Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

nifti1Read(): unsupported slice timing pattern 5 -- mri_convert fix?
by Alex Kell 23 Oct '15

23 Oct '15

Hi, I'm analyzing data from a collaborator who used SPM to generate some niftis, and freesurfer is unable to read these. I get the following error: nifti1Read(): unsupported slice timing pattern 5 Someone previously <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29542.html> had the same problem that I currently have, and Doug sent them a modified version of mri_convert. Could you send me the modified version of mri_convert? Thanks, Alex

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Longitudinal analysis with QDEC
by Wrobel, Pawel 23 Oct '15

23 Oct '15

Hello Dear FreeSurfer Developers, Thank You once again for helping me a couple of months ago. Today I came across a new obstacle, as I have been trying to analyse longitudinal material. I have performed all preparation steps and I started performing statistical analysis in Qdec when receiving following message: Error in Analyze: Couldn't open .../FreeSurfer_output/subjects/CT_10/BLD013_/surf/lh.thickness.fwhm15.fsaverage.mgz or .mgh file. I have checked in the surface directory and I could not find this file. There were several variations of it, but not a file with this particular name. I have been working with Freesurfer5.3. Thank You for Your help! Pawel

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Re: [Freesurfer] Sulcal depth units
by Simon Vandekar 22 Oct '15

22 Oct '15

Hi Bruce, I chose a random subject from the ADNI dataset and computed the mean and variance for the left and right hemispheres separately. It looks like the mean is close to 0, however the variance is not 1. Do you think it is possible that the surfaces are demeaned, but the units are still something meaningful (i.e. not unitless)? sulc = read.table('rh.sulc.asc', header=FALSE, col.names=c('v', 'x', 'y', 'z', 'sulc')) > mean(sulc$sulc) [1] -1.236923e-08 > var(sulc$sulc) [1] 0.3276958 > quantile(sulc$sulc) 0% 25% 50% 75% 100% -1.72503 -0.42128 -0.03963 0.40072 1.80980 Thanks again, Simon Hi Simon they are originally mm, but I believe we z-score normalize them so that the sulc file is 0 mean and unit variance. cheers Bruce On Wed, 21 Oct 2015, Simon Vandekar wrote: > Dear Freesurfer experts, > > I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System" by Fischl, Sereno, and Dale (1999) where the estimation of sulcal depth is described on page 199, however from the description I am still unsure of the exact units of sulcal depth. > Are the units for sulcal depth in mm or are they in arbitrary units? > > Thanks in advance, > Simon > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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FSFAST -per-run question
by dgw 22 Oct '15

22 Oct '15

Hi, I know that -per-run is the recommended motion correction option, and that it uses the middle frame as the reference for motion correction for each run. I was wondering, if there is a reference, or explanation as to why that was chosen and not some other timepoint. Thanks, d

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How to compute the measures on the average brain?
by Mathieu Dubois 22 Oct '15

22 Oct '15

Hi, I'm a beginner with freesurfer so I apologize if it's a trivial question. I recently run recon-all with the -all on many subjects. As far as I can say, all the steps worked. However, the measures on the average brain (output of mris_preproc and friends) were not computed. A colleague told me that he usually re-run recon-all with the -qcache flag to compute those. This seems to work but I don't understand if it is the recommended way to run mris_preproc and why it is not included with -all. Is it possible to get those measures in one call to recon-all? I don't think that the issue comes from the data (e.g. that the failing of a step stops some branch of the pipeline) because it seems to run correctly with -qcache. I haven't found any help on -qcache and the help of recon-all doesn't mention mris_preproc or mri_surf2surf. Thanks in advance, Mathieu

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Postdoctoral position available - quantitative imaging in epilepsy
by Brinkmann, Benjamin H. (Ben) 22 Oct '15

22 Oct '15

The Mayo Systems Electrophysiology Lab within the Departments of Neurology and Physiology & Biomedical Engineering at Mayo Clinic in Rochester, Minnesota has a postdoctoral position for a computational scientist interested in analysis of structural & functional imaging in epilepsy. http://www.mayo-clinic-jobs.com/job/Rochester-Research-Fellow-Job-MN-55901/…

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per analysis with covariates
by marica.padula＠libero.it 22 Oct '15

22 Oct '15

Hi, I am running a vertex-wise correlation analysis between local gyrification (-- y) and thickness (--pvr) using as covariates age and gender. I want to control for the effect of age and gender both the lGI and the thickness values. Does the command does this? Or the effect of the covariates is only taken into account for the lGI? Here my command line: mri_glmfit --glmdir left --y lh.lGI.mgh --fsgd fsgd_control.txt --pvr lh. thickness.mgh --C contrast_control.txt --surface fsaverage lh And my contrast: 0 0 0 1 (first 0 for the class, second and third for the 2 covariates). Thanks, Marica

2 1

normalization of hippocampal volume
by geschwind2013 22 Oct '15

22 Oct '15

Hi, FS Experts, I’m using version 5.3 and have performed hippo-subfields analysis. To perform the statistics, shall I get the normalized volumes of each hippo-subfields? or just to do correction for ICV is enough ? thanks.. Hyon

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Talairach_afd error
by Anna I. Garcia Diaz 22 Oct '15

22 Oct '15

Dear all, I am having problems running the recon-all process. The error log is attached to this e-mail. This error appears only when I run recon-all in a machine able to parallelize preprocesses, however, if I use the same reconstructed oriented image in a machine sent as a normal job directly to the terminal, the preprocess runs without any errors and the output looks correct. I have tried to use the -notal-check flag as the error log suggests, but it fails anyway. Since our team is working in a longitudinal study, and the images from the other time points have been preprocessed with the parallelizing machine, we are concerned that using the non-parallelizing machine could add significant methodological variabilities to our studies, and we would rather be consistent with the previous procedures. Do you have any comments or further suggestions on how we might be able to fix this error? Thanks in advance for your time and help Anna Garcia

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mris_expand - problem reading thickness file?
by Alex Puckett 22 Oct '15

22 Oct '15

Hello! I'm having trouble with mris_expand using the -thickness flag. ?If I expand by a fixed distance instead of % thickness then mris_expand works no problem - the program seems to be hanging up when reading the thickness file. Has anyone else experienced this? The command I'm running (from the surf folder) is: mris_expand -thickness lh.white 0.5 lh.expandWhiteThick0p5 The output from this is: "?using distance as a % of thickness expanding surface lh.white by 50.0% of thickness and writing it to lh.expandWhiteThick0p5 reading thickness..." And then...nothing! Watching the CPU usage it appears that resources are used for about 10 -12 minutes and then drops to 0 and just sits there for as long as I'll let it (>4 days) - no error. Also, the thickness files do not appear to be corrupt. I can overlay the thickness data onto a surface no problem. Any help would be appreciated. Cheers, Alex --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS Linux release 7.1.1503 (Core) Kernel info: Linux 3.10.0-229.1.2.el7.x86_64 x86_64 --------------------------------------------------------------------- ?

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