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Hello Freesurfer Experts!
Thank you in advance for considering this question.
I did a cortical thickness analysis (surface-based), and found a significant cluster. I found the average cortical thickness in* this group*, in the .*y.ocn.dat* file, which is great.
Now I want to find the average cortical thickness in the same cluster, in a separate group of subjects.
I tried using mri_segstats, but it doesn't seem to work:
mri_segstats --slabel $label --i $input --nonempty --excludeid 0 --avgwf test.dat --sum Test_SupParietal.sum
The error I am getting is:
ERROR: cannot do frame average without input volume
Any thoughts about a better way to approach this analysis?
Thanks again in advance! -T
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What are $label and $input set to?
On January 2, 2019 at 9:13 PM Tamara Sussman tsussman@gmail.com wrote:
External Email - Use CautionHello Freesurfer Experts!
Thank you in advance for considering this question.
I did a cortical thickness analysis (surface-based), and found a significant cluster. I found the average cortical thickness in* this group*, in the .*y.ocn.dat* file, which is great.
Now I want to find the average cortical thickness in the same cluster, in a separate group of subjects.
I tried using mri_segstats, but it doesn't seem to work:
mri_segstats --slabel $label --i $input --nonempty --excludeid 0 --avgwf test.dat --sum Test_SupParietal.sum
The error I am getting is:
ERROR: cannot do frame average without input volume
Any thoughts about a better way to approach this analysis?
Thanks again in advance! -T _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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Thanks for your response - yes, I should have included this information before. :)
$label was set to a label I made by 1. binarizing the cluster results from the previous analysis, and then 2. using mri_vol2label to convert this into a label
label=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
$input was set to an individual's thickness data (analogous data that I used in the initial analysis): input= /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
On Wed, Jan 2, 2019 at 4:09 PM ts+ml@rcmd.org wrote:
External Email - Use CautionWhat are $label and $input set to?
On January 2, 2019 at 9:13 PM Tamara Sussman tsussman@gmail.com wrote:
External Email - Use CautionHello Freesurfer Experts!
Thank you in advance for considering this question.
I did a cortical thickness analysis (surface-based), and found a significant cluster. I found the average cortical thickness in* this
group*,
in the .*y.ocn.dat* file, which is great.
Now I want to find the average cortical thickness in the same cluster,
in a
separate group of subjects.
I tried using mri_segstats, but it doesn't seem to work:
mri_segstats --slabel $label --i $input --nonempty --excludeid 0 --avgwf test.dat --sum Test_SupParietal.sum
The error I am getting is:
ERROR: cannot do frame average without input volume
Any thoughts about a better way to approach this analysis?
Thanks again in advance! -T _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Can you include the full command line (no $variables) and the full terminal output?
On 1/2/19 4:22 PM, Tamara Sussman wrote:
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Thanks for your response - yes, I should have included this information before. :)
$label was set to a label I made by 1. binarizing the cluster results from the previous analysis, and then 2. using mri_vol2label to convert this into a label
label=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
$input was set to an individual's thickness data (analogous data that I used in the initial analysis): input=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
On Wed, Jan 2, 2019 at 4:09 PM <ts+ml@rcmd.org mailto:ts%2Bml@rcmd.org> wrote:
External Email - Use Caution What are $label and $input set to? > On January 2, 2019 at 9:13 PM Tamara Sussman <tsussman@gmail.com <mailto:tsussman@gmail.com>> wrote: > > > External Email - Use Caution > > Hello Freesurfer Experts! > > Thank you in advance for considering this question. > > I did a cortical thickness analysis (surface-based), and found a > significant cluster. I found the average cortical thickness in* this group*, > in the .*y.ocn.dat* file, which is great. > > Now I want to find the average cortical thickness in the same cluster, in a > separate group of subjects. > > I tried using mri_segstats, but it doesn't seem to work: > > mri_segstats --slabel $label --i $input --nonempty --excludeid 0 --avgwf > test.dat --sum Test_SupParietal.sum > > The error I am getting is: > > ERROR: cannot do frame average without input volume > > Any thoughts about a better way to approach this analysis? > > Thanks again in advance! > -T > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks so much for your suggestion, Douglas.
Here is the whole input and output:
Tamara-Posner-lab:~ posnerlab$ mri_segstats --slabel /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label --i /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh --nonempty --excludeid 0 --avgwf test.dat --sum Test_SupParietal.sum
ERROR: cannot do frame average without input volume
I was using --slabel instead of --seg because I am using surfaces, and not volumes. Just to test it out, I tried using the --seg aseg too, and got the same error:
Tamara-Posner-lab:~ posnerlab$ mri_segstats --seg /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/mri/aseg.mgz --mask /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label --nonempty --excludeid 0 --avgwf test.dat --sum Test_SupParietal.sum
ERROR: cannot do frame average without input volume
Thank you again for your help! Tamara
On Thu, Jan 3, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Can you include the full command line (no $variables) and the full terminal output?
On 1/2/19 4:22 PM, Tamara Sussman wrote:
External Email - Use CautionThanks for your response - yes, I should have included this information before. :)
$label was set to a label I made by 1. binarizing the cluster results from the previous analysis, and then 2. using mri_vol2label to convert this into a label
label=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
$input was set to an individual's thickness data (analogous data that I used in the initial analysis):
input=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
On Wed, Jan 2, 2019 at 4:09 PM <ts+ml@rcmd.org mailto:ts%2Bml@rcmd.org> wrote:
External Email - Use Caution What are $label and $input set to? > On January 2, 2019 at 9:13 PM Tamara Sussman <tsussman@gmail.com <mailto:tsussman@gmail.com>> wrote: > > > External Email - Use Caution > > Hello Freesurfer Experts! > > Thank you in advance for considering this question. > > I did a cortical thickness analysis (surface-based), and found a > significant cluster. I found the average cortical thickness in* this group*, > in the .*y.ocn.dat* file, which is great. > > Now I want to find the average cortical thickness in the same cluster, in a > separate group of subjects. > > I tried using mri_segstats, but it doesn't seem to work: > > mri_segstats --slabel $label --i $input --nonempty --excludeid 0 --avgwf > test.dat --sum Test_SupParietal.sum > > The error I am getting is: > > ERROR: cannot do frame average without input volume > > Any thoughts about a better way to approach this analysis? > > Thanks again in advance! > -T > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The first command does not work because --slabel requires three options and it is interpreting "--i" and "/Volumes...mgh" as those two so it thinks you have not included. It is probably better to use something like mri_segstats --seg ocn.mgh --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum --i lh.thickness.fwhm10.fsaverage.mgh
On 1/3/19 2:41 PM, Tamara Sussman wrote:
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Thanks so much for your suggestion, Douglas. Here is the whole input and output:
Tamara-Posner-lab:~ posnerlab$ mri_segstats --slabel /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label --i/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh --nonempty --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum
ERROR: cannot do frame average without input volume
I was using --slabel instead of --seg because I am using surfaces, and not volumes. Just to test it out, I tried using the --seg aseg too, and got the same error:
Tamara-Posner-lab:~ posnerlab$ mri_segstats --seg /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/mri/aseg.mgz --mask /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label --nonempty --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum
ERROR: cannot do frame average without input volume
Thank you again for your help! Tamara
On Thu, Jan 3, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Can you include the full command line (no $variables) and the full terminal output? On 1/2/19 4:22 PM, Tamara Sussman wrote: > > External Email - Use Caution > > Thanks for your response - yes, I should have included this > information before. :) > > $label was set to a label I made by 1. binarizing the cluster results > from the previous analysis, and then 2. using mri_vol2label to convert > this into a label > > label=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label > > > $input was set to an individual's thickness data (analogous data that > I used in the initial analysis): > input=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh > > On Wed, Jan 2, 2019 at 4:09 PM <ts+ml@rcmd.org <mailto:ts%2Bml@rcmd.org> > <mailto:ts%2Bml@rcmd.org <mailto:ts%252Bml@rcmd.org>>> wrote: > > External Email - Use Caution > > What are $label and $input set to? > > > On January 2, 2019 at 9:13 PM Tamara Sussman <tsussman@gmail.com <mailto:tsussman@gmail.com> > <mailto:tsussman@gmail.com <mailto:tsussman@gmail.com>>> wrote: > > > > > > External Email - Use Caution > > > > Hello Freesurfer Experts! > > > > Thank you in advance for considering this question. > > > > I did a cortical thickness analysis (surface-based), and found a > > significant cluster. I found the average cortical thickness in* > this group*, > > in the .*y.ocn.dat* file, which is great. > > > > Now I want to find the average cortical thickness in the same > cluster, in a > > separate group of subjects. > > > > I tried using mri_segstats, but it doesn't seem to work: > > > > mri_segstats --slabel $label --i $input --nonempty --excludeid > 0 --avgwf > > test.dat --sum Test_SupParietal.sum > > > > The error I am getting is: > > > > ERROR: cannot do frame average without input volume > > > > Any thoughts about a better way to approach this analysis? > > > > Thanks again in advance! > > -T > > _______________________________________________ > > 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 > > -- > Dr. Tim Schäfer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am > Main, Germany > > _______________________________________________ > 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 > > > _______________________________________________ > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you so much, Douglas, it works!!
On Thu, Jan 3, 2019 at 3:10 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
The first command does not work because --slabel requires three options and it is interpreting "--i" and "/Volumes...mgh" as those two so it thinks you have not included. It is probably better to use something like mri_segstats --seg ocn.mgh --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum --i lh.thickness.fwhm10.fsaverage.mgh
On 1/3/19 2:41 PM, Tamara Sussman wrote:
External Email - Use CautionThanks so much for your suggestion, Douglas. Here is the whole input and output:
Tamara-Posner-lab:~ posnerlab$ mri_segstats --slabel
/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
--i/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
--nonempty --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum
ERROR: cannot do frame average without input volume
I was using --slabel instead of --seg because I am using surfaces, and not volumes. Just to test it out, I tried using the --seg aseg too, and got the same error:
Tamara-Posner-lab:~ posnerlab$ mri_segstats --seg
/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/mri/aseg.mgz
--mask
/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
--nonempty --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum
ERROR: cannot do frame average without input volume
Thank you again for your help! Tamara
On Thu, Jan 3, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Can you include the full command line (no $variables) and the full terminal output? On 1/2/19 4:22 PM, Tamara Sussman wrote: > > External Email - Use Caution > > Thanks for your response - yes, I should have included this > information before. :) > > $label was set to a label I made by 1. binarizing the cluster results > from the previous analysis, and then 2. using mri_vol2label to convert > this into a label > >label=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
> > > $input was set to an individual's thickness data (analogous data that > I used in the initial analysis): >input=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
> > On Wed, Jan 2, 2019 at 4:09 PM <ts+ml@rcmd.org <mailto:ts%2Bml@rcmd.org> > <mailto:ts%2Bml@rcmd.org <mailto:ts%252Bml@rcmd.org>>> wrote: > > External Email - Use Caution > > What are $label and $input set to? > > > On January 2, 2019 at 9:13 PM Tamara Sussman <tsussman@gmail.com <mailto:tsussman@gmail.com> > <mailto:tsussman@gmail.com <mailto:tsussman@gmail.com>>>wrote:
> > > > > > External Email - Use Caution > > > > Hello Freesurfer Experts! > > > > Thank you in advance for considering this question. > > > > I did a cortical thickness analysis (surface-based), and found a > > significant cluster. I found the average cortical thickness in* > this group*, > > in the .*y.ocn.dat* file, which is great. > > > > Now I want to find the average cortical thickness in the same > cluster, in a > > separate group of subjects. > > > > I tried using mri_segstats, but it doesn't seem to work: > > > > mri_segstats --slabel $label --i $input --nonempty--excludeid
> 0 --avgwf > > test.dat --sum Test_SupParietal.sum > > > > The error I am getting is: > > > > ERROR: cannot do frame average without input volume > > > > Any thoughts about a better way to approach this analysis? > > > > Thanks again in advance! > > -T > > _______________________________________________ > > 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 > > -- > Dr. Tim Schäfer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am > Main, Germany > > _______________________________________________ > 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 > > > _______________________________________________ > 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>
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