External Email - Use Caution
Hi Freesurfers,
the number of my parcels increases after extending them into the WM with
mri_aparc2aseg \
--s s001 \
--annot 500.aparc \
--wmparc-dmax 2 \
--labelwm \
--hypo-as-wm \
--o mri/aparc.500+2mm.nii.gz
Could that really be the case? And if so, what can I do to keep the original
number of parcels?
(See more detailed description of my approach below)
I would be very grateful for some suggestions!
Thanks a lot,
Stephanie Winkelbeiner
-----------------------------------------------
Stephanie Winkelbeiner, PhD
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-8267
Email: swinkel...@northwell.edu<mailto:swinkel...@northwell.edu>
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Winkelbeiner, Stephanie A
<swinkel...@northwell.edu>
Sent: Friday, 24 May 2019 6:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [EXTERNAL] Re: Checking number of parcels after
transformation of an annotation file into a .nii.gz file
External Email. Use Caution.
External Email - Use Caution
Hi Doug,
thanks again for the great tip with MRIread - worked perfectly (after
gunzipping the parc300.nii.gz).
So, this means I have the next problem now: instead of 300 parcels this image
contains 638 parcels...
How I created parc300.nii.gz:
1. MATLAB script to create annotation file with 150 parcels/hemisphere
2. extending the parcels 2mm into the WM with mri_aparc2aseg (see 1st email)
3. coregistering to the T1 to get the transformation matrix (bbregister)
4. coregistering to DWI space (mri_vol2vol)
I found in an earlier answer of yours that the extention into the WM might
duplicate the parcels/labels
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/055952.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_pipermail__freesurfer_2018-2DFebruary_055952.html&d=DwMFAw&c=vq5m7Kktb9l80A_wDJ5D-g&r=ycrYUdKGMCyTnsIy5TvOdBwS8HE5ZtmVMesLULEN8xE&m=O04ejT4OMCoABZuHtxcNBFTV5kd2I3iNoEfTbDuX5Q8&s=JeMKgrHrp_mkwc0hI-lKcpr8YPLuQKG9Cqg1-e73Cds&e=>)
Following your suggestions in that email exchange, I did the following:
## 1. Create a mask of the wm labels:
mri_binarize \
--i aparc.500+2mm.nii.gz \
--min 2999.5 \
--max 4035.5 \
--o wm.mask.500.nii.gz
## 2. Mask the wmparc:
mri_mask \
aparc.500+2mm.nii.gz \
wm.mask.500.nii.gz \
aparc.500+2mm.masked.nii.gz
This results in only two parcels... What am I doing wrong or overlooking here?
Thanks a lot for your help (as always)!
Cheers,
Stephanie
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Winkelbeiner, Stephanie A
<swinkel...@northwell.edu>
Sent: Wednesday, 22 May 2019 6:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [EXTERNAL] Re: Checking number of parcels after
transformation of an annotation file into a .nii.gz file
External Email. Use Caution.
External Email - Use Caution
That sounds like a perfect plan!
I gonna try that immediately! Thanks so much, Doug!
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu>
Sent: Wednesday, 22 May 2019 6:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer] Checking number of parcels after
transformation of an annotation file into a .nii.gz file
External Email. Use Caution.
the way that pops to mind is to use matlab
a = MRIread('aparc.250+2mm.nii.gz');
u = unique(a.vol(:));
length(u) will give you the number of unique segmentation number
(including 0)
On 5/22/19 5:54 PM, Winkelbeiner, Stephanie A wrote:
>
> External Email - Use Caution
>
> Hi Freesurfers,
>
> I'm struggling to find out if the number of parcels during a process
> of transformations from annot -> nii.gz has changed.
>
> I extended the parcels from 500.annot 2mm into the WM with
> mri_aparc2aseg \
> --s s001 \
> --annot 500.aparc \
> --wmparc-dmax 2 \
> --labelwm \
> --hypo-as-wm \
> --o mri/aparc.250+2mm.nii.gz
> and coregistered the resulting file to the DWI image using bbregister
> and mri_vol2vol.
>
> Using afni's probilistic tractography pipeline, I end up with more
> parcels than I thought I had.
>
> Is there a way to check the number of parcels after extension into the
> WM (mri_aparc2aseg)?
>
> I would be extremely grateful for some insight!
> Thanks,
> Stephanie
>
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