Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30133 discussions

BEM Surfaces
by obregon＠nmr.mgh.harvard.edu 17 Jan '14

17 Jan '14

Hi, Happy New Year everyone! I'm having issues creating the BEM meshes for one of my subjects using mne_watershed_bem: the outer skull surface is crossing the inner skull surface and cutting into the brain (image attached). I know this program employs Freesurfer's watershed algorithm, though I'm not entirely sure how it does so. Could someone please advise me on how to fix this issue? Thanks! --G

1 0

Desikan atlas in MNI space (in a nii file)?
by Fred Sampedro 17 Jan '14

17 Jan '14

Dear FreeSurfer users, I am searching for the Desikan atlas (which I have in the tailarach space) in the MNI space, as a file (Desikan_mni.nii). I am aware that transforming from one space to the other is not a very good idea but nevertheless I would like to test some computations. Anyone can attach/send a link/know of if exists such a file? Thanks a lot Fred Sampedro Hospital de Sant Pau (Barcelona)

2 1

xhemi correct for multiple comparisons
by krista kelly 17 Jan '14

17 Jan '14

Hello, I'm analysing interhemispheric differences using xhemi. I have followed the instructions on the webpage with no problems. I do have a few questions though. 1) When viewing the results in tksurfer, which color represents "left hemisphere is larger" and which represents "right hemisphere is larger"? 2) I have no idea how to view the results in tksurfer AFTER performing the step of correcting for multiple comparisons. Any suggestions? 3) I've noticed from the archives that some people are performing laterality indices. How would I calculate laterality indices? Thanks! Krista

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V1.thresh
by krista kelly 17 Jan '14

17 Jan '14

Hi all, Can anyone provide information regarding how v1.thresh.label and v2.thresh.label that are automatically implemented in FreeSurfer are thresholded? Thanks! Krista

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xyztrans error
by Tessa Vuper 17 Jan '14

17 Jan '14

Hi all, I receive the following error when I run the selxavg3 -sess command: ERROR: cannot find /usr/local/freesurfer/stable5/bin/fsl. 5.0.2.xyztrans.sch Any thoughts on how to fix this? Thank you so much for your help, tessa Tessa Vuper Clinical Research Coordinator, Manoach Lab Psychiatric Neuroimaging, MGH Martinos Center for Biomedical Imaging 617-726-1908

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Standalone Freeview?
by Jeni Chen 17 Jan '14

17 Jan '14

Hi! I'm wondering if the latest version of Freeview is available in standalone version. I'm currently using FreeSurfer v5.1's tktools for correcting the recon-all outputs, but would like to switch to Freeview. However the version that I have doesn't seem to have the Recon tools, and if I install the latest FS, I will have to rerun the preprocessing... So is it possible to install the latest Freeview separately? Thanks. Jeni Chen

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aseg.stats vs. volumes in native T1 space
by Gabor Perlaki 17 Jan '14

17 Jan '14

Dear all, I've run the freesurfer on 3 subjects and converted the aseg.mgz into *.nii.gz in the native space: "mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii.gz" I've did a stats on left and right hippocampal volumes in the native space using fslstats: "fslstats aseg2raw.nii.gz -l 16.5 -u 17.5 -V" for the left hippocampus and "fslstats aseg2raw.nii.gz -l 52.5 -u 53.5 -V" for the right hippocampus The volumes given by fslstats was about 3% higher than the values reported in the aseg.stats file. The native resolution of the T1 images is 0.45*0.45*0.9 mm^3. I thought that observing a minimal difference could be the consequence of reslicing, but I really don't understand why fslstats gives consequently greater values (for both hippocampi in all three subjects). Thanks, Gabor

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Converting .thickness into nifti volume
by Muhammad Naveed Iqbal Qureshi 16 Jan '14

16 Jan '14

Dear Experts, I need to know how can I convert the .thickness files into volume file that can be opened in SPM and show the thickness of each voxel in the standard templete of the brain. Thank you Best Regards, Muhammad Naveed Iqbal Qureshi

2 1

CUDA problem with FreeSurfer 5.3.0 on CentOS6
by Tran, Kevin (NIH/NIMH) [C] 16 Jan '14

16 Jan '14

Hi, We have encountered a serious problem running recon-all FREESURFER_HOME: /opt/freesurfer-530 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.el6.x86_64 x86_64 The entire command-line executed: /opt/freesurfer-530/bin/recon-all -use-gpu -all -s surface_1 The problem happened when it came to this point mri_ca_register_cuda -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer-530/average/RB_all_2008-03-26.gca transforms/talairach.m3z nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 6.0 Runtime : 5.50 Acquiring CUDA device Using default device CUDA device: Tesla K20m not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer-530/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.22 (predicted orig area = 6.5) freeing gibbs priors...done. average std[0] = 5.0 AllocateHost: Warning - not thread safe! RecvAll: Did not reset gca in dst GCAMcopyNodePositions: On GPU RecvAll: Did not reset gca in dst GCAMcopyNodePositions: On GPU RecvAll: Did not reset gca in dst The same error message kept on repeating and, then, it said ============================================= GPU MRI Label timers -------------------- MarkLabelBorderVoxels Total : -nan ms (avg) 0 ms (tot) VoxInLabelWithPartialVolume Compute : -nan ms (avg) 0 ms (tot) Total : -nan ms (avg) 0 ms (tot) ============================================= CUDA Error in file 'mriconvolve_cuda.cu' on line 945 : unload of CUDA runtime failed. Abort (core dumped) ERROR: mri_ca_register with non-zero status 134 but continuing despite the error We have tried the same data with two different GPUs (Tesla K20m and Quadro K4000). They both had the same problem. Any suggestions? Thanks, -- Kevin Tran, Contractor UNIX System Administrator The National Institutes of Health NIMH, Laboratory of Brain and Cognition 10 Center Drive, Room 4C215 Bethesda MD 20892-1366

2 1

Control point failure - CA Normalize
by Mark Plantz 16 Jan '14

16 Jan '14

Hello freesurfers, I am running into a problem during the "CA Normalize" sequence of autorecon-2. It looks like freesurfer is having a hard time creating control points based off the atlas I am using. The output is as follows: "finding control points in <Left_Cerebral_White_Matter>...found 0 control points" This repeated for the other various regions included in the atlas. The only control points found were "168 control points" in the "Right_Cerebral_White_Matter". Could this possibly be an alignment issue? If so, is there an easy way to check the alignment? Thank you, Mark

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