Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you!
-Shannon K.
Hi Shannon
You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin
Shannon Kogachi skogachi@gmail.com wrote:
Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you!
-Shannon K.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Martin, When I used the long_mris_slopes command for the thickness, the average thickness calculated in FreeSurfer was pretty similar to averaging the values in FreeSurfer. Does this command only work thickness measures and not for volume or area? Thanks!
-Shannon
On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:
Hi Shannon
You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin
Shannon Kogachi skogachi@gmail.com wrote:
Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you!
-Shannon K.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Sent from my phone, please excuse brevity.
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.
Hi Shannon,
long_mris_slopes works for surface maps (both thickness and volume should work). In both cases it should compute the temporal average.
I have another scripts that works for stats files (long_stats_slopes) in the same way.
How many time points do you have, how far apart (equally spaced?).
Best, Martin
On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote:
Hi Martin, When I used the long_mris_slopes command for the thickness, the average thickness calculated in FreeSurfer was pretty similar to averaging the values in FreeSurfer. Does this command only work thickness measures and not for volume or area? Thanks!
-Shannon
On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Shannon
You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin Shannon Kogachi <skogachi@gmail.com> wrote: Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K. ______________________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity. 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.-- Shannon Kogachi Clinical Research Coordinator
Neuroscience and MRI Research Program Department of Medicine JABSOM, University of Hawaii 1356 Lusitana Street, 7th Floor Honolulu, HI 96813 (808) 691 - 8763
Hi Martin, Each subject has 3-6 timepoints. They are all about one year apart. Here's an example of the discrepancy: one subject with 5 timepoints had volumes that ranged from 2.2-2.4. However, from the long_mris_slopes command, the temporal average volume was calculated to be 1.67. Thanks for your help!
-Shannon K.
On Thu, Sep 27, 2012 at 6:21 AM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:
Hi Shannon,
long_mris_slopes works for surface maps (both thickness and volume should work). In both cases it should compute the temporal average.
I have another scripts that works for stats files (long_stats_slopes) in the same way.
How many time points do you have, how far apart (equally spaced?).
Best, Martin
On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote:
Hi Martin, When I used the long_mris_slopes command for the thickness, the average thickness calculated in FreeSurfer was pretty similar to averaging the values in FreeSurfer. Does this command only work thickness measures and not for volume or area? Thanks!
-Shannon
On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Shannon
You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin Shannon Kogachi <skogachi@gmail.com> wrote: Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K. ______________________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Sent from my phone, please excuse brevity. 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.--
Hi Shannon,
that cannot be. It either indicates a serious bug (which we have not yet encountered in our data) or a problem with your processing.
Can you send me: - the version you use - the command line you run - the output you get
Also long_mris_slopes is designed for analyzing surface maps (analysis on a vertex by vertex basis). This is usually thickness. So I don't understand what 'volumes' you mean? For an ROI analysis based on stats files you need to use long_stats_slopes.
Best, Martin
On Thu, 2012-09-27 at 11:37 -1000, Shannon Kogachi wrote:
Hi Martin, Each subject has 3-6 timepoints. They are all about one year apart. Here's an example of the discrepancy: one subject with 5 timepoints had volumes that ranged from 2.2-2.4. However, from the long_mris_slopes command, the temporal average volume was calculated to be 1.67. Thanks for your help!
-Shannon K.
On Thu, Sep 27, 2012 at 6:21 AM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Shannon,
long_mris_slopes works for surface maps (both thickness and volume should work). In both cases it should compute the temporal average. I have another scripts that works for stats files (long_stats_slopes) in the same way. How many time points do you have, how far apart (equally spaced?). Best, Martin On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote: > Hi Martin, > When I used the long_mris_slopes command for the thickness, the > average thickness calculated in FreeSurfer was pretty similar to > averaging the values in FreeSurfer. Does this command only work > thickness measures and not for volume or area? Thanks! > > -Shannon > > On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter > <mreuter@nmr.mgh.harvard.edu> wrote: > Hi Shannon > > You probably mean average thickness. > My scripts compute the temporal average from the linear fit > (at mid time), which can be differed from simply averaging > values. > Best Martin > > Shannon Kogachi <skogachi@gmail.com> wrote: > Hi, > I had a question about how the temporal average is > calculated for subjects with multiple timepoints. I > used the long_mris_slopes command on a longitudinal > set of data. However, when I compared the average > volumes calculated through this command to the average > volumes calculated in excel after extracting the same > vertices at the individual timepoints, these values > did not match up. The average volumes calculated > through long_mris_slopes were smaller. Please let me > know if there is a way to explain this discrepancy. > Thank you! > > -Shannon K. > > > > ______________________________________________________ > > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Sent from my phone, please excuse brevity. > 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. > > > > > > --
Hi Martin, I am running FS version 5.1. This is the command line I ran:
long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas volume --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage
These are the outputs I get, which are located in the subjects' base template surf folders:
lh.long.volume-rate.fwhm10.mgh lh.long.volume-pc1.fwhm10.mgh lh.long.volume-avg.fwhm10.mgh lh.long.volume-spc.fwhm10.mgh I also get the files that end in fsaverage.mgh.
I'm a little confused about this volume issue. In a previous post you said that "long_mris_slopes works for surface maps (both thickness and volume should work)." Therefore I used the long_mris_slopes for the volumes for a VBM analysis. Please let me know if this would not work. Thank you!
-Shannon
On Fri, Sep 28, 2012 at 4:02 AM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:
Hi Shannon,
that cannot be. It either indicates a serious bug (which we have not yet encountered in our data) or a problem with your processing.
Can you send me:
- the version you use
- the command line you run
- the output you get
Also long_mris_slopes is designed for analyzing surface maps (analysis on a vertex by vertex basis). This is usually thickness. So I don't understand what 'volumes' you mean? For an ROI analysis based on stats files you need to use long_stats_slopes.
Best, Martin
On Thu, 2012-09-27 at 11:37 -1000, Shannon Kogachi wrote:
Hi Martin, Each subject has 3-6 timepoints. They are all about one year apart. Here's an example of the discrepancy: one subject with 5 timepoints had volumes that ranged from 2.2-2.4. However, from the long_mris_slopes command, the temporal average volume was calculated to be 1.67. Thanks for your help!
-Shannon K.
On Thu, Sep 27, 2012 at 6:21 AM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Shannon,
long_mris_slopes works for surface maps (both thickness and volume should work). In both cases it should compute the temporal average. I have another scripts that works for stats files (long_stats_slopes) in the same way. How many time points do you have, how far apart (equally spaced?). Best, Martin On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote: > Hi Martin, > When I used the long_mris_slopes command for the thickness, the > average thickness calculated in FreeSurfer was pretty similar to > averaging the values in FreeSurfer. Does this command only work > thickness measures and not for volume or area? Thanks! > > -Shannon > > On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter > <mreuter@nmr.mgh.harvard.edu> wrote: > Hi Shannon > > You probably mean average thickness. > My scripts compute the temporal average from the linear fit > (at mid time), which can be differed from simply averaging > values. > Best Martin > > Shannon Kogachi <skogachi@gmail.com> wrote: > Hi, > I had a question about how the temporal average is > calculated for subjects with multiple timepoints. I > used the long_mris_slopes command on a longitudinal > set of data. However, when I compared the average > volumes calculated through this command to the average > volumes calculated in excel after extracting the same > vertices at the individual timepoints, these values > did not match up. The average volumes calculated > through long_mris_slopes were smaller. Please let me > know if there is a way to explain this discrepancy. > Thank you! > > -Shannon K. > > > > ______________________________________________________ > > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Sent from my phone, please excuse brevity. > 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. > > > > > > --
I see, Usually people look at thickness maps and volume on an ROI basis. Volume on the surface I think is simply area times thickness. Not sure how meaningful that is as area of a vertex depends on the triangle mesh.
Anyway, you look at smoothed maps on fsaverage. The average volume for each vertex should be somewhere in the middle of the individual values across time after they have been resampled to fsaverage. You can find the mapped files in the base directories. Can you double check that the average is in the middle of the time points? Best Martin
Shannon Kogachi skogachi@gmail.com wrote:
Hi Martin, I am running FS version 5.1. This is the command line I ran:
long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas volume --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage
These are the outputs I get, which are located in the subjects' base template surf folders:
lh.long.volume-rate.fwhm10.mgh lh.long.volume-pc1.fwhm10.mgh lh.long.volume-avg.fwhm10.mgh lh.long.volume-spc.fwhm10.mgh I also get the files that end in fsaverage.mgh.
I'm a little confused about this volume issue. In a previous post you said that "long_mris_slopes works for surface maps (both thickness and volume should work)." Therefore I used the long_mris_slopes for the volumes for a VBM analysis. Please let me know if this would not work. Thank you!
-Shannon
On Fri, Sep 28, 2012 at 4:02 AM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:
Hi Shannon,
that cannot be. It either indicates a serious bug (which we have not
yet
encountered in our data) or a problem with your processing.
Can you send me:
- the version you use
- the command line you run
- the output you get
Also long_mris_slopes is designed for analyzing surface maps
(analysis
on a vertex by vertex basis). This is usually thickness. So I don't understand what 'volumes' you mean? For an ROI analysis based on
stats
files you need to use long_stats_slopes.
Best, Martin
On Thu, 2012-09-27 at 11:37 -1000, Shannon Kogachi wrote:
Hi Martin, Each subject has 3-6 timepoints. They are all about one year
apart.
Here's an example of the discrepancy: one subject with 5
timepoints
had volumes that ranged from 2.2-2.4. However, from the long_mris_slopes command, the temporal average volume was
calculated
to be 1.67. Thanks for your help!
-Shannon K.
On Thu, Sep 27, 2012 at 6:21 AM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Shannon,
long_mris_slopes works for surface maps (both thickness and volume should work). In both cases it should compute the temporal average. I have another scripts that works for stats files (long_stats_slopes) in the same way. How many time points do you have, how far apart (equally spaced?). Best, Martin On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote: > Hi Martin, > When I used the long_mris_slopes command for the thickness, the > average thickness calculated in FreeSurfer was pretty similar to > averaging the values in FreeSurfer. Does this commandonly
work > thickness measures and not for volume or area? Thanks! > > -Shannon > > On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter > <mreuter@nmr.mgh.harvard.edu> wrote: > Hi Shannon > > You probably mean average thickness. > My scripts compute the temporal average from the linear fit > (at mid time), which can be differed from simply averaging > values. > Best Martin > > Shannon Kogachi <skogachi@gmail.com> wrote: > Hi, > I had a question about how the temporal average is > calculated for subjects with multiple timepoints. I > used the long_mris_slopes command on a longitudinal > set of data. However, when I compared the average > volumes calculated through this commandto
the average > volumes calculated in excel afterextracting
the same > vertices at the individual timepoints,these
values > did not match up. The average volumes calculated > through long_mris_slopes were smaller. Please let me > know if there is a way to explain this discrepancy. > Thank you! > > -Shannon K. > > > > ______________________________________________________ > > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > -- > Sent from my phone, please excuse brevity. > The information in this e-mail is intended onlyfor
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. > > > > > > ---- Shannon Kogachi Clinical Research Coordinator
Neuroscience and MRI Research Program Department of Medicine JABSOM, University of Hawaii 1356 Lusitana Street, 7th Floor Honolulu, HI 96813 (808) 691 - 8763
Hi Martin, I am a little confused about these mapped files in the base directories you are referring to. How would I check them?
-Shannon K.
On Fri, Sep 28, 2012 at 4:08 PM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:
I see, Usually people look at thickness maps and volume on an ROI basis. Volume on the surface I think is simply area times thickness. Not sure how meaningful that is as area of a vertex depends on the triangle mesh.
Anyway, you look at smoothed maps on fsaverage. The average volume for each vertex should be somewhere in the middle of the individual values across time after they have been resampled to fsaverage. You can find the mapped files in the base directories. Can you double check that the average is in the middle of the time points?
Best Martin
Shannon Kogachi skogachi@gmail.com wrote:
Hi Martin, I am running FS version 5.1. This is the command line I ran:
long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas volume --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage
These are the outputs I get, which are located in the subjects' base template surf folders:
lh.long.volume-rate.fwhm10.mgh lh.long.volume-pc1.fwhm10.mgh lh.long.volume-avg.fwhm10.mgh lh.long.volume-spc.fwhm10.mgh I also get the files that end in fsaverage.mgh.
I'm a little confused about this volume issue. In a previous post you said that "long_mris_slopes works for surface maps (both thickness and volume should work)." Therefore I used the long_mris_slopes for the volumes for a VBM analysis. Please let me know if this would not work. Thank you!
-Shannon
On Fri, Sep 28, 2012 at 4:02 AM, Martin Reuter < mreuter@nmr.mgh.harvard.edu> wrote:
Hi Shannon,
that cannot be. It either indicates a serious bug (which we have not yet encountered in our data) or a problem with your processing.
Can you send me:
- the version you use
- the command line you run
- the output you get
Also long_mris_slopes is designed for analyzing surface maps (analysis on a vertex by vertex basis). This is usually thickness. So I don't understand what 'volumes' you mean? For an ROI analysis based on stats files you need to use long_stats_slopes.
Best, Martin
On Thu, 2012-09-27 at 11:37 -1000, Shannon Kogachi wrote:
Hi Martin, Each subject has 3-6 timepoints. They are all about one year apart. Here's an example of the discrepancy: one subject with 5 timepoints had volumes that ranged from 2.2-2.4. However, from the long_mris_slopes command, the temporal average volume was calculated to be 1.67. Thanks for your help!
-Shannon K.
On Thu, Sep 27, 2012 at 6:21 AM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Shannon,
long_mris_slopes works for surface maps (both thickness and volume should work). In both cases it should compute the temporal average. I have another scripts that works for stats files (long_stats_slopes) in the same way. How many time points do you have, how far apart (equally spaced?). Best, Martin On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote: > Hi Martin, > When I used the long_mris_slopes command for the thickness, the > average thickness calculated in FreeSurfer was pretty similar to > averaging the values in FreeSurfer. Does this command only work > thickness measures and not for volume or area? Thanks! > > -Shannon > > On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter > <mreuter@nmr.mgh.harvard.edu> wrote: > Hi Shannon > > You probably mean average thickness. > My scripts compute the temporal average from the linear fit > (at mid time), which can be differed from simply averaging > values. > Best Martin > > Shannon Kogachi <skogachi@gmail.com> wrote: > Hi, > I had a question about how the temporal average is > calculated for subjects with multiple timepoints. I > used the long_mris_slopes command on a longitudinal > set of data. However, when I compared the average > volumes calculated through this command to the average > volumes calculated in excel after extracting the same > vertices at the individual timepoints, these values > did not match up. The average volumes calculated > through long_mris_slopes were smaller. Please let me > know if there is a way to explain this discrepancy. > Thank you! > > -Shannon K. > > > > ______________________________________________________ > > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Sent from my phone, please excuse brevity. > 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. > > > > > > ---- Sent from my phone, please excuse brevity.
freesurfer@nmr.mgh.harvard.edu
-
Martin Reuter -
Shannon Kogachi