Hello all,
I want to run a Monte Carlo simulation within a volume ROI and I am running into a problem when I use the --mask flag while running glmfit. My question is very similar to the question asked in "[Freesurfer] Volume-based Monte Carlo Restricted to a within mask area" but I could not find the response to this question.
Here is my code.
First, I created a volume mask with mri_binarize:
mri_binarize --match 18 --i home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri/aseg.mgz --o /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz
I checked the mask and it looked good. Then I use the mask in glmfit.
mri_glmfit --y ces.nii.gz --osgm --glmdir glm.amygdala_lh --mask /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz
When I do this, I get the following error:
ERROR: dimension mismatch 1 between y and mask
I guess this means that the ces.nii.gz file and mask file don't match, but I have no idea how to solve this. Any thoughts?
Thanks! Suzanne
Hi suzanne, you'll need to use the 2mm version fsaverage/mri.2mm/aseg.mgz doug
On 10/29/2013 11:46 AM, Suzanne Oosterwijk wrote:
Hello all,
I want to run a Monte Carlo simulation within a volume ROI and I am running into a problem when I use the --mask flag while running glmfit. My question is very similar to the question asked in "[Freesurfer] Volume-based Monte Carlo Restricted to a within mask area" but I could not find the response to this question.
Here is my code.
First, I created a volume mask with mri_binarize:
mri_binarize --match 18 --i home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri/aseg.mgz --o /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz
I checked the mask and it looked good. Then I use the mask in glmfit.
mri_glmfit --y ces.nii.gz --osgm --glmdir glm.amygdala_lh --mask /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz
When I do this, I get the following error:
ERROR: dimension mismatch 1 between y and mask
I guess this means that the ces.nii.gz file and mask file don't match, but I have no idea how to solve this. Any thoughts?
Thanks! Suzanne
--
Suzanne Oosterwijk, Ph.D.
Postdoctoral Researcher
Department of Social Psychology
University of Amsterdam
s.oosterwijk@u mailto:s.oosterwijk@neu.eduva.nl http://va.nl
https://sites.google.com/site/suzanneoosterwijk/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello again,
I am stuck again in my analysis and I am not sure that my code is right. I want to do the following. With a Monte Carlo simulation I search for significant clusters within a particular ROI in my all conditions vs baseline contrast. Then I want to translate this functional cluster to each individuals native space (as a label) and extract percent signal change for each condition separately from that label. This is no problem in my surface analysis, but I am not sure how to do this in the volume. I ran the Monte Carlo simulation within the mask, which provides a segmentation called mc-z.pos.23.lh.sig.ocn.mgh. I assume that this would be the label that would go into mri_vol2vol to translate the cluster to native space. I found on the website, however, that you need to use tkregister first. So I used the following code, but I am doubtful about whether I am doing this right.
tkregister2 --mov /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol /omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh --s ff_01_030512 --regheader --reg ff_01_030512/register.dat --surf
The results of this command do not look good at all....(see attached image). The cluster in the -mov file does not overlap with the amygdala. For the next step, I assumed to use mri_vol2vol to save the cluster as a native space label, although I'd like to make sure the first step is correct before continuing with this step.
mri_vol2vol --mov /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol
/omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh --reg ff_01_030512/register.dat --fstarg --interp nearest --o ff_01_030512/label/lh.amygdala.imact.mgz --s ff_01_030512
What am I missing? Is the translation off because I did something wrong, or does that point to a deeper issue?
Any help is much appreciated!
Suzanne
On Tue, Oct 29, 2013 at 6:04 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi suzanne, you'll need to use the 2mm version fsaverage/mri.2mm/aseg.mgz doug
On 10/29/2013 11:46 AM, Suzanne Oosterwijk wrote:
Hello all,
I want to run a Monte Carlo simulation within a volume ROI and I am running into a problem when I use the --mask flag while running glmfit. My question is very similar to the question asked in "[Freesurfer] Volume-based Monte Carlo Restricted to a within mask area" but I could not find the response to this question.
Here is my code.
First, I created a volume mask with mri_binarize:
mri_binarize --match 18 --i
home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri/aseg.mgz
--o
/home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz
I checked the mask and it looked good. Then I use the mask in glmfit.
mri_glmfit --y ces.nii.gz --osgm --glmdir glm.amygdala_lh --mask
/home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz
When I do this, I get the following error:
ERROR: dimension mismatch 1 between y and mask
I guess this means that the ces.nii.gz file and mask file don't match, but I have no idea how to solve this. Any thoughts?
Thanks! Suzanne
--
Suzanne Oosterwijk, Ph.D.
Postdoctoral Researcher
Department of Social Psychology
University of Amsterdam
s.oosterwijk@u mailto:s.oosterwijk@neu.eduva.nl http://va.nl
https://sites.google.com/site/suzanneoosterwijk/
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: 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.
Hi Suzanne, there is probably an easier way to do this. If you create contrasts of each condition vs baseline then run isxconcat-sess on each, you can then run something like
mri_segstats --seg mc-z.pos.23.lh.sig.ocn.mgh --i condition1.nii.gz --avgwf condition1.table.dat --excludeid 0
where condition1.nii.gz is the output of isxconcat-sess for condition 1. The output fo mri_segstats will be condition1.table.dat which will have a row for each subject and a column for each of the clusters
doug
On 11/01/2013 09:51 AM, Suzanne Oosterwijk wrote:
Hello again,
I am stuck again in my analysis and I am not sure that my code is right. I want to do the following. With a Monte Carlo simulation I search for significant clusters within a particular ROI in my all conditions vs baseline contrast. Then I want to translate this functional cluster to each individuals native space (as a label) and extract percent signal change for each condition separately from that label. This is no problem in my surface analysis, but I am not sure how to do this in the volume. I ran the Monte Carlo simulation within the mask, which provides a segmentation called mc-z.pos.23.lh.sig.ocn.mgh. I assume that this would be the label that would go into mri_vol2vol to translate the cluster to native space. I found on the website, however, that you need to use tkregister first. So I used the following code, but I am doubtful about whether I am doing this right.
tkregister2 --mov /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol /omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh --s ff_01_030512 --regheader --reg ff_01_030512/register.dat --surf
The results of this command do not look good at all....(see attached image). The cluster in the -mov file does not overlap with the amygdala. For the next step, I assumed to use mri_vol2vol to save the cluster as a native space label, although I'd like to make sure the first step is correct before continuing with this step.
mri_vol2vol --mov /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol
/omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh --reg ff_01_030512/register.dat --fstarg --interp nearest --o ff_01_030512/label/lh.amygdala.imact.mgz --s ff_01_030512
What am I missing? Is the translation off because I did something wrong, or does that point to a deeper issue?
Any help is much appreciated!
Suzanne
On Tue, Oct 29, 2013 at 6:04 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi suzanne, you'll need to use the 2mm version fsaverage/mri.2mm/aseg.mgz doug On 10/29/2013 11:46 AM, Suzanne Oosterwijk wrote: > Hello all, > > I want to run a Monte Carlo simulation within a volume ROI and I am > running into a problem when I use the --mask flag while running > glmfit. My question is very similar to the question asked in > "[Freesurfer] Volume-based Monte Carlo Restricted to a within mask > area" but I could not find the response to this question. > > Here is my code. > > First, I created a volume mask with mri_binarize: > > mri_binarize --match 18 --i > home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri/aseg.mgz > --o > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz > > I checked the mask and it looked good. Then I use the mask in glmfit. > > mri_glmfit --y ces.nii.gz --osgm --glmdir glm.amygdala_lh --mask > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz > > When I do this, I get the following error: > > ERROR: dimension mismatch 1 between y and mask > > I guess this means that the ces.nii.gz file and mask file don't match, > but I have no idea how to solve this. Any thoughts? > > Thanks! > Suzanne > > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu <mailto:s.oosterwijk@neu.edu>>va.nl <http://va.nl> <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <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 . 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.--
Suzanne Oosterwijk, Ph.D.
Postdoctoral Researcher
Department of Social Psychology
University of Amsterdam
s.oosterwijk@u mailto:s.oosterwijk@neu.eduva.nl http://va.nl
Hi Doug,
Thanks for the code, this works. Nevertheless, I am a bit unsure about whether the masks that are used as input into this command are correct. I like to check all the stages of the process and when I open the mask.mgh file within the appropriate glm folder, the segmentation is totally off (the putamen is somewhere in the OFC). Furthermore, even though the file that holds the output cluster from the Monte Carlo simulation (mc-z.pos.23.lh.sig.cluster.mgh) seems correct, the segmentation file that I use as input into the mri_segstats command is also totally off (mc-z.pos.23.lh.sig.ocn.mgh) when I load it in tkmedit. Am I loading it incorrectly as a segmentation? Does this have anything to do with the fact that you advised me to use the 2mm version fsaverage/mri.2mm/aseg.mgz? Should I adapt for that in my tkmedit command?
Finally, I also run into a problem with the nucleus accumbens specifically. For some reason I get an error when I run the glmfit and mc simulation within this specific mask. First I make the mask:
mri_binarize --match 26 --i /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri.2mm/aseg.mgz --o /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/accumb_lh.mgz
Then I run glmfit:
set labels = (accumb) foreach label ($labels) mri_glmfit --y ces.nii.gz --osgm --glmdir glm.${label} --mask /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/${label}_lh.mgz mri_glmfit-sim --glmdir glm.${label} --sim mc-z 10000 2.3 mc-z.pos.23.lh --sim-sign pos end
But I get an error saying:
FWHM = -nan ERROR: input FWHM is NaN (not a number). Check the mask in the glm directory.
Any ideas what I am doing wrong?
Thanks again!
Suzanne
On Tue, Nov 5, 2013 at 12:04 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Suzanne, there is probably an easier way to do this. If you create contrasts of each condition vs baseline then run isxconcat-sess on each, you can then run something like
mri_segstats --seg mc-z.pos.23.lh.sig.ocn.mgh --i condition1.nii.gz --avgwf condition1.table.dat --excludeid 0
where condition1.nii.gz is the output of isxconcat-sess for condition 1. The output fo mri_segstats will be condition1.table.dat which will have a row for each subject and a column for each of the clusters
doug
On 11/01/2013 09:51 AM, Suzanne Oosterwijk wrote:
Hello again,
I am stuck again in my analysis and I am not sure that my code is right. I want to do the following. With a Monte Carlo simulation I search for significant clusters within a particular ROI in my all conditions vs baseline contrast. Then I want to translate this functional cluster to each individuals native space (as a label) and extract percent signal change for each condition separately from that label. This is no problem in my surface analysis, but I am not sure how to do this in the volume. I ran the Monte Carlo simulation within the mask, which provides a segmentation called mc-z.pos.23.lh.sig.ocn.mgh. I assume that this would be the label that would go into mri_vol2vol to translate the cluster to native space. I found on the website, however, that you need to use tkregister first. So I used the following code, but I am doubtful about whether I am doing this right.
tkregister2 --mov /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/ feedback_functional/ff_image/feedback_gamma_image_vol /omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh --s ff_01_030512 --regheader --reg ff_01_030512/register.dat --surf
The results of this command do not look good at all....(see attached image). The cluster in the -mov file does not overlap with the amygdala. For the next step, I assumed to use mri_vol2vol to save the cluster as a native space label, although I'd like to make sure the first step is correct before continuing with this step.
mri_vol2vol --mov /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/ feedback_functional/ff_image/feedback_gamma_image_vol
/omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh --reg ff_01_030512/register.dat --fstarg --interp nearest --o ff_01_030512/label/lh.amygdala.imact.mgz --s ff_01_030512
What am I missing? Is the translation off because I did something wrong, or does that point to a deeper issue?
Any help is much appreciated!
Suzanne
On Tue, Oct 29, 2013 at 6:04 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi suzanne, you'll need to use the 2mm version fsaverage/mri.2mm/aseg.mgz doug On 10/29/2013 11:46 AM, Suzanne Oosterwijk wrote: > Hello all, > > I want to run a Monte Carlo simulation within a volume ROI and I am > running into a problem when I use the --mask flag while running > glmfit. My question is very similar to the question asked in > "[Freesurfer] Volume-based Monte Carlo Restricted to a within mask > area" but I could not find the response to this question. > > Here is my code. > > First, I created a volume mask with mri_binarize: > > mri_binarize --match 18 --i > home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri/aseg.mgz > --o > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/ feedback_structural/ROI_handmade_labels/amygdala_lh.mgz > > I checked the mask and it looked good. Then I use the mask in glmfit. > > mri_glmfit --y ces.nii.gz --osgm --glmdir glm.amygdala_lh --mask > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/ feedback_structural/ROI_handmade_labels/amygdala_lh.mgz > > When I do this, I get the following error: > > ERROR: dimension mismatch 1 between y and mask > > I guess this means that the ces.nii.gz file and mask file don't match, > but I have no idea how to solve this. Any thoughts? > > Thanks! > Suzanne > > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu mailto:s.oosterwijk@neu.edu>va.nl http://va.nl http://va.nl
> > https://sites.google.com/site/suzanneoosterwijk/ > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto:Freesurfer@nmr.mgh.harvard.eduhttps://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.--
Suzanne Oosterwijk, Ph.D.
Postdoctoral Researcher
Department of Social Psychology
University of Amsterdam
s.oosterwijk@u mailto:s.oosterwijk@neu.eduva.nl http://va.nl
-- 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: 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/
What is your tkmedit command used to view the segmentation? doug
On 11/14/2013 07:10 AM, Suzanne Oosterwijk wrote:
Hi Doug,
Thanks for the code, this works. Nevertheless, I am a bit unsure about whether the masks that are used as input into this command are correct. I like to check all the stages of the process and when I open the mask.mgh file within the appropriate glm folder, the segmentation is totally off (the putamen is somewhere in the OFC). Furthermore, even though the file that holds the output cluster from the Monte Carlo simulation (mc-z.pos.23.lh.sig.cluster.mgh) seems correct, the segmentation file that I use as input into the mri_segstats command is also totally off (mc-z.pos.23.lh.sig.ocn.mgh) when I load it in tkmedit. Am I loading it incorrectly as a segmentation? Does this have anything to do with the fact that you advised me to use the 2mm version fsaverage/mri.2mm/aseg.mgz? Should I adapt for that in my tkmedit command?
Finally, I also run into a problem with the nucleus accumbens specifically. For some reason I get an error when I run the glmfit and mc simulation within this specific mask. First I make the mask:
mri_binarize --match 26 --i /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri.2mm/aseg.mgz --o /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/accumb_lh.mgz
Then I run glmfit:
set labels = (accumb) foreach label ($labels) mri_glmfit --y ces.nii.gz --osgm --glmdir glm.${label} --mask /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/${label}_lh.mgz mri_glmfit-sim --glmdir glm.${label} --sim mc-z 10000 2.3 mc-z.pos.23.lh --sim-sign pos end
But I get an error saying:
FWHM = -nan ERROR: input FWHM is NaN (not a number). Check the mask in the glm directory.
Any ideas what I am doing wrong?
Thanks again!
Suzanne
On Tue, Nov 5, 2013 at 12:04 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Suzanne, there is probably an easier way to do this. If you create contrasts of each condition vs baseline then run isxconcat-sess on each, you can then run something like mri_segstats --seg mc-z.pos.23.lh.sig.ocn.mgh --i condition1.nii.gz --avgwf condition1.table.dat --excludeid 0 where condition1.nii.gz is the output of isxconcat-sess for condition 1. The output fo mri_segstats will be condition1.table.dat which will have a row for each subject and a column for each of the clusters doug On 11/01/2013 09:51 AM, Suzanne Oosterwijk wrote: Hello again, I am stuck again in my analysis and I am not sure that my code is right. I want to do the following. With a Monte Carlo simulation I search for significant clusters within a particular ROI in my all conditions vs baseline contrast. Then I want to translate this functional cluster to each individuals native space (as a label) and extract percent signal change for each condition separately from that label. This is no problem in my surface analysis, but I am not sure how to do this in the volume. I ran the Monte Carlo simulation within the mask, which provides a segmentation called mc-z.pos.23.lh.sig.ocn.mgh. I assume that this would be the label that would go into mri_vol2vol to translate the cluster to native space. I found on the website, however, that you need to use tkregister first. So I used the following code, but I am doubtful about whether I am doing this right. tkregister2 --mov /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol /omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh --s ff_01_030512 --regheader --reg ff_01_030512/register.dat --surf The results of this command do not look good at all....(see attached image). The cluster in the -mov file does not overlap with the amygdala. For the next step, I assumed to use mri_vol2vol to save the cluster as a native space label, although I'd like to make sure the first step is correct before continuing with this step. mri_vol2vol --mov /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol /omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh --reg ff_01_030512/register.dat --fstarg --interp nearest --o ff_01_030512/label/lh.amygdala.imact.mgz --s ff_01_030512 What am I missing? Is the translation off because I did something wrong, or does that point to a deeper issue? Any help is much appreciated! Suzanne On Tue, Oct 29, 2013 at 6:04 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: Hi suzanne, you'll need to use the 2mm version fsaverage/mri.2mm/aseg.mgz doug On 10/29/2013 11:46 AM, Suzanne Oosterwijk wrote: > Hello all, > > I want to run a Monte Carlo simulation within a volume ROI and I am > running into a problem when I use the --mask flag while running > glmfit. My question is very similar to the question asked in > "[Freesurfer] Volume-based Monte Carlo Restricted to a within mask > area" but I could not find the response to this question. > > Here is my code. > > First, I created a volume mask with mri_binarize: > > mri_binarize --match 18 --i > home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri/aseg.mgz > --o > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz > > I checked the mask and it looked good. Then I use the mask in glmfit. > > mri_glmfit --y ces.nii.gz --osgm --glmdir glm.amygdala_lh --mask > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz > > When I do this, I get the following error: > > ERROR: dimension mismatch 1 between y and mask > > I guess this means that the ces.nii.gz file and mask file don't match, > but I have no idea how to solve this. Any thoughts? > > Thanks! > Suzanne > > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu <mailto:s.oosterwijk@neu.edu> <mailto:s.oosterwijk@neu.edu <mailto:s.oosterwijk@neu.edu>>>va.nl <http://va.nl> <http://va.nl> <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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 . 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. -- Suzanne Oosterwijk, Ph.D. Postdoctoral Researcher Department of Social Psychology University of Amsterdam s.oosterwijk@u <mailto:s.oosterwijk@neu.edu <mailto:s.oosterwijk@neu.edu>>va.nl <http://va.nl> <http://va.nl> https://sites.google.com/site/suzanneoosterwijk/ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/--
Suzanne Oosterwijk, Ph.D.
Postdoctoral Researcher
Department of Social Psychology
University of Amsterdam
s.oosterwijk@u mailto:s.oosterwijk@neu.eduva.nl http://va.nl
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Suzanne Oosterwijk