what do you mean? On 5/31/19 3:00 PM, Winkelbeiner, Stephanie A wrote: > > 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 (*MailScanner has detected a > possible fraud attempt from "urldefense.proofpoint.com" claiming to > be* > 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 > > > > The information contained in this electronic e-mail transmission and > > any attachments are intended only for the use of the individual or > > entity to whom or to which it is addressed, and may contain > > information that is privileged, confidential and exempt from > > disclosure under applicable law. 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If you have received this transmission in error, please > notify the sender immediately by telephone and electronic mail, and > delete the original communication and any attachment from any > computer, server or other electronic recording or storage device or > medium. Receipt by anyone other than the intended recipient is not a > waiver of any attorney-client, physician-patient or other privilege. > > The information contained in this electronic e-mail transmission and > any attachments are intended only for the use of the individual or > entity to whom or to which it is addressed, and may contain > information that is privileged, confidential and exempt from > disclosure under applicable law. If the reader of this communication > is not the intended recipient, or the employee or agent responsible > for delivering this communication to the intended recipient, you are > hereby notified that any dissemination, distribution, copying or > disclosure of this communication and any attachment is strictly > prohibited. If you have received this transmission in error, please > notify the sender immediately by telephone and electronic mail, and > delete the original communication and any attachment from any > computer, server or other electronic recording or storage device or > medium. Receipt by anyone other than the intended recipient is not a > waiver of any attorney-client, physician-patient or other privilege. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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