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)
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- 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 Message-ID: < MN2PR04MB575785A35596BD0BB37BF85A8AC10@MN2PR04MB5757.namprd04.prod.outlook.com
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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 CautionHi 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