Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

extracting segmented images with exact values for GM-WM-VL-CSF
by Alexander Lebedev 23 Mar '11

23 Mar '11

Sorry, that's of course directed to FREESURFER users and developers, and maybe there is a possibility to extract such images cerebellum-stripped?

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From scanner to freesurfer
by Knut J Bjuland 23 Mar '11

23 Mar '11

Hi I am now imported my first dicom files into freesurfer. I have followed the protocol as described in the tutorial. I have some questions. Does recon-all -i /path/to/subject's/mprage.dcm -i /second/mprage/if/you/had/one -all -s subj001 import all dicoms if you pint it to hte first in serie if you are using a Simmens MPRAGE/T1 scan? Is there any other way to make sure all dicom in series is imported or if there are several series in subject. How can I import several series for just one subject. Knut J

2 1

Longitudinal FS References
by Martin Reuter 23 Mar '11

23 Mar '11

Hi everyone, we are preparing a list of papers that make use of the unbiased longitudinal stream in FreeSurfer (in version 4.4 and up). This helps us to keep track of impact and application fields (and it helps you to advertise your research on our Wiki :-) Please sent me your references (if possible with doi link). I also have an update. So far people could only cite our inverse consistent registration paper: Highly Accurate Inverse Consistent Registration: A Robust Approach, M. Reuter, H.D. Rosas, B. Fischl. NeuroImage 53 (4), pp. 1181-1196, 2010. http://dx.doi.org/10.1016/j.neuroimage.2010.07.020 http://reuter.mit.edu/papers/reuter-robreg10.pdf Now we published a small (3 page) comment, containing an overview on several of the steps in FS longitudinal processing: Avoiding Asymmetry-Induced Bias in Longitudinal Image Processing, M. Reuter, B. Fischl. NeuroImage, 2011. http://dx.doi.org/10.1016/j.neuroimage.2011.02.076 http://reuter.mit.edu/papers/reuter-bias11.pdf We plan to publish a more detailed description in the near future. Thanks for using the longitudinal stream and let me know if you have any questions. See you at HBM. Best, Martin

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changing tksurfer window font size...
by Gonzalo Rojas Costa 23 Mar '11

23 Mar '11

Hi: How can I change the font size used in the tksurfer dialogs ?... such as "Configure Overlay Display" dialog ?... Because I changed the font size in Ubuntu GNOME, but it didn't changed the font size used in tksurfer... I asking that because in the "Configure Overlay Display" didn't appears the "Apply", "Close", and "Help" buttons, and I think that it could be for the font size in the GUI, or the screen resolution... Sincerely, Gonzalo Rojas Costa

2 1

autorecon1 memory error
by Paige Scalf 23 Mar '11

23 Mar '11

Hello, I'm getting the memory allocation error that is causing autorecon1 to abort. I've also attached the log file. Please help! \n mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz \n mri_gcut(6855) malloc: *** vm_allocate(size=8421376) failed (error code=3) mri_gcut(6855) malloc: *** error: can't allocate region mri_gcut(6855) malloc: *** set a breakpoint in szone_error to debug terminate called after throwing an instance of 'std::bad_alloc' what(): St9bad_alloc reading mask... use voxels with intensity 110 as WM mask threshold set to: 110.000000*0.360000=39.600000 calculating weights... doing mincut... Abort Thanks, Paige

2 1

changing tksurfer window font size...
by Gonzalo Rojas Costa 23 Mar '11

23 Mar '11

1 0

[Fressurfer] fMRI and anatomical T1
by leonardo kay 23 Mar '11

23 Mar '11

Hi all Can anyone help me overlaying fMRI activations from fsl on a anatomical T1 volume in freesurfer. Is there any previous format conversion to do before? Thanks in advance best regards, -- Leo Kay.

2 1

recon-all errors
by Alfredo Damasceno 23 Mar '11

23 Mar '11

Hello, I had some problems with 3 images of different patients running the recon-all comand. With one of them, I received the following message: ERROR: vbmAMIPP.nii exists but is not readable With the others two there were no error messages, but both stopped at the same point: gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.10 x + 0 estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.85 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux tupa.neuroimg.hc.unicamp.br 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Mar 18 17:24:55 BRT 2011 Could anyone help in solving these problems? Thanks in advance Alfredo

1 1

Calculating BPF
by Andrew Dumas 22 Mar '11

22 Mar '11

Hi, I've been looking through the mailing list archives for anything on calculating BPF (Brain Parenchymal Fraction) and have only found some fuzzy descriptions of how to calculate this using FreeSurfer. I know I can get ICV from the aseg.stats, but how can I obtain the volumes of total white and gray matter (i.e. total brain parenchyma volume)? One possible method I saw suggested mris_anatomical_stats-- but that looks like it only calculates gray matter volumes. Any ideas? Thanks in advance for your help! Andrew

2 1

average_thickness&mris_anatomical_stats
by Liukarl 22 Mar '11

22 Mar '11

Hello, Freesurfer experts: I am using the mris_anatomical_stats to extract the average cortical thickness: mris_anatomical_stats -l lh.cortex.label -f subject1.txt subject1 lh the output is number of vertices = 127190 total surface area = 84246 mm^2 total gray matter volume = 257279 mm^3 average cortical thickness = 2.628 mm +- 0.698 mm average integrated rectified mean curvature = 0.158 average integrated rectified Gaussian curvature = 0.146 folding index = 6266 intrinsic curvature index = 403.9 My question is whether the average cortical thickness here is from white matter surface or pial surface? How can I get the pial surface average thickness? Our goal is to use average cortical thickness as a covariate to examine the possible local thickness difference, like in the prefrontal lobe. Which average cortical thickness, pial or white, is a better fit in our case? Thanks in advance Karl

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