Hi Venkat,
in 5.0 images are not aligned as longitudinal runs are done in their native (cross sectional spaces). since 5.1 we map everything to the base in the initial conform reslicing step to make visualization and debugging easier. this further decreases variability. Although 5.0 does not align the images it should still work. So maybe you have no problem at all.
If you rerun, make sure you re-run the base and the longitudinal directories from scratch, not on top of the old ones.
About processing stats files, there are several options: 1. grab the measures from the stats files yourself and input them into any statistic package you desire. For this asegstats2table may be helpful (also aparcstats2table). This is recommended as it is most flexible, e.g. you can run linear mixed models, which is better than looking simply at slopes. In your case (only 2 time points) it may not matter much, but linear mixed models can deal with missing data (e.g. if you have subjects with a single time point only). 2. (some quick stuff I implemented for simple analysis, similar to long_mris_slopes) get long_stats_slopes (and all the other files there) from: http://martinos.org/~mreuter/long/ backup yours and replace with these. long_stats_slopes works the same way as long_mris_slopes. You can run the output (e.g. rate/year or percent change) through glm_fit for your group analysis (there is a tutorial about glm_fit).
We are working on making available more powerful statistical tools for longitudinal analyses in the future. Then we will also create a better tutorial for it.
Best, Martin
On Fri, 2012-08-03 at 10:31 -0400, Rajagopalan, Venkateswaran wrote:
Hi Martin,
Thanks for your immediate response.
are you using version 5.1 ? No version 5.0 I am undating it. After the upgarde I will run the program again and see whether the same problem persists.
The most common reason is that skull strip fails in the cross sectional runs. Large chunks of skull can throw off the registration in the base.
I verified my skull strip (I always do) and it is fine in this case. In your case, you have only 2 time points and an error in the registration would immediately result in a messed up norm.mgz image in the base:nonhyper_24_templ/mri/norm.mgz would be very blurry or show two ghost images.
I didn't see base image being messed up in my case though.
Also I am interested in seeing whether is there any reduction in cortical thickness between the two time points. In that case how to do stats. I am unable to find guidelines to do stats after the longitudinal processing (processing steps for longitudinal is very good but unfortunately I am unable to find one for stats part).
Thanks
Venkat
From: Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] Sent: Thu 8/2/2012 3:37 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal cortical thickness analysis
Hi Venkat,
are you using version 5.1 ? In earlier versions, time points were not aligned to the base, so they don't align. Since 5.1 they should perfectly align. If not it can have several reasons. The most common reason is that skull strip fails in the cross sectional runs. Large chunks of skull can throw off the registration in the base.
In your case, you have only 2 time points and an error in the registration would immediately result in a messed up norm.mgz image in the base:
nonhyper_24_templ/mri/norm.mgz would be very blurry or show two ghost images.
So take a look at that and also the skull strip in nonhyper_24_06/mri/brainmask.mgz nonhyper_24_07/mri/brainmask.mgz
and fix them if it they are bad.
Best, Martin
On Thu, 2012-08-02 at 13:48 -0400, Rajagopalan, Venkateswaran wrote:
Dear All,
I ran the following steps in a patient of mine at two time points nonhyper_24_06 and nonhyper_24_07
recon-all -autorecon1 -subjid nonhyper_24_06 recon-all -autorecon1 -subjid nonhyper_24_07 recon-all -autorecon2 -subjid nonhyper_24_06 recon-all -autorecon3 -subjid nonhyper_24_06 recon-all -autorecon2 -subjid nonhyper_24_07 recon-all -autorecon3 -subjid nonhyper_24_07
# template creation
recon-all -base nonhyper_24_templ -tp nonhyper_24_06 -tp nonhyper_24_07 -all
recon-all -long nonhyper_24_06 nonhyper_24_templ -all recon-all -long nonhyper_24_07 nonhyper_24_templ -all
When I tried to inspect my longitudinal result using freeview -v nonhyper_24_06.long.nonhyper_24_templ/mri/norm.mgz \ nonhyper_24_07.long.nonhyper_24_templ/mri/norm.mgz \ -f nonhyper_24_06.long.nonhyper_24_templ/surf/lh.pial:edgecolor=red \
nonhyper_24_06.long.nonhyper_24_templ/surf/lh.white:edgecolor=blue \
nonhyper_24_07.long.nonhyper_24_templ/surf/lh.pial:edgecolor=255,128,128 \
nonhyper_24_07.long.nonhyper_24_templ/surf/lh.white:edgecolor=lightblue
My norm images from two time points doesn't overlap (so does the
pial
and white surfaces from two points they appear on two distinct
places
on the freeview instead of being overlaped as shown in tutorial)
when
I load then it looks like there is some registration problem. I
don't
know where I made a mistake and how to correct for this. Any help will be greatly appreciated.
Thanks Venkat
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010). Visit us online at http://www.clevelandclinic.org for a complete listing of our
services,
staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed
and
may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message
is
not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard
copy.
Thank you.
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.