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Il giorno 16 gen 2020, alle ore 6:00 PM, freesurfer-request@nmr.mgh.harvard.edu ha scritto:
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Today's Topics:
1. Qdec and TkSurfer input boxes (Marcos Martins da Silva)
2. FreeSurfer analyses in MatLab (Graduate Imaging)
3. Re: Oval shape in average subject inflated (Marina Fern?ndez)
4. Segfault in mris_topo_fixer (Christian O'Reilly, Dr)
5. Re: Segfault in mris_topo_fixer (Hoopes, Andrew)
6. Segmentation Fault during recon-all using FLAIR Image
(Swanson,Clayton)
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Message: 1
Date: Wed, 15 Jan 2020 14:02:26 -0300
From: Marcos Martins da Silva <marcosm@hucff.ufrj.br>
Subject: [Freesurfer] Qdec and TkSurfer input boxes
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CANXLKP7HxjOjLShobVkYr+eDGNuh+PksDM1Aio=9XgKm_NaXeg@mail.gmail.com>
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Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with
input/entry/edit boxes in Qdec and TkSurfer. I can see box content, click
inside the box and even select the content but it seems read only: I can't
change it. So it is impossible to see the scatter plot from a specific
vertex inputing its number. Any clue about what happened and how to fix it?
Thank you for your attention.
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Message: 2
Date: Wed, 15 Jan 2020 16:08:12 -0500
From: Graduate Imaging <graduate.imaging@gmail.com>
Subject: [Freesurfer] FreeSurfer analyses in MatLab
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CA+yW3sSV=E5M1_cbOJfecPMCeCePjtZy_isFL8vzmRMDX55Pfw@mail.gmail.com>
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Hello,
I recently ran a vertex wise analysis on two different projects the first
had three groups with three co-variates that looked at if group membership
was associated with brain volume. The second project had two groups with
three co-variates looking at psychiatric x BMI interaction effect on brain
volume. I'm interested in running ROI analyses in matlab to ensure the same
matrices were used.
To run the ROI analyses I'm going to important the design matrix from the
vertex wise analysis and use the fast_glmfit and fast_fratio commands as
shown below:
X = load('Xg.dat');
C = load('C.dat');
y = load('ROI.dat'); text file containing participant ROI values from the
DKT atlas.
[beta rvar] = fast_glmfit(y,X);
[F pvalues] = fast_fratio(beta,X,rvar,C
My first question is the beta values that are calculated from fast_glmfit
are unstandardized is there anyway way to have it compute standardized
values?
My second question is when I ran the ROI analyses looking at the diagnosis
x BMI interaction effect it outputs an array of beta values for each
regressor. In addition to each groups beta value (for BMI) I'm interested
in the beta value of the interaction (ie diagnosis x BMI). I was wondering
how do i go about obtaining this? Would I have to create a new matrix with
the interaction term included in it?
If so would the analysis essentially be one group with the diagnosis x BMI
interaction term plus the three co-variates?
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Message: 3
Date: Thu, 16 Jan 2020 12:58:41 +0100
From: Marina Fern?ndez <marina.fdez.alvarez@gmail.com>
Subject: Re: [Freesurfer] Oval shape in average subject inflated
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAALjZmeP2eKby4GGLJn_X6uOfCwPgNfnE3WUq5kmbv0-nqHi6Q@mail.gmail.com>
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It works! Thank you very much Bruce!
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Message: 4
Date: Thu, 16 Jan 2020 14:57:00 +0000
From: "Christian O'Reilly, Dr" <christian.oreilly@mcgill.ca>
Subject: [Freesurfer] Segfault in mris_topo_fixer
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<YQBPR0101MB10125047A377D0AD8F34D349E1360@YQBPR0101MB1012.CANPRD01.PROD.OUTLOOK.COM>
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Hi,
I got the following error running mris_topo_fixer:
~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh
INFO: assuming .mgz format
verbose mode on (medium mode): printing warnings
reading input surface /usr/local/freesurfer/subjects/ANTS6-0Months3T/work/ANTS6-0Months3T/surf/lh.orig...
Before topology correction, eno=0 (nv=43656, nf=87312, ne=130968, g=1)
Surface Diagnostics:
eno=0 (nv=43656, nf=87312, ne=130968)
# of border vertices [ #v ~ #f ] 0
# of edges with single face 0
# of edges with more than 2 faces 0
# of corner configurations 0
The original surface is a valid manifold
Counting the number of connected components
The original surface has one component
The original surface does not self-intersect
The surface has 1 loops (X=0)
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
identify defects...
marking ambiguous vertices...
1527 ambiguous faces found in tessellation
segmenting defects...
analyzing defects for overlaps...
reading brain volume from brain...
reading wm segmentation from wm...
Detecting contrast direction: right direction [ GM (129.46) < WM (134.73) ]
ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0
ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0
Segmentation fault (core dumped)
Any idea what in the data file could cause the assert "vt->nsizeMax > 0" to be triggered? Any idea how to go around it?
Thank you,
Christian
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Message: 5
Date: Thu, 16 Jan 2020 15:39:32 +0000
From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] Segfault in mris_topo_fixer
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BN8PR04MB56979DB2BBFD5A0BAB3E280EF9360@BN8PR04MB5697.namprd04.prod.outlook.com>
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Hi Christian, if you send me that surface, I can take a look at what's going wrong.
best
Andrew
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Christian O'Reilly, Dr <christian.oreilly@mcgill.ca>
Sent: Thursday, January 16, 2020 9:57 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Segfault in mris_topo_fixer
External Email - Use Caution
Hi,
I got the following error running mris_topo_fixer:
~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh
INFO: assuming .mgz format
verbose mode on (medium mode): printing warnings
reading input surface /usr/local/freesurfer/subjects/ANTS6-0Months3T/work/ANTS6-0Months3T/surf/lh.orig...
Before topology correction, eno=0 (nv=43656, nf=87312, ne=130968, g=1)
Surface Diagnostics:
eno=0 (nv=43656, nf=87312, ne=130968)
# of border vertices [ #v ~ #f ] 0
# of edges with single face 0
# of edges with more than 2 faces 0
# of corner configurations 0
The original surface is a valid manifold
Counting the number of connected components
The original surface has one component
The original surface does not self-intersect
The surface has 1 loops (X=0)
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
identify defects...
marking ambiguous vertices...
1527 ambiguous faces found in tessellation
segmenting defects...
analyzing defects for overlaps...
reading brain volume from brain...
reading wm segmentation from wm...
Detecting contrast direction: right direction [ GM (129.46) < WM (134.73) ]
ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0
ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0
Segmentation fault (core dumped)
Any idea what in the data file could cause the assert "vt->nsizeMax > 0" to be triggered? Any idea how to go around it?
Thank you,
Christian
------------------------------
Message: 6
Date: Thu, 16 Jan 2020 15:55:44 +0000
From: "Swanson,Clayton" <Clayton.Swanson@colostate.edu>
Subject: [Freesurfer] Segmentation Fault during recon-all using FLAIR
Image
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <A95D6E27-F818-45F7-9391-C5B130978013@colostate.edu>
Content-Type: text/plain; charset="us-ascii"
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Hello FreeSurfer Developers,
I am attempting to perform a recon-all using a T2-FLAIR image. I have already run this particular participant through recon-all with their T1 image without error. While running the recon-all using the T2 the process exited with error stating a segmentation fault.
Is there any way to run fix this problem on my end or better understand why this would be occurring?
I have uploaded the recon-all.log for your convenience.
Thank you,
Clayton
________________________________
Clayton Swanson MS
Graduate Research Assistant & PhD Student
Sensorimotor Neuroimaging Laboratory
Colorado State University
Office: (970) 491-6160
Clayton.Swanson@colostate.edu<mailto:Clayton.Swanson@colostate.edu>
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