New subject: Overlap of vertices in downsampled data

9 Apr 2020

      External Email - Use Caution
We calculated p-value/tstat overlays using FSL PALM comparing the cortical
thickness of different groups. We aim for a measure of similarity in
cortical thickness between some of the groups. Our idea was to use dice
overlap between groups to test similarity in atrophy patterns.
We tried to use ‚mri_compute_overlap‘ to obtain these measures but when we
used the p-value overlays we found that mrs_compute_overlap returned us the
dice overlap for cortical regions and also white matter and unknown labeled
regions what is not expected in a cortical thickness stats map I guess. So
we doubt that is the correct way to use these overlays.
Do you have any idea how to calculate the dice overlap of statistical
overlays (vertex wise)?
Thanks,
Ersin Ersözlü
freesurfer-request@nmr.mgh.harvard.edu adresine sahip kullanıcı 9 Nis
2020 Per, 18:01 tarihinde şunu yazdı:
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Today's Topics:

Re: Error in Tracula-all -prep (Yendiki, Anastasia)
Re: Tracula: tract length meaning (Yendiki, Anastasia)
Re: Hippocampal Subfield Segmentation Error
(Lab of Autism and Developmental Neuroscience,    Lab of Autism and

Developmental Neuroscience)
   4. Re: mri_convert input files (Douglas N. Greve)
   5. Re: mri_glmfit-sim FWHM error (Douglas N. Greve)
   6. Re: Aseg file issue (Douglas N. Greve)
   7. Overlap of vertices in downsampled data (Ersin Ers?zl?)
   8. Re: Overlap of vertices in downsampled data (Douglas N. Greve)
   9. Re: Fwd: Is it possible to load flatmaps in freeview and draw
      ROI's on them? (Ruopeng Wang)
  10. Re: Aseg file issue
      (Lab of Autism and Developmental Neuroscience,    Lab of Autism and
Developmental Neuroscience)

Message: 1
Date: Thu, 9 Apr 2020 02:34:53 +0000
From: "Yendiki, Anastasia" AYENDIKI@mgh.harvard.edu
Subject: Re: [Freesurfer] Error in Tracula-all -prep
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
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Hi Salah - It looks like it didn't find your subject's freesurfer recon
when it was doing the pre-processing, so it skipped some steps that you
need to go beyond that point. Based on your SUBJECTS_DIR and your subject
name, it looked for this file:
/Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/mri/brain.mgz
Any chance this was missing or unreadable?
a.y
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <
freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salah Showiheen <
sshowiheen@gmail.com>
Sent: Monday, April 6, 2020 11:49 PM
To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error in Tracula-all -prep
    External Email - Use Caution

Hi Freesurfer community,
I have an issue that I spent ages trying to figure out and this error has
been asked about back in (17/12/2016) and the title is ([Freesurfer]
Tracula trac -all preprocessing error.
my error is:
ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni
There is an issue that the mini folder is empty.
Attached is the log file and the configuration file (tracula_conf.txt)
Regards,
Salah

Re: [Freesurfer] Overlap of vertices in downsampled data