Hi Freesurfers,
I have two unrelated questions.
1. I want to pre-whiten some functional data without running a GLM on them (we're going to run the GLM in matlab). It looks like fsfast does autocorrelation correction as a part of the selxavg3-sess wrapper. I tried poking around on the wiki and mailing archives, but I can't find how to pre-whiten the data without running a GLM. Is there a straightforward way? If not, I guess we could just do it in matlab.
2. Separately, we're bringing some volume masks to the surface and are preprocessing them with dilation and erosion to clean them up. We're trying to get a sense of how much is a reasonable amount to dilate and erode by, and it would be helpful to know about how far apart the adjacent surface vertices are. Roughly, what's the mean distance between adjacent vertices?
Thanks in advance.
Best, Alex
Hi Alex
the vertices are about 1mm apart. I'll leave 1 for Doug Bruce On Sat, 19 Jan 2013, Alex Kell wrote:
Hi Freesurfers, I have two unrelated questions.
- I want to pre-whiten some functional data without running a GLM on them
(we're going to run the GLM in matlab). It looks like fsfast does autocorrelation correction as a part of the selxavg3-sess wrapper. I tried poking around on the wiki and mailing archives, but I can't find how to pre-whiten the data without running a GLM. Is there a straightforward way? If not, I guess we could just do it in matlab.
- Separately, we're bringing some volume masks to the surface and are
preprocessing them with dilation and erosion to clean them up. We're trying to get a sense of how much is a reasonable amount to dilate and erode by, and it would be helpful to know about how far apart the adjacent surface vertices are. Roughly, what's the mean distance between adjacent vertices?
Thanks in advance.
Best, Alex
On 01/19/2013 03:18 PM, Alex Kell wrote:
Hi Freesurfers,
I have two unrelated questions.
- I want to pre-whiten some functional data without running a GLM on
them (we're going to run the GLM in matlab). It looks like fsfast does autocorrelation correction as a part of the selxavg3-sess wrapper. I tried poking around on the wiki and mailing archives, but I can't find how to pre-whiten the data without running a GLM. Is there a straightforward way? If not, I guess we could just do it in matlab.
FSFAST uses an AR1 model. It computes the AR1 from the residuals (thus needing to run the GLM first). The voxel-wise AR1 is spatially smoothed, then binned into 10 bins. All the voxels in each bin are then analyzed in the same way.
- Separately, we're bringing some volume masks to the surface and are
preprocessing them with dilation and erosion to clean them up. We're trying to get a sense of how much is a reasonable amount to dilate and erode by, and it would be helpful to know about how far apart the adjacent surface vertices are. Roughly, what's the mean distance between adjacent vertices?
About 1mm doug
Thanks in advance.
Best, Alex
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks for the information about how FS whitens the data. Is there a way to temporally whiten data without running a GLM (i.e., without running selxavg3-sess)?
Alex
On Tue, Jan 22, 2013 at 9:58 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
On 01/19/2013 03:18 PM, Alex Kell wrote:
Hi Freesurfers,
I have two unrelated questions.
- I want to pre-whiten some functional data without running a GLM on
them (we're going to run the GLM in matlab). It looks like fsfast does autocorrelation correction as a part of the selxavg3-sess wrapper. I tried poking around on the wiki and mailing archives, but I can't find how to pre-whiten the data without running a GLM. Is there a straightforward way? If not, I guess we could just do it in matlab.
FSFAST uses an AR1 model. It computes the AR1 from the residuals (thus needing to run the GLM first). The voxel-wise AR1 is spatially smoothed, then binned into 10 bins. All the voxels in each bin are then analyzed in the same way.
- Separately, we're bringing some volume masks to the surface and are
preprocessing them with dilation and erosion to clean them up. We're trying to get a sense of how much is a reasonable amount to dilate and erode by, and it would be helpful to know about how far apart the adjacent surface vertices are. Roughly, what's the mean distance between adjacent vertices?
About 1mm doug
Thanks in advance.
Best, Alex
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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Whoops, I just saw your response in your response. My bad -- please ignore.
Alex
On Fri, Jan 25, 2013 at 10:37 AM, Alex Kell alexkell@mit.edu wrote:
Hi Doug,
Thanks for the information about how FS whitens the data. Is there a way to temporally whiten data without running a GLM (i.e., without running selxavg3-sess)?
Alex
On Tue, Jan 22, 2013 at 9:58 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
On 01/19/2013 03:18 PM, Alex Kell wrote:
Hi Freesurfers,
I have two unrelated questions.
- I want to pre-whiten some functional data without running a GLM on
them (we're going to run the GLM in matlab). It looks like fsfast does autocorrelation correction as a part of the selxavg3-sess wrapper. I tried poking around on the wiki and mailing archives, but I can't find how to pre-whiten the data without running a GLM. Is there a straightforward way? If not, I guess we could just do it in matlab.
FSFAST uses an AR1 model. It computes the AR1 from the residuals (thus needing to run the GLM first). The voxel-wise AR1 is spatially smoothed, then binned into 10 bins. All the voxels in each bin are then analyzed in the same way.
- Separately, we're bringing some volume masks to the surface and are
preprocessing them with dilation and erosion to clean them up. We're trying to get a sense of how much is a reasonable amount to dilate and erode by, and it would be helpful to know about how far apart the adjacent surface vertices are. Roughly, what's the mean distance between adjacent vertices?
About 1mm doug
Thanks in advance.
Best, Alex
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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Hi Doug,
I've attached the isxconcat-sess log. I'm able to concatenate the subjects into one file, and generate the masks. I'm not able to obtain the rho values because the subject design matrix could not be sourced.
$Id: isxconcat-sess,v 1.60 2011/03/10 15:58:15 greve Exp $ Fri Jan 25 11:04:10 EST 2013 Linux audrey 2.6.32-279.14.1.el6.x86_64 #1 SMP Tue Nov 6 23:43:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux /autofs/space/audrey_001/users/FSFASTFC /usr/local/freesurfer/stable5_1_0/fsfast/bin/isxconcat-sess -a noGMrhDGmc6 -sf matchedCTRLSCHIZ.txt -d /autofs/space/audrey_001/users/FSFASTFC -o matchedCTRLSCHIZ.rhDG.newest -all-contrasts -m pcc
Do you know what went wrong?
Thanks, Newfei
Hi NewFei, canyou run the following commands and send me dng.log ? cd /autofs/space/audrey_001/users/FSFASTFC isxconcat0-sess -m pcc -o matchedCTRLSCHIZ.rhDG.newest/noGMrhDGmc6/X/mni305.pcc.nii.gz -sf matchedCTRLSCHIZ.txt -d /autofs/space/audrey_001/users/FSFASTFC -c X -a noGMrhDGmc6 -split -interp trilin -reg register.dof6.dat -talres 2 |& tee dng.log
doug
On 01/25/2013 11:49 AM, New Fei Ho wrote:
Hi Doug,
I've attached the isxconcat-sess log. I'm able to concatenate the subjects into one file, and generate the masks. I'm not able to obtain the rho values because the subject design matrix could not be sourced.
$Id: isxconcat-sess,v 1.60 2011/03/10 15:58:15 greve Exp $ Fri Jan 25 11:04:10 EST 2013 Linux audrey 2.6.32-279.14.1.el6.x86_64 #1 SMP Tue Nov 6 23:43:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux /autofs/space/audrey_001/users/FSFASTFC /usr/local/freesurfer/stable5_1_0/fsfast/bin/isxconcat-sess -a noGMrhDGmc6 -sf matchedCTRLSCHIZ.txt -d /autofs/space/audrey_001/users/FSFASTFC -o matchedCTRLSCHIZ.rhDG.newest -all-contrasts -m pcc
Do you know what went wrong?
Thanks, Newfei
There's a bunch of stuff in the analysis folder (noGMrhDGmc6) including some .mat files. FSFAST sees these .mat files and thinks they are contrasts. So, you can remove all the extra stuff in that folder or you can spec the contrast with -contrast.
doug
On 01/25/2013 11:49 AM, New Fei Ho wrote:
Hi Doug,
I've attached the isxconcat-sess log. I'm able to concatenate the subjects into one file, and generate the masks. I'm not able to obtain the rho values because the subject design matrix could not be sourced.
$Id: isxconcat-sess,v 1.60 2011/03/10 15:58:15 greve Exp $ Fri Jan 25 11:04:10 EST 2013 Linux audrey 2.6.32-279.14.1.el6.x86_64 #1 SMP Tue Nov 6 23:43:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux /autofs/space/audrey_001/users/FSFASTFC /usr/local/freesurfer/stable5_1_0/fsfast/bin/isxconcat-sess -a noGMrhDGmc6 -sf matchedCTRLSCHIZ.txt -d /autofs/space/audrey_001/users/FSFASTFC -o matchedCTRLSCHIZ.rhDG.newest -all-contrasts -m pcc
Do you know what went wrong?
Thanks, Newfei
freesurfer@nmr.mgh.harvard.edu
-
Alex Kell -
Bruce Fischl -
Douglas N Greve -
New Fei Ho