlaying my functional volume on the surface. I'm getting this warning -iMac1-2:~ aarslan$ tksurfer KS02sess1 lh inflated –ovreg $V1/register.dat -overlay $V1/spmT_0001.mgz WARNING: flag –ovreg unrecognized WARNING: flag /Users/aarslan/mypath/register.dat unrecognized surfer: current subjects dir: /path/anat surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/aarslan surfer: Reading header info from /path/anat/KS02sess1/mri/T1.mgz surfer: vertices=142381, faces=284758 surfer: Interpreting overlay volume /Users/aarslan/mypath/spmT_0001.mgz as registered functional volume. surfer: curvature read: min=-1.260472 max=2.154594 I also tried with -overlay-reg flag but got the same warning. The results are the same with or without the registration file, so I'm sure that I'm failing to load it. Loading the registration.dat from gui menus also doesn't make a difference visually. Does this indicate that my registration.dat file is bad or am I making an error in the tksurfer call? Any help would be appreciated. Regards, Ali Arslan

2 1

mri_convert question: converting dicom to mgz
by Kenichiro Tanaka 15 Jul '10

15 Jul '10

Hello, all. I have not been able to convert dicom files to a mgz file using mri_convert. Could you tell me how to use mri_convert to do that and the example? I typed the following command and run: mri_convert -it dicom -ot mgz 001/ 001.mgz Then I got the following message: mri_convert -it dicom -ot mgz 001/ 001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 001/... Starting DICOMRead2() dcmfile = 001 dcmdir = . ERROR: 001 is not a dicom file There are 126 dicom files in the directory "001/". OS is CentOS 4.8(64bit), and the version of the Freesurfer I am using is 4.5. Thank you for all your help. Kenichiro Tanaka.

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