Hi, I am interested in just obtaining the subcortical segmentation labels and not generating surfaces. I would like to do this in as little time as possible and since I am only looking for label volumes (ie. hippocampal volumes) i figured that there must be some steps I can leave out of -autorecon2. Can anyone tell me the flags I should set to get the fastest way to generate these label files? I found: autorecon-all -subcortseg -subjid <subject> on the wiki, but it says this may take 11+ hours to complete so I thought I would just check before I batched things to run. many thanks, mishkin
yes, sorry. The subcortical segmentation is early in the processing stream, and pretty much the slowest step.
Bruce On Fri, 1 Jun 2007, Mishkin Derakhshan wrote:
Hi, I am interested in just obtaining the subcortical segmentation labels and not generating surfaces. I would like to do this in as little time as possible and since I am only looking for label volumes (ie. hippocampal volumes) i figured that there must be some steps I can leave out of -autorecon2. Can anyone tell me the flags I should set to get the fastest way to generate these label files? I found: autorecon-all -subcortseg -subjid <subject> on the wiki, but it says this may take 11+ hours to complete so I thought I would just check before I batched things to run. many thanks, mishkin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On this topic, if I *don't* want subcortical segmentation, but rather only surface generation and thickness maps, what's the best option to use for that? It seems like it might be -noaseg, but I couldn't find any references to this flag being used with human data, only with non- human primates, so I thought I'd ask before I assumed I'd figured it out.
On Jun 1, 2007, at 1:49 PM, Bruce Fischl wrote:
yes, sorry. The subcortical segmentation is early in the processing stream, and pretty much the slowest step.
-- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe
unfortunately, you have to go thru the segmentation as that is part of the surface-based stream.
doug
David Perlman wrote:
On this topic, if I *don't* want subcortical segmentation, but rather only surface generation and thickness maps, what's the best option to use for that? It seems like it might be -noaseg, but I couldn't find any references to this flag being used with human data, only with non- human primates, so I thought I'd ask before I assumed I'd figured it out.
On Jun 1, 2007, at 1:49 PM, Bruce Fischl wrote:
yes, sorry. The subcortical segmentation is early in the processing stream, and pretty much the slowest step.
-- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, After running the -subcortseg option, i see the output volumes of certain structures on the screen. Are they stored anywhere in a text file? I checked stats/aseg.stats, and while the column headers indicate that there should be values for NVoxels and Volume_mm3, in the table those two fields are blank for all labels. Is this a bug, or is there another option I need to set to get those fields filled in? thanks, mishkin
On 6/1/07, Doug Greve greve@nmr.mgh.harvard.edu wrote:
unfortunately, you have to go thru the segmentation as that is part of the surface-based stream.
doug
David Perlman wrote:
On this topic, if I *don't* want subcortical segmentation, but rather only surface generation and thickness maps, what's the best option to use for that? It seems like it might be -noaseg, but I couldn't find any references to this flag being used with human data, only with non- human primates, so I thought I'd ask before I assumed I'd figured it out.
On Jun 1, 2007, at 1:49 PM, Bruce Fischl wrote:
yes, sorry. The subcortical segmentation is early in the processing stream, and pretty much the slowest step.
-- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Mishkin,
Are all the fields blank in the aseg.stats table, or just for some things? It shouldn't be like this. It may be that there are some structures listed in that file that are not labeled in the aseg and then reported as a zero, but it shouldn't be all of them. Were there any error messages at the end of this particular subject's scripts/recon-all.log?
Jenni
On Tue, 5 Jun 2007, Mishkin Derakhshan wrote:
Hi, After running the -subcortseg option, i see the output volumes of certain structures on the screen. Are they stored anywhere in a text file? I checked stats/aseg.stats, and while the column headers indicate that there should be values for NVoxels and Volume_mm3, in the table those two fields are blank for all labels. Is this a bug, or is there another option I need to set to get those fields filled in? thanks, mishkin
On 6/1/07, Doug Greve greve@nmr.mgh.harvard.edu wrote:
unfortunately, you have to go thru the segmentation as that is part of the surface-based stream.
doug
David Perlman wrote:
On this topic, if I *don't* want subcortical segmentation, but rather only surface generation and thickness maps, what's the best option to use for that? It seems like it might be -noaseg, but I couldn't find any references to this flag being used with human data, only with non- human primates, so I thought I'd ask before I assumed I'd figured it out.
On Jun 1, 2007, at 1:49 PM, Bruce Fischl wrote:
yes, sorry. The subcortical segmentation is early in the processing stream, and pretty much the slowest step.
-- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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
Hi Jenni, thanks for the reply. The log file says it finished without any eroors. In the aseg.stats file, none of the structures have the NVoxels of Volume_mm3 reported. I attached the file so you can see what I mean. I am using freesurfer-Linux-rh9-stable-pub-v3.0.5 on debian sarge. I ran another subject as well and my aseg.stats file appears to be the same.
The command lines I ran were: recon-all -i hippo_test_subject1_t1g_nu.mnc -autorecon1 -subjid subject1 recon-all -subcortseg -subjid subject1
did I miss anything? thanks, mishkin
On 6/5/07, Jenni Pacheco jpacheco@nmr.mgh.harvard.edu wrote:
Hi Mishkin,
Are all the fields blank in the aseg.stats table, or just for some things? It shouldn't be like this. It may be that there are some structures listed in that file that are not labeled in the aseg and then reported as a zero, but it shouldn't be all of them. Were there any error messages at the end of this particular subject's scripts/recon-all.log?
Jenni
On Tue, 5 Jun 2007, Mishkin Derakhshan wrote:
Hi, After running the -subcortseg option, i see the output volumes of certain structures on the screen. Are they stored anywhere in a text file? I checked stats/aseg.stats, and while the column headers indicate that there should be values for NVoxels and Volume_mm3, in the table those two fields are blank for all labels. Is this a bug, or is there another option I need to set to get those fields filled in? thanks, mishkin
On 6/1/07, Doug Greve greve@nmr.mgh.harvard.edu wrote:
unfortunately, you have to go thru the segmentation as that is part of the surface-based stream.
doug
David Perlman wrote:
On this topic, if I *don't* want subcortical segmentation, but rather only surface generation and thickness maps, what's the best option to use for that? It seems like it might be -noaseg, but I couldn't find any references to this flag being used with human data, only with non- human primates, so I thought I'd ask before I assumed I'd figured it out.
On Jun 1, 2007, at 1:49 PM, Bruce Fischl wrote:
yes, sorry. The subcortical segmentation is early in the processing stream, and pretty much the slowest step.
-- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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
what do you mean? The 3rd and 4th columns have that info:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 2 2 263489 263489.0 Left-Cerebral-White-Matter 107.2167 8.7619 52.0000 140.0000 88.0000 3 3 245645 245645.0 Left-Cerebral-Cortex 86.6194 10.8034 13.0000 132.0000 119.0000 4 4 5227 5227.0 Left-Lateral-Ventricle 46.7893 13.3922 18.0000 92.0000 74.0000
Mishkin Derakhshan wrote:
Hi Jenni, thanks for the reply. The log file says it finished without any eroors. In the aseg.stats file, none of the structures have the NVoxels of Volume_mm3 reported. I attached the file so you can see what I mean. I am using freesurfer-Linux-rh9-stable-pub-v3.0.5 on debian sarge. I ran another subject as well and my aseg.stats file appears to be the same.
The command lines I ran were: recon-all -i hippo_test_subject1_t1g_nu.mnc -autorecon1 -subjid subject1 recon-all -subcortseg -subjid subject1
did I miss anything? thanks, mishkin
On 6/5/07, Jenni Pacheco jpacheco@nmr.mgh.harvard.edu wrote:
Hi Mishkin,
Are all the fields blank in the aseg.stats table, or just for some things? It shouldn't be like this. It may be that there are some structures listed in that file that are not labeled in the aseg and then reported as a zero, but it shouldn't be all of them. Were there any error messages at the end of this particular subject's scripts/recon-all.log?
Jenni
On Tue, 5 Jun 2007, Mishkin Derakhshan wrote:
Hi, After running the -subcortseg option, i see the output volumes of certain structures on the screen. Are they stored anywhere in a text file? I checked stats/aseg.stats, and while the column headers indicate that there should be values for NVoxels and Volume_mm3, in the table those two fields are blank for all labels. Is this a bug, or is there another option I need to set to get those fields filled in? thanks, mishkin
On 6/1/07, Doug Greve greve@nmr.mgh.harvard.edu wrote:
unfortunately, you have to go thru the segmentation as that is
part of
the surface-based stream.
doug
David Perlman wrote:
On this topic, if I *don't* want subcortical segmentation, but
rather
only surface generation and thickness maps, what's the best
option to
use for that? It seems like it might be -noaseg, but I couldn't
find
any references to this flag being used with human data, only
with non-
human primates, so I thought I'd ask before I assumed I'd
figured it
out.
On Jun 1, 2007, at 1:49 PM, Bruce Fischl wrote:
yes, sorry. The subcortical segmentation is early in the
processing
stream, and pretty much the slowest step.
--
-dave----------------------------------------------------------------
Science arose from poetry... when times change the two can meet
again
on a higher level as friends. -Göthe
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Very embarrassing. I thought the column headings were 1. Col 2.Headers 3.Index 4.SegId as that is how they lined up in my text editor. Now I realize that the fourth column is indeed my volume. sorry for all the confusion. mishkin
On 6/5/07, Doug Greve greve@nmr.mgh.harvard.edu wrote:
what do you mean? The 3rd and 4th columns have that info:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 2 2 263489 263489.0 Left-Cerebral-White-Matter 107.2167 8.7619 52.0000 140.0000 88.0000 3 3 245645 245645.0 Left-Cerebral-Cortex 86.6194 10.8034 13.0000 132.0000 119.0000 4 4 5227 5227.0 Left-Lateral-Ventricle 46.7893 13.3922 18.0000 92.0000 74.0000
Mishkin Derakhshan wrote: Hi Jenni, thanks for the reply. The log file says it finished without any eroors. In the aseg.stats file, none of the structures have the NVoxels of Volume_mm3 reported. I attached the file so you can see what I mean. I am using freesurfer-Linux-rh9-stable-pub-v3.0.5 on debian sarge. I ran another subject as well and my aseg.stats file appears to be the same.
The command lines I ran were: recon-all -i hippo_test_subject1_t1g_nu.mnc -autorecon1 -subjid subject1 recon-all -subcortseg -subjid subject1
did I miss anything? thanks, mishkin
On 6/5/07, Jenni Pacheco jpacheco@nmr.mgh.harvard.edu wrote:
Hi Mishkin,
Are all the fields blank in the aseg.stats table, or just for some things? It shouldn't be like this. It may be that there are some structures listed in that file that are not labeled in the aseg and then reported as a zero, but it shouldn't be all of them. Were there any error messages at the end of this particular subject's scripts/recon-all.log?
Jenni
On Tue, 5 Jun 2007, Mishkin Derakhshan wrote:
Hi, After running the -subcortseg option, i see the output volumes of certain structures on the screen. Are they stored anywhere in a text file? I checked stats/aseg.stats, and while the column headers indicate that there should be values for NVoxels and Volume_mm3, in the table those two fields are blank for all labels. Is this a bug, or is there another option I need to set to get those fields filled in? thanks, mishkin
On 6/1/07, Doug Greve greve@nmr.mgh.harvard.edu wrote:
unfortunately, you have to go thru the segmentation as that is part of the surface-based stream.
doug
David Perlman wrote:
On this topic, if I *don't* want subcortical segmentation, but rather only surface generation and thickness maps, what's the best option to use for that? It seems like it might be -noaseg, but I couldn't find any references to this flag being used with human data, only with non- human primates, so I thought I'd ask before I assumed I'd figured it out.
On Jun 1, 2007, at 1:49 PM, Bruce Fischl wrote:
yes, sorry. The subcortical segmentation is early in the processing stream, and pretty much the slowest step.
--
-dave----------------------------------------------------------------
Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
you can do that, but the aseg is used to automate generation of surfaces (e.g. ventricle filling), so you would be trading computer time for human time.
Bruce On Fri, 1 Jun 2007, David Perlman wrote:
On this topic, if I *don't* want subcortical segmentation, but rather only surface generation and thickness maps, what's the best option to use for that? It seems like it might be -noaseg, but I couldn't find any references to this flag being used with human data, only with non-human primates, so I thought I'd ask before I assumed I'd figured it out.
On Jun 1, 2007, at 1:49 PM, Bruce Fischl wrote:
yes, sorry. The subcortical segmentation is early in the processing stream, and pretty much the slowest step.
-- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
David Perlman -
Doug Greve -
Jenni Pacheco -
Mishkin Derakhshan