Re: [Freesurfer] Multiple Comparison Question for surface-based analyses

Hi Doug, Thank you very much for your update regarding this issue. 1)Just curious, will LGI be included in this report as this is another analysis of interest? 2)As for the cortical thickness I originally used 15mm in the analysis so based on your email I think using 5-10mm may be more prudent

Re: [Freesurfer] brain mask and T1 are not the same size

as scrubbed... Name: Screen Shot 2016-08-03 at 10.41.31 AM.png Type: image/png Size: 222427 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/b575e32f/attachment-0001.png -- Message: 10 Date: Wed, 3 Aug 2016 02:

Re: [Freesurfer] Coordinates in TRACULA group analysis

Hi Anastasia, Thank you for your kind explanation. I can be understanding how TRACULA tracts white matter pathways. At each position (in training subjects, not in new subjects of my data) probability that next goes for which direction to every labels in the aparc+aseg (not with setting a certain R

Re: [Freesurfer] mapping error

what is your command line? On 8/3/16 6:00 AM, Caroline Beelen wrote: Dear FS, An aparc.annot ctab file was created but I got the following error: Colortable:aparc.annot.ctab Annotname: myaparc Nhitsfile nhits.mgh Nlabels 6 Labeltresh 0 0.0 Loading freesurfer/fsaverage/surf/lh.orig

Re: [Freesurfer] Multiple Comparison Question for surface-based analyses

On 8/3/16 3:45 AM, Ajay Kurani wrote: Hi Doug, Thank you very much for your update regarding this issue. 1)Just curious, will LGI be included in this report as this is another analysis of interest? I was not planning to. The 809 subjects that I used for thickness do not have lGI run on th

Re: [Freesurfer] Coordinates in TRACULA group analysis

That's correct! On Wed, 3 Aug 2016, Anri WATANABE wrote: Hi Anastasia, Thank you for your kind explanation. I can be understanding how TRACULA tracts white matter pathways.  At each position (in training subjects, not in new subjects of my data) probability that next goes for which direction

Re: [Freesurfer] brain mask and T1 are not the same size

W. 8th Street >> Miami, FL 33199 >> Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 >> Email: ad...@fiu.edu >> Webpage: http://myweb.fiu.edu/adick >> Join the Society for the Study of Human Development: >> http://www.

Re: [Freesurfer] Freesurfer Digest, Vol 150, Issue 6

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[Freesurfer] mri_label2label

Hello, i used mri_annotation2label to extract individual parcellations for my subjects. Do I need to register my subjects to fsaverage using mri_label2label before creating a mask for ROI surface based analysis using GLM dods? Thanks Best, Paul ___ Frees

[Freesurfer] Anonymizing FreeSurfer files

Hi, I'm involved in a project that requires anonymizing FreeSurfer data to remove all patient information. I've found that the subject folder number is sometimes included in text files and logs in a FreeSurfer folder. Is there any patient information stored in any of the non-text files? Is the

Re: [Freesurfer] Anonymizing FreeSurfer files

If you passed DICOMS directly to recon-all, then the only place that would have subject info would be the scripts/recon-all.log file; that file would captures the conversion, and the subject name and date of scan will show up there (might be some other info stored in the dicom file that gets pr

Re: [Freesurfer] mri_normalize, 110 is too dark

Hi Bruce, > You can't just change which peak is the WM - lots of things downstream would > fail That is unfortunate. I've send you the subject files and the raw files via filedrop (per these instructions https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange) On Fri, Jul 29, 2016 at 4:38 P

Re: [Freesurfer] mri_label2label

You should just run mri_annotation2label on fsaverage and use the label you want On 08/03/2016 01:55 PM, miracle ozzoude wrote: > Hello, > i used mri_annotation2label to extract individual parcellations for my > subjects. Do I need to register my subjects to fsaverage using > mri_label2label be

Re: [Freesurfer] brain mask and T1 are not the same size

n mask and T1 are not the same size (Douglas N Greve) >> >> >> -- >> >> Message: 1 >> Date: Wed, 3 Aug 2016 10:50:30 + >> From: Isabelle Deschamps >> Subject: Re: [Freesurfer]

Re: [Freesurfer] Coordinates in TRACULA group analysis

Thanks so much!! ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ***