Dear all,
In group analysis, how are the various thresholds (min, mid, max) related to p-values?
Thanks, Sasha
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Hi Sasha,
they are -log10(p), with a sign added to show the direction of the effect. e.g. 1e-4 shows up as 4 (or -4)
cheers, Bruce
On Tue, 27 Dec 2005, Sasha Wolosin wrote:
Dear all,
In group analysis, how are the various thresholds (min, mid, max) related to p-values?
Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Is there any way to load a colour look-up table through tksurfer scripting? I can't seem to see any options in the usage. Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Thanks Kevin. Is it possible to load overlays through a script as well?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Kevin Teich [mailto:kteich@nmr.mgh.harvard.edu] Sent: Wed 28/12/2005 11:40 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer script
labl_load_color_table <filename>
On Wed, Dec 28, 2005 at 04:06:08PM +1100, Fornito, Alexander wrote:
Is there any way to load a colour look-up table through tksurfer scripting? I can't seem to see any options in the usage.
If you have a .w file:
set val <filename> sclv_read_from_dotw <layer>
If it's a volume:
sclv_read_from_volume <layer> <filename> <registration type> [registration file name]
Where <layer> is an index 0-8 for the layer to load it into, <registration type> is 0 for file, 1 for find, and 2 for identity, and the registration file name is optional if you choose 0 for the reg type.
On Thu, Dec 29, 2005 at 10:55:19AM +1100, Fornito, Alexander wrote:
Thanks Kevin. Is it possible to load overlays through a script as well?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Kevin Teich [mailto:kteich@nmr.mgh.harvard.edu] Sent: Wed 28/12/2005 11:40 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer script
labl_load_color_table <filename>
On Wed, Dec 28, 2005 at 04:06:08PM +1100, Fornito, Alexander wrote:
Is there any way to load a colour look-up table through tksurfer scripting? I can't seem to see any options in the usage.
-- Kevin Teich
Hi, I'm trying to run mris_anatomical_stats on a custom parcellation, but am having problems because I don't know what the flag to speficy the appropriate colour table is. If I run the -b option, I get output but with no labels. If I run -f, I get a message saying that no colour table is loaded. Commands and output are below. Thanks, Alex
mris_anatomical_stats -mgz -a acc.annot -b 1000908 lh white INFO: assuming MGZ format for volumes. computing statistics for each annotation in acc.annot. reading volume /data/flanders/work/alex/freesurfer/subjects_fe/1000908/mri/wm.mgz... reading input surface /data/flanders/work/alex/freesurfer/subjects_fe/1000908/surf/lh.white... INFO: Volume /tmp/mritotal_1614/nu_8_dxyz.mnc cannot be found. done. computing second fundamental form... ... done. total white matter volume = 442238 mm^3
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
111575 75355 185201 2.472 +- 0.836 0.190 0.061 1980.885 250.831 ** annotation 003c1400 444 269 715 2.685 +- 0.637 0.110 0.021 1.601 0.402 ** annotation 00dc3c3c 891 578 1588 2.777 +- 0.537 0.187 0.034 15.162 1.149 ** annotation 003c3c8c 213 126 392 3.145 +- 0.924 0.152 0.034 2.943 0.297 ** annotation 003c6464 82 40 152 3.785 +- 0.634 0.070 0.011 0.196 0.034 ** annotation 00b4648c 567 334 906 2.723 +- 0.503 0.103 0.020 2.385 0.434 ** annotation 00b48c3c 1093 709 2195 3.051 +- 0.793 0.206 0.078 20.688 3.225 ** annotation 003c643c 240 139 311 2.247 +- 0.872 0.085 0.010 0.454 0.149 ** annotation 008c143c
*OR*
mris_anatomical_stats -mgz -a acc.annot -f ./1000908.txt 1000908 lh white INFO: assuming MGZ format for volumes. computing statistics for each annotation in acc.annot. reading volume /data/flanders/work/alex/freesurfer/subjects_fe/1000908/mri/wm.mgz... reading input surface /data/flanders/work/alex/freesurfer/subjects_fe/1000908/surf/lh.white... INFO: Volume /tmp/mritotal_1614/nu_8_dxyz.mnc cannot be found. done. computing second fundamental form... ... done. total white matter volume = 442238 mm^3 mris_anatomical_stats: no color table loaded - cannot translate annot file
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Hi Alex,
did you run mris_ca_train with -t <color table>? If so, it should embed the color table in the .gcs file, then get probagated to the .annot, so you shouldn't have to specify anything to mris_anatomical_stats.
cheers, Bruce On Fri, 30 Dec 2005, Fornito, Alexander wrote:
Hi, I'm trying to run mris_anatomical_stats on a custom parcellation, but am having problems because I don't know what the flag to speficy the appropriate colour table is. If I run the -b option, I get output but with no labels. If I run -f, I get a message saying that no colour table is loaded. Commands and output are below. Thanks, Alex
mris_anatomical_stats -mgz -a acc.annot -b 1000908 lh white INFO: assuming MGZ format for volumes. computing statistics for each annotation in acc.annot. reading volume /data/flanders/work/alex/freesurfer/subjects_fe/1000908/mri/wm.mgz... reading input surface /data/flanders/work/alex/freesurfer/subjects_fe/1000908/surf/lh.white... INFO: Volume /tmp/mritotal_1614/nu_8_dxyz.mnc cannot be found. done. computing second fundamental form... ... done. total white matter volume = 442238 mm^3
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
111575 75355 185201 2.472 +- 0.836 0.190 0.061 1980.885 250.831 ** annotation 003c1400 444 269 715 2.685 +- 0.637 0.110 0.021 1.601 0.402 ** annotation 00dc3c3c 891 578 1588 2.777 +- 0.537 0.187 0.034 15.162 1.149 ** annotation 003c3c8c 213 126 392 3.145 +- 0.924 0.152 0.034 2.943 0.297 ** annotation 003c6464 82 40 152 3.785 +- 0.634 0.070 0.011 0.196 0.034 ** annotation 00b4648c 567 334 906 2.723 +- 0.503 0.103 0.020 2.385 0.434 ** annotation 00b48c3c 1093 709 2195 3.051 +- 0.793 0.206 0.078 20.688 3.225 ** annotation 003c643c 240 139 311 2.247 +- 0.872 0.085 0.010 0.454 0.149 ** annotation 008c143c
*OR*
mris_anatomical_stats -mgz -a acc.annot -f ./1000908.txt 1000908 lh white INFO: assuming MGZ format for volumes. computing statistics for each annotation in acc.annot. reading volume /data/flanders/work/alex/freesurfer/subjects_fe/1000908/mri/wm.mgz... reading input surface /data/flanders/work/alex/freesurfer/subjects_fe/1000908/surf/lh.white... INFO: Volume /tmp/mritotal_1614/nu_8_dxyz.mnc cannot be found. done. computing second fundamental form... ... done. total white matter volume = 442238 mm^3 mris_anatomical_stats: no color table loaded - cannot translate annot file
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi. I was wondering if anybody out there has made other parcellations of the entire brain besides the standard freesurfer one with 81 named regions? For instance, did anybody go to the painful trouble of making a 4 lobe parcellation?
Thanks Daniel Goldenholz
This isn't for an annotation automatically labelled using mris_ca_label; I've simply manually traced my ROIs then saved out an annotation by assigning labels from the colour table in tksurfer. At this stage I'd like to get stats on my manual ROIs. Does -b only give labels if the automatic parcellation is used? If so, would the order of ROIs appearing in the stats output table (e.g., the one below) always be the same as the order in the colour table?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
________________________________
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sat 31/12/2005 12:54 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_anatomical_stats on custom annot
Hi Alex,
did you run mris_ca_train with -t <color table>? If so, it should embed the color table in the .gcs file, then get probagated to the .annot, so you shouldn't have to specify anything to mris_anatomical_stats.
cheers, Bruce On Fri, 30 Dec 2005, Fornito, Alexander wrote:
Hi, I'm trying to run mris_anatomical_stats on a custom parcellation, but am having problems because I don't know what the flag to speficy the appropriate colour table is. If I run the -b option, I get output but with no labels. If I run -f, I get a message saying that no colour table is loaded. Commands and output are below. Thanks, Alex
mris_anatomical_stats -mgz -a acc.annot -b 1000908 lh white INFO: assuming MGZ format for volumes. computing statistics for each annotation in acc.annot. reading volume /data/flanders/work/alex/freesurfer/subjects_fe/1000908/mri/wm.mgz... reading input surface /data/flanders/work/alex/freesurfer/subjects_fe/1000908/surf/lh.white... INFO: Volume /tmp/mritotal_1614/nu_8_dxyz.mnc cannot be found. done. computing second fundamental form... ... done. total white matter volume = 442238 mm^3
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
111575 75355 185201 2.472 +- 0.836 0.190 0.061 1980.885 250.831 ** annotation 003c1400 444 269 715 2.685 +- 0.637 0.110 0.021 1.601 0.402 ** annotation 00dc3c3c 891 578 1588 2.777 +- 0.537 0.187 0.034 15.162 1.149 ** annotation 003c3c8c 213 126 392 3.145 +- 0.924 0.152 0.034 2.943 0.297 ** annotation 003c6464 82 40 152 3.785 +- 0.634 0.070 0.011 0.196 0.034 ** annotation 00b4648c 567 334 906 2.723 +- 0.503 0.103 0.020 2.385 0.434 ** annotation 00b48c3c 1093 709 2195 3.051 +- 0.793 0.206 0.078 20.688 3.225 ** annotation 003c643c 240 139 311 2.247 +- 0.872 0.085 0.010 0.454 0.149 ** annotation 008c143c
*OR*
mris_anatomical_stats -mgz -a acc.annot -f ./1000908.txt 1000908 lh white INFO: assuming MGZ format for volumes. computing statistics for each annotation in acc.annot. reading volume /data/flanders/work/alex/freesurfer/subjects_fe/1000908/mri/wm.mgz... reading input surface /data/flanders/work/alex/freesurfer/subjects_fe/1000908/surf/lh.white... INFO: Volume /tmp/mritotal_1614/nu_8_dxyz.mnc cannot be found. done. computing second fundamental form... ... done. total white matter volume = 442238 mm^3 mris_anatomical_stats: no color table loaded - cannot translate annot file
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Does the 'threshold midpoint' value in tksurfer's curvature display control correspond to values in the .sulc file (assuming the .sulc file is loaded), or are they arbitrary values? For example, if I set the value to .50, does this make all vertices with a .sulc value of .50 or less lighter (lighter, if using binary colouring)? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
the threshold midpoint in the curvature display just sets where the transition is from red to green (or light gray to dark gray if using binary colors)
On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi, Does the 'threshold midpoint' value in tksurfer's curvature display control correspond to values in the .sulc file (assuming the .sulc file is loaded), or are they arbitrary values? For example, if I set the value to .50, does this make all vertices with a .sulc value of .50 or less lighter (lighter, if using binary colouring)? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce, I'm trying to extract thickness for sulci and gyri separately. From what I understand, positive .sulc values suggest sulci and negative .sulc values suggest gyri. I'd like to play around with this distinction (e.g., call everything with a .sulc value < .35 'gyral'), and am wandering if adjusting the midpoint in tksurfer allows me to precisly visualize what changing this threshold does. Basically, I'd like to know if it's correct for me to pick a midpoint I'm happy with in tksurfer, say .35, than go back and split the .thickness file into vertices with .sulc values above and below .35, knowing that this distinction between sulcal and gyral will correspond to the one shown by the colour display I visualized in tksurfer.
I'm pretty sure the values in the tksurfer threshold midpoint scale correspond to those in the curvature file, since they seem to change depednig on the curvature file loaded (e.g., the range for .sulc files is different to the range for .thickness files). Just want to double-check. Hope this makes sense, Alex
the threshold midpoint in the curvature display just sets where the transition is from red to green (or light gray to dark gray if using binary colors)
On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi, Does the 'threshold midpoint' value in tksurfer's curvature display control correspond to values in the .sulc file (assuming the .sulc file is loaded), or are they arbitrary values? For example, if I set the value to .50, does this make all vertices with a .sulc value of .50 or less lighter (lighter, if using binary colouring)? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, that makes sense. On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi Bruce, I'm trying to extract thickness for sulci and gyri separately. From what I understand, positive .sulc values suggest sulci and negative .sulc values suggest gyri. I'd like to play around with this distinction (e.g., call everything with a .sulc value < .35 'gyral'), and am wandering if adjusting the midpoint in tksurfer allows me to precisly visualize what changing this threshold does. Basically, I'd like to know if it's correct for me to pick a midpoint I'm happy with in tksurfer, say .35, than go back and split the .thickness file into vertices with .sulc values above and below .35, knowing that this distinction between sulcal and gyral will correspond to the one shown by the colour display I visualized in tksurfer.
I'm pretty sure the values in the tksurfer threshold midpoint scale correspond to those in the curvature file, since they seem to change depednig on the curvature file loaded (e.g., the range for .sulc files is different to the range for .thickness files). Just want to double-check. Hope this makes sense, Alex
the threshold midpoint in the curvature display just sets where the transition is from red to green (or light gray to dark gray if using binary colors)
On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi, Does the 'threshold midpoint' value in tksurfer's curvature display control correspond to values in the .sulc file (assuming the .sulc file is loaded), or are they arbitrary values? For example, if I set the value to .50, does this make all vertices with a .sulc value of .50 or less lighter (lighter, if using binary colouring)? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I am trying to run nu_correct inside of a script using perl. It keeps crashing with a "Termination Status=512".
Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Cannot open .imp file: nu1.imp nu_correct: crashed while running nu_estimate_np_and_em (termination status=512)
Anyone have any ideas where this may be coming from?
-Eric
Great, thanks.
On another issue, I've noticed that using mris_convert to convert ?h.area to ascii produces the same area values in the resulting file, irrepsective of whether pial or white surfaces are specified in the command. This contrasts mris_anatomical_stats, which gives different values. Is it possible to extract pial and white surface area separately for sulcal and gyral regions? Thanks again, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
________________________________
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/01/2006 12:42 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] .sulc in tksurfer
yes, that makes sense. On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi Bruce, I'm trying to extract thickness for sulci and gyri separately. From what I understand, positive .sulc values suggest sulci and negative .sulc values suggest gyri. I'd like to play around with this distinction (e.g., call everything with a .sulc value < .35 'gyral'), and am wandering if adjusting the midpoint in tksurfer allows me to precisly visualize what changing this threshold does. Basically, I'd like to know if it's correct for me to pick a midpoint I'm happy with in tksurfer, say .35, than go back and split the .thickness file into vertices with .sulc values above and below .35, knowing that this distinction between sulcal and gyral will correspond to the one shown by the colour display I visualized in tksurfer.
I'm pretty sure the values in the tksurfer threshold midpoint scale correspond to those in the curvature file, since they seem to change depednig on the curvature file loaded (e.g., the range for .sulc files is different to the range for .thickness files). Just want to double-check. Hope this makes sense, Alex
the threshold midpoint in the curvature display just sets where the transition is from red to green (or light gray to dark gray if using binary colors)
On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi, Does the 'threshold midpoint' value in tksurfer's curvature display control correspond to values in the .sulc file (assuming the .sulc file is loaded), or are they arbitrary values? For example, if I set the value to .50, does this make all vertices with a .sulc value of .50 or less lighter (lighter, if using binary colouring)? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yeah, the ?h.area file is the area of the ?h.white surface. The surface specified for mris_convert is only used to get the # of vertices/faces/etc... I think the only way to write out the area of other surfaces is to read them into tksurfer and use the tcl commands:
% set area lh.pial_area % write_binary_areas
cheers, Bruce
On Thu, 5 Jan 2006, Fornito, Alexander wrote:
Great, thanks.
On another issue, I've noticed that using mris_convert to convert ?h.area to ascii produces the same area values in the resulting file, irrepsective of whether pial or white surfaces are specified in the command. This contrasts mris_anatomical_stats, which gives different values. Is it possible to extract pial and white surface area separately for sulcal and gyral regions? Thanks again, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/01/2006 12:42 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] .sulc in tksurfer
yes, that makes sense. On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi Bruce, I'm trying to extract thickness for sulci and gyri separately. From what I understand, positive .sulc values suggest sulci and negative .sulc values suggest gyri. I'd like to play around with this distinction (e.g., call everything with a .sulc value < .35 'gyral'), and am wandering if adjusting the midpoint in tksurfer allows me to precisly visualize what changing this threshold does. Basically, I'd like to know if it's correct for me to pick a midpoint I'm happy with in tksurfer, say .35, than go back and split the .thickness file into vertices with .sulc values above and below .35, knowing that this distinction between sulcal and gyral will correspond to the one shown by the colour display I visualized in tksurfer.
I'm pretty sure the values in the tksurfer threshold midpoint scale correspond to those in the curvature file, since they seem to change depednig on the curvature file loaded (e.g., the range for .sulc files is different to the range for .thickness files). Just want to double-check. Hope this makes sense, Alex
the threshold midpoint in the curvature display just sets where the transition is from red to green (or light gray to dark gray if using binary colors)
On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi, Does the 'threshold midpoint' value in tksurfer's curvature display control correspond to values in the .sulc file (assuming the .sulc file is loaded), or are they arbitrary values? For example, if I set the value to .50, does this make all vertices with a .sulc value of .50 or less lighter (lighter, if using binary colouring)? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu