Re: [Freesurfer] Fcseed-sess
Use aparc.a2009s+aseg.mgz
On 05/11/2015 02:01 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
I want to use the command fcseed-config to configure the segment 1126 (in
aparc+aseg) as a seed to pass it to connectivity analysis. I ran the command
line:
fcseed-config -segid 1126 -fcname L_G_Precentralgyrus.dat -fsd bold -mean
-cfg mean.L_G_Precentralgyrus.config
Then I ran the command fcseed-sess -s ${i} -cfg
mean.L_G_Precentralgyrus.config to create the FC seed for every subject.
The final message for the previous command line was Found 0 voxels in final
mask
I changed the configuration file as the following : FillThresh I make it (0)
, Domean I make it (0)... and I got the same result Found 0 voxels in
final mask
I tried to run mri_binarize --i aparc+aseg.mgz --o L_G_Precentralgyrus.mgz
--match 1126 I got the same result Found 0 voxels in final mask
When I ran the previous command line using the flag -binval 0 I got voxels
in the final mask.
Regarding the command fcseed-sess how can I force it to find voxels in the
final mask?
Thanks,
Mohamad
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Fwd: OHBM 2015 Council Election Deadline
Forwarded Message Subject:OHBM 2015 Council Election Deadline Date: Mon, 11 May 2015 10:52:06 -0500 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu The election process to select your organizational leadership who in turn represent you on the OHBM Council and Program Committee closes on*Friday, May 15, 2015 at 11:59 PM CST*. Remember to cast your vote by completing anelection ballot https://www.humanbrainmapping.org/i4a/forms/index.cfm?id=61. Thank you for taking the time to show your support of the OHBM. If you have any questions, please contact the Executive Office at i...@humanbrainmapping.org mailto:i...@humanbrainmapping.org. Sincerely, JoAnn Taie Executive Director Organization for Human Brain Mapping (OHBM) *Organization for Human Brain Mapping* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 Fax: 1 952-545-6073 www.humanbrainmapping.org http://www.humanbrainmapping.org i...@humanbrainmapping.org mailto:i...@humanbrainmapping.org To opt out of OHBM emails, contact the OHBM Executive Office at i...@humanbrainmapping.org mailto:i...@humanbrainmapping.org?subject=Opt%20Out%20of%20Emails. ___ 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] Demeaning both covariates of interest as well as nuisance for only one group
Greetings Freesurfer experts, I've looked over the FS mailing list, as well as other resources (such as Mumford's page on demeaning and fMRI data), but I was still a bit confused, so apologizes in advance. I have a datatset that consists of only 1 group (an expert trained group), and I'd like to investigate how the years of training correlates to cortical thickness. I thus have two covariates I'd like to include: the years of training (ranging from 6 to 18 years), and their age (ranging from 18 to 22 years old), where I want to regress out age (treat it as a nuisance variable). From my understanding, I am interested in the slope rather than the intercept of this one group. I assume that demeaning would at least bring the intercept to the mean of this group and not at 0 (which isn't applicable to this group), but wasn't sure if demeaning is still necessary to investigate the correlation between cortical thickness and years of training, while holding age as a nuisance variable (as according to Mumford: mean centering a covariate will never change the inference for that covariate). Any input would be great. Thank you. Paul ___ 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.
Re: [Freesurfer] Taking a measure of cluster width and length on flat surface
Hi Sarah the unfolding tries very hard to preserve exactly this - the metric properties. If you cut off the occipital third of cortex and flatten it (after introducing some cut along the axis of the cone) you should be able to get to around 10% distortion or below, which I assume is good enough. cheers Bruce On Mon, 11 May 2015, Sarah Finnegan wrote: Dear all, I am looking to take two measures within the visual cortex. 1) A measure of width and length for each activation cluster overlaid onto the flattened cortical surface. 2) A measure of spacing between each cluster I can find how to take measures of area but I specifically want to know the width and length separately to correlate this to potential stripe systems. My plan was to fit an oval to each of these clusters and measure length through the cardinal axis and width through the minor, spacing would be calculated from a line fit to the minor axis of each cluster. Unfortunately I think the unfolding process will have changed the spacing relationships between clusters to make this inappropriate. I wonder if there is a command or established pipeline to take such measures? Thanks for your help! Sarah ___ 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] Fcseed-sess
Hi Doug,
I want to use the command fcseed-config to configure the segment 1126 (in
aparc+aseg) as a seed to pass it to connectivity analysis. I ran the command
line:
fcseed-config -segid 1126 -fcname L_G_Precentralgyrus.dat -fsd bold -mean -cfg
mean.L_G_Precentralgyrus.config
Then I ran the command fcseed-sess -s ${i} -cfg
mean.L_G_Precentralgyrus.config to create the FC seed for every subject.
The final message for the previous command line was Found 0 voxels in final
mask
I changed the configuration file as the following : FillThresh I make it (0) ,
Domean I make it (0)... and I got the same result Found 0 voxels in final
mask
I tried to run mri_binarize --i aparc+aseg.mgz --o L_G_Precentralgyrus.mgz
--match 1126 I got the same result Found 0 voxels in final mask
When I ran the previous command line using the flag -binval 0 I got voxels in
the final mask.
Regarding the command fcseed-sess how can I force it to find voxels in the
final mask?
Thanks,
Mohamad
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] Fcseed-sess
oh, the 1126 is for the 2005 atlas, try 11129 (ctx_lh_G_precentral) instead
On 05/11/2015 03:00 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
Here is the output:
cmdline mri_binarize --i aparc.a2009s+aseg.mgz --binval 1 --o
L_G_Precentralgyrus.mgz --match 1126
sysname Linux
hostname glia
machine x86_64
user malshikh
input aparc.a2009s+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output L_G_Precentralgyrus.mgz
Binarizing based on matching values
nMatch 1
0 1126
binval1
binvalnot 0
Found 0 values in range
Counting number of voxels
Found 0 voxels in final mask
mri_binarize done
and I ran the following command line by changing
bival to 0
mri_binarize --i aparc.a2009s+aseg.mgz --binval 0 --o 111.mgz --match 1126
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cmdline mri_binarize --i aparc.a2009s+aseg.mgz --binval 0 --o
L_G_Precentralgyrus.mgz --match 1126
sysname Linux
hostname glia
machine x86_64
user malshikh
input aparc.a2009s+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output L_G_Precentralgyrus.mgz
Binarizing based on matching values
nMatch 1
0 1172
binval0
binvalnot 0
Found 0 values in range
Counting number of voxels
Found 16777216 voxels in final mask
mri_binarize done
Thank you for any advice?
Mohamad
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 11, 2015 2:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fcseed-sess
Use aparc.a2009s+aseg.mgz
On 05/11/2015 02:01 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
I want to use the command fcseed-config to configure the segment 1126 (in
aparc+aseg) as a seed to pass it to connectivity analysis. I ran the command
line:
fcseed-config -segid 1126 -fcname L_G_Precentralgyrus.dat -fsd bold -mean
-cfg mean.L_G_Precentralgyrus.config
Then I ran the command fcseed-sess -s ${i} -cfg
mean.L_G_Precentralgyrus.config to create the FC seed for every subject.
The final message for the previous command line was Found 0 voxels in final
mask
I changed the configuration file as the following : FillThresh I make it (0)
, Domean I make it (0)... and I got the same result Found 0 voxels in
final mask
I tried to run mri_binarize --i aparc+aseg.mgz --o L_G_Precentralgyrus.mgz
--match 1126 I got the same result Found 0 voxels in final mask
When I ran the previous command line using the flag -binval 0 I got voxels
in the final mask.
Regarding the command fcseed-sess how can I force it to find voxels in the
final mask?
Thanks,
Mohamad
___
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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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
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Re: [Freesurfer] Fcseed-sess
Fabulous!!! It worked
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, May 11, 2015 5:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fcseed-sess
oh, the 1126 is for the 2005 atlas, try 11129 (ctx_lh_G_precentral) instead
On 05/11/2015 03:00 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
Here is the output:
cmdline mri_binarize --i aparc.a2009s+aseg.mgz --binval 1 --o
L_G_Precentralgyrus.mgz --match 1126 sysname Linux hostname glia
machine x86_64
user malshikh
input aparc.a2009s+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output L_G_Precentralgyrus.mgz
Binarizing based on matching values
nMatch 1
0 1126
binval1
binvalnot 0
Found 0 values in range
Counting number of voxels
Found 0 voxels in final mask
mri_binarize done
and I ran the following command line by
changing bival to 0
mri_binarize --i aparc.a2009s+aseg.mgz --binval 0 --o 111.mgz --match
1126
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cmdline
mri_binarize --i aparc.a2009s+aseg.mgz --binval 0 --o
L_G_Precentralgyrus.mgz --match 1126 sysname Linux hostname glia
machine x86_64
user malshikh
input aparc.a2009s+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output L_G_Precentralgyrus.mgz
Binarizing based on matching values
nMatch 1
0 1172
binval0
binvalnot 0
Found 0 values in range
Counting number of voxels
Found 16777216 voxels in final mask
mri_binarize done
Thank you for any advice?
Mohamad
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 11, 2015 2:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fcseed-sess
Use aparc.a2009s+aseg.mgz
On 05/11/2015 02:01 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
I want to use the command fcseed-config to configure the segment 1126 (in
aparc+aseg) as a seed to pass it to connectivity analysis. I ran the command
line:
fcseed-config -segid 1126 -fcname L_G_Precentralgyrus.dat -fsd bold
-mean -cfg mean.L_G_Precentralgyrus.config
Then I ran the command fcseed-sess -s ${i} -cfg
mean.L_G_Precentralgyrus.config to create the FC seed for every subject.
The final message for the previous command line was Found 0 voxels in final
mask
I changed the configuration file as the following : FillThresh I make it (0)
, Domean I make it (0)... and I got the same result Found 0 voxels in
final mask
I tried to run mri_binarize --i aparc+aseg.mgz --o L_G_Precentralgyrus.mgz
--match 1126 I got the same result Found 0 voxels in final mask
When I ran the previous command line using the flag -binval 0 I got voxels
in the final mask.
Regarding the command fcseed-sess how can I force it to find voxels in the
final mask?
Thanks,
Mohamad
___
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Re: [Freesurfer] FSFAST_Paradigm file
You only need to make it once for mni305. The analysis is not lateralized.
doug
On 05/04/2015 05:19 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
I wanted to run FSFAST without using the paradigm file in the analysis
using the following command lines:
1.preproc-sess -s ${i} -fwhm 5 -surface fsaverage lhrh -mni305-1mm
-fsd bold -per-run
2.fcseed-config -segid 1024 -fcname L_Precentralgyrus.dat -fsd bold
-mean -cfg mean.L_Precentralgyrus.config
fcseed-config -segid 2024 -fcname R_Precentralgyrus.dat -fsd bold
-mean -cfg mean.R_Precentralgyrus.config
3.fcseed-sess -s ${i} -cfg mean.L_Precentralgyrus.config
4.fcseed-sess -s ${i} -cfg mean.R_Precentralgyrus.config
5.fcseed-config -wm -fcname wm.dat -fsd bold -pca -cfg wm.config
fcseed-sess -s ${i} -cfg wm.config
fcseed-config -vcsf -fcname vcsf.dat -fsd bold -pca -cfg vcsf.config
fcseed-sess -s ${i} -cfg vcsf.config
Now :
I want to configure analysis for lh , rh , and mni305 using the
following command lines:
_For lh I used the command:_
mkanalysis-sess -analysis precentralgyrus.lh -surface fsaverage lh
-fwhm 5 -notask -taskreg L_Precentralgyrus.dat 1 -nuisreg vcsf.dat 13
-nuisreg wm.dat 13 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2.01
-per-run -force
_For rh I used the command:_
mkanalysis-sess -analysis precentralgyrus.rh -surface fsaverage rh
-fwhm 5 -notask -taskreg R_Precentralgyrus.dat 1 -nuisreg vcsf.dat 13
-nuisreg wm.dat 13 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2.01
-per-run –force
*_My Question is :_*
how can I configure an analysis for mni305 without the paradigm file?
Is it correct to make it twice for the right and left hemispheres?
mkanalysis-sess -analysis precentralgyrus.305.lh –mni305 1 -fwhm 5
-notask -taskreg L_Precentralgyrus.dat 1 -nuisreg vcsf.dat 13 -nuisreg
wm.dat 13 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2.01 -per-run
-force
mkanalysis-sess -analysis precentralgyrus.305.rh –mni305 1 -fwhm 5
-notask -taskreg R_Precentralgyrus.dat 1 -nuisreg vcsf.dat 13 -nuisreg
wm.dat 13 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2.01 -per-run
-force
Thanks
Mohamad__
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Re: [Freesurfer] question regarding the contrast in mri_glmfit
On 05/04/2015 09:29 PM, Alena Piovar wrote: Hello, I am trying to establish contrast for direct statistical analysis in FS. if I have for example three subject and I want to correlate thickness with age the fsgd file is set GroupDescriptorFile 1 Title G1V2 Class Patient Variables age Input002Patient9 Input003Patient10 Input004Patient15 I wil set up contrast 1 0 for main effect of group and then 0 1 for slope being positive *My question is - do I have to specify also contrast* * * *0 -1* * * *for slope being negative??* No, it computes two-sided tests. When you to to correct for multiple comparisons, you can choose a sign then. * * Moreover, *I have a question regarding --cache option* in mri_glmfit-sim I hope I understand correctly that value 2 mean that the p is set to 0.01, but I am not sure whether I should use pos, neg or absolute and what difference this will make. Yes, the clusterforming threshold of 2 means p.01 (not the same as the threshold used to report clusters, the --cwp). If you have an apriori hypothesis about the sign, then use it. Otherwise specify abs doug Sorry for these - probably dummy questions, but I am doing this for the first time and I would like to avoid any mistake. Sincerely, Alena ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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.
Re: [Freesurfer] aparc labels to grey white ratio
You can try mri_segstats with the label or annotation option
doug
On 05/05/2015 09:21 AM, Corinna Bauer wrote:
Hi all,
What command would I use to apply the aparc labels to a different
surface (e.g. to $h.ratio.mgh)??
The ratio file was created as follows:
mri_vol2surf --src ${nu_mgz} --projfrac +0.35 --surf white --hemi
lh --out ${subj_dir}/mri/lh.white.projfrac.pos35.mgh --regheader
${subject} --noreshape
mri_vol2surf --src ${nu_mgz} --projdist -1 --surf white --hemi lh
--out ${subj_dir}/mri/lh.white.projdist.neg1.mgh --regheader
${subject} --noreshape
fscalc ${subj_dir}/mri/lh.white.projfrac.pos35.mgh div
${subj_dir}/mri/lh.white.projdist.neg1.mgh -o ${subj_dir}/mri/lh.ratio.mgh
Thanks
Corinna
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Re: [Freesurfer] Fcseed-sess
Hi Doug,
Here is the output:
cmdline mri_binarize --i aparc.a2009s+aseg.mgz --binval 1 --o
L_G_Precentralgyrus.mgz --match 1126
sysname Linux
hostname glia
machine x86_64
user malshikh
input aparc.a2009s+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output L_G_Precentralgyrus.mgz
Binarizing based on matching values
nMatch 1
0 1126
binval1
binvalnot 0
Found 0 values in range
Counting number of voxels
Found 0 voxels in final mask
mri_binarize done
and I ran the following command line by changing bival
to 0
mri_binarize --i aparc.a2009s+aseg.mgz --binval 0 --o 111.mgz --match 1126
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cmdline mri_binarize --i aparc.a2009s+aseg.mgz --binval 0 --o
L_G_Precentralgyrus.mgz --match 1126
sysname Linux
hostname glia
machine x86_64
user malshikh
input aparc.a2009s+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output L_G_Precentralgyrus.mgz
Binarizing based on matching values
nMatch 1
0 1172
binval0
binvalnot 0
Found 0 values in range
Counting number of voxels
Found 16777216 voxels in final mask
mri_binarize done
Thank you for any advice?
Mohamad
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 11, 2015 2:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fcseed-sess
Use aparc.a2009s+aseg.mgz
On 05/11/2015 02:01 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
I want to use the command fcseed-config to configure the segment 1126 (in
aparc+aseg) as a seed to pass it to connectivity analysis. I ran the command
line:
fcseed-config -segid 1126 -fcname L_G_Precentralgyrus.dat -fsd bold -mean
-cfg mean.L_G_Precentralgyrus.config
Then I ran the command fcseed-sess -s ${i} -cfg
mean.L_G_Precentralgyrus.config to create the FC seed for every subject.
The final message for the previous command line was Found 0 voxels in final
mask
I changed the configuration file as the following : FillThresh I make it (0)
, Domean I make it (0)... and I got the same result Found 0 voxels in
final mask
I tried to run mri_binarize --i aparc+aseg.mgz --o L_G_Precentralgyrus.mgz
--match 1126 I got the same result Found 0 voxels in final mask
When I ran the previous command line using the flag -binval 0 I got voxels
in the final mask.
Regarding the command fcseed-sess how can I force it to find voxels in the
final mask?
Thanks,
Mohamad
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Re: [Freesurfer] Taking a measure of cluster width and length on flat surface
Hi Bruce, Is there some way to know when cuts have been made correctly so that distortion can be minimized? (Or conversely, some way to know when a given patch has or will undergo too much distortion during flattening? Thanks! Michael On Mon, May 11, 2015 at 12:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Sarah the unfolding tries very hard to preserve exactly this - the metric properties. If you cut off the occipital third of cortex and flatten it (after introducing some cut along the axis of the cone) you should be able to get to around 10% distortion or below, which I assume is good enough. cheers Bruce On Mon, 11 May 2015, Sarah Finnegan wrote: Dear all, I am looking to take two measures within the visual cortex. 1) A measure of width and length for each activation cluster overlaid onto the flattened cortical surface. 2) A measure of spacing between each cluster I can find how to take measures of area but I specifically want to know the width and length separately to correlate this to potential stripe systems. My plan was to fit an oval to each of these clusters and measure length through the cardinal axis and width through the minor, spacing would be calculated from a line fit to the minor axis of each cluster. Unfortunately I think the unfolding process will have changed the spacing relationships between clusters to make this inappropriate. I wonder if there is a command or established pipeline to take such measures? Thanks for your help! Sarah ___ 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 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.
Re: [Freesurfer] xhemi final iteration
Use --lh instead of --hemi lh On 05/10/2015 03:32 PM, Derek James Dean wrote: Dear Freesurfer community, I am trying to complete the final iteration described in the Xhemi wiki page to compare left-right hemisphere symmetry between a patient and control group but I get an error when I run make_average_subject. Basic information: FREESURFER_HOME: /projects/ics/software/freesurfer/5.3.0 Build stamp: free surfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Red Hat Enterprise Linux Server release 6.6 (Santiago) Kernel info: Linux 2.6.32-504.8.1.el6.x8664 x86_64 Current working directory: data/images Command: make_average_subject --out myatlas.i3 --surf-reg myatlas.i2.sphere.reg --fsgd laterality.fsgd --xhemi --hemi lh Error message: ERROR: Flag --hemi unrecognized. To my knowledge, previous steps described on the Xhemi wiki have completed without error. Additionally, I am able to run the command if I do not include --hemi lh flag. Thank you for your help. Kind Regards, Derek Dean Department of Psychology and Neuroscience University of Colorado Boulder ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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.
Re: [Freesurfer] references for qdec/mcsim methods
This is an example where the method was used in a study (but it did not try to verify it) Greve, Douglas N., Lise Van der Haegen, Qing Cai, Steven Stufflebeam, Mert R. Sabuncu, Bruce Fischl, and Marc Bysbaert. A surface-based analysis of language lateralization and cortical asymmetry. (2013). Journal of Cognitive Neuroscience 25.9: 1477-1492. You could just say it was implemented as described Greve, et al. Or you could just look inside to see how we reference it. On 05/11/2015 03:46 AM, Alain Imaging wrote: Dear all, I have performed vertex-wise analysis of cortical thickness using qdec following the tutorial on the wiki, and then I have performed the MC simulation method for correction of multiple comparison only within a certain region of interest, again following the tutorial for mri_mcsim and then mri_glmfit-sim. The smoothing was of 14 mm FWHM. Which study can I reference for glmfit and MC simulation method in freesurfer ? Thank in advance Alain ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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.
Re: [Freesurfer] dt_recon
It sounds like you did the right thing. On 05/10/2015 02:41 PM, Pedro Rosa - GMail wrote: Dear developers, I am running an analysis with dt_recon, and it seems that my DWI files are organized into three series (one larger, and two smaller, that I believe are ADC and Trace). Inputing a DICOM file to dt_recon generates a .nii file from one of the series only (the larger one, once it has many more .dcm files). Thus, it ignores the smaller series. This is the first time I am working with DWI series, so I not quite sure if this way of organizing data is usual. I would appreciate help in regard of how to deal with this data and input it into dt_recon. Regards, Pedro Rosa. ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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.
Re: [Freesurfer] a mkanalysis-sess question
what is the error? On 05/04/2015 01:56 PM, Xiaomin Yue wrote: I am having another problem with mkanalysis-sess, here is my command: mkanalysis-sess -funcstem fmc.so.sm2 -analysis volanalysis -native -paradigm human_curv.par -event-related -gammafit 2.25 1.25 -refeventdur 16 -polyfit 2 -TR 2 -nconditions 8 -fsd bold -per-run -tpexclude xy_tpexclude. it got erros as running selxxavg3-sess. It turns out that the analysis.info under volanalysis directory has the following nurisreg mcextreg 3. Since the data was processing as per run, there is no mcextreg, but mcprextreg file. The analysis file generated for surface based analysis has correct analysis.info with mcprextreg. I am using fs5.3. Did I do anything wrong with the mkanalysis-sess command? Thanks, Xiaomin On Sun, May 3, 2015 at 8:55 AM -0700, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: If you just want to exclude those time points then you can use a time point exclude file. To do this, create a text file with the time in seconds of the time points you want to exclude (t=0 is first time point), put this file in the run folder (where the raw data is) then when making the analysis, specify -tpexclude filename. If you want to create a nuisance regressor, then create a text file with a value for each time point and put it in the run folder then run mkanalysis-sess with -nuisreg filename 1 doug On 5/3/15 11:17 AM, Xiaomin Yue wrote: Hi Doug, Thanks for your response. I want to treat it as a nuisance variable. If so, should the #3 is best choice? Xiaomin Date: Sun, 3 May 2015 11:06:01 -0400 From: gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] a mkanalysis-sess question #1 and #3 are basically the same. If used as a task regressor, then a contrast for it will be created. #2 is a parametric modulation. Probably not what you want but see http://freesurfer.net/fswiki/FsFastParametricModulation Do you want to treat it as a nuisance variable or task? In any event, I would probably recode it to make fixation=0 and non-fixation something else On 5/2/15 5:34 PM, Xiaomin Yue wrote: Hi, I have a question related to how to make an appropriate design matrix using fs-fast 5.3. Subjects’ eye movement was collected during an experiment. Then, the data has been transformed to a continuous variable with a number for each TR. The better fixation performance has higher number. For example, a number would be 0 if subjects look away from a target within a TR. In ideal situation, subjects should keep his eyes on target all the time, so the variable should be 1 for all TR. According to mkanalysis-sess documents, it seems that there are three different ways to take into account of eye fixation performance: 1) use it as an external task regressor; 2) use it as a weight in the paradigm file (the fourth column); 3) use it as a nuisance regressor. My question is what’s the difference between the three methods? In my situation, which one is the best choice in my situation? I hope the question is clear. Thanks so much for your help. Xiaomin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] interpreting glmfit-sim results
There is no one place you can get it from. You can go to cache.th30.abs.y.ocn.dat. this will have a column for each cluster. Each row is an input/subject. If you compute the mean of the rows, you'll get the mean effect in each cluster. On 05/04/2015 03:03 PM, Hirsch, Gabriella wrote: Hi FS experts, I had a couple quick questions about interpreting glmfit-sim results. For context, I’m interesting in analyzing surface-based morphology differences (cortical thickness, volume, surface area) between two groups. I ran a simple t-test contrast (1 -1) using glmfit on two groups (control and patient) and then corrected for multiple comparisons with glmfit-sim using mc-z. My question is 1) I assume this is a two-tailed t-test (I used “absolute” in the clusterwise correction)? And 2) Is there a place where the direction of the results is easily readable (other than visualizing the cluster colors)? Apologies if this is trivial – I couldn’t find anything in the archive. Thanks! Gabriella ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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.
[Freesurfer] Freeview
Dear Freesurfer Users,I am trying to update the freeview file. However, I cannot find the folder$FREESURFER_HOME/Freeview.app/Contents/MacOS/FreeviewWhen I go into my Freesurfer folder, I cannot find Freeview.app.Any help would be greatly appreciated.Thanks,Isabelle *Isabelle Deschamps,Chercheure postdoctorale,Faculté de MédecineDépartement de réadaptationUniversité Laval Pavillon Ferdinand-Vandry1050 avenue de la Médecine Québec(Québec)G1V 0A6Centre de Recherche de l'Institutuniversitaire en santé mentale deQuébec (CRIUMSQ)2601, chemin de laCanardière, bureau F-2424AQuébec (Québec) G1J 2G3Téléphone : 418 663-5000 poste 6857 ___ 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] Taking a measure of cluster width and length on flat surface
Dear all, I am looking to take two measures within the visual cortex. 1) A measure of width and length for each activation cluster overlaid onto the flattened cortical surface. 2) A measure of spacing between each cluster I can find how to take measures of area but I specifically want to know the width and length separately to correlate this to potential stripe systems. My plan was to fit an oval to each of these clusters and measure length through the cardinal axis and width through the minor, spacing would be calculated from a line fit to the minor axis of each cluster. Unfortunately I think the unfolding process will have changed the spacing relationships between clusters to make this inappropriate. I wonder if there is a command or established pipeline to take such measures? Thanks for your help! Sarah ___ 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] Segmentation of hippocampal subfields / version 6.0 release date
Hello, I wanted to inquire about when you think that this new package for freesurfer 6.0 will be complete? I am interested in pursuing hippocampal segmentation, but it seems that I should not use the segmentation from your older program and I should wait, would you agree? Thank you, Josh -- Josh Gray Graduate Student Psychology Dept. - Clinical Program Experimental Clinical Psychopharmacology Laboratory University of Georgia ___ 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] freesurfer ROIs for network analysis
Hello, I'm looking for some help to generate connectivity matrices using Freesurfer segmented volumes and my DTI data. Firstly, the output from Freesurfer required for network analysis in ExploreDTI needs a label volume file in .nii format. Then, I need a coordinate .txt file and two column label names .txt file. The output from Freesurfer separates left and right hemispheres in .label format. Do I need to merge lh. rh. labels, then convert labels to a volume file in order to get a .nii? Or is there an alternative step? Next, is there a downloadable x,y,z coordinate .txt file to correspond with the label volumes? I'm looking for a simplified x,y,z coordinate file for about the 68 structures, rather than the grayordinates with every vertex. Finally, would the label names file be generated with both left and right hemispheres in the one file? Kind Regards, Stefani O'Donoghue PhD Candidate Clinical Neuroimaging Laboratory Department of Psychiatry National University of Ireland, Galway ___ 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.
