Dear FS experts
I have done group comparisons wrt thickness and surface area. The found clusters were written out as annotations, transformed into each individual space, and then the corresponding values were extracted.
When using mris_anatomical_stats, values are different for thickness maps depending whether I used the --nsmooth 15 option or not. So good so far.
However, when using the same command (see below) for ?h.area files, extracted values are the same whether or not I used the --nsmooth option.
It seems that the --nsmooth option in mris_anatomical_stats does not affect (smooth) the surface area maps.
Is there any solution to also smooth surface area maps with mris_anatomical_stats?
I use the Mac FS 5.1.0 version
Thanks in advance Best regards Jürgen Hänggi
---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------
what is your command line? doug
On 6/6/12 5:25 AM, Jürgen Hänggi wrote:
Dear FS experts
I have done group comparisons wrt thickness and surface area. The found clusters were written out as annotations, transformed into each individual space, and then the corresponding values were extracted.
When using mris_anatomical_stats, values are different for thickness maps depending whether I used the --nsmooth 15 option or not. So good so far.
However, when using the same command (see below) for ?h.area files, extracted values are the same whether or not I used the --nsmooth option.
It seems that the --nsmooth option in mris_anatomical_stats does not affect (smooth) the surface area maps.
Is there any solution to also smooth surface area maps with mris_anatomical_stats?
I use the Mac FS 5.1.0 version
Thanks in advance Best regards Jürgen Hänggi
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
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Hi Doug
This is my command line:
mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area -nsmooth 15 -f $s/stats/lh.aparc.a2005s.stats $s lh
In the past, you recommended smoothing the data with mri_surf2surf instead of with mris_anatomical_stats.
For that purpose, I run the following command:
mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex
But the following error occurred:
[Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% foreach s ( MOREA_* ) foreach? mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex foreach? end srcsubject = MOREA_KG002 srcval = (null) srctype = trgsubject = MOREA_KG002 trgval = lh.area.15.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.sphere.reg Loading source data Reading surface file /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area nquads=9895939, nvertices=399 ERROR: MRISread: file '/Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area' has many more faces than vertices! Probably trying to use a scalar data file as a surface!
Thanks for help in advance Cheers Jürgen
On [DATE], "Douglas Greve" <[ADDRESS]> wrote:
what is your command line? doug
On 6/6/12 5:25 AM, Jürgen Hänggi wrote:
Dear FS experts
I have done group comparisons wrt thickness and surface area. The found clusters were written out as annotations, transformed into each individual space, and then the corresponding values were extracted.
When using mris_anatomical_stats, values are different for thickness maps depending whether I used the --nsmooth 15 option or not. So good so far.
However, when using the same command (see below) for ?h.area files, extracted values are the same whether or not I used the --nsmooth option.
It seems that the --nsmooth option in mris_anatomical_stats does not affect (smooth) the surface area maps.
Is there any solution to also smooth surface area maps with mris_anatomical_stats?
I use the Mac FS 5.1.0 version
Thanks in advance Best regards Jürgen Hänggi
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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Use "--sval lh.area". Also, why do you want to smooth it before averaging over the ROI? doug
On 06/07/2012 01:29 AM, Jürgen Hänggi wrote:
Hi Doug
This is my command line:
mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area -nsmooth 15 -f $s/stats/lh.aparc.a2005s.stats $s lh
In the past, you recommended smoothing the data with mri_surf2surf instead of with mris_anatomical_stats.
For that purpose, I run the following command:
mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex
But the following error occurred:
[Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% foreach s ( MOREA_* ) foreach? mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex foreach? end srcsubject = MOREA_KG002 srcval = (null) srctype = trgsubject = MOREA_KG002 trgval = lh.area.15.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.sphere.reg Loading source data Reading surface file /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area nquads=9895939, nvertices=399 ERROR: MRISread: file '/Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area' has many more faces than vertices! Probably trying to use a scalar data file as a surface!
Thanks for help in advance Cheers Jürgen
On [DATE], "Douglas Greve"<[ADDRESS]> wrote:
what is your command line? doug
On 6/6/12 5:25 AM, Jürgen Hänggi wrote:
Dear FS experts
I have done group comparisons wrt thickness and surface area. The found clusters were written out as annotations, transformed into each individual space, and then the corresponding values were extracted.
When using mris_anatomical_stats, values are different for thickness maps depending whether I used the --nsmooth 15 option or not. So good so far.
However, when using the same command (see below) for ?h.area files, extracted values are the same whether or not I used the --nsmooth option.
It seems that the --nsmooth option in mris_anatomical_stats does not affect (smooth) the surface area maps.
Is there any solution to also smooth surface area maps with mris_anatomical_stats?
I use the Mac FS 5.1.0 version
Thanks in advance Best regards Jürgen Hänggi
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
Freesurfer mailing list 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
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.
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
Hi Doug
I correlated a behavioural measure with cortical thickness and surface area using mri_preroc, mri_surf2surf and mri_glmfit. Now I would like to extract the individual values of the clusters that correlated with the behavioural measure. Because the individual values should be comparable with the results of the group, I have to smooth them too.
When using --sval lh.area, the following error occurred:
[Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% foreach s ( MOREA_* ) foreach? mri_surf2surf --hemi lh --s $s --sval lh.area --fwhm 15 --tval lh.area.15.mgh --cortex foreach? end ERROR: could not determine type of lh.area ....... ....... ....... ERROR: could not determine type of lh.area [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
Thanks Cheers Jürgen
On [DATE], "Douglas N Greve" <[ADDRESS]> wrote:
Use "--sval lh.area". Also, why do you want to smooth it before averaging over the ROI? doug
On 06/07/2012 01:29 AM, Jürgen Hänggi wrote:
Hi Doug
This is my command line:
mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area -nsmooth 15 -f $s/stats/lh.aparc.a2005s.stats $s lh
In the past, you recommended smoothing the data with mri_surf2surf instead of with mris_anatomical_stats.
For that purpose, I run the following command:
mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex
But the following error occurred:
[Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% foreach s ( MOREA_* ) foreach? mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex foreach? end srcsubject = MOREA_KG002 srcval = (null) srctype = trgsubject = MOREA_KG002 trgval = lh.area.15.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.sphere.reg Loading source data Reading surface file /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area nquads=9895939, nvertices=399 ERROR: MRISread: file '/Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area' has many more faces than vertices! Probably trying to use a scalar data file as a surface!
Thanks for help in advance Cheers Jürgen
On [DATE], "Douglas Greve"<[ADDRESS]> wrote:
what is your command line? doug
On 6/6/12 5:25 AM, Jürgen Hänggi wrote:
Dear FS experts
I have done group comparisons wrt thickness and surface area. The found clusters were written out as annotations, transformed into each individual space, and then the corresponding values were extracted.
When using mris_anatomical_stats, values are different for thickness maps depending whether I used the --nsmooth 15 option or not. So good so far.
However, when using the same command (see below) for ?h.area files, extracted values are the same whether or not I used the --nsmooth option.
It seems that the --nsmooth option in mris_anatomical_stats does not affect (smooth) the surface area maps.
Is there any solution to also smooth surface area maps with mris_anatomical_stats?
I use the Mac FS 5.1.0 version
Thanks in advance Best regards Jürgen Hänggi
--------------------------------------------------------------------------->>>> -
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------
Hi Juegen, there will be a file called something like cache.th20.abs.y.ocn.dat in the glm output directory. This will be a text file with number of columns equal to the number of significant clusters (after correction) and number of rows equal to the number of subjects. The value will be the average over that cluster for that subject. Is this what you want? This will correspond exactly with the map-based data, which you'll never be able to do by mapping the clusters back to each individual subject because of resampling issues. doug
On 06/08/2012 02:37 AM, Jürgen Hänggi wrote:
Hi Doug
I correlated a behavioural measure with cortical thickness and surface area using mri_preroc, mri_surf2surf and mri_glmfit. Now I would like to extract the individual values of the clusters that correlated with the behavioural measure. Because the individual values should be comparable with the results of the group, I have to smooth them too.
When using --sval lh.area, the following error occurred:
[Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% foreach s ( MOREA_* ) foreach? mri_surf2surf --hemi lh --s $s --sval lh.area --fwhm 15 --tval lh.area.15.mgh --cortex foreach? end ERROR: could not determine type of lh.area ....... ....... ....... ERROR: could not determine type of lh.area [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
Thanks Cheers Jürgen
On [DATE], "Douglas N Greve"<[ADDRESS]> wrote:
Use "--sval lh.area". Also, why do you want to smooth it before averaging over the ROI? doug
On 06/07/2012 01:29 AM, Jürgen Hänggi wrote:
Hi Doug
This is my command line:
mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area -nsmooth 15 -f $s/stats/lh.aparc.a2005s.stats $s lh
In the past, you recommended smoothing the data with mri_surf2surf instead of with mris_anatomical_stats.
For that purpose, I run the following command:
mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex
But the following error occurred:
[Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% foreach s ( MOREA_* ) foreach? mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex foreach? end srcsubject = MOREA_KG002 srcval = (null) srctype = trgsubject = MOREA_KG002 trgval = lh.area.15.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.sphere.reg Loading source data Reading surface file /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area nquads=9895939, nvertices=399 ERROR: MRISread: file '/Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area' has many more faces than vertices! Probably trying to use a scalar data file as a surface!
Thanks for help in advance Cheers Jürgen
On [DATE], "Douglas Greve"<[ADDRESS]> wrote:
what is your command line? doug
On 6/6/12 5:25 AM, Jürgen Hänggi wrote:
Dear FS experts
I have done group comparisons wrt thickness and surface area. The found clusters were written out as annotations, transformed into each individual space, and then the corresponding values were extracted.
When using mris_anatomical_stats, values are different for thickness maps depending whether I used the --nsmooth 15 option or not. So good so far.
However, when using the same command (see below) for ?h.area files, extracted values are the same whether or not I used the --nsmooth option.
It seems that the --nsmooth option in mris_anatomical_stats does not affect (smooth) the surface area maps.
Is there any solution to also smooth surface area maps with mris_anatomical_stats?
I use the Mac FS 5.1.0 version
Thanks in advance Best regards Jürgen Hänggi
--------------------------------------------------------------------------->>>>
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
--------------------------------------------------------------------------->>>>
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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hi doug,
i am loading 917 subjects in qdec.....i already made qdec.table.dat which consist the list of subjid, age, gender, lh & rh thickness......
for some reason, it is only displaying the first subject.....others are not been detected by qdec..... i also looked into tutorial and compared the tutorial qdec.table.dat file with the one i made....both r identical and look good......$SUBJECTS_DIR already has glm, qdec and fsaverage folders....Still; it displaying only one subject.....
any idea why is it doing as i tried several ways to find the fix but hasnt been successful yet....please let me know
thanks kk
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jürgen Hänggi" j.haenggi@psychologie.uzh.ch Cc: "Freesurfer Mailinglist" freesurfer@nmr.mgh.harvard.edu Sent: Friday, June 8, 2012 4:17:02 PM Subject: Re: [Freesurfer] Mris_anatomical_stats: smoothing does not work with surface area maps
Hi Juegen, there will be a file called something like cache.th20.abs.y.ocn.dat in the glm output directory. This will be a text file with number of columns equal to the number of significant clusters (after correction) and number of rows equal to the number of subjects. The value will be the average over that cluster for that subject. Is this what you want? This will correspond exactly with the map-based data, which you'll never be able to do by mapping the clusters back to each individual subject because of resampling issues. doug
On 06/08/2012 02:37 AM, Jürgen Hänggi wrote:
Hi Doug
I correlated a behavioural measure with cortical thickness and surface area using mri_preroc, mri_surf2surf and mri_glmfit. Now I would like to extract the individual values of the clusters that correlated with the behavioural measure. Because the individual values should be comparable with the results of the group, I have to smooth them too.
When using --sval lh.area, the following error occurred:
[Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% foreach s ( MOREA_* ) foreach? mri_surf2surf --hemi lh --s $s --sval lh.area --fwhm 15 --tval lh.area.15.mgh --cortex foreach? end ERROR: could not determine type of lh.area ....... ....... ....... ERROR: could not determine type of lh.area [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
Thanks Cheers Jürgen
On [DATE], "Douglas N Greve"<[ADDRESS]> wrote:
Use "--sval lh.area". Also, why do you want to smooth it before averaging over the ROI? doug
On 06/07/2012 01:29 AM, Jürgen Hänggi wrote:
Hi Doug
This is my command line:
mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area -nsmooth 15 -f $s/stats/lh.aparc.a2005s.stats $s lh
In the past, you recommended smoothing the data with mri_surf2surf instead of with mris_anatomical_stats.
For that purpose, I run the following command:
mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex
But the following error occurred:
[Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% foreach s ( MOREA_* ) foreach? mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex foreach? end srcsubject = MOREA_KG002 srcval = (null) srctype = trgsubject = MOREA_KG002 trgval = lh.area.15.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.sphere.reg Loading source data Reading surface file /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area nquads=9895939, nvertices=399 ERROR: MRISread: file '/Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area' has many more faces than vertices! Probably trying to use a scalar data file as a surface!
Thanks for help in advance Cheers Jürgen
On [DATE], "Douglas Greve"<[ADDRESS]> wrote:
what is your command line? doug
On 6/6/12 5:25 AM, Jürgen Hänggi wrote:
Dear FS experts
I have done group comparisons wrt thickness and surface area. The found clusters were written out as annotations, transformed into each individual space, and then the corresponding values were extracted.
When using mris_anatomical_stats, values are different for thickness maps depending whether I used the --nsmooth 15 option or not. So good so far.
However, when using the same command (see below) for ?h.area files, extracted values are the same whether or not I used the --nsmooth option.
It seems that the --nsmooth option in mris_anatomical_stats does not affect (smooth) the surface area maps.
Is there any solution to also smooth surface area maps with mris_anatomical_stats?
I use the Mac FS 5.1.0 version
Thanks in advance Best regards Jürgen Hänggi
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Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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Hi Doug
Yes, this is exactly what I looked for. Thanks a lot
Cheers Jürgen
On [DATE], "Douglas N Greve" <[ADDRESS]> wrote:
Hi Juegen, there will be a file called something like cache.th20.abs.y.ocn.dat in the glm output directory. This will be a text file with number of columns equal to the number of significant clusters (after correction) and number of rows equal to the number of subjects. The value will be the average over that cluster for that subject. Is this what you want? This will correspond exactly with the map-based data, which you'll never be able to do by mapping the clusters back to each individual subject because of resampling issues. doug
On 06/08/2012 02:37 AM, Jürgen Hänggi wrote:
Hi Doug
I correlated a behavioural measure with cortical thickness and surface area using mri_preroc, mri_surf2surf and mri_glmfit. Now I would like to extract the individual values of the clusters that correlated with the behavioural measure. Because the individual values should be comparable with the results of the group, I have to smooth them too.
When using --sval lh.area, the following error occurred:
[Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% foreach s ( MOREA_* ) foreach? mri_surf2surf --hemi lh --s $s --sval lh.area --fwhm 15 --tval lh.area.15.mgh --cortex foreach? end ERROR: could not determine type of lh.area ....... ....... ....... ERROR: could not determine type of lh.area [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
Thanks Cheers Jürgen
On [DATE], "Douglas N Greve"<[ADDRESS]> wrote:
Use "--sval lh.area". Also, why do you want to smooth it before averaging over the ROI? doug
On 06/07/2012 01:29 AM, Jürgen Hänggi wrote:
Hi Doug
This is my command line:
mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area -nsmooth 15 -f $s/stats/lh.aparc.a2005s.stats $s lh
In the past, you recommended smoothing the data with mri_surf2surf instead of with mris_anatomical_stats.
For that purpose, I run the following command:
mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex
But the following error occurred:
[Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% foreach s ( MOREA_* ) foreach? mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex foreach? end srcsubject = MOREA_KG002 srcval = (null) srctype = trgsubject = MOREA_KG002 trgval = lh.area.15.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.sphere.reg Loading source data Reading surface file /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area nquads=9895939, nvertices=399 ERROR: MRISread: file '/Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area' has many more faces than vertices! Probably trying to use a scalar data file as a surface!
Thanks for help in advance Cheers Jürgen
On [DATE], "Douglas Greve"<[ADDRESS]> wrote:
what is your command line? doug
On 6/6/12 5:25 AM, Jürgen Hänggi wrote:
Dear FS experts
I have done group comparisons wrt thickness and surface area. The found clusters were written out as annotations, transformed into each individual space, and then the corresponding values were extracted.
When using mris_anatomical_stats, values are different for thickness maps depending whether I used the --nsmooth 15 option or not. So good so far.
However, when using the same command (see below) for ?h.area files, extracted values are the same whether or not I used the --nsmooth option.
It seems that the --nsmooth option in mris_anatomical_stats does not affect (smooth) the surface area maps.
Is there any solution to also smooth surface area maps with mris_anatomical_stats?
I use the Mac FS 5.1.0 version
Thanks in advance Best regards Jürgen Hänggi
--------------------------------------------------------------------------->>
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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