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Hello Doug and other experts:
I have done QDEC analysis between two groups (healthy controls vs disease) and obtained different .mgh and .annot files. I got one big cluster covering most part of the brain. I wanted to extract the number of vertices for Yeo's 7 Networks in that big cluster and therefore I ran this:
mri_segstats --i cache.th30.pos.sig.masked.mgh --annot fsaverage rh Yeo2011_7Networks_N1000 --excludeid 0 --sum network_param.dat
The result was:
Col Headers Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 1 22519 14950.0 7Networks_1 1.4816 1.8126 0.0000 3.6990 3.6990 2 2 30207 12514.7 7Networks_2 2.6658 1.6596 0.0000 3.6990 3.6990 3 3 17604 8224.3 7Networks_3 2.6278 1.6778 0.0000 3.6990 3.6990 4 4 19402 8357.2 7Networks_4 3.3453 1.0877 0.0000 3.6990 3.6990 5 5 11614 6205.0 7Networks_5 2.1434 1.7750 0.0000 3.6990 3.6990 6 6 22330 12170.7 7Networks_6 2.6315 1.6761 0.0000 3.6990 3.6990 7 7 26056 13826.2 7Networks_7 3.0249 1.4229 0.0000 3.6990 3.6990
I ran the same code for different --i (input) .mgh files and everytime the NVertices were the same, which means this is not the one I am looking for.
Can you please help me in getting the number of vertices of Yeo's each network that fall in that big cluster?
Thanks.
Anwar
--
Anwar S. Shatil
Research Assistant Department of Medical Imaging Sunnybrook Health Sciences Centre Room AB204, 2075 Bayview Avenue Toronto, ON M4N 3M5 Tel: 416.480.6100 ext. 89617 Email: anwar.shatil@sunnybrook.ca This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.
The input (--i) only supplies information for use in computing the Mean, StdDev, etc. The number of vertices willcome from the annot. Or am I misunderstanding something?
On 08/15/2018 10:44 AM, Shatil, Anwar Shahadat wrote:
External Email - Use Caution
Hello Doug and other experts:
I have done QDEC analysis between two groups (healthy controls vs disease) and obtained different .mgh and .annot files. I got one big cluster covering most part of the brain. I wanted to extract the number of vertices for Yeo's 7 Networks in that big cluster and therefore I ran this:
mri_segstats --i cache.th30.pos.sig.masked.mgh --annot fsaverage rh Yeo2011_7Networks_N1000 --excludeid 0 --sum network_param.dat
The result was:
Col Headers Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 1 22519 14950.0 7Networks_1 1.4816 1.8126 0.0000 3.6990 3.6990 2 2 30207 12514.7 7Networks_2 2.6658 1.6596 0.0000 3.6990 3.6990 3 3 17604 8224.3 7Networks_3 2.6278 1.6778 0.0000 3.6990 3.6990 4 4 19402 8357.2 7Networks_4 3.3453 1.0877 0.0000 3.6990 3.6990 5 5 11614 6205.0 7Networks_5 2.1434 1.7750 0.0000 3.6990 3.6990 6 6 22330 12170.7 7Networks_6 2.6315 1.6761 0.0000 3.6990 3.6990 7 7 26056 13826.2 7Networks_7 3.0249 1.4229 0.0000 3.6990 3.6990
I ran the same code for different --i (input) .mgh files and everytime the NVertices were the same, which means this is not the one I am looking for.
Can you please help me in getting the number of vertices of Yeo's each network that fall in that big cluster?
Thanks.
Anwar
--
*Anwar S. Shatil*
Research Assistant Department of Medical Imaging Sunnybrook Health Sciences Centre Room AB204, 2075 Bayview Avenue Toronto, ON M4N 3M5 Tel: 416.480.6100 ext. 89617 Email: anwar.shatil@sunnybrook.ca
*/This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies./*
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Hi Doug:
Thanks for your reply. I think you are correct.
Is there any way to extract the number of vertices from the cluster spanning each of Yeo's 7 networks? I tried to overlay Yeo2011_7Networks_N1000.annot on the .mgh file and use my cursor to get information, but that does not give me the number of vertices.
Thanks,
Anwar
--------
Date: Wed, 15 Aug 2018 11:18:50 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Extracting number of vertices in Yeo's 7Networks from significant clusters To: freesurfer@nmr.mgh.harvard.edu Message-ID: 0870c8a6-0a29-b748-500a-3cbfbc39b8f0@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"; format=flowed
The input (--i) only supplies information for use in computing the Mean, StdDev, etc. The number of vertices willcome from the annot. Or am I misunderstanding something? ________________________________ From: Shatil, Anwar Shahadat Sent: August 15, 2018 10:44 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Extracting number of vertices in Yeo's 7Networks from significant clusters
Hello Doug and other experts:
I have done QDEC analysis between two groups (healthy controls vs disease) and obtained different .mgh and .annot files. I got one big cluster covering most part of the brain. I wanted to extract the number of vertices for Yeo's 7 Networks in that big cluster and therefore I ran this:
mri_segstats --i cache.th30.pos.sig.masked.mgh --annot fsaverage rh Yeo2011_7Networks_N1000 --excludeid 0 --sum network_param.dat
The result was:
Col Headers Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 1 22519 14950.0 7Networks_1 1.4816 1.8126 0.0000 3.6990 3.6990 2 2 30207 12514.7 7Networks_2 2.6658 1.6596 0.0000 3.6990 3.6990 3 3 17604 8224.3 7Networks_3 2.6278 1.6778 0.0000 3.6990 3.6990 4 4 19402 8357.2 7Networks_4 3.3453 1.0877 0.0000 3.6990 3.6990 5 5 11614 6205.0 7Networks_5 2.1434 1.7750 0.0000 3.6990 3.6990 6 6 22330 12170.7 7Networks_6 2.6315 1.6761 0.0000 3.6990 3.6990 7 7 26056 13826.2 7Networks_7 3.0249 1.4229 0.0000 3.6990 3.6990
I ran the same code for different --i (input) .mgh files and everytime the NVertices were the same, which means this is not the one I am looking for.
Can you please help me in getting the number of vertices of Yeo's each network that fall in that big cluster?
Thanks.
Anwar
--
Anwar S. Shatil
Research Assistant Department of Medical Imaging Sunnybrook Health Sciences Centre Room AB204, 2075 Bayview Avenue Toronto, ON M4N 3M5 Tel: 416.480.6100 ext. 89617 Email: anwar.shatil@sunnybrook.ca This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.
Use the --mask option to mri_segstats and pass it a surface overlay with just the cluster of interest in it. You can use --maskthresh and --masksign to fine-tune the masking process.
On 08/15/2018 02:17 PM, Shatil, Anwar Shahadat wrote:
External Email - Use Caution
Hi Doug:
Thanks for your reply. I think you are correct.
Is there any way to extract the number of vertices from the cluster spanning each of Yeo's 7 networks? I tried to overlay Yeo2011_7Networks_N1000.annot on the .mgh file and use my cursor to get information, but that does not give me the number of vertices.
Thanks,
Anwar
Date: Wed, 15 Aug 2018 11:18:50 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Extracting number of vertices in Yeo's 7Networks from significant clusters To: freesurfer@nmr.mgh.harvard.edu Message-ID: 0870c8a6-0a29-b748-500a-3cbfbc39b8f0@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"; format=flowed
The input (--i) only supplies information for use in computing the Mean, StdDev, etc. The number of vertices willcome from the annot. Or am I misunderstanding something?
*From:* Shatil, Anwar Shahadat *Sent:* August 15, 2018 10:44 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Extracting number of vertices in Yeo's 7Networks from significant clusters
Hello Doug and other experts:
I have done QDEC analysis between two groups (healthy controls vs disease) and obtained different .mgh and .annot files. I got one big cluster covering most part of the brain. I wanted to extract the number of vertices for Yeo's 7 Networks in that big cluster and therefore I ran this:
mri_segstats --i cache.th30.pos.sig.masked.mgh --annot fsaverage rh Yeo2011_7Networks_N1000 --excludeid 0 --sum network_param.dat
The result was:
Col Headers Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 1 22519 14950.0 7Networks_1 1.4816 1.8126 0.0000 3.6990 3.6990 2 2 30207 12514.7 7Networks_2 2.6658 1.6596 0.0000 3.6990 3.6990 3 3 17604 8224.3 7Networks_3 2.6278 1.6778 0.0000 3.6990 3.6990 4 4 19402 8357.2 7Networks_4 3.3453 1.0877 0.0000 3.6990 3.6990 5 5 11614 6205.0 7Networks_5 2.1434 1.7750 0.0000 3.6990 3.6990 6 6 22330 12170.7 7Networks_6 2.6315 1.6761 0.0000 3.6990 3.6990 7 7 26056 13826.2 7Networks_7 3.0249 1.4229 0.0000 3.6990 3.6990
I ran the same code for different --i (input) .mgh files and everytime the NVertices were the same, which means this is not the one I am looking for.
Can you please help me in getting the number of vertices of Yeo's each network that fall in that big cluster?
Thanks.
Anwar
--
*Anwar S. Shatil*
Research Assistant Department of Medical Imaging Sunnybrook Health Sciences Centre Room AB204, 2075 Bayview Avenue Toronto, ON M4N 3M5 Tel: 416.480.6100 ext. 89617 Email: anwar.shatil@sunnybrook.ca
*/This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies./*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Shatil, Anwar Shahadat