[Freesurfer] 1 Group (2 Levels) 2 Covariates
Hello, I want to do an analysis with 1 Group (Control and HIV) with two covariates (Age and ICV). Qdec only lets me choose one covariate. So instead I choose two nuisance variables. No matter how many different permutations I run on this, I can not get it to duplicate my SAS results, and the Qdec results look suspiciously wrong. Also, when I do it manually with the mri_glmfit command, I still can not duplicate the SAS results. I have tried both demeaning and not demeaning. This should be pretty straight forward? Am I missing something obvious? How would one do a 1 Group (2 levels) 2 Covariate analysis in QDEC? Thank you, Jeff ___ 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] In Qdec, what does the 'area' mean within 'Measure' menu in 'Design' tab
Hello FreeSurfers, I am following up on a previous question by another poster: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21700.html In here, Doug says that the mris_preproc script was patched to help with mapping the surface area to a common space, but Doug also hints that it might also help with the volume. I am using FreeSurfer 5.0.0, mris_preproc release date 10-13-09, Revision 1.53. If I want to do a qdec analysis in fsaverage space on just the thickness and volume, can I go ahead with files previously created using my current mris_preproc, or do I need to download the updated one at ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc? We also have some people using FreeSurfer 5.1.0, mris_preproc release date 5-17-11, Revision 1.59.2.1. Do they need to update their mris_preproc script? Thank you very much, Jeff Sadino ___ 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] Covary for categorical variable in QDEC
Hello, Is it possible to covary for a categorical variable in QDEC? I see other posters have said it is not possible, but I did not see any official documentation or response regarding the issue. Thank You, Jeff Sadino ___ 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] Covary for a categorical variable in mri_glmfit
Hello, I am trying to covary for Gender in mri_glmfit, but I am having errors pop up. I tried to follow Doug's suggesting in this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html but after modifying my Xg.dat file and rerunning mri_glmfit, it says: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07 I can run it using the --illcond flag, but then I get a bunch of: *** CEPHES ERROR: fdtrc domain error *** Can anyone please give advice on how to covary for Gender in mri_glmfit (or qdec)? As always, thank you for all of your great help!! Jeff Sadino ___ 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] Covary for a categorical variable in mri_glmfit
Hello, I think our emails were getting crossed in cyberspace. I have a group that has a disproportionate number of females, and so there is a significant difference in the number of females as compared to males (chi-square p=.01). This must be accounted for. If I find that one group has a smaller brain volume, etc., then it could be attributed to one group having fewer females than the others. My ultimate goal is to run an analysis on the thickness, taking into account these sex differences (and ICV and age). My plan was to covary for sex, icv, and age. I have covaried for icv and age lots of times, but I am having trouble covarying (if that is the right word) for this categorical sex variable. Any help would be greatly appreciated! Jeff On Wed, Sep 5, 2012 at 10:44 AM, Jeff Sadino wrote: > Hello, > > I am trying to covary for Gender in mri_glmfit, but I am having errors pop > up. I tried to follow Doug's suggesting in this post: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html > but after modifying my Xg.dat file and rerunning mri_glmfit, it says: > ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07 > > I can run it using the --illcond flag, but then I get a bunch of: > *** > CEPHES ERROR: fdtrc domain error > *** > > Can anyone please give advice on how to covary for Gender in mri_glmfit > (or qdec)? > > As always, thank you for all of your great help!! > Jeff Sadino > ___ 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] Longitudinal Subject/Base name errors
Hello Experts,
I am using fs 5.0.0. My naming convention is similar to 11_S01 and
11_S02 for subject, and then 11 for the base. Now when I process
the runs longitudinally, I get: ERROR: longitudinal base ID cannot be the
same as a timepoint. I believe this is because of line 4845 in recon-all:
grep $longbaseid ${longbasedir}/${BaseSubjsListFname} >& /dev/null. I can
just as easily cut out this part of the code, or I could manipulate the
base-tps file, or rename the base folder. But I do not know if there are
other spots in the code that rely on the original naming conventions. Can
anyone recommend one approach over the other?
Thank you very much,
Jeff Sadino
___
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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
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Re: [Freesurfer] Longitudinal Subject/Base name errors
Thank you all for your help. Nick, I installed fs 5.1.0, and it is running
correctly now. This brings up another question though. We have about 200
subjects (600 scans) we are doing reconstruction on. We are done with the
cross-sectional, and have completed 20 of the base templates, all in fs
5.0.0. My fs 5.0 installation is running mri_robust_register 1.31.2.1 and
mri_robust_template 1.18.2.3, both dated 7/22/10. Should I update those
binaries with the ones from fs 5.1.0, or would it be better to just do the
rest of the processing (180 templates and 600 long runs) in fs 5.1.0?
Thank You!
Jeff Sadino
On Wed, Aug 10, 2011 at 10:27 AM, Nick Schmansky
wrote:
> stable 5.1 contains the fix, which is the addition of -w to the grep on
> line 5428. that particular fix works for the example names given
> (11 as the basename, 11_S0 and 11_S1 in the base-tps file).
>
> can someone give me the basename and base-tps contents so that i can
> replicate the problem?
>
> n.
>
> On Wed, 2011-08-10 at 14:45 -0400, Martin Reuter wrote:
> > Hi Nick,
> > can you look into this? I think we fixed this bug in 5.0 or is it
> > something different? Is it still not fixed in 5.1?
> >
> > Thanks, Martin
> >
> > On Wed, 2011-08-10 at 11:19 -0700, Irwin, William wrote:
> > > Hi-
> > >
> > > Note, this bug still exists in 5.1. Below is my exchange with Martin
> and Nick a several months ago.
> > >
> > > -Wil
> > >
> > > ---
> > > |-Original Message-
> > > |From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
> > > |Sent: Wednesday, May 25, 2011 3:52 PM
> > > |To: Irwin, William; Martin Reuter
> > > |Subject: RE: 5.1.0 Longitudial syntax question
> > > |
> > > |Martin,
> > > |
> > > |attached is his log. it seems like it will fail if the basename
> > > |partially matches a timepoint name.
> > > |
> > > |
> > > |
> > > |Wil, there are two possible workarounds:
> > > |
> > > |1) edit line 5421 of recon-all to change:
> > > |if ( ! $status) then
> > > |
> > > |to
> > > |
> > > |if ( 0 ) then
> > > |
> > > |
> > > |so that this block is never run
> > > |
> > > |or
> > > |
> > > |2) change the name of the basename so that its not a sub-match, for
> > > |instance change to xxx_base
> > > |
> > > |
> > > |we'll have to figure out how this happened.
> > > |
> > > |n.
> > > ---
> > > |-Original Message-
> > > |From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu]
> > > |Sent: Wednesday, August 10, 2011 10:10 AM
> > > |To: Jeff Sadino
> > > |Cc: freesurfer@nmr.mgh.harvard.edu
> > > |Subject: Re: [Freesurfer] Longitudinal Subject/Base name errors
> > > |
> > > |Hi Jeff,
> > > |
> > > |this was a known bug in 5.0 and there are fixes on the web (release
> notes),
> > > |just download the recon all from there (and did you grab the robust
> template
> > > |binary)?.
> > > |
> > > |http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
> > > |
> > > |Best, Martin
> > > |
> > > |On Mon, 2011-08-08 at 17:43 -1000, Jeff Sadino wrote:
> > > |> Hello Experts,
> > > |>
> > > |>
> > > |> I am using fs 5.0.0. My naming convention is similar to 11_S01
> > > |> and 11_S02 for subject, and then 11 for the base. Now when
> I
> > > |> process the runs longitudinally, I get: ERROR: longitudinal base ID
> > > |> cannot be the same as a timepoint. I believe this is because of
> line
> > > |> 4845 in recon-all: grep $longbaseid
> > > |> ${longbasedir}/${BaseSubjsListFname} >& /dev/null. I can just as
> > > |> easily cut out this part of the code, or I could manipulate the
> > > |> base-tps file, or rename the base folder. But I do not know if
> there
> > > |> are other spots in the code that rely on the original naming
> > > |> conventions. Can anyone recommend one approach over the other?
> > > |>
> > > |>
> > > |> Thank you very much,
> > > |> Jeff Sadino
> > > |> ___
> > > |> Freesurfer mailing list
> > > |> Freesurfer@nmr.mgh.harvard.edu
> > > |> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > |
> > >
> > >
> > >
> >
>
Re: [Freesurfer] Memory allocation problem with mri_robust_template
Hello,
I am having a problem with mri_robust_template using too much RAM and
causing my computers to freeze. I am using fs510. I think I would like to
try to convert the inputs to uchar as Martin suggested, but I am not sure
exactly where to do this. Would I issue this command:
For each timepoint:
mv tp1/mri/norm.mgz tp1/mri/norm.orig.mgz
mri_convert -i tp1/mri/norm.orig.mgz -o tp1/mri/norm/mgz -odt uchar
recon-all -base -tp 1 -tp 2 -all
Also, my computers have two AMD processors and 4GB of DDR RAM running at
333MHZ. I dropped them down so they each only do one job, but they are
still freezing. Besides upgrading the entire cluster to something more
current, would doubling the RAM to 8GB be worthwhile?
As always, thank you so very much!
Jeff Sadino
Mahen
Fri, 11 Feb 2011 09:16:27 -0800
To Martin,
Thanks a bunch. I haven't tested out all the recommendations, but at least I
know what's going on. If I did want to convert to uchar, how would I go
about this? Is there a function included in the Freesurfer package, or would
I have to write my own function to do so? It's not a concern, as I'm
probably not going to explore this avenue, but if I get time, I might enjoy
trying to write such a function...
Regards,
Mahen
On Wed, Feb 9, 2011 at 7:07 AM, Martin Reuter
wrote:
> Hi Mahen,
>
> 4.5 is based on flirt registration which does a pairwise registration to
> the first image. Since 5.0 we use the mri_robust_template tool (as it
> can ignore outlier regions and produces more accurate registrations, see
> Reuter et al Neuroimage 2010 "..robust registration"), but it is more
> memory hungry and time consuming.
>
> If your input images are large, it can happen that mri_robust_template
> uses a lot of memory. I tested that tool in the longitudinal stream
> where I successfully ran it on > 10 images on a 4 gig machine (those
> images are probably smaller than yours).
>
> So you have the following options:
>
> 1. use only the best 2 input images. This has been recommended in the
> past, 5 inputs are usually not improving anything (see old emails on
> this list from Bruce)
>
> 2. pass the flag -flirt-motioncor to recon-all and it will revert back
> to using flirt (but accuracy of the registration might suffer, since the
> inputs are full head images with potentially a lot of differences in
> jaw, tongue, neck, eyes, scalp and cropping planes).
>
> Another option would be to convert the inputs to uchar and see if that
> fits into the memory. They will be converted to uchar anyway in the
> conform step.
>
> Best, Martin
>
> On Tue, 2011-02-08 at 23:21 +0800, Mahen wrote:
> > Hi all,
> >
> > Since upgrading to Freesurfer v5.0, I have been unable to complete the
> > first step of recon-all ('recon-all -autorecon1 -subjid ...') when
> > using 5 anatomical datasets (our typical load for surface
> > reconstruction). The problem seems to come when the third dataset is
> > being registered, at which point recon-all exits with the following
> > error message:
> > =
> > Resolution: 0
> > Iteration(single-prec): 1 (subsample 200) mri_robust_template(47536)
> > malloc: *** mmap(size=921600) failed (error code=12)
> > *** error: can't allocate region
> > *** set a breakpoint in malloc_error_break to debug
> > MRIalloc(480, 480, 248): could not allocate 921600 bytes for 207th
> > slice
> >
> > Cannot allocate memory
> > /Users/mahen/fMRI/Surfaces/cck_kmu
> > \n
> > mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
> /Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform \n
> > mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
> /Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform
> > mghRead(/Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz, -1): could
> > not open file
> > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
> > reading from /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz...
> > Darwin MahenWillEatYourChildren.local 10.6.0 Darwin Kernel Version
> > 10.6.0: Wed Nov 10 18:13:17 PST 2010;
> > root:xnu-1504.9.26~3/RELEASE_I386 i386
> >
> > recon-all -s cck_kmu exited with ERRORS at Tue Feb 8 20:50:00 CST
> > 2011
> > =
> > My machine has 4gb of RAM, and I've ssh'd into my advisor's machine
> > (which has 16gb) and had the same problem.
> > I tryed updating the binaries for recon-all and mri_robust_template
> > (from
> >
> http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/),
> but the problem remained unsolved.
> > My advisor informs me that it is now running with version 4
Re: [Freesurfer] Inaccurate Surfaces Generated
Hi Bruce, Thank you very much for taking a look at this for us. I uploaded it to your ftp server under the name JeffSadino_050089_S05.tar. About 70 of our subjects are showing similar problems. It seems to be happening more frequently in fs5 as compared to fs4. If you can find anything that will help, that would be great. Thank you again! Jeff On Wed, Oct 5, 2011 at 2:41 PM, Bruce Fischl wrote: > Hi jeff > Sorry, this slipped through the cracks. If you upload the dataset we will > take a look > Bruce > > > > On Oct 5, 2011, at 8:32 PM, Jeff Sadino wrote: > > Hello FreeSurfer Experts, > > Does anyone have any ideas about how to salvage this data? > > Thank you very much! > Jeff > > On Sun, Oct 2, 2011 at 5:10 PM, Jeff Sadino < > jsadino.que...@gmail.com> wrote: > >> Hi Freesurfer Team, >> When we tried to process some subjects in FS 5.0.0 through the >> cross-sectional step in the longitudinal processing stream, we got >> inaccurate surfaces generated. Also, after doing skullstripping or adding >> control points and re-running the cross-sectional reconstruction, inaccurate >> pial and white matter surfaces were generated (see attached pictures). We >> are not sure how to fix this problem and this has affected about 70 of our >> scans. Several of these subjects we also processed in FS 3 and FS 4.3.1, >> and the surfaces were generated fine. Are there any known solutions to >> fixing the surfaces in the newer FreeSurfer? If not, then could we feed the >> 4.3.1 cross-sectionals into FS 5 to create the base template, and then use >> FS 5 to create the longitudinal reconstructions? >> >> Thank you, >> Jeff Sadino >> >> > <050089_S05rhlh.png> > > ___ > 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.
Re: [Freesurfer] Inaccurate Surfaces Generated
Hello Bruce, Thank you very much for this. It led me exactly to where I needed to look. In regards to this specific subject, it ran through reconstruction with a bad skullstrip but accurate surfaces. We then fixed the skullstrip and reran autorecon 2 & 3, but then the bad surfaces appeared. Today, when I reran mri_em_register (from fs5.0.0) on the fixed skullstrip, I got the talairach.lta file that was way, way off. However, when I use the fs 5.1.0 mri_em_register, I get a talairach.lta that is almost identical to yours. The talairach.lta file seemed to be way off for the rest of these subjects as well. Not sure if anyone else is having problems with the mri_em_register between 5.0.0 and 5.1.0. We will reprocess these in 5.1.0 and hopefully that will fix it. Thank you again for taking a look! Jeff On Thu, Oct 6, 2011 at 4:13 AM, Bruce Fischl wrote: > Hi Jeff, > > it's hard to sort out what happened as it looks like you invoked recon-all > over 50 times for this subject! In any case, the talairach.lta was way, way > off, but when I just reran mri_em_register it worked perfectly, so I can't > reconstruct what you did. Can you try running recon-all -autorecon2 > -autorecon3 and see if it fixes things? Did the skull strip fail for you > initially? Maybe em_register and the aseg stuff were run on a bad skull > strip? > > I'll attach the output of my mri_em_register run (called test.lta). You can > compare it to the talairach.lta in that subject's transforms dir using > tkmedit or tkregister2. > > cheers > Bruce > > > On Wed, 5 Oct 2011, Jeff Sadino wrote: > > Hi Bruce, >> Thank you very much for taking a look at this for us. I uploaded it to >> your >> ftp server under the name JeffSadino_050089_S05.tar. About 70 of our >> subjects are showing similar problems. It seems to be happening more >> frequently in fs5 as compared to fs4. If you can find anything that will >> help, that would be great. Thank you again! >> >> Jeff >> >> On Wed, Oct 5, 2011 at 2:41 PM, Bruce Fischl >> wrote: >> Hi jeff >> Sorry, this slipped through the cracks. If you upload the dataset we >> will take a look >> Bruce >> >> >> >> On Oct 5, 2011, at 8:32 PM, Jeff Sadino >> wrote: >> >> Hello FreeSurfer Experts, >> Does anyone have any ideas about how to salvage this data? >> >> Thank you very much! >> Jeff >> >> On Sun, Oct 2, 2011 at 5:10 PM, Jeff Sadino >> wrote: >> Hi Freesurfer Team, >> When we tried to process some subjects in FS 5.0.0 through >> the cross-sectional step in the longitudinal processing >> stream, we got inaccurate surfaces generated. Also, after >> doing skullstripping or adding control points and >> re-running the cross-sectional reconstruction, inaccurate >> pial and white matter surfaces were generated (see >> attached pictures). We are not sure how to fix this >> problem and this has affected about 70 of our scans. >> Several of these subjects we also processed in FS 3 and >> FS 4.3.1, and the surfaces were generated fine. Are there >> any known solutions to fixing the surfaces in the newer >> FreeSurfer? If not, then could we feed the 4.3.1 >> cross-sectionals into FS 5 to create the base template, >> and then use FS 5 to create the longitudinal >> reconstructions? >> >> Thank you, >> Jeff Sadino >> >> >> <050089_S05rhlh.png> >> >> __**_ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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] Resize window using Tcl command
Hello, I was wondering if there is a Tcl command to resize the window. I saw this thread, but it would not work on my computer, and I don't see any documentation in the tkmedit tcl scripting guide. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02600.html Thank you, Jeff Sadino ___ 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] Fixing Talairach.lta
Hello, I have several subjects with bad surfaces in fs 5.0.0. After checking their talairach.lta file, these transforms are all bad. I tried using tkregister2 to create a good talairach.lta file, but it just wasn't working. I tried rerunning these subjects in fs 5.1.0, and their talairach.lta files are all good. Can I just copy the fs510 talairach.lta file to the fs500 subject folder, or will that cause other issues that are not obvious? As a side note, what would the tkregister2 command be to create the lta file? Thank you, Jeff Sadino ___ 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] Brain Volume measures
Hello, Thank you Bruce and Doug for your answers to my previous question about a bad talairach.lta file. I am now grabbing volumes using fs5.0.0 and would like to ask for clarification. On the Morphometry Stats page at http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats, it says that the cortex is based on the pial surface. I am wondering what this includes. I loaded up the pial surface in tkmedit along with aseg.mgz. It looks like the following regions are completely outside the pial surface: cerebellum, 4th ventricle, Brain-Stem, optic chiasm. Is it correct that these regions are excluded? And then it looks like the hippocampus, amygdala, and inferior-lateral-ventricle are only halfway outside the pial surface. Is that correct? If it is, then is there a recommended way to exclude the hippocampus, amygdala, and inferior-lateral-ventricle regions in the cortical gray matter? Do these regions get properly accounted for in the subcortical gray calculation? And then for the white matter, the webpage says that it is based on the white surface. Looking at the white surface (lh.white), all of the subcortical gray matter and ventricles are enclosed in the surface. Can someone explain how the subcortical gray gets excluded? Finally, for the SubCortGray reported in aseg.stats file, does that exclude the following areas: Left-Lateral-Ventricle Left-Inf-Lat-Vent 3rd-Ventricle 4th-Ventricle CSF Left-vessel Right-Lateral-Ventricle Right-Inf-Lat-Vent Right-vessel 5th-Ventricle Left-Cerebellum-White-Matter Right-Cerebellum-White-Matter WM-hypointensities What about the brain stem? Why is the cerebellum Gray Matter included? I ask because the only way I can get close to the SubCortGray by using the aseg file is by excluding those regions. Once again, thank you for your invaluable help! Jeff Sadino ___ 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] Brain Volume measures
Thank you Doug for your answer. After reading the wiki more, it has led me to another question. I am trying to duplicate the White Matter value from aseg.stats using FreeSurfer 5.0.0. The value from aseg.stats is 220804 (as it is also when running mris_wm_volume). By hand, when I run mris_volume subject lh.white, I get 239035. From this, I subtract: Left-Lateral-Ventricle Left-Inf-Lat-Vent Left-vessel Left-Thalamus-Proper Left-Caudate Left-Putamen Left-Pallidum Left-Accumbens-area Left-VentralDC Left-choroid-plexus and then I am left with 209832. Can someone please give more detail about how or which areas mris_wm_volume excludes? Thank you very much, Jeff On Wed, Nov 30, 2011 at 7:46 AM, Douglas N Greve wrote: > Hi Jeff, the total cortical gray matter is based on the volume between the > white and pial surfaces. The other structures you mention below are based > on the automatic volume segmentation. > doug > > Jeff Sadino wrote: > >> Hello, >> >> Thank you Bruce and Doug for your answers to my previous question about a >> bad talairach.lta file. I am now grabbing volumes using fs5.0.0 and would >> like to ask for clarification. On the Morphometry Stats page at >> http://surfer.nmr.mgh.harvard.**edu/fswiki/MorphometryStats<http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats>, >> it says that the cortex is based on the pial surface. I am wondering what >> this includes. I loaded up the pial surface in tkmedit along with >> aseg.mgz. It looks like the following regions are completely outside the >> pial surface: cerebellum, 4th ventricle, Brain-Stem, optic chiasm. Is it >> correct that these regions are excluded? And then it looks like the >> hippocampus, amygdala, and inferior-lateral-ventricle are only halfway >> outside the pial surface. Is that correct? If it is, then is there a >> recommended way to exclude the hippocampus, amygdala, and >> inferior-lateral-ventricle regions in the cortical gray matter? Do these >> regions get properly accounted for in the subcortical gray calculation? >> >> And then for the white matter, the webpage says that it is based on the >> white surface. Looking at the white surface (lh.white), all of the >> subcortical gray matter and ventricles are enclosed in the surface. Can >> someone explain how the subcortical gray gets excluded? >> >> Finally, for the SubCortGray reported in aseg.stats file, does that >> exclude the following areas: >> Left-Lateral-Ventricle >> Left-Inf-Lat-Vent >> 3rd-Ventricle >> 4th-Ventricle >> CSF >> Left-vessel >> Right-Lateral-Ventricle >> Right-Inf-Lat-Vent >> Right-vessel >> 5th-Ventricle >> Left-Cerebellum-White-Matter >> Right-Cerebellum-White-Matter >> WM-hypointensities >> >> What about the brain stem? Why is the cerebellum Gray Matter included? >> I ask because the only way I can get close to the SubCortGray by using the >> aseg file is by excluding those regions. >> >> Once again, thank you for your invaluable help! >> Jeff Sadino >> --**--** >> >> >> __**_ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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<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] Verifying ICV in FS5
Hello, Thank you Nick, Martin, and Doug for your previous feedback about ICV. I have a couple more questions that I am hoping you could clarify for me. To verify my ICV value, some pages on the mailing list and wiki say to use this command: tkregister2 --s subject --fstal --surf Other places say to use this: tkregister2 --xfm talairach.xfm --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov ../nu_noneck.mgz --reg junk However, on this wiki page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV), it says that post fs4.2.0, the template is this file: 711-2C_as_mni_average_305.4dfp.img. In the first tkregister2 command above, doesn't the --fstal flag use the talairach template? But shouldn't it be using the 711 template? And since I am using fs5.0.0, does that mean that I should not be using the RB template? Ultimately, what is the correct way to verify the ICV in fs 5.0.0? Thank you very much, Jeff Sadino On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve wrote: > It's hard to tell from the coronal, but it looks ok. The problem is more > visible in the sagittal. > > doug > > Jeff Sadino wrote: >> >> Hello Doug, >> >> I loaded up the tkregister2 program and I think I see some poor >> transformations. I've never really used it before though. Am I just >> looking at whether or not the green line lines up with the target image wm? >> Can you look at my pictures real quick? 040002_S04_test is from fs4 that >> is having problems. 040002_S04 is from fs3 and has a good icv value. Some >> of the blank spots are from my graphics drivers and unrelated to fs. >> tkregister2 also said the determinant of 040002_S04_test was 1.49544. >> >> Martin, >> >> Thank you for the idea. I did this, and got a much better icv. On fs3, >> where the icv was good, the number was 1,767,481. On fs4, it was 1,302,696. >> Using your idea on fs4, it was 1,819,485. >> >> Thank you so much to everyone for your help! >> Jeff >> >> On Thu, Feb 25, 2010 at 8:53 PM, Martin Kavec > <mailto:martin.ka...@gmail.com>> wrote: >> >> Hi Jeff, >> >> I see this relatively often. Eventhough the talairach registration >> is fine, the >> ICV is underestimated. In this case I take old ICV, which helps. >> >> mri_segstats --subject $MYSUBJECT --old-etiv-only >> >> This is in 99% of these cases a cure. This is not just a blind >> attempt. In >> these cases I then compare each ICV normalized aseg volume against >> an age >> matched group and only if the old-etiv-only ICV gives better >> estimates I use >> it. >> >> Cheers, >> >> Martin >> >> On Thursday 25 February 2010 23:05:10 Jeff Sadino wrote: >> > Thanks Doug. That is very good news to hear! >> > >> > Maybe I spoke too soon about fixing the problem. I looked at 4 more >> > subjects, and even though the icv value is unique, its magnitude >> seems >> > wrong. Often times, it is smaller than the BrainSegVol, which >> doesn't make >> > much sense and it is also low overall. >> > >> > >> > # subjectname 090167_F01 >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1639959, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1639959.00, mm^3 >> > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain >> Segmentation Volume >> > Without Ventricles, 1289194.00, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1299686, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1299686.00, >> > mm^3 >> > # Measure IntraCranialVol, ICV, Intracranial Volume, >> 1105595.114652, mm^3 >> > >> > # subjectname 090182_S01 >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1599981, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1599981.00, mm^3 >> > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain >> Segmentation Volume >> > Without Ventricles, 1199694.00, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1205382, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1205382.00, >> > mm^3 >> > # Measure IntraCranialVol, I
Re: [Freesurfer] Verifying ICV in FS5
bump :) any feedback on this would be very much appreciated. Thank you! Jeff On Mon, Jan 23, 2012 at 6:56 PM, Jeff Sadino wrote: > Hello, > > Thank you Nick, Martin, and Doug for your previous feedback about ICV. > I have a couple more questions that I am hoping you could clarify for > me. > > To verify my ICV value, some pages on the mailing list and wiki say to > use this command: > tkregister2 --s subject --fstal --surf > > Other places say to use this: > tkregister2 --xfm talairach.xfm --targ > $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov > ../nu_noneck.mgz --reg junk > > However, on this wiki page > (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV), it says that post > fs4.2.0, the template is this file: > 711-2C_as_mni_average_305.4dfp.img. In the first tkregister2 command > above, doesn't the --fstal flag use the talairach template? But > shouldn't it be using the 711 template? And since I am using fs5.0.0, > does that mean that I should not be using the RB template? > Ultimately, what is the correct way to verify the ICV in fs 5.0.0? > > Thank you very much, > Jeff Sadino > > On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve > wrote: >> It's hard to tell from the coronal, but it looks ok. The problem is more >> visible in the sagittal. >> >> doug >> >> Jeff Sadino wrote: >>> >>> Hello Doug, >>> >>> I loaded up the tkregister2 program and I think I see some poor >>> transformations. I've never really used it before though. Am I just >>> looking at whether or not the green line lines up with the target image wm? >>> Can you look at my pictures real quick? 040002_S04_test is from fs4 that >>> is having problems. 040002_S04 is from fs3 and has a good icv value. Some >>> of the blank spots are from my graphics drivers and unrelated to fs. >>> tkregister2 also said the determinant of 040002_S04_test was 1.49544. >>> >>> Martin, >>> >>> Thank you for the idea. I did this, and got a much better icv. On fs3, >>> where the icv was good, the number was 1,767,481. On fs4, it was 1,302,696. >>> Using your idea on fs4, it was 1,819,485. >>> >>> Thank you so much to everyone for your help! >>> Jeff >>> >>> On Thu, Feb 25, 2010 at 8:53 PM, Martin Kavec >> <mailto:martin.ka...@gmail.com>> wrote: >>> >>> Hi Jeff, >>> >>> I see this relatively often. Eventhough the talairach registration >>> is fine, the >>> ICV is underestimated. In this case I take old ICV, which helps. >>> >>> mri_segstats --subject $MYSUBJECT --old-etiv-only >>> >>> This is in 99% of these cases a cure. This is not just a blind >>> attempt. In >>> these cases I then compare each ICV normalized aseg volume against >>> an age >>> matched group and only if the old-etiv-only ICV gives better >>> estimates I use >>> it. >>> >>> Cheers, >>> >>> Martin >>> >>> On Thursday 25 February 2010 23:05:10 Jeff Sadino wrote: >>> > Thanks Doug. That is very good news to hear! >>> > >>> > Maybe I spoke too soon about fixing the problem. I looked at 4 more >>> > subjects, and even though the icv value is unique, its magnitude >>> seems >>> > wrong. Often times, it is smaller than the BrainSegVol, which >>> doesn't make >>> > much sense and it is also low overall. >>> > >>> > >>> > # subjectname 090167_F01 >>> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >>> 1639959, >>> > unitless >>> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >>> 1639959.00, mm^3 >>> > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain >>> Segmentation Volume >>> > Without Ventricles, 1289194.00, mm^3 >>> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >>> Voxels, >>> > 1299686, unitless >>> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >>> 1299686.00, >>> > mm^3 >>> > # Measure IntraCranialVol, ICV, Intracranial Volume, >>> 1105595.114652, mm^3 >>> > >>> > # subjectname 090182_S01 >>> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >>> 15
[Freesurfer] Comparing Cortical Thickness
Hello FreeSurfers, I want to compare cortical thickness differences between my two groups. Is this the correct pipeline? I ran make_average_subject on each group. To get the study thickness file in control space, I did this: mri_surf2surf --srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control --trgsurfval control/surf/study.thickness.mgh --hemi lh And then to calculate the differences, I used: mris_thickness_diff -out diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial control/surf/study.thickness.mgh. Is this the right way to do this? mris_thickness_diff says it should only be used on the same subject. mris_diff says it is still being tested. I also see mris_thickness_comparison. Which command is the best to use to get a thickness difference map? Thank you very much, Jeff Sadino ___ 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] Exclude cortical region for one subject during qdec analysis
Hello, I have 200 subjects and I am analyzing their cortex in qdec. I have several subjects that have poor cortical surfaces on a local basis. Is there a way for exclude just one area for just one subject during qdec analysis? For example, on some images, the patient nose is in their occipital lobe...no pathologies, just image wraparound during acquisition :). This makes the cortical surfaces unreliable in this area. Is there a way to tell qdec to ignore the occipital regions in this one subject in its analysis? Thank you very much, Jeff Sadino ___ 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 with cluster-wise p=.1
Hello FreeSurfers, I want to do several cluster-wise corrections at a p value of .1, preferably in QDEC. To create the new "template cluster", I am using this command: mri_mcsim --o test --base mc-z --surf fsaverage lh --nreps 1 --fwhm 10 Is there a way that I can tell mri_mcsim to do a threshold of 1.00 (p=.1) and only the "abs" sign? Thank you, Jeff Sadino ___ 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] Jacobian Questions
Hello, Since the jacobian files contain only positive numbers, is there any way to make a distinction between a brain area that needs to be stretched bigger to fit the template versus a brain area that needs to be squished smaller? fsaverage is comprised of 40 subjects, but I wonder if the jacobian is most accurate only for my subjects that have the same age as the fsaverage mean? If so, then the younger subjects would need to be squished and the older subjects would need to be stretched. But since the jacobian is always positive, then on a scatterplot of jacobian versus age, this would look like a hump centered on the fsaverage mean age. Am I on the right track with this? Thank you, Jeff ___ 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] Cortical Normalization Questions
Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus? For cortical volume, it is pretty standard to normalize to eTIV. For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations? Thank you, Jeff ___ 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] mri_segstats memory corruption error
-linux-gnu/libz.so.1.2.3.4 b78a4000-b78a5000 rwxp 00013000 08:15 11666324 /lib/i386-linux-gnu/libz.so.1.2.3.4 b78ac000-b78b5000 r-xp 08:15 11666291 /lib/i386-linux-gnu/ libnss_nis-2.13.so b78b5000-b78b6000 r-xp 8000 08:15 11666291 /lib/i386-linux-gnu/ libnss_nis-2.13.so b78b6000-b78b7000 rwxp 9000 08:15 11666291 /lib/i386-linux-gnu/ libnss_nis-2.13.so b78b7000-b78bd000 r-xp 08:15 11666283 /lib/i386-linux-gnu/ libnss_compat-2.13.so b78bd000-b78be000 r-xp 5000 08:15 11666283 /lib/i386-linux-gnu/ libnss_compat-2.13.so b78be000-b78bf000 rwxp 6000 08:15 11666283 /lib/i386-linux-gnu/ libnss_compat-2.13.so b78bf000-b78c2000 rwxp 00:00 0 b78c2000-b78de000 r-xp 08:15 11666228 /lib/i386-linux-gnu/ ld-2.13.so b78de000-b78df000 r-xp 0001b000 08:15 11666228 /lib/i386-linux-gnu/ ld-2.13.so b78df000-b78e rwxp 0001c000 08:15 11666228 /lib/i386-linux-gnu/ ld-2.13.so b78e-b78e1000 r-xp 00:00 0 [vdso] bf87f000-bf8a1000 rwxp 00:00 0 [stack] Writing to rhFwhm12Sig13/rh-Diff-M-F-Intercept-volume/mc-z.abs.13.jls.y.ocn.dat Abort Thank you for your help! Jeff Sadino ___ 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] Cortical Normalization Questions
Thank you everyone for your great input. After reading through all of the suggestions and references, I like the idea of using ICV rather than global averages, at least for this current study. However, I do have one more question. All the papers normalize on surface area. If we want to present the Jacobian values, does it make sense to normalize the Jacobian values to the ICV? Or are the Jacobians conceptionally too different from surface areas to do this? Thank you, Jeff On Fri, Mar 23, 2012 at 1:29 AM, Michael Harms wrote: > > Our reply to that is here > http://bjp.rcpsych.org/content/196/5/414.2.long > > which reminded me of other papers that have also used a global thickness > measure to covary for mean cortical thickness and thereby "address whether > any regional thickness differences were in excess of global cortical > thickness differences between groups" -- see references [1,4] in our > Reply. > > cheers, > -MH > > > Hi Michael and others, > > > > maybe it's this one: > > > > http://bjp.rcpsych.org/content/196/5/414.1.long > > > > best, > > -joost > > > > > > On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms > > wrote: > > > >> > >> Hi Jeff, > >> I personally like the idea of using average thickness as a covariate to > >> control for a reduction in "whole brain" thickness, and have used that > >> approach in a paper. If the Abstract that you mentioned indicated that > >> this is flawed, I'd be curious to know what the reason was... > >> > >> cheers, > >> -MH > >> > >> On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote: > >> > Hi Jeff > >> > > >> > yes, I think this is still our recommendation for thickness, although > >> > perhaps David Salat can verify. As far as surface area, you might get > >> > Anderson Winkler to send you a preprint of his newly accepted paper on > >> > surface area comparisons and how to do them properly. I would have > >> said > >> > normalize by the 2/3 root of ICV (maybe David can comment on this as > >> well) > >> > > >> > cheers > >> > Bruce > >> > > >> > > >> > On Thu, 22 Mar 2012, Jeff Sadino wrote: > >> > > >> > > Hello, > >> > > For cortical thickness normalizations, Bruce said not to normalize > >> based on a HBM > >> > > abstract > >> > > ( > >> > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). > >> Is > >> > > this still the consensus? > >> > > > >> > > For cortical volume, it is pretty standard to normalize to eTIV. > >> > > > >> > > For cortical surface area (jacobian), I couldn't find any > >> information > >> on the wiki. > >> > > Does anyone have any recommendations? > >> > > > >> > > Thank you, > >> > > Jeff > >> > > > >> > > > >> > ___ 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 > >> > > > > ___ 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] Cortical Normalization Questions
Hello, Thank you Michael for your input. My feeling was that surface area would scale with ICV. In any case, is there any recommendation on how to normalize the Jacobian? My other ramble is that since it is already mapped into a common space, would I normalize the Jacobian, or would I have to normalize its precurser (surface area) measurement and then re-calculate the Jacobian? My last ramble is that since the Jacobian is non-linear, is it possible to normalize it in a simple linear manner, or would it be a more complicated non-linear normalization? I hope that makes sense. Any feedback would be very greatly helpful! Mahalo, Jeff Hi Jeff, I'm confused here. ICV and surface area are two very different things. cheers, -MH On Thu, Apr 12, 2012 at 12:06 PM, Jeff Sadino wrote: > Thank you everyone for your great input. After reading through all of the > suggestions and references, I like the idea of using ICV rather than global > averages, at least for this current study. However, I do have one more > question. All the papers normalize on surface area. If we want to present > the Jacobian values, does it make sense to normalize the Jacobian values to > the ICV? Or are the Jacobians conceptionally too different from surface > areas to do this? > > Thank you, > Jeff > > > On Fri, Mar 23, 2012 at 1:29 AM, Michael Harms wrote: > >> >> Our reply to that is here >> http://bjp.rcpsych.org/content/196/5/414.2.long >> >> which reminded me of other papers that have also used a global thickness >> measure to covary for mean cortical thickness and thereby "address whether >> any regional thickness differences were in excess of global cortical >> thickness differences between groups" -- see references [1,4] in our >> Reply. >> >> cheers, >> -MH >> >> > Hi Michael and others, >> > >> > maybe it's this one: >> > >> > http://bjp.rcpsych.org/content/196/5/414.1.long >> > >> > best, >> > -joost >> > >> > >> > On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms >> > wrote: >> > >> >> >> >> Hi Jeff, >> >> I personally like the idea of using average thickness as a covariate to >> >> control for a reduction in "whole brain" thickness, and have used that >> >> approach in a paper. If the Abstract that you mentioned indicated that >> >> this is flawed, I'd be curious to know what the reason was... >> >> >> >> cheers, >> >> -MH >> >> >> >> On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote: >> >> > Hi Jeff >> >> > >> >> > yes, I think this is still our recommendation for thickness, although >> >> > perhaps David Salat can verify. As far as surface area, you might get >> >> > Anderson Winkler to send you a preprint of his newly accepted paper >> on >> >> > surface area comparisons and how to do them properly. I would have >> >> said >> >> > normalize by the 2/3 root of ICV (maybe David can comment on this as >> >> well) >> >> > >> >> > cheers >> >> > Bruce >> >> > >> >> > >> >> > On Thu, 22 Mar 2012, Jeff Sadino wrote: >> >> > >> >> > > Hello, >> >> > > For cortical thickness normalizations, Bruce said not to normalize >> >> based on a HBM >> >> > > abstract >> >> > > ( >> >> >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html >> ). >> >> Is >> >> > > this still the consensus? >> >> > > >> >> > > For cortical volume, it is pretty standard to normalize to eTIV. >> >> > > >> >> > > For cortical surface area (jacobian), I couldn't find any >> >> information >> >> on the wiki. >> >> > > Does anyone have any recommendations? >> >> > > >> >> > > Thank you, >> >> > > Jeff >> >> > > >> >> > > >> >> > ___ 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 >&
[Freesurfer] Count non-zero voxels without matlab
Hello surfers, I would like to count the number of non-zero voxels in the image brain.mgz. Does anybody have any ideas what the easiest way to do this would be without using matlab? Thank you all! Jeff Sadino _ Want to do more with Windows Live? Learn “10 hidden secrets” from Jamie. http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!550F681DAD532637!5295.entry?ocid=TXT_TAGLM_WL_domore_092008 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Count non-zero voxels without matlab
Hello surfers, We are trying to normalize volumes of different regions of the brain to brain size. By brain size, we would be shooting for everything inside the skull - brain, CSF, and dura. After looking at the four different measurements in aseg.stats and comparing what each of these measures include and also how much each of these measures vary between scans on the same subject, none of them really achieve the consistency that we would like. ICV had a variability of 7.4% with 5 subjects each with 3 scans. The others were at about 3%. We are thinking that if we count the non-zero voxels in brain.mgz, this should be the most accurate measure of ICV. It will include a little bit of the skull and maybe some outside the skull, but since the size of the skull itself should be constant from scan to scan, that should not really matter. This measure gave a variability of only 1.51% Does anybody see any potential errors in using this approach to measure ICV, or suggest improvements or ver! ify its validity? Thank you so much! Jeff Sadino mri_label_volume -a brain.mgz should do the trick. cheers, Bruce On Mon, 22 Sep 2008, Jeff Sadino wrote: > > Hello surfers, > > I would like to count the number of non-zero voxels in the image brain.mgz. > Does anybody have any ideas what the easiest way to do this would be without > using matlab? Thank you all! > > Jeff Sadino _ See how Windows connects the people, information, and fun that are part of your life. http://clk.atdmt.com/MRT/go/msnnkwxp1020093175mrt/direct/01/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] -normalization error
Hello all, I am receiving an error when trying to run autorecon1. When trying to step through it manually step-by-step, everything is fine up to -nuintensitycor. After running that command and looking at nu.mgz in tkmedit, the picture starts to fade out pretty bad above 120 intensity. When I lower the intensity down to about 30, I can see the picture just fine. Next, I skip -talairach (even though and run -normalization. But it exits with an error: [EMAIL PROTECTED] mri]$ recon-all -s 070046_S01 -normalization INFO: SUBJECTS_DIR is /data Actual FREESURFER_HOME /apps/freesurfer -rw-rw-r-- 1 FSuser FSuser 90352 Sep 24 16:10 /data/070046_S01/scripts/recon-all.log Linux cluster.mrilab.net 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 14:14:47 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux # [EMAIL PROTECTED] Intensity Normalization Wed Sep 24 16:15:19 HST 2008 /data/070046_S01/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux cluster.mrilab.net 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 14:14:47 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 16:15:21 HST 2008 Also, I have some of the -talairach files from a previous run: [EMAIL PROTECTED] mri]$ ls transforms/ bak talairach.auto.xfm talairach.log talairach.xfm Any ideas? Thank you. Jeff _ Get more out of the Web. Learn 10 hidden secrets of Windows Live. http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!550F681DAD532637!5295.entry?ocid=TXT_TAGLM_WL_domore_092008 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Calculate corticol thickness
Hello all,
Real basic question: How do I calculate the thickness of the cortex, preferably
at each vertex/face? I have tried read_curv.m, but get this error:
[thickness, f] = read_curv('lh.thickness')
??? Undefined function or method 'fread3' for input arguments of type 'double'.
Error in ==> read_curv at 21
vnum = fread3(fid) ;
This should be simple, but the discussion board starts one step after me I
think :) Any help would be appreciate!
Second, when I try to load it in freesurfer, I get an error:
[fsu...@cluster ~]$ tksurfer 050080_S01 lh thickness
surfer: current subjects dir: /share/apps/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /export/home/FSuser
Talairach transform
/home/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm does not
exist ...
Loading tal xfm file
/share/apps/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm
surfer: Reading header info from
/share/apps/freesurfer/subjects/050080_S01/mri/T1.mgz
I tried loading the inflated first, then loading the thickness, which works,
but the surface just turns all red. Are the minimum thicknesses maxing out my
color map? This seems unlikely. Can anybody help me?
[fsu...@cluster ~]$ tksurfer 050080_S01 lh inflated
surfer: current subjects dir: /share/apps/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /export/home/FSuser
Talairach transform
/home/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm does not
exist ...
Loading tal xfm file
/share/apps/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm
surfer: Reading header info from
/share/apps/freesurfer/subjects/050080_S01/mri/T1.mgz
surfer: vertices=144686, faces=289368
Talairach transform
/home/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm does not
exist ...
Loading tal xfm file
/share/apps/freesurfer/subjects/050080_S01/surf/../mri/transforms/talairach.xfm
surfer: single buffered window
libGL error: open DRM failed (Operation not permitted)
libGL error: reverting to (slow) indirect rendering
surfer: using interface /share/apps/freesurfer/lib/tcl/tksurfer.tcl
Reading /share/apps/freesurfer/lib/tcl/tkm_common.tcl
Reading /share/apps/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /share/apps/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /share/apps/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
(And then File -> Load Curvature -> lh.thickness)
% surfer: curvature read: min=0.226951 max=5.00
Thanks you very much,
Jeff Sadino
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[Freesurfer] Calculate Corticol Thickness
Nevermind, I figured out my mistake. Thanks for your help! _ Windows Live™: E-mail. Chat. Share. Get more ways to connect. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t2_allup_explore_012009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Measuring regional cortical thickness
Hello, I would like to measure the cortical thickness for each region. All I can find is how to do it for user-defined ROI's, but not for each auto-segmented region. Can anyone point me in the right direction? Also, can you manually add and subtract pixels from region labels from the surface in tksurfer in a similar way that you can in tkmedit? Thank you very much. Jeff Sadino _ Windows Live™ Hotmail®…more than just e-mail. http://windowslive.com/howitworks?ocid=TXT_TAGLM_WL_t2_hm_justgotbetter_howitworks_012009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] lh.aparc.a2005s.stats and lh.aparc.stats differences
Hello all, Thank you for your quick replies to my previous posts. One more question. I am wondering what the difference is and if I should be taking average thickness measurements for cortical regions from lh.aparc.a2005s.stats or lh.aparc.stats. I think the main difference is that lh.aparc.a2005s.stats was made with ?h.atlas2005_simple.gcs and lh.aparc.stats was made with ?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs. Which one is more accurate? I am using freesurfer 3.0.5. Thank you, Jeff Sadino _ Windows Live™ Hotmail®…more than just e-mail. http://windowslive.com/howitworks?ocid=TXT_TAGLM_WL_t2_hm_justgotbetter_howitworks_012009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Group Cortical Thickness
Hello, I want to run group statistics on the cortical thickness for a study with 3 groups, each with about 30 subjects. To do this, I need to create an average cort thickness map for each group. We are interested in basic statistics, so nothing too advanced. I am wondering what would be the most efficient way to go about this. From what I can tell, FsFast is the program used to do group analysis. Would it be fastest to learn FsFast to process all my group data, or I am thinking since we only need basic stats, it may be faster and easier to register each subject's ?h.thickness file to an average sphere and then load the registered thickness file into matlab to do the stats? I think I would need to modify the commands from auto-recon stage 3 to use the thickness file, for example: mris_sphere ?h.thickness ?h.thickness.sphere mris_register -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.thickness.sphere.reg mris_jacobian ?h.white ?h.thickness.sphere.reg ?h.jacobian_white mrisp_paint -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.thickness.sphere.reg ?h.thickness.avg_curvWe have a cluster, so the processing could be done fairly quickly. Thank you in advance for your advice! Jeff Sadino _ Stay up to date on your PC, the Web, and your mobile phone with Windows Live. http://clk.atdmt.com/MRT/go/msnnkwxp1020093185mrt/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
FW: [Freesurfer] Group Cortical Thickness
Thank you for your quick reply Doug. After looking, I think you are referring to the mri_glmfit tool? Is this the webpage to look at first to get started learning about how to do cortical thickness group analysis? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis Thank you, Jeff Sadino > Date: Wed, 18 Feb 2009 19:25:21 -0500 > From: gr...@nmr.mgh.harvard.edu > To: jsad...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Group Cortical Thickness > > If this is just a thickness study, then you dont need fsfast. There are > examples/tutorials of this type of analysis in the wiki. Look through > that and see if you still have questions. > > doug > > Jeff Sadino wrote: > > Hello, > > I want to run group statistics on the cortical thickness for a study > > with 3 groups, each with about 30 subjects. To do this, I need to > > create an average cort thickness map for each group. We are > > interested in basic statistics, so nothing too advanced. I am > > wondering what would be the most efficient way to go about this. From > > what I can tell, FsFast is the program used to do group analysis. > > Would it be fastest to learn FsFast to process all my group data, or I > > am thinking since we only need basic stats, it may be faster and > > easier to register each subject's ?h.thickness file to an average > > sphere and then load the registered thickness file into matlab to do > > the stats? I think I would need to modify the commands from > > auto-recon stage 3 to use the thickness file, for example: > > > > mris_sphere ?h.thickness ?h.thickness.sphere > > mris_register <http://surfer.nmr.mgh.harvard.edu/fswiki/mris_register> > > -curv ?h.sphere > > $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif > > ?h.thickness.sphere.reg > > mris_jacobian <http://surfer.nmr.mgh.harvard.edu/fswiki/mris_jacobian> > > ?h.white ?h.thickness.sphere.reg ?h.jacobian_white > > > > mrisp_paint <http://surfer.nmr.mgh.harvard.edu/fswiki/mrisp_paint> -a > > 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 > > ?h.thickness.sphere.reg ?h.thickness.avg_curv > > > > We have a cluster, so the processing could be done fairly quickly. > > Thank you in advance for your advice! > > > > Jeff Sadino > > > > > > Stay up to date on your PC, the Web, and your mobile phone with > > Windows Live. See Now > > <http://clk.atdmt.com/MRT/go/msnnkwxp1020093185mrt/direct/01/> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Get more out of the Web. Learn 10 hidden secrets of Windows Live. http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!550F681DAD532637!5295.entry?ocid=TXT_TAGLM_WL_domore_092008___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] GLM Contrast
Hello, I am running the mri_glmfit and would like to doublecheck my contrast file. This is my fsgd file: MeasurementName thickness Class ctrl Class cd Class nc Variables age ed Input 040002_S04 nc 42.62 18 Input 040005_HG01 nc 45.26 15 Input 040008_S01 nc 26.92 16 Input 050015_S01 nc 46.65 12 .. .. .. with values for cd and ctrl as well. I want to see if there are differences in thickness between my control group and my cognitive deficit group after taking into account for age and education. This is my matrix file: 1 -1 0 0 0 0 0 0 0 for ctrl, cd, nc, ctrl age, cd age, nc age, ctrl ed, cd ed, nc ed Will this matrix file work for my hypothesis? It seems like if the last 6 are zeros, then it will not be taking age and education into account? And then also, since I have 90 subjects in all, will I need to correct for multiple comparisons? Thank you in advance, Jeff Sadino _ Access your email online and on the go with Windows Live Hotmail. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_AE_Access_022009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Configure Overlay Display for >2 Colors
Hello Surfers, I have an overlay file with values ranging from -4.63 (n=138477) to 1.34 (n=25365). I would like to display this data with more than the two colors of the Green/Red, Heat, Blue/Red, or complex Color Scales in the Configure Overlay dialog. So far, no luck, even with toying with the min, max, mid, and piecewise options every way I can think of. Is there some way to get a fuller color spectrum on my overlay? Thank you, Jeff Sadino _ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Configure Overlay Display for >2 Colors
Hi Bruce, Thanks for your quick reply. I tried fine-tuning the offset and the midpoint. I guess what I would like to have happen is to have a couple more colors come out beyond the blue-to-light blue range for the thinning. If I could get some greens in there too, that would make the picture much more descriptive to look at. Thanks for your help! Regards, Jeff Sadino > Date: Mon, 2 Mar 2009 17:28:08 -0500 > From: fis...@nmr.mgh.harvard.edu > To: jsad...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Configure Overlay Display for >2 Colors > > Hi Jeff, > > have you tried setting the offset in the configure functional overlay > panel to be around the middle of your range (-1.5 or so I guess)? > > cheers, > Bruce > On Mon, 2 > Mar 2009, Jeff Sadino wrote: > > > > > Hello Surfers, > > I have an overlay file with values ranging from -4.63 (n=138477) to 1.34 > > (n=25365). I would like to display this data with more than the two colors > > of the Green/Red, Heat, Blue/Red, or complex Color Scales in the Configure > > Overlay dialog. So far, no luck, even with toying with the min, max, mid, > > and piecewise options every way I can think of. Is there some way to get a > > fuller color spectrum on my overlay? > > > > Thank you, > > Jeff Sadino > > > > _ > > Hotmail® is up to 70% faster. Now good news travels really fast. > > http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009 _ Express your personality in color! Preview and select themes for Hotmail®. http://www.windowslive-hotmail.com/LearnMore/personalize.aspx?ocid=TXT_MSGTX_WL_HM_express_032009#colortheme___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Are accurate volumes necessary for accurate surfaces?
Hello Surfers, I want to do a study on the cortical thickness for some new subjects. As I understand the Recon process, the surface files get their information from the volume files. If I want to increase the accuracy of my thickness files, do I first need to manually check the accuracy of the volume segmentations? Thank you, Jeff _ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer Load Group Descriptor File error
Hello, Can someone help me get scatterplots of my data? I am using freesurfer 3.0.5. I have ran these commands: mris_preproc --fsgd try1.fsgd --target fsaverage --hemi lh --meas thickness --out lh.try1.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.try1.mgh --fwhm 10 --tval lh.try1.fw.mgh mri_glmfit --y lh.try1.fw.mgh --fsgd try1.fsgd dods --C try1.mtx --surf fsaverage lh --glmdir lh.try1.dir tksurfer fsaverage lh inflated -annot aparc.atlas2005_simple -overlay lh.try1.dir/try1.mtx/sig.mgh Then selected a vertex, then File->Load Group Descriptor File and selected try1.fsgd, but I get this error: WARNING: Marker for class ctrl was invalid. WARNING: Color for class ctrl was invalid. WARNING: Marker for class cd was invalid. WARNING: Color for class cd was invalid. This is try1.fsgd: GroupDescriptorFile 1 Title try1 MeasurementName thickness Class ctrl Class cd Variables Age Input 040004_P02 ctrl 55.18 Input 050046_S02 ctrl 37.45 ... ... Input 070073_S01 cd 20.54 Input 070114_OGM01 cd 46.03 I also tried with lh.try1.dir/y.fsgd, but get a similar error: INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: gdfRead: reshaping WARNING: Marker for class ctrl was invalid. WARNING: Color for class ctrl was invalid. WARNING: Marker for class cd was invalid. WARNING: Color for class cd was invalid. y.fsgd looks like this: GroupDescriptorFile 1 Title try1 MeasurementName external Tessellation surface PlotFile /data/Jeff/glmtut/pass5/try1/lh.try1.fw.mgh DesignMatFile fsgd.X.mat dods ResidualFWHM 22.331472 Class ctrl Class cd Variables Age Input 040004_P02 ctrl 55.18 Input 050046_S02 ctrl 37.45 ... ... Input 070073_S01 cd 20.54 Input 070114_OGM01 cd 46.03 Creator mri_glmfit SUBJECTS_DIR /share/apps/freesurfer/subjects SynthSeed1237057379 In both cases, a graph pops up, but it is blank. Thank you in advance for your suggestions, Jeff Sadino _ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Changing from 1.4x1.4x1.4 mm slices to 1x1x1
Hello, I am analyzing some subjects from several years ago when we had a protocol that called for slices 1.4x1.4x1.4mm. I am also including in the study more recent scans with a protocol for 1x1x1mm slices. I am using freesurfer 3.0.5. I am wondering if the different slice dimensions will cause differences in the analysis. As I read on a previous post, freesurfer resamples all its input data into 1mm isovolumetric voxels anyways, so I should be ok? Regards, Jeff Sadino _ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Changing from 1.4x1.4x1.4 mm slices to 1x1x1
Hi Bruce, Yes, we are going to combine them into a single study. Is there a place on the wiki I can read about how to error check for these problems? Thank you, Jeff > Date: Tue, 17 Mar 2009 19:39:34 -0400 > From: fis...@nmr.mgh.harvard.edu > To: jsad...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Changing from 1.4x1.4x1.4 mm slices to 1x1x1 > > Hi Jeff, > > are you intending to combine them into a single study? This can be > problematic as you'll get differential sensitivity and possibly bias. > > cheers, > Bruce > > On Tue, 17 Mar 2009, Jeff Sadino wrote: > > > > > Hello, > > > > I am analyzing some subjects from several years ago when we had a protocol > > that called for slices 1.4x1.4x1.4mm. I am also including in the study > > more recent scans with a protocol for 1x1x1mm slices. I am using > > freesurfer 3.0.5. I am wondering if the different slice dimensions will > > cause differences in the analysis. As I read on a previous post, > > freesurfer resamples all its input data into 1mm isovolumetric voxels > > anyways, so I should be ok? > > > > Regards, > > Jeff Sadino > > > > _ > > Hotmail® is up to 70% faster. Now good news travels really fast. > > http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009 _ Windows Live™: Life without walls. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_allup_1a_explore_032009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] New Tutorial Attachments
Hello, I wanted to review the FreeSurfer attachments on the wiki's tutorial page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial Whenever I try to click on an attachment, it brings me to a page and says: Attached FilesNo attachments stored for FsTutorial/April2009CourseSchedule You are not allowed to attach a file to this page. I see the page was recently updated for the new class. Are the powerpoints still available to view somewhere? Mahalo, Jeff Sadino _ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] tksurfer Load Group Descriptor File error
Thank you for the advice Sid. I added those lines, and now my errors disappear, but I still get a blank screen where there should be a scatterplot. Is this a graphics issue with my hardware, or do I need to do something differently? This is my fsgd file: GroupDescriptorFile 1 Title try1 MeasurementName thickness Class nc circle red Variables Age Input 060017_HG01 nc .5 Input 060023_F01 nc .8 Input 060024_HG01 nc .1 Input 060025_HG01 nc .5 ... ... The screen that pops up has thickness on the y-axis, but a range of only 0-1 and Age on x-axis with range 0-1. My ages were "real" (50.8, 40.8, 50.1, etc.), but I changed them to between 0 and 1 to see if that helped, but no good. Thanks in advance for your help, Jeff Sadino Date: Thu, 12 Mar 2009 18:52:45 -0700 Subject: Re: [Freesurfer] tksurfer Load Group Descriptor File error From: sid...@gmail.com To: jsad...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Class ctrl should be followed by marker and color specification (Class ctrl circle red, for e.g). ditto for cd . sid. On Thu, Mar 12, 2009 at 6:37 PM, Jeff Sadino wrote: Hello, Can someone help me get scatterplots of my data? I am using freesurfer 3.0.5. I have ran these commands: mris_preproc --fsgd try1.fsgd --target fsaverage --hemi lh --meas thickness --out lh.try1.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.try1.mgh --fwhm 10 --tval lh.try1.fw.mgh mri_glmfit --y lh.try1.fw.mgh --fsgd try1.fsgd dods --C try1.mtx --surf fsaverage lh --glmdir lh.try1.dir tksurfer fsaverage lh inflated -annot aparc.atlas2005_simple -overlay lh.try1.dir/try1.mtx/sig.mgh Then selected a vertex, then File->Load Group Descriptor File and selected try1.fsgd, but I get this error: WARNING: Marker for class ctrl was invalid. WARNING: Color for class ctrl was invalid. WARNING: Marker for class cd was invalid. WARNING: Color for class cd was invalid. This is try1.fsgd: GroupDescriptorFile 1 Title try1 MeasurementName thickness Class ctrl Class cd Variables Age Input 040004_P02 ctrl 55.18 Input 050046_S02 ctrl 37.45 ... ... Input 070073_S01 cd 20.54 Input 070114_OGM01 cd 46.03 I also tried with lh.try1.dir/y.fsgd, but get a similar error: INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: gdfRead: reshaping WARNING: Marker for class ctrl was invalid. WARNING: Color for class ctrl was invalid. WARNING: Marker for class cd was invalid. WARNING: Color for class cd was invalid. y.fsgd looks like this: GroupDescriptorFile 1 Title try1 MeasurementName external Tessellation surface PlotFile /data/Jeff/glmtut/pass5/try1/lh.try1.fw.mgh DesignMatFile fsgd.X.mat dods ResidualFWHM 22.331472 Class ctrl Class cd Variables Age Input 040004_P02 ctrl 55.18 Input 050046_S02 ctrl 37.45 ... ... Input 070073_S01 cd 20.54 Input 070114_OGM01 cd 46.03 Creator mri_glmfit SUBJECTS_DIR /share/apps/freesurfer/subjects SynthSeed1237057379 In both cases, a graph pops up, but it is blank. Thank you in advance for your suggestions, Jeff Sadino Hotmail® is up to 70% faster. Now good news travels really fast. Find out more. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Windows Live™: Keep your life in sync. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_allup_1a_explore_042009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Extracting Thickness Vertex Values
Hello all again, I am displaying the sig.mgh file after running mris_glm. I can also see the fsgdf scatterplot when clicking on a vertex. What I would like is to be able to copy the thickness values for each subject in the group for the vertex I clicked on to an ascii/matlab/excel file. Otherwise, I'll use the mris_convert command on each subject to make an ascii file. As always, thanks for your expert help! Jeff Sadino _ Windows Live™: Life without walls. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_allup_1b_explore_042009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_preproc really averages?
Hello, I think my message got scrubbed from my last post with the pictures. I ran mris_preproc on 56 subjects and then graphed the concatenated image. I also read this image into matlab and did the averaging using matlab, and then graphed the resulting image. When I did this, the two average pictures were slightly different. I thought that mris_preproc just simply averages all the subjects into common space. I noticed that its vector in matlab keeps the thickness value for all vertex's for all 56 subjects. I want to have the matlab capability for some custom processing I am doing, but the discrepancy leads me to think that mris_preproc is not a simple average. Can anyone elucidate this for me? Thank you! Matlab script. Only place I would suspect a wrong assumption is when I throw out the rest of the subjects at curv4=curv3(1,:,:,1) %Select your input thickness file path='/mnt/users/Jeff/fs/lc/HIV/pass2pics/416/diff/nc.rh.ave.mgh'; %Read the thickness file curv=MRIread(path); %Select the volume attribute curv2=curv.vol; %Create a duplicate thickness array for manipulation curv3=curv2; %Get the number of concatanated subjects tmp=size(curv2); m=tmp(4) clear 'tmp' %Sum each vertex for all your subjects for im=2:m for in=1:7 curv3(1,:,in,1)=curv3(1,:,in,1)+curv2(1,:,in,im); end end %Select just the first frame curv4=curv3(1,:,:,1); %Compute the average thickness curv.vol=curv4/m; %Write to thickness file MRIwrite(curv,'nc.rh.ave1.tmp.mgh'); _ Windows Live™ SkyDrive™: Get 25 GB of free online storage. http://windowslive.com/online/skydrive?ocid=TXT_TAGLM_WL_skydrive_042009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_glmfit significiance verification outside freesurfer
Hello Surfers, I am trying to verify the p-value sig.mgh maps outputted from the mri_glmfit command as the first part of a more advanced analysis. We have been extracting the thickness data for a single vertex from each of our 58 subjects in two control groups and then running a significiance analysis is SAS. We thought that the output from SAS should match the p-value in the sig.mgh file, but the p-values do not match at all. We have tested multiple data points. Does freesurfer do some sort of a more advanced significance analysis that is not in the standard documentation? Thank you very much, Jeff Sadino _ Windows Live™ SkyDrive™: Get 25 GB of free online storage. http://windowslive.com/online/skydrive?ocid=TXT_TAGLM_WL_SD_25GB_062009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] mri_glmfit significiance verification outside freesurfer
Hello Everyone, Thank you all for your replies. We converted the values into -log10(p) and accounted for two-tailed, but the values were still off, and they are not even off in any consistent pattern. For example: FS: .1541 .1109 .0749 .0641 .0514 .0281 .0182 .0141 .0132 .0025 .0007 .0006 SAS: .3226 .0852 .2131 .0818 .0760 .2425 .6196 .0020 .0458 .0039 .0003 .0020 Our SAS program only gives output to four digits. Could the discrepencies be coming from rounding errors? Mahalo, Jeff > Date: Mon, 8 Jun 2009 19:21:53 -0400 > From: gr...@nmr.mgh.harvard.edu > To: ni...@nmr.mgh.harvard.edu > CC: jsad...@hotmail.com; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_glmfit significiance verification outside > freesurfer > > Also, p-values for t-tests are two-sided. > > Nick Schmansky wrote: > > Jeff, > > > > sig.mgh actually stores the -log10(p), not p, so to get the true p-value > > of say, -2 (in the sig.mgh), take 10^-2 (giving you the true p-value of > > 0.01). > > > > Nick > > > > > > On Mon, 2009-06-08 at 16:48 -0600, Jeff Sadino wrote: > > > >> Hello Surfers, > >> > >> I am trying to verify the p-value sig.mgh maps outputted from the > >> mri_glmfit command as the first part of a more advanced analysis. We > >> have been extracting the thickness data for a single vertex from each > >> of our 58 subjects in two control groups and then running a > >> significiance analysis is SAS. We thought that the output from SAS > >> should match the p-value in the sig.mgh file, but the p-values do not > >> match at all. We have tested multiple data points. Does freesurfer > >> do some sort of a more advanced significance analysis that is not in > >> the standard documentation? > >> > >> Thank you very much, > >> Jeff Sadino > >> > >> > >> __ > >> Windows Live™ SkyDrive™: Get 25 GB of free online storage. Get it on > >> your BlackBerry or iPhone. > >> ___ > >> 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 > gr...@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 > > _ Insert movie times and more without leaving Hotmail®. http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutorial_QuickAdd_062009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Co-vary
Hello Freesurfers, My apologies for this very basic question more about statistics than freesurfer, but I have not found an answer anywhere on the wikis, or the web (maybe it is too basic :-) ) I am interested in age-related effects of hiv and I wanted to covary for age and education in mri_glmfit. For example, if my fsgd file is: class control class hiv variables age ed input subj1 control 40 13 input subj2 hiv 35 12 ... ... and I use dods, is my contrast matrix the place where I would tell it to covary? Something like: 0 0-1 1 1 11 1 (y-int) (age slope) (covary for age) (covary for ed) As always, thank you for your help, Jeff _ Hotmail® has ever-growing storage! Don’t worry about storage limits. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutorial_Storage_062009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_nu_correct.mni intensity correction problem
Hello, I am running FS 3 and am having problems with auto-recon1, in particular the mri_nu_correct.mni step. My orig volume has intensities around 150-250, but my nu.mgz image has intensities all below 20. I am having errors further down the line, but I think they are all due to this step. Can anyone help me get my intensity values to work out right? Thank you! Jeff Sadino _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141664/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] QA Cortex
Hello, I want to do a quality check of the cortex for 140 subjects, as far as making sure it is segmented correctly. What files are the best ones to load up to check this in fs 3? If I load the aseg.mgz file up in tkmedit and look at the cortical regions, there are some regions where there is no cortex at all. Would I make the edits on this file, or is there some other file that would be better to use. Thank you, Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_nu_correct.mni intensity correction problem
Hello, I asked this question a couple days ago, but never got an answer. Please excuse the double posting. I am running FS 3 and am having problems with auto-recon1, in particular the mri_nu_correct.mni step. My orig volume has intensities around 150-250, but my nu.mgz image has intensities all below 20. I am having errors further down the line, but I think they are all due to this step. Can anyone help me get my intensity values to work out right? Thank you! Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Smaller
Hello Surfers, I have a number of subjects that are displaying a large number of small holes in the superior region of their white matter. I believe the medical term for them is virchow-robin spaces. We would like to try to quantify the volume that these holes occupy. Is there any way to break down the Right-Cerebral-White-Matter and Left-Cerebral-White-Matter segmentation labels in aseg.mgz into finer regions so that we can quantify the volume of these holes? Or would it simply be easier to go through the volumes and manually label the holes as a label that is not being used? Thank you, Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Measuring Cortical Volume
Hello, I want to measure the volume of my groups' cortex, n=139, mostly males. I am using fs 3.0.5. >From the aseg.stats file, lh + rh white matter is 548,000 and gray matter is 487,000, for a ratio of 1.1. I know the aseg.stats file is not a good place to go for gray matter volume, as it is usually underestimated. Looking in the aparc.a2005.stats file, the average white matter is 606,000 and gray matter is 463,000, for a ratio of 1.3. I was surprised the gray matter actually went down, and the ratio of 1.3 seems a bit high. Is this normal? I see in the aseg.stats file, skin left over after the watershed is counted as cortex and so is a fair amount around the cerebellum. Could partial volumeing also be a possible explanation? I would think that the aparc file would be most accurate, but with these results, I wanted to doublecheck. Thanks Bruce for answering my earlier question. I am still looking at the pallidum differences and will let you know soon. Thanks! Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ICV Error fs 4.3.1
Hello, I reconed 149 subjects using freesurfer 4.3.1 automatically using our cluster. When I did asegstats2table, all 149 subjects had the exact same icv: # Measure IntraCranialVol, ICV, Intracranial Volume, 1948106.00, mm^3 Running mri_segstats manually, here is the beginning of the output: mri_segstats --seg mri/aseg.mgz --sum stats/aseg2.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject 040002_S04 atlas_icv (eTIV) = 1948106 mm^3 (det: 1.00 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 246101 rh white matter volume 251160 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1766623 # brainmaskvolume 1766623.0 # nbrainsegvoxels 1310448 # brainsegvolume 1310448.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 1 2 Left-Cerebral-White-Matter 247216 247216 Looking at the log files for several other subjects, they all have a determinant of 1. However, all of the other numbers - brainmask, brain seg volume, individual regions - are all unique and correct. It is just the icv. Can anyone point me in the right direction of how to investigate the determinant value? Here is the mri_segstats version: # cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks Exp $ Thanks! Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ICV Error fs 4.3.1
Hi Doug, Thanks for the quick reply. It just seems like an error that all 149 subjects would line up exactly with the talairach transform (that would give a determinant of 1.00?). The following commands I used from my script were: recon-all -sd /scratch/data431 -s 040002_S04 -autorecon1 *code to check for errors* recon-all -sd /scratch/data431 -s 040002_S04 -autorecon2 *code to check for errors* recon-all -sd /scratch/data431 -s 040002_S04 -autorecon3 *code to check for errors* I searched the recon-all log for "-notalairach" and came up with no hits. Any other ideas? I ran all of these subjects in fs3 a while ago using an older version of my script, and they all came out with unique icv values. Thank you again for your suggestions! Jeff Sadino On Fri, Feb 19, 2010 at 12:04 PM, Douglas N Greve wrote: > The ICV is *estimated* from the talairach transform. Did you happen to run > recon-all with -notalairach? You can check that the talairach transforms are > all different. > > doug > > Jeff Sadino wrote: > >> Hello, >> I reconed 149 subjects using freesurfer 4.3.1 automatically using our >> cluster. When I did asegstats2table, all 149 subjects had the exact same >> icv: >> # Measure IntraCranialVol, ICV, Intracranial Volume, 1948106.00, mm^3 >> >> Running mri_segstats manually, here is the beginning of the output: >> >> mri_segstats --seg mri/aseg.mgz --sum stats/aseg2.stats --pv mri/norm.mgz >> --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in >> mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv >> --surf-wm-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject 040002_S04 >> atlas_icv (eTIV) = 1948106 mm^3 (det: 1.00 ) >> Loading mri/aseg.mgz >> Getting Cerebral WM volumes from surface >> lh white matter volume 246101 >> rh white matter volume 251160 >> Loading mri/norm.mgz >> Loading mri/norm.mgz >> Loading mri/brainmask.mgz >> # nbrainmaskvoxels 1766623 >> # brainmaskvolume 1766623.0 >> # nbrainsegvoxels 1310448 >> # brainsegvolume 1310448.0 >> Voxel Volume is 1 mm^3 >> Generating list of segmentation ids >> Found 50 segmentations >> Computing statistics for each segmentation >> 1 2 Left-Cerebral-White-Matter 247216 247216 >> >> Looking at the log files for several other subjects, they all have a >> determinant of 1. However, all of the other numbers - brainmask, brain seg >> volume, individual regions - are all unique and correct. It is just the >> icv. Can anyone point me in the right direction of how to investigate the >> determinant value? >> >> Here is the mri_segstats version: # cvs_version $Id: mri_segstats.c,v >> 1.33.2.5 2009/02/11 22:38:51 nicks Exp $ >> >> Thanks! >> Jeff Sadino >> >> >> ___ >> 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
Re: [Freesurfer] ICV Error fs 4.3.1
Doug - Thank you for your suggestion. I looked, and the talairach_with_skull.lta file was unique to each subject. However, the talairach.xfm file was actually a shortcut to /apps/freesurfer3/subjects/fsaverage/mri/transforms/talairach.xfm. This is because of some in-house legacy code that we use to do some preprocessing. After fixing this, the icv value came out unique. Too bad it is in the beginning of the reconstruction stream. 149 subjects is going to take a while to redo. Besides the icv measurements, will this file effect other outputs, or could I just rerun the segstats command? Nick - Sorry, I should have been more clear. I reran them in fs4 from scratch, using a different subject directory, so the two recons should hopefully be completely independent of each other. Thanks Everyone! Jeff On Fri, Feb 19, 2010 at 12:47 PM, Nick Schmansky wrote: > also note that if the subjects were processed by a prior version, then > when re-run with v4.X, talairach.xfm will not get overwritten, as it is > assuming it was edited. so you should check of talairach.xfm and > talairach.auto.xfm are the same, and if not either re-run with > -clean-tal, or just copy talairach.auto.xfm to talairach.xfm. > > n. > > > On Fri, 2010-02-19 at 17:41 -0500, Douglas N Greve wrote: > > Can you check the talairach.xfm and the talairach_with_skull.lta to make > > sure that they are different across subject? > > > > Jeff Sadino wrote: > > > Hi Doug, > > > > > > Thanks for the quick reply. It just seems like an error that all 149 > > > subjects would line up exactly with the talairach transform (that > > > would give a determinant of 1.00?). > > > > > > The following commands I used from my script were: > > > recon-all -sd /scratch/data431 -s 040002_S04 -autorecon1 > > > *code to check for errors* > > > recon-all -sd /scratch/data431 -s 040002_S04 -autorecon2 > > > *code to check for errors* > > > recon-all -sd /scratch/data431 -s 040002_S04 -autorecon3 > > > *code to check for errors* > > > > > > I searched the recon-all log for "-notalairach" and came up with no > > > hits. Any other ideas? > > > > > > I ran all of these subjects in fs3 a while ago using an older version > > > of my script, and they all came out with unique icv values. > > > > > > Thank you again for your suggestions! > > > Jeff Sadino > > > > > > On Fri, Feb 19, 2010 at 12:04 PM, Douglas N Greve > > > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > The ICV is *estimated* from the talairach transform. Did you > > > happen to run recon-all with -notalairach? You can check that the > > > talairach transforms are all different. > > > > > > doug > > > > > > Jeff Sadino wrote: > > > > > > Hello, > > > I reconed 149 subjects using freesurfer 4.3.1 automatically > > > using our cluster. When I did asegstats2table, all 149 > > > subjects had the exact same icv: > > > # Measure IntraCranialVol, ICV, Intracranial Volume, > > > 1948106.00, mm^3 > > > > > > Running mri_segstats manually, here is the beginning of the > > > output: > > > > > > mri_segstats --seg mri/aseg.mgz --sum stats/aseg2.stats --pv > > > mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask > > > mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm > > > --in-intensity-units MR --etiv --surf-wm-vol --ctab > > > $FREESURFER_HOME/ASegStatsLUT.txt --subject 040002_S04 > > > atlas_icv (eTIV) = 1948106 mm^3 (det: 1.00 ) > > > Loading mri/aseg.mgz > > > Getting Cerebral WM volumes from surface > > > lh white matter volume 246101 > > > rh white matter volume 251160 > > > Loading mri/norm.mgz > > > Loading mri/norm.mgz > > > Loading mri/brainmask.mgz > > > # nbrainmaskvoxels 1766623 > > > # brainmaskvolume 1766623.0 > > > # nbrainsegvoxels 1310448 > > > # brainsegvolume 1310448.0 > > > Voxel Volume is 1 mm^3 > > > Generating list of segmentation ids > > > Found 50 segmentations > > > Computing statistics for each segmentation >
Re: [Freesurfer] ICV Error fs 4.3.1
Thanks Doug. That is very good news to hear! Maybe I spoke too soon about fixing the problem. I looked at 4 more subjects, and even though the icv value is unique, its magnitude seems wrong. Often times, it is smaller than the BrainSegVol, which doesn't make much sense and it is also low overall. # subjectname 090167_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1639959, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1639959.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1289194.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1299686, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1299686.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1105595.114652, mm^3 # subjectname 090182_S01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1599981, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1599981.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1199694.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1205382, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1205382.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1114008.197334, mm^3 # subjectname 090187_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1826694, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1826694.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1381871.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1388801, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1388801.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1307759.303915, mm^3 # subjectname 100014_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1948121, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1948121.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1467582.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1488088, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1488088.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1637915.031593, mm^3 # subjectname 040002_S04_test # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1774481, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1774481.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1288022.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1312132, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1312132.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1302696.178406, mm^3 I had also done 040002_S04 in fs 3.0.5, and this is the result: # subjectname 040002_S04 # BrainMaskFile mri/brainmask.mgz # BrainMaskFileTimeStamp 2008/29/08 15:44:46 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1753272, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1753272.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1310474, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1310474.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1767481.547316, mm^3 All of the values are similar except the icv. Do you guys have any ideas where I can look for the answer? Thank you very much, Jeff On Thu, Feb 25, 2010 at 11:14 AM, Jeff Sadino wrote: > Doug - > Thank you for your suggestion. I looked, and the talairach_with_skull.lta > file was unique to each subject. However, the talairach.xfm file was > actually a shortcut to > /apps/freesurfer3/subjects/fsaverage/mri/transforms/talairach.xfm. This is > because of some in-house legacy code that we use to do some preprocessing. > After fixing this, the icv value came out unique. > > Too bad it is in the beginning of the reconstruction stream. 149 subjects > is going to take a while to redo. Besides the icv measurements, will this > file effect other outputs, or could I just rerun the segstats command? > > Nick - > Sorry, I should have been more clear. I reran them in fs4 from scratch, > using a different subject directory, so the two recons should hopefully be > completely independent of each other. > > Thanks Everyone! > Jeff > > > On Fri, Feb 19, 2010 at 12:47 PM, Nick Schmansky < > ni...@nmr.mgh.harvard.edu> wrote: > >> also note that if the subjects were processed by a prior version, then >> when re-run with v4.X, talairach.xfm will not get overwritten, as it is >> assuming it was ed
[Freesurfer] qdec Font Error
Hello, When I get to the last step of qdec 1.2, when I choose the "Description" under "Scalers" on the "Display" tab, I get a couple of errors relating to fonts: ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Rendering/vtkFreeTypeUtilities.cxx, line 1659 vtkTextProperty (0x217178e0): Unable to create font ! (family: 0, bold: 1, italic: 1, length: 36128) ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Rendering/vtkOpenGLFreeTypeTextMapper.cxx, line 366 vtkOpenGLFreeTypeTextMapper (0x21717710): Render - No font I installed vtk 5.2.0, and also the newest vtk, but neither one worked. I also installed all of the windows fonts on my Linux. Haven't looked at OpenGL yet. Am I just missing the right font, or is there a deeper problem? btw, Freesurfer 4.3.1 is installed on a server that I log into. Thank you again! Jeff Sadino ___ 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] Cerebellum Segmentations
Hello, I am processing a large number of scans with the goal of segmenting the cerebellum into subregions, particularly the Vermis. Without editing each scan individually using tkmedit, what is the best way to achieve this subregion segmentation for a large number of subjects? Thank you in advance, Jeff Sadino JABSOM University of Hawaii at Manoa _ Want to do more with Windows Live? Learn “10 hidden secrets” from Jamie. http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!550F681DAD532637!5295.entry?ocid=TXT_TAGLM_WL_domore_092008 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] What is included in the ICV value
Hello, I am measuring the shrinkage of the limbic system over time for several subjects and need to know what is included in the ICV value in aseg.stats to do this. We are putting our raw scans into freesurfer without any manual edits until after QA at the end. My understanding is that the brain gets registered to the talairach template, the skull gets stripped, and then everything inside the skull - wm, gm, csf, cerebellum - gets included in the ICV (via scaling of the determinant of talairach_with_skull.lta)? Can someone confirm this work flow for us? Thank you very much, Jeff _ See how Windows Mobile brings your life together—at home, work, or on the go. http://clk.atdmt.com/MRT/go/msnnkwxp1020093182mrt/direct/01/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Calc stats on ROI in qdec
Hello, I am wondering if it is possible to calculate t-values and significance of a whole ROI in qdec, version 1.2. Right now, I have no problem doing it on a point-by-point basis, but I want to do whole ROI analysis within qdec. For example, I want to know the p-value of the whole lh_superiorparietal region for the "Does the average thickness differ between HIV and Control?" contrast. Your help is always appreciated! Mahalo, Jeff ___ 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] Calc stats on ROI in qdec
Hello, I am wondering if it is possible to calculate t-values and significance of a whole ROI in qdec, version 1.2. Right now, I have no problem doing it on a point-by-point basis, but I want to do whole ROI analysis within qdec. For example, I want to know the p-value of the whole lh_superiorparietal region for the "Does the average thickness differ between HIV and Control?" contrast. Your help is always appreciated! Mahalo, Jeff ___ 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] Mixing fs 4.3.1 with fs 4.5.0 longitudinally
Hello, I processed a 200 subject dataset cross-sectionally using fs 4.3.1 with the intention of running them longitudinally. I now read that the longitudinal stream in 4.3.1 is biased towards the initial timepoint and the 4.5.0 is the recommended version to do longitudinally. Can I just send my 4.3.1 subjects into the 4.5.0 longitudinal stream, or will I have have to redo the cross-sectional reconstruction in 4.5.0? Thank you very much, Jeff Sadino ___ 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] 3-Way Anova in Qdec
Hello, I would like to be able to do 3-way anova in qdec, freesurfer version 4.3.1 and measure the cortical thickness and volume. Is this possible? I have 3 discrete factors, each with two levels: age group: less/more than 50 HIV: yes/no Alzheimers: yes/no When I try to click on the third discrete factor in the qdec design tab, it deselects one of the others. Does it max out at two? Thank you very much, Jeff Sadino ___ 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] make_average_surface error?
Hello, I issued this command to make an average subject: make_average_subject --subjects 2101 2102 2103 --out uh3 I wanted to verify the average thickness file is what it sounds like. I used the recon-all -qcache on each subject individually, read the fwhm0 thickness files into matlab, and averaged vertex #100. However, when I look at vertex #100 from the uh3 surf folder, the numbers don't match. What is the reason for this? I am using freesurfer 4.3.1. Thank you, Jeff Sadino ___ 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] Surface Area and Cortical Volume
Hello, As I understand it, the surface area measure is not a real surface area measure. It is more a measure of how much the brain has to be stretched in order to get into a common space. My question is that if the cortical volume is calculated by multiplying the thickness and the surface area (right?), then is it a real volume that can be compared between subjects? Also, is it is more accurate to use the cortical volume measures from the aparc files rather than the aseg files, since the aseg files overestimate the white matter due to the manual tracing it is based on? Thank you, Jeff ___ 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] fs450 Longitudinal edits, varied data, and other questions
Thank you for your feedback on my previous question regarding the surface area measurement. We found it very helpful to move forward. I am beginning (again) to do longitudinal processing using fs4.5.0, but I just want to make sure that I understand everything right before starting this time. We have about 150 subjects with timepoints varying from 2-7, for a total of somewhere around 750 scans. All have already been processed cross-sectionally. 1. Reading through the wiki, the main thing to check on the cross-sectional runs are the control points. I'm confused by this though because the base creation only needs the reconstruction ran through the norm.mgz step to start. But we won't know if we need to add control points to the cross-sectional scan until after the surfaces are made, later in the stream. So it seems like I need to run the cross-sectionals through the norm.mgz step to start the base creation, but then before I run the -long part, I need to run the cross-sectionals through the surface reconstruction so that I can check the control points so that they can be copied from the cross-sectional run to the -long run? Are there any other edits I need to look at before starting the -base run? The cross-sectional brainmasks? The brainmask QA is just to make sure that the skull and other things are correctly stripped away? What about intensity normalization and gm/wm contrast on the norm.mgz image? 2. Also, in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12895.html, Martin says "the cross sectional asegs are 'fused' (probabilistic voting), to initialize the labeling in the longitudinal runs." Can someone explain what this 'fused' means? This is the only place I have read this besides the short description in recon-all --help. So it seems like I need to finish the cross-sectionals pretty much completely before doing the -long run. 3. Why is the brainmask from the -base run used in the -long run? I can see how this increases consistency between timepoints, but it seems like there would be a larger benefit of using the brainmask from the cross-sectional run? 4. I read that if the -base is stopped halfway through due to earthquakes, then it can be restarted from some point in the stream. I will just restart it from the beginning for ease of use. My question is what if the -long stops halfway through? I forget the command I use to restart from the last step in the cross-sectional stream (our cluster is down now), but can I do the same thing: recon-all -long tp1 longbase -restart_from_last_step_command? And then I had some questions specific to our data, if you would permit me =) 1. We have timepoints from the past 6 years, and so our scanning parameters have changed. Our old data is 1x1x1.4mm and 144 slices and our new data is 1x1x1mm and 160 slices. Some subjects have an acceleration of 2, while most have no acceleration. Our scanner is a Siemens 3T Trio. Will I need to exclude any of these timepoints? From both -base and -long? The thread http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14014.htmlsays that the new stream significantly reduces these effects, but I just wanted to doublecheck. 2. Because of the way our group is set up, sometimes subjects will have more than one mprage - from different days, say one week apart - for each timepoint. Even though I will only use one of these mprages for each -long timepoint, will the -base be better if I include all of them? As a tangential question, could I use these close together visits and average their mprages in the -motioncor step? My feeling would be no, that I could only do that if the subject does not move, but I wanted to check. Sorry for the long questions! Thank you for all of your great help all the time! Jeff Sadino ___ 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] BrainSegVol different in wmparc and aseg
Hello, When I look at the BrainSegVol and BrainSegVolNotVent in wmparc.stats, the values are around 200,000 - 300,000. However, when I look at the same measures in aseg.stats, the values are around 1,100,000 - 1,500,000. When I sum up the individual ROIs in wmparc, it comes out to >1L. I am currently using freesurfer 4.3.1. When I look at the aseg.stats files from freesurfer 3.0.5, ran on the same subjects, the values are up around that 1 - 1.5L range. This is consistent across all of our subjects: > 100 and from two different scanners at two locations. >From my wmparc file: # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1774481, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1774481.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 243312.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 275688, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 275688.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1302696.178406, mm^3 My question is why would wmparc so severely underestimate the BrainSegVol measure? If I can not fix it, should I take the BrainSegVol from the aseg.stats file? Thank you! Jeff Sadino ___ 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] BrainSegVol different in wmparc and aseg
bump :) On Tue, Nov 9, 2010 at 11:38 AM, Jeff Sadino wrote: > Hello, > > When I look at the BrainSegVol and BrainSegVolNotVent in wmparc.stats, the > values are around 200,000 - 300,000. However, when I look at the same > measures in aseg.stats, the values are around 1.1L - 1.5L. When I sum up > the individual ROIs in wmparc, it comes out to >1L. I am currently using > freesurfer 4.3.1. When I look at the aseg.stats files from freesurfer > 3.0.5, ran on the same subjects, the values are up around that 1 - 1.5L > range. This is consistent across all of our subjects: > 100 and from two > different scanners at two locations. > > From my wmparc file: > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1774481, > unitless > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1774481.00, mm^3 > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume > Without Ventricles, 243312.00, mm^3 > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, > 275688, unitless > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 275688.00, > mm^3 > # Measure IntraCranialVol, ICV, Intracranial Volume, 1302696.178406, mm^3 > > > My question is why would wmparc so severely underestimate the BrainSegVol > measure? If I can not fix it, should I take the BrainSegVol from the > aseg.stats file? > > Thank you! > Jeff Sadino > ___ 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] Reprocessing subjects with new freesurfer
Hello, I have an easy question: If I want to reprocess my fs 4.3.1 and fs 4.5.0 subjects with the newest fs 5.0 (btw, I thought we had fs 5.1 and 5.2 out already?), but I also want to keep the 4.3.1 and 4.5.0 subject folders for future reference, how do I do that? Do I copy all the 4.3.1 and 4.5.0 subjects to a new fs 5.0 subjects folder and then run fs 5.0? Thank you! Jeff Sadino ___ 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] recon-all -make all error?
Hello, I am reprocessing a number of subjects from fs 4.5.0 to fs 5.0.0. I am doing this by issuing the "recon-all -make all -s subject" command. It stops right away with the message: make: Nothing to be done for `all'. There exists the wmparc.stats file from the fs450 recon, but there is no label/?h.BA*.label or label/?h.entorhinal_exvivo.label files. Looking at the recon table, it looks like these are supposed to be part of the standard recon. Is my -make all broken, or can I ignore this message? Thank you, Jeff Sadino ___ 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] QA on wmparc.mgz
Hello, I am trying to verify the wmparc.mgz segmentations. I have identified outlier regions statistically, but then when I load up the wmparc.mgz file to QA visually, I find it is very difficult to QA the white matter regions. The problem is that because there is no contrast in the white matter, it is difficult to decide where one region ends and another one begins. I would like to ask if anybody has any suggestions as to a better way to visually verify the wmparc.mgz file. Thank you, Jeff ___ 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] Resampling Question
Hello, I have a question about the effects of FreeSurfer's resampling algorithms. The way our pipeline goes is that we convert our DICOM images into .nii.gz format using FSL tools. One of the commands we use is FSLCPGEOM. I was never sure why, but our script would always break without it. Looking into it in more detail now, I see that it is replacing the voxel size information in the Nifti header with the voxel size in the template that FSLCPGEOM is copying from. This is causing all of our data to show isovolumetric 1x1x1 information in the header, even if the voxels really are non-isovolumetric. I have been having a difficult time combining FreeSurfer results across our different studies and I am wondering if this might be the reason why. All of our studies have voxels acquired near 1x1x1 isovolumetric, usually no more than .3mm away in any direction. What would the effect be of pushing data through the FreeSurfer reconstruction pipeline that is not really 1x1x1 isovolumetric? Thank you, Jeff Sadino ___ 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] Resampling Question
One more thing that might be useful: for my current dataset, everything was processed in FreeSurfer 4.3.1. Thank you, Jeff On Mon, Mar 7, 2011 at 12:41 PM, Jeff Sadino wrote: > Hello, > > I have a question about the effects of FreeSurfer's resampling algorithms. > The way our pipeline goes is that we convert our DICOM images into .nii.gz > format using FSL tools. One of the commands we use is FSLCPGEOM. I was > never sure why, but our script would always break without it. Looking into > it in more detail now, I see that it is replacing the voxel size information > in the Nifti header with the voxel size in the template that FSLCPGEOM is > copying from. This is causing all of our data to show isovolumetric 1x1x1 > information in the header, even if the voxels really are non-isovolumetric. > I have been having a difficult time combining FreeSurfer results across our > different studies and I am wondering if this might be the reason why. All > of our studies have voxels acquired near 1x1x1 isovolumetric, usually no > more than .3mm away in any direction. What would the effect be of pushing > data through the FreeSurfer reconstruction pipeline that is not really 1x1x1 > isovolumetric? > > Thank you, > Jeff Sadino > ___ 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] Visualizing Subcortical Volume Differences
Hello, I am interested in a way to visualize the differences in the volume in subcortical structures, preferably in 3D. For example, I would like to view the Thalamus of controls. And then I would like to overlay a color-coded map that shows the difference between the volume of the Control Thalamus and the Study Thalamus. I have seen a couple of different ways to do this, but they all seem rather clunky. Can anyone recommend a method for this? Thank you very much, Jeff Sadino ___ 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] Visualizing Subcortical Volume Differences
Hello, I found a couple of scripts that might work, namely the mri_hausdorff_dist, mri_distance_transform, the mri_compute commands, and the mri_seg_diff. They all seem to do one part of what I want, but none all together. Has anyone done this before and could they point me in the right direction? Thank you, Jeff Sadino On Mon, Apr 11, 2011 at 1:07 PM, Jeff Sadino wrote: > Hello, > > I am interested in a way to visualize the differences in the volume in > subcortical structures, preferably in 3D. For example, I would like to view > the Thalamus of controls. And then I would like to overlay a color-coded > map that shows the difference between the volume of the Control Thalamus and > the Study Thalamus. I have seen a couple of different ways to do this, but > they all seem rather clunky. Can anyone recommend a method for this? > > Thank you very much, > Jeff Sadino > ___ 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] ICV smaller than the brain
Hello, I asked a question similar to this last year when working with FS 4.3.1, and I'm hoping that there is something new in FS 5 that can help. I am having a problem where a lot of my subjects' brains are larger than the eICV. In FS 4.3.1, it is happening in about 70/140 subjects, and in FS 5, it is happening in about 30/140 subjects. I checked them in tkregister2, and they look ok. I can use the --old-etiv-only command, but then the problem is that my ICV shoots up to 1.7L, and my brain/ICV ratio drops to .65, way to low to be reasonable. What could the reason for this be, and are there any other tricks that I could use? Thank you, Jeff Sadino ___ 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] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences
Hello, When FS5 came out, I copied over my FS4 reconstructions to my FS5 Subjects Directory, and then reran them using the FS5 recon-all stream. This updated their subject folders with the FS5 changes, but not in as many places as I would have thought. For example, on 6 test subjects, I created their FS5 folders from FS4 folders that I copied over and then ran the FS5 recon-all stream. I also created another copy of their FS5 folders from scratch. The average difference in their ICV values was -12,000 mm^3. Is it to be expected that FS5 reconstructions running on FS4 folders will not include all possible improvements? If I want to get an accurate an ICV measurement as possible, is it advisable to rerun all of my subjects in FS5, starting from scratch? As always, thank you for your valuable assistance! Jeff Sadino ___ 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] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences
Hello Bruce, Thank you for your reply. I used recon-all -make all -s subject. Thanks, Jeff On Thu, Jun 16, 2011 at 3:11 PM, Bruce Fischl wrote: > Hi Jeff > > what command did you run to run them over? > > cheers > Bruce > > On Thu, 16 Jun 2011, Jeff Sadino wrote: > > Hello, >> >> When FS5 came out, I copied over my FS4 reconstructions to my FS5 Subjects >> Directory, and then reran them using the FS5 recon-all stream. This >> updated >> their subject folders with the FS5 changes, but not in as many places as I >> would have thought. For example, on 6 test subjects, I created their FS5 >> folders from FS4 folders that I copied over and then ran the FS5 recon-all >> stream. I also created another copy of their FS5 folders from scratch. >> The >> average difference in their ICV values was -12,000 mm^3. Is it to be >> expected that FS5 reconstructions running on FS4 folders will not include >> all possible improvements? If I want to get an accurate an ICV >> measurement >> as possible, is it advisable to rerun all of my subjects in FS5, starting >> from scratch? >> >> As always, thank you for your valuable assistance! >> Jeff Sadino >> >> > > 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] Pial Edits on Base Template
Hello, I have a subject with three timepoints I am putting through the longitudinal stream in fs 5.0.0. After the base template was created, I edited some of the pial surfaces on the base. Now when I run the command: "recon-all -base subject -autorecon2-pial -autorecon3", it says: "ERROR: /mnt/fs5/050079 exists, delete or re-run with -force" This is confusing to me because if I delete the folder, then wont my edits also be deleted? I ran it using the force flag, and it seems to be going ok. I just want to ask if this is the best way to do this. Thank you, Jeff Sadino ___ 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.
