Freesurfer October 2010

freesurfer@nmr.mgh.harvard.edu

100 participants
129 discussions

Cluster Multiple Comparison Correction
by Jay Ives 10 Oct '10

10 Oct '10

Hi Experts, Which option is best to use: mc-z or perm? I have read that perm gives more accurate results than mc-z, as it uses the actual data rather than fake data to estimate the null distribution. When I use perm, I get no significant clusters. When I use mc-z, almost all clusters are significant. Thanks......J

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Side swapped results?
by Jay Ives 10 Oct '10

10 Oct '10

Hi Experts, I have experienced a possible problem with sided-ness within Freesurfer. I have 2 groups which have been processed through the pipeline without error. I have used the lh.aparc and rh.aparc files to extract parcellated cortex volumes, and analysed the mean differences with SPSS. >From this I get significantly different volumes in the RIGHT fusiform gyrus (amongst others). I then used QDEC to look at vertex based volume differences and found a large significant clusters at the LEFT fusiform gyrus, but not the RIGHT. I'm certain I haven't mixed up the analysis. Can anyone comment on this? Thanks........J

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mri/orig File naming requirements
by Matt Russell 10 Oct '10

10 Oct '10

Hello All, I'm currently working an automation program to setup a FreeSurfer file system for processing. I was wondering if I put a quality check pipeline in the code, deleting files that fail an inspection, would I have problems if the file name order ceased to be 001.mgz, 002.mgz, 003.mgz and was changed to just 002.mgz, 003.mgz? Best, Matthew Russell

3 2

dura flag in fsv5.0.0
by Juranek, Jenifer 08 Oct '10

08 Oct '10

Since the -dura flag is not recognized in FSv5.0.0, how should mempr data (4 echoes) be passed to the latest version of FS? Many Thanks, Jenifer

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Upscaling Functional Data
by Luis Lafer-Sousa 08 Oct '10

08 Oct '10

Using jip-align, we have successfully registered functional data to templates we created from high resolution anatomical scans. To create the templates though, we had to downsample the original scans and lose resolution. Ideally we would like to maintain the resolution of the anatomicals, and upsample the functionals. When trying to do this we run into an error using mri-convert since they are 4-dimensional. How do we upsample the dimensions of functional data? Or how do other groups resolve the resolution differences? Thanks, Luis

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FW: Extracting coordinates of segmented volume
by Eggebrecht, Adam 08 Oct '10

08 Oct '10

Hello there, I am just getting started with learning the ways of FreeSurfer. I am hoping you can help explain how (and if) FreeSurfer can give me the information I need. I want to use FS's segmentation to better label optical properties in the head for optical reconstructions. Does FS output the coordinates and labels for the segmented volume (gray matter, white matter, csf)? Also good would be the affine transform so it can be inverted to put the coordinates of the segmented and labelled nodes (voxels?) back into native space. I am performing our head segmentation and optical analysis in MATLAB. Any help supplied is greatly appreciated. Many thanks! Adam Adam T. Eggebrecht, Ph.D. Dept. of Radiology Washington University School of Medicine St. Louis, MO 314-362-6942 The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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mri_convert with flash - FS 4.5.0 vs 5.0
by Ellen Lau 08 Oct '10

08 Oct '10

Hi, We're having trouble using mri_convert as wrapped within mne_flash_bem to create the bem surfaces from our FLASH volumes. The script runs but the inner_skull and outer_skull surfaces that it outputs seem to be rotated, for example if we display the surfaces on the T1 coronal, we see what looks like the sagittal inner_skull surface. I'm guessing this is some kind of registration problem. I noticed that we are getting a warning at one point in the process when the flash is being registered with the MPRAGE, which I've pasted below. I am wondering if this might have something to do with the switch to version 5.0.0. For this dataset, we ran the reconstruction and all the subsequent processing on v5.0.0. However, I have gotten the exact same error (rotated inner and outer skull surfaces) when I accidentally ran mne_flash_bem in v5.0 with a previous dataset that was reconstructed in v4.5.0. When I re-ran mne_flash_bem in v4.5.0 the surfaces came out correctly for the previous dataset. But I was reluctant to try this with my new dataset since ideally we'd like to be able to switch completely over to v5.0.0. Thanks, Ellen --------------- [kerryave:test] (nmr-std-env) which mri_convert /usr/local/freesurfer/stable5/bin/mri_convert setenv SUBJECTS_DIR /cluster/kuperberg/SemPrMM/MRI/structurals/subjects/ selected output from mne_flash_bem containing the warning: /autofs/cluster/kuperberg/SemPrMM/MRI/structurals/subjects/ya1/mri/flash/parameter_maps mri_convert ./fsl_rigid_register.7595/outvol.fsl_rigid_register.nii flash5_reg.mgz mri_convert ./fsl_rigid_register.7595/outvol.fsl_rigid_register.nii flash5_reg.mgz $Id: mri_convert.c,v 1.166.2.4 2010/09/20 17:29:33 nicks Exp $ reading from ./fsl_rigid_register.7595/outvol.fsl_rigid_register.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 5.63785e-17) j_ras = (0, 3.67872e-08, -1) k_ras = (0, 1, -1.5134e-08) writing to flash5_reg.mgz... /autofs/cluster/kuperberg/SemPrMM/MRI/structurals/subjects/ya1/mri/flash/parameter_maps mri_copy_params flash5_reg.mgz flash5.mgz flash5_reg.mgz WARNING: volume sizes are different in_vol : 256, 256, 256 temp_vol : 256, 256, 176 Cleaning up

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error loading averaged brain in QDEC (2)
by Ilana Hairston 08 Oct '10

08 Oct '10

sorry - on further inspection i changed "Common-Space Subject" to the new averaged subject folder. However, when trying to run analyses, i get an error message: Error in Analyze: Couldn't open file /usr/local/FS5/subjects/FS080920cr/surf/lh.thickness.fwhm10.avgsubject.mgh (where"avgsubject" was the output name of the averaged subject template). Indeed, there are ?h.?.fwhm?.fsaverage.mgh in my subject folders (presumable from the previous preproc), but no new ones. thanks ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Sentimental Insomnia and Nostalgia Disorders Sciences ********************

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Creating Brainmaps for Significant Regression
by Adam Nitenson 08 Oct '10

08 Oct '10

Hi all, So far I have only been using Freesurfer analyses to look at the functional activation for individuals, single groups, and subtractions between 2 groups. We now want to investigate a possible linear relationship between allele load (Three levels: 0,1,2) and functional activation. Is there a way to create a brainmap using glmfit or some other command that displays voxels that display a significant regression of genotype (such as red for positive / blue for negative linear relationship)? Basically, it would be a map that shows significant "r" instead of significant difference. Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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error loading averaged brain in QDEC
by Ilana Hairston 08 Oct '10

08 Oct '10

Hi there, i ran "make_average_subject", and then tried to load the averaged brain to QDEC 1.4. I get this error message: ERROR: MRISread: file '/usr/local/FS5/subjects/avgsubject/surf/lh.avg_thickness' has many more faces than vertices! Probably trying to use a scalar data file as a surface! What am i missing? Note - the data was originally processed using FS version 4.5. thanks ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Sentimental Insomnia and Nostalgia Disorders Sciences ********************

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Freesurfer October 2010