Dear Freesurfer experts,
I am a beginner in using Freesurfer. I did an explorative study where I correlated cotical thickness with different neuropsychological parameters: I found positive correlations between cortical thickness and higher scores on different neuropsychological scales in different brain regions. However, some of these brain regions (clusters) with cortical thinning are only covering a very small surface area (blue color). I was now wondering if there is a possibility in Qdec to manually define the minimal and maximal cluster size, which I want to show?
Thanks in advance! Dusan
I don't think tthere is a way in qdec to define either. You can run mri_surfcluster externally to remove clusters under a certain size. With a few tricks you can remove the ones over a certain size too. doug
Dusan Hirjak wrote:
Dear Freesurfer experts,
I am a beginner in using Freesurfer. I did an explorative study where I correlated cotical thickness with different neuropsychological parameters: I found positive correlations between cortical thickness and higher scores on different neuropsychological scales in different brain regions. However, some of these brain regions (clusters) with cortical thinning are only covering a very small surface area (blue color). I was now wondering if there is a possibility in Qdec to manually define the minimal and maximal cluster size, which I want to show? Thanks in advance! Dusan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Freesurfer experts,
after a partial correlation (cortical thickness in different brain regions of 24 Subjects correalted with socres on different neuropsychological scales) I tried to define the minimal and maximal cluster size in Qdec in order to show only the largest effects. I run "mri_surfcluster" and other commands described on http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster. Unfortunately, it did not work. Should I use all the command lines? What is exactly meant by "inputfile" and "csd csdfile"? I guess my inputfile should be the "table.dat" File and T1-weighted images of all 24 Subjects...?
Thanks in advance!
Dusan
Date: Wed, 7 Mar 2012 16:34:02 -0500 From: greve@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cluster-Size in Qdec
I don't think tthere is a way in qdec to define either. You can run mri_surfcluster externally to remove clusters under a certain size. With a few tricks you can remove the ones over a certain size too. doug
Dusan Hirjak wrote:
I am a beginner in using Freesurfer. I did an explorative study where I correlated cotical thickness with different neuropsychological parameters: I found positive correlations between cortical thickness and higher scores on different neuropsychological scales in different brain regions. However, some of these brain regions (clusters) with cortical thinning are only covering a very small surface area (blue color). I was now wondering if there is a possibility in Qdec to manually define the minimal and maximal cluster size, which I want to show? Thanks in advance! Dusan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
In this case, the input file would be the sig.mgh file that you want to extract clusters from. For this, you would not use a csd file (which is created by the simulation, unless you want to exclude clusters based on their p-values instead of size). You would set the --thmin to set the voxel-wise threshold. You would also set --minarea to exclude clusters smaller than a certain size. doug
Dusan Hirjak wrote:
Dear Freesurfer experts,
after a partial correlation (cortical thickness in different brain regions of 24 Subjects correalted with socres on different neuropsychological scales) I tried to define the minimal and maximal cluster size in Qdec in order to show only the largest effects. I run "mri_surfcluster" and other commands described on http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster. Unfortunately, it did not work. Should I use all the command lines? What is exactly meant by "inputfile" and "csd csdfile"? I guess my inputfile should be the "table.dat" File and T1-weighted images of all 24 Subjects...?
Thanks in advance!
Dusan
Date: Wed, 7 Mar 2012 16:34:02 -0500 From: greve@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cluster-Size in Qdec
I don't think tthere is a way in qdec to define either. You can run mri_surfcluster externally to remove clusters under a certain size.
With
a few tricks you can remove the ones over a certain size too. doug
Dusan Hirjak wrote:
I am a beginner in using Freesurfer. I did an explorative study where I correlated cotical thickness with different
neuropsychological
parameters: I found positive correlations between cortical thickness and higher scores on different neuropsychological scales in different brain regions. However, some of these brain regions (clusters) with cortical thinning are only covering a very small surface area (blue color). I was now wondering if there is a possibility in Qdec to manually define the minimal and maximal cluster size, which I want to show? Thanks in advance! Dusan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Freesurfer Experts,
thanks for helping me! I run the following comand line:
mri_surfcluster --in qdec/lh-Avg-thickness-XXX_TOTAL-Cor/sig.mgh --no-adjust --subject fsaverage --hemi lh --thmin 2 --minarea 100 --sum TestClusters
After a while, I got this answer:
thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.48 2010/04/12 17:36:58 greve Exp $ hemi = lh srcid = qdec/lh-Avg-thickness-XXX_TOTAL-Cor/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr = -1 minarea = 100 xfmfile = talairach.xfm nth = -1 sumfile = TestClusters subjectsdir = /Users/dhirjak/MRI/Freesurfer/XXX FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /Users/dhirjak/MRI/Freesurfer/XXX/fsaverage/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /Users/dhirjak/MRI/Freesurfer/XXX/fsaverage/surf/lh.white Done reading source surface Computing metric properties Loading source values mghRead(qdec/lh-Avg-thickness-XXX_TOTAL-Cor/sig.mgh, -1): could not open file ERROR: could not read qdec/lh-Avg-thickness-XXX_TOTAL-Cor/sig.mgh as type
However, as you can see, it is still not functionning. What am I doing wrong? How should I correct my command line? Which other commands do I have to use?
Thanks for your help!
Dusan
Date: Mon, 12 Mar 2012 11:38:07 -0400 From: greve@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cluster-Size in Qdec
In this case, the input file would be the sig.mgh file that you want to extract clusters from. For this, you would not use a csd file (which is created by the simulation, unless you want to exclude clusters based on their p-values instead of size). You would set the --thmin to set the voxel-wise threshold. You would also set --minarea to exclude clusters smaller than a certain size. doug
Dusan Hirjak wrote:
Dear Freesurfer experts,
after a partial correlation (cortical thickness in different brain regions of 24 Subjects correalted with socres on different neuropsychological scales) I tried to define the minimal and maximal cluster size in Qdec in order to show only the largest effects. I run "mri_surfcluster" and other commands described on http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster. Unfortunately, it did not work. Should I use all the command lines? What is exactly meant by "inputfile" and "csd csdfile"? I guess my inputfile should be the "table.dat" File and T1-weighted images of all 24 Subjects...?
Thanks in advance!
Dusan
Date: Wed, 7 Mar 2012 16:34:02 -0500 From: greve@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cluster-Size in Qdec
I don't think tthere is a way in qdec to define either. You can run mri_surfcluster externally to remove clusters under a certain size.
With
a few tricks you can remove the ones over a certain size too. doug
Dusan Hirjak wrote:
I am a beginner in using Freesurfer. I did an explorative study where I correlated cotical thickness with different
neuropsychological
parameters: I found positive correlations between cortical thickness and higher scores on different neuropsychological scales in different brain regions. However, some of these brain regions (clusters) with cortical thinning are only covering a very small surface area (blue color). I was now wondering if there is a possibility in Qdec to manually define the minimal and maximal cluster size, which I want to show? Thanks in advance! Dusan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Dusan Hirjak