[Freesurfer] longitudinal analysis: rate of change
Hi, I had a question about the rate of change (thickening in mm/year) for the longitudinal processing. How is this value calculated when there are more than two timepoints per subject? Thank you! -Shannon K. ___ 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.
[Freesurfer] qdec analyses without interaction effect
Hi, I was wondering if there is a way to run statistical tests, such as a 2-way ANCOVA, on QDEC but without the interaction effect. I ran a 2-way ANCOVA for thickness measures for a longitudinal study, and no interaction effect was found. Therefore, I would like to run the same test but without the interaction effect and see if there are other group effects. Please let me know if there is a way to do this in QDEC or any other statistical programs in FreeSurfer. Thank you! -Shannon ___ 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.
[Freesurfer] repeated measures ANOVA with two groups
Hi, Is there a way to set up a repeated measures ANOVA and ANCOVA with two different groups (ex: study group v. controls) and each subject has more than two timepoints? Would it be possible to assign each Input in the fsgd file to two classes (ex: timepoint scan and group) or is there another way to set up the fsgd file and contrast matrices? I've already used qdec in freesurfer 5.1 to calculate rates of change and symmetrized percent changes between the timepoints (using long_mris_slopes) but now would like to perform a repeated measures test. Thank you! -Shannon K. ___ 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.
[Freesurfer] error in long_mris_slopes command
Hi Freesurfers, I've just tried to use the long_mris_slopes command on some longitudinal data. I've created my long.qdec.table.dat file. I've run this command before without any problems but I need to re-run it again. This time when I try to re-run it this error pops up: ERROR 1 : mris_label_calc intersect did not work? Is there any way to fix this? it also tells me the following: cp: target 'path/subjectID/lh.long.cortex.label' is not a directory Please let me know if there is any way to fix this. thank you!! -Shannon K. ___ 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.
Re: [Freesurfer] qdec analyses without interaction effect
Hi Doug, I just wanted to double check on what you mean. I want to run statistical models without the interaction term. When I ran a test using DOSS and co-varying for sex, age, and ICV, I chose two discrete factors (study, sex), 1 covariate (age), and 1 nuisance factor (ICV). The results I got were the same as when I ran this in SAS but with the interaction term included: model &yvar = study Sex study*sex age ICV Is there a way in QDEC to run models without the interaction term (ex: study*sex)? Thanks! -Shannon On Fri, Aug 24, 2012 at 1:05 PM, Douglas N Greve wrote: > Hi Shannon, you can use the DOSS (different offset/same slope) instead > of DODS > doug > > On 08/20/2012 03:47 PM, Shannon Kogachi wrote: > > Hi, > > I was wondering if there is a way to run statistical tests, such as > > a 2-way ANCOVA, on QDEC but without the interaction effect. I ran a > > 2-way ANCOVA for thickness measures for a longitudinal study, and no > > interaction effect was found. Therefore, I would like to run the same > > test but without the interaction effect and see if there are other > > group effects. Please let me know if there is a way to do this in QDEC > > or any other statistical programs in FreeSurfer. Thank you! > > > > > > -Shannon > > > > > > > > ___ > > 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 > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > ___ > 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. > > ___ 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.
[Freesurfer] long_mris_slopes command: temporal average calculation
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 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.
Re: [Freesurfer] long_mris_slopes command: temporal average calculation
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 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 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 ___ 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.
Re: [Freesurfer] long_mris_slopes command: temporal average calculation
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 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 > > 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 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. > > > > > > > > > > > > -- > > > > ___ 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.
Re: [Freesurfer] long_mris_slopes command: temporal average calculation
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 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 > > 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 > > > 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 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! > >
Re: [Freesurfer] long_mris_slopes command: temporal average calculation
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 wrote: > 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 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 < >> mreu...@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 >>> > 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 >>> > > wrote: >>> > > Hi Shannon >>> > > >>> >
