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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: swinkelbei@northwell.edumailto:swinkelbei@northwell.edu
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Winkelbeiner, Stephanie A Swinkelbei@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....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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Winkelbeiner, Stephanie A Swinkelbei@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
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External Email - Use Caution
That sounds like a perfect plan!
I gonna try that immediately! Thanks so much, Doug! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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 CautionHi 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. 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.
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
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.
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.
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:swinkelbei@northwell.edu mailto:swinkelbei@northwell.edu
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Winkelbeiner, Stephanie A Swinkelbei@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:
- MATLAB script to create annotation file with 150 parcels/hemisphere
- extending the parcels 2mm into the WM with mri_aparc2aseg (see 1st email)
- coregistering to the T1 to get the transformation matrix (bbregister)
- 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.... 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Winkelbeiner, Stephanie A Swinkelbei@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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. 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://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
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.
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.
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Greve, Douglas N.,Ph.D. -
Winkelbeiner, Stephanie A