Is the normalization software called N3 a standard part of the dev release of Freesurfer? Michele
Michele,
Yes, the N3 package, and other MNI tools, is included with the dev release of Freesurfer. nu_correct, part of this N3 package, is run early in the FreeSurfer processing stream.
Nick
On Wed, 2005-11-30 at 08:12 -0800, Michele Perry wrote:
Is the normalization software called N3 a standard part of the dev release of Freesurfer? Michele _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, I've created some labels in tkmedit, but it seems that I can only load one at a time in tksurfer.I can load eithe individually, but if I try to load one label while another is already loaded, tksurfer closes automatically. The output is below. Thanks, Alex
tksurfer 1000040 lh inflated surfer: current subjects dir: /data/flanders/work/alex/freesurfer/subjects_fe surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/flanders/work/alex/freesurfer/subjects_fe ERROR: cound not stat /data/flanders/work/alex/freesurfer/subjects_fe/1000040/mri/T1/COR-.info. Does it exist? mghRead(/data/flanders/work/alex/freesurfer/subjects_fe/1000040/mri/T1.mgh, -1): could not open file surfer: Reading header info from /data/flanders/work/alex/freesurfer/subjects_fe/1000040/mri/T1.mgz INFO: Volume /tmp/mritotal_14746/nu_8_dxyz.mnc cannot be found. INFO: Volume /tmp/mritotal_14746/nu_8_dxyz.mnc cannot be found. surfer: vertices=127270, faces=254536 corRead(): can't open file /data/flanders/work/alex/freesurfer/subjects_fe/1000040/surf/../mri/orig/COR-.info surfer: single buffered window Xlib: extension "XFree86-DRI" missing on display ":0.0". surfer: using interface /usr/local/freesurfer-dev20050905/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer-dev20050905/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer-dev20050905/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer-dev20050905/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer-dev20050905/lib/tcl/tkUtils.tcl Read /usr/local/freesurfer-dev20050905/surface_labels.txt, found 95 structures Successfully parsed tksurfer.tcl % 220 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... 366 unassigned vertices in label - building spatial LUT...
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, I'm wandering if its possible to convert a label into a volume so that it fills the space between the white and pial surfaces used in calculating thickness. That is, if the label is drawn on the wm surface, is is possible to determine what points on the pial surface are used to calculate the thickness of that label? I've been playing with the --proj option in mr_label2vol. The --help states that --proj frac "means that start, stop, and delta are relative to the thickness at each vertex." I tried using the start, stop and delta values provided in the example (0, 1 .1), but it doesn't seem to completely fill the area between the two surfaces. I've also tried plugging in other values and can't seem to get it right.Is there soemthing I'm missing? 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
This is done in the newer versions of recon all. It creates subject/mri/?h.ribbon.mgz using mri_surf2vol. Here's what recon-all does:
set cmd = (mri_surf2vol --mkmask --hemi $hemi) set cmd = ($cmd --fillribbon --template orig$MGZ) set cmd = ($cmd --volregidentity $subjid --outvol $hemi.ribbon.mgz)
doug
On Sat, 3 Dec 2005, Fornito, Alexander wrote:
Hi, I'm wandering if its possible to convert a label into a volume so that it fills the space between the white and pial surfaces used in calculating thickness. That is, if the label is drawn on the wm surface, is is possible to determine what points on the pial surface are used to calculate the thickness of that label? I've been playing with the --proj option in mr_label2vol. The --help states that --proj frac "means that start, stop, and delta are relative to the thickness at each vertex." I tried using the start, stop and delta values provided in the example (0, 1 .1), but it doesn't seem to completely fill the area between the two surfaces. I've also tried plugging in other values and can't seem to get it right.Is there soemthing I'm missing? 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 see. The ribbon actually looks like the result I got when i used mri_label2vol. So would I be correct in saying that a that using the flag -proj frac 0, 1, .1 will extract that protion of ?h.ribbon.mgz that is associated with the label? What exactly does delta (eg., .1) correspond to? How come the ribbon.mgz appears 'splotchy' (ie., the space between the white and pial surfaces is not completely filled.) 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
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Sat 3/12/2005 9:43 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol
This is done in the newer versions of recon all. It creates subject/mri/?h.ribbon.mgz using mri_surf2vol. Here's what recon-all does:
set cmd = (mri_surf2vol --mkmask --hemi $hemi) set cmd = ($cmd --fillribbon --template orig$MGZ) set cmd = ($cmd --volregidentity $subjid --outvol $hemi.ribbon.mgz)
doug
On Sat, 3 Dec 2005, Fornito, Alexander wrote:
Hi, I'm wandering if its possible to convert a label into a volume so that it fills the space between the white and pial surfaces used in calculating thickness. That is, if the label is drawn on the wm surface, is is possible to determine what points on the pial surface are used to calculate the thickness of that label? I've been playing with the --proj option in mr_label2vol. The --help states that --proj frac "means that start, stop, and delta are relative to the thickness at each vertex." I tried using the start, stop and delta values provided in the example (0, 1 .1), but it doesn't seem to completely fill the area between the two surfaces. I've also tried plugging in other values and can't seem to get it right.Is there soemthing I'm missing? 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
From --help on mri_label2vol:
--proj type start stop delta
Project the label along the surface normal. type can be abs or frac. abs means that the start, stop, and delta are measured in mm. frac means that start, stop, and delta are relative to the thickness at each vertex. The label definition is changed to fill in label points in increments of delta from start to stop. Requires subject and hemi in order to load in a surface and thickness. Uses the white surface. The label MUST have been defined on the surface.
Not sure why it's splotchy. Can you lower the delta?
doug
Fornito, Alexander wrote:
I see. The ribbon actually looks like the result I got when i used mri_label2vol. So would I be correct in saying that a that using the flag -proj frac 0, 1, .1 will extract that protion of ?h.ribbon.mgz that is associated with the label? What exactly does delta (eg., .1) correspond to? How come the ribbon.mgz appears 'splotchy' (ie., the space between the white and pial surfaces is not completely filled.) 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
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Sat 3/12/2005 9:43 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol
This is done in the newer versions of recon all. It creates subject/mri/?h.ribbon.mgz using mri_surf2vol. Here's what recon-all does:
set cmd = (mri_surf2vol --mkmask --hemi $hemi) set cmd = ($cmd --fillribbon --template orig$MGZ) set cmd = ($cmd --volregidentity $subjid --outvol $hemi.ribbon.mgz)doug
On Sat, 3 Dec 2005, Fornito, Alexander wrote:
Hi, I'm wandering if its possible to convert a label into a volume so that it fills the space between the white and pial surfaces used in calculating thickness. That is, if the label is drawn on the wm surface, is is possible to determine what points on the pial surface are used to calculate the thickness of that label? I've been playing with the --proj option in mr_label2vol. The --help states that --proj frac "means that start, stop, and delta are relative to the thickness at each vertex." I tried using the start, stop and delta values provided in the example (0, 1 .1), but it doesn't seem to completely fill the area between the two surfaces. I've also tried plugging in other values and can't seem to get it right.Is there soemthing I'm missing? 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 Doug,
I tried lowering delta to really low values, eg., .001, but it doesn't seem change things much. Under ideal circumstances, would I expect the space between the white and pial surfaces to be completely filled?
Also, I noted the -help states that delta is relative to the thickness at each vertex if -frac is used, but am a bit unsure of what this means. Does it mean that, for eg., if the vertex thickness is 3mm, then start = 0, stop = 1, delta = 0.5 will fill the entire 3mm space in increments of 1.5mm? Whereas if -abs is specified, start = 0, stop = 1, delta = 0.5 means that the space between 0 and 1mm from the specified surface will be filled, in increments of 0.5mm? Hope this makes sense and thanks again for your help, 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: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 6/12/2005 6:10 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol
From --help on mri_label2vol:
--proj type start stop delta
Project the label along the surface normal. type can be abs or frac. abs means that the start, stop, and delta are measured in mm. frac means that start, stop, and delta are relative to the thickness at each vertex. The label definition is changed to fill in label points in increments of delta from start to stop. Requires subject and hemi in order to load in a surface and thickness. Uses the white surface. The label MUST have been defined on the surface.
Not sure why it's splotchy. Can you lower the delta?
doug
Fornito, Alexander wrote:
I see. The ribbon actually looks like the result I got when i used mri_label2vol. So would I be correct in saying that a that using the flag -proj frac 0, 1, .1 will extract that protion of ?h.ribbon.mgz that is associated with the label? What exactly does delta (eg., .1) correspond to? How come the ribbon.mgz appears 'splotchy' (ie., the space between the white and pial surfaces is not completely filled.) 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 -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Sat 3/12/2005 9:43 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol This is done in the newer versions of recon all. It creates subject/mri/?h.ribbon.mgz using mri_surf2vol. Here's what recon-all does: set cmd = (mri_surf2vol --mkmask --hemi $hemi) set cmd = ($cmd --fillribbon --template orig$MGZ) set cmd = ($cmd --volregidentity $subjid --outvol $hemi.ribbon.mgz) doug On Sat, 3 Dec 2005, Fornito, Alexander wrote:
Hi, I'm wandering if its possible to convert a label into a volume so that it fills the space between the white and pial surfaces used in calculating thickness. That is, if the label is drawn on the wm surface, is is possible to determine what points on the pial surface are used to calculate the thickness of that label? I've been playing with the --proj option in mr_label2vol. The --help states that --proj frac "means that start, stop, and delta are relative to the thickness at each vertex." I tried using the start, stop and delta values provided in the example (0, 1 .1), but it doesn't seem to completely fill the area between the two surfaces. I've also tried plugging in other values and can't seem to get it right.Is there soemthing I'm missing? 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
Hmmm, when you say it looks "splotch" do you mean that it just looks pixelated? or that there are wholes in it? I would expect that the ribbon would fill in all the space between the two surfaces with some voxels jutting out beyond the surface.
Your interpretation of delta is correct
doug
Fornito, Alexander wrote:
Hi Doug,
I tried lowering delta to really low values, eg., .001, but it doesn't seem change things much. Under ideal circumstances, would I expect the space between the white and pial surfaces to be completely filled?
Also, I noted the -help states that delta is relative to the thickness at each vertex if -frac is used, but am a bit unsure of what this means. Does it mean that, for eg., if the vertex thickness is 3mm, then start = 0, stop = 1, delta = 0.5 will fill the entire 3mm space in increments of 1.5mm? Whereas if -abs is specified, start = 0, stop = 1, delta = 0.5 means that the space between 0 and 1mm from the specified surface will be filled, in increments of 0.5mm? Hope this makes sense and thanks again for your help, 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: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 6/12/2005 6:10 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol
From --help on mri_label2vol:
--proj type start stop delta
Project the label along the surface normal. type can be abs or frac. abs means that the start, stop, and delta are measured in mm. frac means that start, stop, and delta are relative to the thickness at each vertex. The label definition is changed to fill in label points in increments of delta from start to stop. Requires subject and hemi in order to load in a surface and thickness. Uses the white surface. The label MUST have been defined on the surface.
Not sure why it's splotchy. Can you lower the delta?
doug
Fornito, Alexander wrote:
I see. The ribbon actually looks like the result I got when i used mri_label2vol. So would I be correct in saying that a that using the flag -proj frac 0, 1, .1 will extract that protion of ?h.ribbon.mgz that is associated with the label? What exactly does delta (eg., .1) correspond to? How come the ribbon.mgz appears 'splotchy' (ie., the space between the white and pial surfaces is not completely filled.) 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
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Sat 3/12/2005 9:43 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol
This is done in the newer versions of recon all. It creates subject/mri/?h.ribbon.mgz using mri_surf2vol. Here's what recon-all does:
set cmd = (mri_surf2vol --mkmask --hemi $hemi) set cmd = ($cmd --fillribbon --template orig$MGZ) set cmd = ($cmd --volregidentity $subjid --outvol $hemi.ribbon.mgz)doug
On Sat, 3 Dec 2005, Fornito, Alexander wrote:
Hi, I'm wandering if its possible to convert a label into a volume so that it fills the space between the white and pial surfaces used in calculating thickness. That is, if the label is drawn on the wm surface, is is possible to determine what points on the pial surface are used to calculate the thickness of that label? I've been playing with the --proj option in mr_label2vol. The --help states that --proj frac "means that start, stop, and delta are relative to the thickness at each vertex." I tried using the start, stop and delta values provided in the example (0, 1 .1), but it doesn't seem to completely fill the area between the two surfaces. I've also tried plugging in other values and can't seem to get it right.Is there soemthing I'm missing? Thanks, AlexAlex 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
From memory, the space between the two surface seems to have holes in it. UnfortunatelyI'm out of state atm, but aybe I can send you a pick when I get back next week to show you what I mean?
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: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 6/12/2005 9:50 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol
Hmmm, when you say it looks "splotch" do you mean that it just looks pixelated? or that there are wholes in it? I would expect that the ribbon would fill in all the space between the two surfaces with some voxels jutting out beyond the surface.
Your interpretation of delta is correct
doug
Fornito, Alexander wrote:
Hi Doug,
I tried lowering delta to really low values, eg., .001, but it doesn't seem change things much. Under ideal circumstances, would I expect the space between the white and pial surfaces to be completely filled?
Also, I noted the -help states that delta is relative to the thickness at each vertex if -frac is used, but am a bit unsure of what this means. Does it mean that, for eg., if the vertex thickness is 3mm, then start = 0, stop = 1, delta = 0.5 will fill the entire 3mm space in increments of 1.5mm? Whereas if -abs is specified, start = 0, stop = 1, delta = 0.5 means that the space between 0 and 1mm from the specified surface will be filled, in increments of 0.5mm? Hope this makes sense and thanks again for your help, 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: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 6/12/2005 6:10 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol
From --help on mri_label2vol:
--proj type start stop delta
Project the label along the surface normal. type can be abs or frac. abs means that the start, stop, and delta are measured in mm. frac means that start, stop, and delta are relative to the thickness at each vertex. The label definition is changed to fill in label points in increments of delta from start to stop. Requires subject and hemi in order to load in a surface and thickness. Uses the white surface. The label MUST have been defined on the surface.
Not sure why it's splotchy. Can you lower the delta?
doug
Fornito, Alexander wrote:
I see. The ribbon actually looks like the result I got when i used mri_label2vol. So would I be correct in saying that a that using the flag -proj frac 0, 1, .1 will extract that protion of ?h.ribbon.mgz that is associated with the label? What exactly does delta (eg., .1) correspond to? How come the ribbon.mgz appears 'splotchy' (ie., the space between the white and pial surfaces is not completely filled.) 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 -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Sat 3/12/2005 9:43 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol This is done in the newer versions of recon all. It creates subject/mri/?h.ribbon.mgz using mri_surf2vol. Here's what recon-all does: set cmd = (mri_surf2vol --mkmask --hemi $hemi) set cmd = ($cmd --fillribbon --template orig$MGZ) set cmd = ($cmd --volregidentity $subjid --outvol $hemi.ribbon.mgz) doug On Sat, 3 Dec 2005, Fornito, Alexander wrote: Hi, I'm wandering if its possible to convert a label into a volume so that it fills the space between the white and pial surfaces used in calculating thickness. That is, if the label is drawn on the wm surface, is is possible to determine what points on the pial surface are used to calculate the thickness of that label? I've been playing with the --proj option in mr_label2vol. The --help states that --proj frac "means that start, stop, and delta are relative to the thickness at each vertex." I tried using the start, stop and delta values provided in the example (0, 1 .1), but it doesn't seem to completely fill the area between the two surfaces. I've also tried plugging in other values and can't seem to get it right.Is there soemthing I'm missing? 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
freesurfer@nmr.mgh.harvard.edu
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