Re: [Freesurfer] Using a2009s.annot as seed masks for tractography

Hi Anastasia, Sorry for not being clearer. According to your email, I have labelled all my regions of interest using this command: mri_binarize --match ID --i aparc.a2009s+aseg.mgz --o labelID.nii.gz Let's take the left putamen as an example: cmdline mri_binarize --match 12 --i

[Freesurfer] help optseq2 question

Dear Doug Greve Hi, I am glad to write to you. I am a graduate student in Institute of Psychology, Chinese Academy of Sciences. It is my first time doing fMRI experiment. Now I meet some difficulties while using Optseq2. I hope you can help me. Thank you very much. The following are

[Freesurfer] PhD position available in Bern

Dear all I hope that it is ok to publish this short neuroimaging-related job offer here. At the Psychiatric University Hospital Bern (Switzerland), we're currently searching for a PhD student who is particularly interested in the neural underpinnings of psychopathology in psychosis

[Freesurfer] White matter and pial surfaces not tracking sulcus

Hi all, I have run into an issue that I am having trouble correcting. http://imgur.com/a/4KqpJ I have checked the aseg to see if it was labeled as ventricle. This does not seem to be the cause. Any other suggestions? I am happy to upload the case if that is necessary. Best regards, Niels

Re: [Freesurfer] functional connectivity maps (correlation and z maps)

Thanks Doug, Hi, I am wondering if you would give some input on this: When we run the buckner scripts for functional connectivity analysis, those scripts: 1. Obtain correlation maps of individual subjects, and convert them to individual subject z-maps using Fisher's r-to-z transformation.

Re: [Freesurfer] getting callosal compartment average thickness / length

Hi Ben I don't think either of those are measured by default. Peng Yu wrote some code some years ago to do this, but I don't think we ever put the effort into making it distributable. Basically you would need to run a medial axis transform and measure the radius of the inscribed circle at

[Freesurfer] Measuring Brain torque

Dear Freesurfer Experts, I wonder if there is anyway in FS to measure the brain torque or if you have any experience with other tools regarding this? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] getting callosal compartment average thickness / length

Hi all, I am trying to parcellate the corpus callosum into 50 compartments using the -d option of the mri_cc command. I first ran recon-all on a DICOM volume for a single subject, then verified things looked good using tkmedit. Is there a way to get the average thickness for each compartment?

[Freesurfer] [FreeSurfer] : Convert asl data from fsaverage (surface) to MNI305 (volume)

Dear experts, I have some asl data on fsaverage surface and would like to compute them on MNI305 volume. So I executed the commands below, but when merging left and right hemispheres it seems that the *--fillribbon *option on *MNI305.asl.nii.gz* output data didn't work for right hemisphere :

[Freesurfer] fs-fast temporal snr

Hi, Does FS-FAST perform any temporal SNR calculations on data? If so, how. Thanks, Dan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is

Re: [Freesurfer] selxavg3-sess svd NaN error

can you send /autofs/cluster/neuromind/dwakeman/mm/subjects/nmr00904/sycabs/sycabs_lh/pr014/Xtmp.mat ? On 03/26/2015 03:51 PM, dgw wrote: Hi, I am having a problem running my selxavg3-sess using Freesurfer 5.3.0 stable. I am getting the following error: Saving X matrix to

Re: [Freesurfer] selxavg3-sess svd NaN error

The duration of the stimuli for condition 4 is only 8 milisec. What's up with that? If this is what you want, then go into the analysis.info file and change the TER to something like .007974 (your TR/153). You'll have to do this for all your analyses. The TER is the basic clock tick of the

Re: [Freesurfer] selxavg3-sess svd NaN error

Actually, I just noticed that I had a flag in mkanalysis-sess that does this. It is -TER doug On 03/26/2015 08:15 PM, Douglas N Greve wrote: The duration of the stimuli for condition 4 is only 8 milisec. What's up with that? If this is what you want, then go into the analysis.info file and

[Freesurfer] selxavg3-sess svd NaN error

Hi, I am having a problem running my selxavg3-sess using Freesurfer 5.3.0 stable. I am getting the following error: Saving X matrix to /autofs/cluster/neuromind/dwakeman/mm/subjects/nmr00904/sycabs/sycabs_lh/pr014/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond

Re: [Freesurfer] fs-fast temporal snr

Yes, look in fsnr.nii.gz On 03/26/2015 03:53 PM, dgw wrote: Hi, Does FS-FAST perform any temporal SNR calculations on data? If so, how. Thanks, Dan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] [FreeSurfer] : Convert asl data from fsaverage (surface) to MNI305 (volume)

That version had a bug. Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol On 03/26/2015 12:16 PM, Matthieu Vanhoutte wrote: Dear experts, I have some asl data on fsaverage surface and would like to compute them on MNI305 volume. So I executed the

Re: [Freesurfer] Fw: longitudinal statistics LGI

Hi Jorge, I have read the previous posts and applied it for my analysis which is longitudinal study go control and patient groups. I have a control group (n=19) with 2.87 ± 0.3 years time difference between scans. and patient group (n=16) who have 1.31 ± 0.6 years time difference. I followed your

[Freesurfer] smoothing for mri_glmfit

When doing connectivity based within group analysis using mri_glmfit. If I already smoothed the data in the first level analysis do I need to again smooth using the --fwhm command? If so, why? Tracy ___ Freesurfer mailing list

Re: [Freesurfer] smoothing for mri_glmfit

No, you should do all the smoothing at the 1st level. doug On 03/26/2015 10:53 AM, Barbour, Tracy,M.D. wrote: When doing connectivity based within group analysis using mri_glmfit. If I already smoothed the data in the first level analysis do I need to again smooth using the --fwhm command?