[Freesurfer] Running A Single Time Point Through Longitudinal Processing
Hello Freesurfer Experts, For a longitudinal dataset we worked on some time ago, in version 5.1, we want to add subjects with only one time point. According to the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing we can do this by passing only a single time point to the base creation and subsequently long step. For a cross-sectionally processed folder 060027_S01, I sent the command recon-all -base 060027 -tp 060027_S01 -all This exited with errors, but looking at the recon-all.log file, it seems to have dumped the 'help' file into the log. recon-all.log is attached. Please advise, Thank you, -Eric Cunningham recon-all.log Description: Binary data ___ 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] (no subject)
Hello Freesurfer Experts, For a longitudinal dataset we worked on some time ago, in version 5.1, we want to add subjects with only one time point. According to the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing we can do this by passing only a single time point to the base creation and subsequently long step. For a cross-sectionally processed folder 060027_S01, I sent the command recon-all -base 060027 -tp 060027_S01 -all This exited with errors, but looking at the recon-all.log file, it seems to have dumped the 'help' file into the log. recon-all.log is attached. Please advise, Thank you, -Eric Cunningham recon-all.log Description: Binary data ___ 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] the effects of cortical edits
Hello Freesurfer Experts, Our group is trying to determine the importance of manual edits on our data. After discovering poor white matter segmentation in the supramarginal/inferiorparietal regions, we performed manual edits as described in the FsTutorial. Surprisingly, the areas we edited had relatively small changes on the aparc.stats table in rh.area (0-8%) and other regions we didn't edit, such as the bankssts, entorhinal, and parsopercularis regions had much larger changes in rh.area (11-20%). Does this mean that the edits (and presumably errors) in one region of the brain affect the entire cortical template? Thanks, -Eric ___ 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] Linear Mixed Effects Models
Hello Freesurfer Experts,
I am currently trying to run the Linear Mixed Effects Models described in
the wiki here:
http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
And I am running into difficulties that are fairly well described by the
last message in this previous mail thread:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25787.html
Can you please clarify the variable "ni"?
the following command:
*[M,Y,ni] = sortData(M,1,Y,sID);*
results in:
??? Error: File: sortData.m Line: 59 Column: 6
Expression or statement is incorrect--possibly unbalanced (, {, or [.
do i need to build "ni" ahead of time?
You probably don't need to know this, but I am using data generated by
Freesurfer version 5.1, on matlab 7.8.0 (R2009a), which I gather will cause
a few problems further down the line.
Thank you for your help,
-Eric
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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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dispose of the e-mail.
[Freesurfer] comparing models
Hello Freesurfer experts, I have a question about how to determine if a covariate is important in a mixed effects model for example: Y1 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) + B5(covariate_1) +B6(covariate_2) Y2 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) + B5(covariate_1) Would it be appropriate to use the lme_mass_LR script? (the script says it is for comparing models with q and q+1 random effects). Thanks, -E ___ 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] comparing models
Sorry! I made a mistake with my example. I meant to say group_effect instead of rand_effect. It should read as follows: Y1 = B1 + B2(time) + B3(group_effect1) + B4(group_effect*time) + B5(covariate_1) +B6(covariate_2) Y2 = B1 + B2(time) + B3(group_effect1) + B4(group_effect*time) + B5(covariate_1) The difference between the two that I was trying to highlight is the presence of the second covariate term. Thanks, -E On Tue, Mar 4, 2014 at 11:18 AM, Eric Cunningham wrote: > Hello Freesurfer experts, > I have a question about how to determine if a covariate is important in a > mixed effects model > for example: > > Y1 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) + > B5(covariate_1) +B6(covariate_2) > Y2 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) + > B5(covariate_1) > > Would it be appropriate to use the lme_mass_LR script? (the script says > it is for comparing models with q and q+1 random effects). > > Thanks, > -E > ___ 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] mris_preproc, mri_surf2surf and lme_mass_vw
Hello Freesurfer experts, The lme_mass_vw script runs for a long time and outputs info into the matlab terminal. Most look like this: Location #: Algorithm did not converge. Initial and final likelihoods: ###, ### Running this script, for almost every line, the initial and final likelihoods are "Inf". Is this indicative of a problem? Getting these results made me wonder if the Y-input was built properly. Using mris_preproc and mri_surf2surf to smooth, we tested 10mm smoothing and no smoothing in addition to the 30mm smoothing we had been doing originally. The results: smoothed to 30 ~ almost every likelihood = Inf, Inf smoothed to 10 ~ some (1 in 5? 10?) likelihood = Inf not smoothed ~ no instances of likelihood = Inf, Inf Thanks, -Eric ___ 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] LME advice
Hello Freesurfer experts, I am getting some unusual results with the lme pipeline, and I would appreciate help with identifying the most likely step in which the problem may have originated. Running lme_fit_FS.m on a single vertex, followed by lme_F on the output of that (stats) yields a p-value of 0. This is because the fcdf function in matlab rounds to 1 if the F-value is big enough (in our case it rounds at about 80, and our F-value is 123). This being the case, we are trying to determine whether this is (1) a problem with the data, (2) a problem with the script somewhere, or (3) a system setting I don't know about. I'm not sure if you have enough information, but can you tell me if the F-values and Beta values look possible (reasonable?)? Thanks for any advice you can provide. -E Starting Fisher scoring iterations Likelihood at FS iteration 1 : 484.5267 Gradient norm: 53.7987 Likelihood at FS iteration 2 : 484.5984 Gradient norm: 1.3858 Likelihood at FS iteration 3 : 484.5985 Gradient norm: 0.02 Likelihood at FS iteration 4 : 484.5985 Gradient norm: 0.00056884 Total elapsed time is 0.24038 seconds stats = Bhat: [7x1 double] CovBhat: [7x7 double] bihat: [1x93 double] Covbihat: [93x1 double] phisqhat: 0.0110 SIGMA: [345x5 double] W: [345x5 double] Dhat: 0.0213 X: [345x7 double] Zcols: 1 re: [345x1 double] ni: [93x1 double] lreml: 484.5985 st = 1 K>> stats.Bhat ans = 3.1531 -0.0559 0.0148 -0.0154 -0.0309 -0.0767 -0.0229 K>> -0.0559 K>> fstats = lme_F(stats,contrastmatrix) fstats = F: 123.4649 pval: 0 sgn: -1 df: [1 284.0811] ___ 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] reproducing sig.mgh
Hello Freesurfer Experts, I am trying to reproduce the values in sig.mgh using matlab, just to confirm that I know what is going on. My numbers do not match exactly, and I am hoping someone can explain my error, or point me in the right direction. With Qdec, I built a model with one discrete factor (A) with groups (A1) and (A2), one continuous covariate (B), and one nuisance factor (C). I extracted the values from sig.mgh from the folder: lh-Diff-A1-A2-Cor-area-B at a specific vertex. I also extracted the values from y.mgh at the same vertex. I then ran an anova with contrast matrix, and expected the -log10(p-value) of the A*B term to match that of sig.mgh. [1 0 0;... (A) 0 1 0;...(B) 0 0 1;...(C) 1 1 0]; (A*B) Thank you for your time, -E ___ 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] subjects_dir
Greetings Freesurfer experts, The README file in the $SUBJECTS_DIR says that a different directory can be specified by setting the env var SUBJECTS_DIR prior to the 'source $FREESURFER_HOME/FreeSurferEnv.csh' statement. Do the original contents of SUBJECTS_DIR (such as fsaverage) need to be moved into the newly specified SUBJECTS_DIR? Thanks, -Eric ___ 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] subjects_dir
Other than fsaverage, are there any other files that need to be linked for recon-all to work? Thanks On Mon, Nov 23, 2015 at 4:57 PM, Bruce Fischl wrote: > Hi Eric > No, you can just symlink fsaverage and such > Cheers > Bruce > > > On Nov 23, 2015, at 9:40 PM, Eric Cunningham wrote: > > > > Greetings Freesurfer experts, > > > > The README file in the $SUBJECTS_DIR says that a different directory can > be specified by setting the env var SUBJECTS_DIR prior to the 'source > $FREESURFER_HOME/FreeSurferEnv.csh' statement. > > > > Do the original contents of SUBJECTS_DIR (such as fsaverage) need to be > moved into the newly specified SUBJECTS_DIR? > > > > Thanks, > > -Eric > > > > ___ > > 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. > > ___ 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 the talairach.xfm
Hi, I have a few very basic clarification questions regarding the recon-all processing pipeline. I am currently following the instructions here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Near the end of the page, it instructs me to rerun the whole process using my new talairach, using the command: recon-all -all -subjid [subjid] Questions: (1) Since the talairach file is created during recon-all, wouldn't rerunning the whole process overwrite my freshly edited file with whatever it came up with the first time? (2) Assuming the answer to question 1 is 'no', can i rerun the process in steps (-autorecon1, then -autorecons 2 and 3) without overwriting my freshly edited file? (3) Are there any files that are unusual in their likelihood of being overwritten? (e.g. running recon-all -all will overwrite aseg.stats but not talairach.xfm) Thank you for your help, -Eric ___ 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] talairach.xfm error frequency
Greetings, I am trying to determine how bad a talairach.xfm registration has to be to warrant a manual edit. I have found that even minor edits can have noticable (9%) effects on major subcortical volumes (such as thalamus or hippocampus). Very few registrations seem to have completely failed, but most seem like they could be made better by a tweak here or there. At what point would I just be adding randomness by manually editing? About what percent of a given dataset would you expect to manually edit? Much appreciated, -Eric Cunningham ___ 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] talairach.xfm error frequency
Hi Bruce, I am running version 5.10 Thanks, -Eric On Wed, Oct 10, 2012 at 3:13 PM, Bruce Fischl wrote: > Hi Eric > > what version are you running? > Bruce > > On Wed, 10 Oct 2012, Eric Cunningham wrote: > > Greetings, >> >> I am trying to determine how bad a talairach.xfm registration has to be to >> warrant a manual edit. I have found that even minor edits can have >> noticable (9%) effects on major subcortical volumes (such as thalamus or >> hippocampus). Very few registrations seem to have completely failed, but >> most seem like they could be made better by a tweak here or there. At >> what >> point would I just be adding randomness by manually editing? >> >> About what percent of a given dataset would you expect to manually edit? >> >> Much appreciated, >> -Eric Cunningham >> >> >> > > 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.
Re: [Freesurfer] talairach.xfm error frequency
Hi all, Ah, good to know that there is a Talairach accuracy problem. What have other groups been doing about this? Do you think it makes sense to manually edit much of our data? From what we've seen so far (registering to ages 3-9 so more errors expected) about 25% of our data have the registration sufficiently far off to push the TARGET volume (our subject's volume and the green lines in the pictures http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach) outside of the skull. Thanks, -Eric On Wed, Oct 10, 2012 at 3:26 PM, Bruce Fischl wrote: > I think 5.1 specifically has a problem with Talairach accuracy (is that > right Nick?). Should be much better with the next release > > On Wed, 10 Oct 2012, Eric Cunningham wrote: > > Hi Bruce, >> I am running version 5.10 >> Thanks, >> -Eric >> >> On Wed, Oct 10, 2012 at 3:13 PM, Bruce Fischl > > >> wrote: >> Hi Eric >> >> what version are you running? >> Bruce >> On Wed, 10 Oct 2012, Eric Cunningham wrote: >> >> Greetings, >> >> I am trying to determine how bad a talairach.xfm >> registration has to be to >> warrant a manual edit. I have found that even minor >> edits can have >> noticable (9%) effects on major subcortical volumes >> (such as thalamus or >> hippocampus). Very few registrations seem to have >> completely failed, but >> most seem like they could be made better by a tweak >> here or there. At what >> point would I just be adding randomness by manually >> editing? >> >> About what percent of a given dataset would you >> expect to manually edit? >> >> Much appreciated, >> -Eric Cunningham >> >> >> >> >> 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.
Re: [Freesurfer] talairach.xfm error frequency
Would you recommend subjects through autorecon1 in freesurfer 5.0 and then through autorecon2 and autorecon3 in 5.1? Thanks, -Eric On Wed, Oct 10, 2012 at 4:35 PM, Eric Cunningham wrote: > Hi all, > Ah, good to know that there is a Talairach accuracy problem. What have > other groups been doing about this? Do you think it makes sense to > manually edit much of our data? From what we've seen so far (registering > to ages 3-9 so more errors expected) about 25% of our data have the > registration sufficiently far off to push the TARGET volume (our subject's > volume and the green lines in the pictures > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach) outside of > the skull. > Thanks, > -Eric > > > On Wed, Oct 10, 2012 at 3:26 PM, Bruce Fischl > wrote: > >> I think 5.1 specifically has a problem with Talairach accuracy (is that >> right Nick?). Should be much better with the next release >> >> On Wed, 10 Oct 2012, Eric Cunningham wrote: >> >> Hi Bruce, >>> I am running version 5.10 >>> Thanks, >>> -Eric >>> >>> On Wed, Oct 10, 2012 at 3:13 PM, Bruce Fischl < >>> fis...@nmr.mgh.harvard.edu> >>> wrote: >>> Hi Eric >>> >>> what version are you running? >>> Bruce >>> On Wed, 10 Oct 2012, Eric Cunningham wrote: >>> >>> Greetings, >>> >>> I am trying to determine how bad a talairach.xfm >>> registration has to be to >>> warrant a manual edit. I have found that even minor >>> edits can have >>> noticable (9%) effects on major subcortical volumes >>> (such as thalamus or >>> hippocampus). Very few registrations seem to have >>> completely failed, but >>> most seem like they could be made better by a tweak >>> here or there. At what >>> point would I just be adding randomness by manually >>> editing? >>> >>> About what percent of a given dataset would you >>> expect to manually edit? >>> >>> Much appreciated, >>> -Eric Cunningham >>> >>> >>> >>> >>> 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] checking talairach.lta
Hi folks, In previous threads, the command provided to check the talairach.lta is... tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca \ --targ ../brainmask.mgz --lta-inv talairach.lta --reg talairach.lta.reg.dat \ --surfs --s $subject When I try to run this command, I run into trouble with the --lta-inv portion. (it is an unknown option). I am running version 5.1. Can anyone help? Thanks, -Eric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] checking talairach.lta
i tried replacing this file in tktools with the new tkregister2.bin, and i get a new error: /lib64/tls/libc.so.6: version GLIBC_2.4 not found On Mon, Nov 5, 2012 at 6:06 PM, Douglas Greve wrote: > > OK, I see the problem. I should have told you to put tkregsiter2.bin into > /apps/fs510/tktools/ (after making a copy of the one there). > doug > > > > > On 11/5/12 5:00 PM, Eric Cunningham wrote: > > [e4fs@cluster bin]$ ls -l `which tkregister2.bin` > -rwxr-xr-- 1 jsadinol fs 21663433 May 22 2011 /apps/fs510/tktools/ > tkregister2.bin > > [e4fs@cluster bin]$ tkregister2 --all-info > ProgramName: tkregister2.in ProgramArguments: --all-info > ProgramVersion: $Name: stable5 $ TimeStamp: 2012/11/05-21:43:36-GMT > BuildtimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 > 2011/03/28 20:25:16 greve Exp $User: e4fs Machine: cluster.mrilab.net > Playform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC > CompilerVersion: 30400 > > > > fyi: /apps/fs510/ = $FREESURFER_HOME > i tried replacing this file in tktools with the new tkregister2.bin, and i > get a new error: > /lib64/tls/libc.so.6: version GLIBC_2.4 not found > > > > On Mon, Nov 5, 2012 at 11:34 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> Can you send me the result of >> >> ls -l `which tkregister2.bin` >> >> and >> >> tkregister2 --all-info >> >> >> doug >> >> >> >> >> On 11/05/2012 03:54 PM, Eric Cunningham wrote: >> >>> retried it, same error >>> >>> new file is .bin, old file is tkregister2, no old tkregister2.bin file >>> appeared to be in the folder $FREESURFER_HOME/bin >>> >>> On Mon, Nov 5, 2012 at 10:49 AM, Douglas N Greve < >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> I'm not sure that was the right thing to do. There should be two >>> files: >>> tkregister2 and tkregister2.bin. tkregister2 is just a script that >>> calls >>> tkregister2.bin after setting up some environment variables. Try >>> keeping >>> the original file name. >>> doug >>> >>> On 11/05/2012 03:43 PM, Eric Cunningham wrote: >>> > i am sure >>> > there is one irregularity, namely that the '.bin' extension is >>> absent >>> > from our old file, so i renamed the new file without it (as >>> > tkregister2) and moved the other one to tkregister2_backup >>> > >>> > the command i listed from previous threads was given to someone >>> else >>> > from our lab (and probably worked), so it is likely that the >>> problem >>> > is somewhere on our side, i was just hoping that it was known and >>> > recognizable from the error >>> > >>> > >>> > >>> > On Mon, Nov 5, 2012 at 10:15 AM, Douglas N Greve >>> > mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >>> > >>> > are you sure you are using the new version? >>> > >>> > >>> > On 11/05/2012 02:38 PM, Eric Cunningham wrote: >>> > >>> > tried the new version, and it errored out at the same step >>> > >>> > ERROR: Option --lta-inv unknown >>> > >>> > thanks again for your help! >>> > >>> > On Mon, Nov 5, 2012 at 8:16 AM, Douglas N Greve >>> > mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu >>> >> >>> > <mailto:gr...@nmr.mgh.harvard.edu >> gr...@nmr.mgh.harvard.edu> >>> > <mailto:gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote: >>> > >>> > Try using this version >>> > >>> >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tkregister2.bin >>> > copy it into $FREESURFER_HOME/bin (but make a back up >>> of >>> > the existing >>> > tkregister2.bin first!) >>> > doug >>> > >>>
[Freesurfer] regarding use-mritotal
Hi, this link: http://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 discusses a solution to bad talairach.xfm transforms, the -use-mritotal flag. this link: http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV mentions that the talairach.xfm is used to calculate the total intracranial volume. is using mritotal likely to result in significantly different intracranial volumes even if the talairach.xfm does not appear to be very different when viewed? thanks much, -eric ___ 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] gray matter surface
oh interesting! i'm not sure if it will apply to me, but how would one go about the hires T2 / FLAIR based refinement? thanks, -eric On Tue, Feb 19, 2013 at 11:44 AM, Bruce Fischl wrote: > Hi Eric > > yes, the bits of dura left around (your red circles) will make the > thickness incorrect in those regions. If you want to fix it you can try the > graph cuts skull stripping, or if you have a hires T2 or FLAIR we can > typically refine the surfaces to avoid dura. As for the yellow arrow, I > can't tell from a single slice if that is an error. Certainly the > intensities look like gray matter, but it could be damaged white matter > instead. > > cheers > Bruce > > > > > On Tue, 19 Feb 2013, Eric Cunningham wrote: > > hello freesurfer experts, >> >> attached is an image drawn from the tutorial page. >> http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/**WhiteMatterEdits<http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits> >> i have circled 3 examples of what i am asking about >> >> sometimes the gray matter surface (the red line) appears to include an >> area >> of membrane or something else that isn't brain. will this adversely >> affect >> the any of the measures in the region? what, if anything, should be done >> about it? >> >> thank you, >> -eric cunningham >> >> >> > > 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] skullstripping outside freesurfer
External Email - Use Caution Dear Freesurfer Experts, I have recently processed some data with the following 2 steps: 1) Perform skullstripping outside freesurfer to generate a nifti file (mostly using AFNI). 2) Run that through freesurfer using the -noskullstrip flag. Comparing the results from this with just running freesurfer alone, I found that the eTIV was significantly smaller, and not terribly well correlated (R^2 of .65). When looking at cortical volume measurements, it is generally considered a good idea to correct for eTIV. How would you recommend doing so in this case? Freesurfer version 5.3. Thanks, -Eric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_glmfit and R
External Email - Use Caution
Hello Freesurfer Experts,
I am trying to plot the ${meas} values at the maximum vertex in a
significant cluster found by the group analysis pipeline (mri_glmfit).
I created an .mgh file with mris_preproc, rh.cbd7.area.10.mgh. I read this
file into matlab using MRIread.
(mgh=MRIread(${path}/rh.cbd7.area.10.mgh);) After running mri_glmfit and
mri_glmfit-sim, I found a significant cluster with maximum at vertex
53263. I read the values at this vertex using matlab again
(values=mgh.vol(1,53263,1,:)). I then tried to duplicate the p value that
mri_glmfit gave me at that vertex in R, and was unsuccessful (the p values
did not match, and were actually quite different).
I had assumed that mri_glmfit ran a glm at every vertex of the smoothed mgh
file created by mris_preproc, and that the p values of that glm were
assembled into sig.mgh. Was this assumption wrong?
Thanks,
-Eric
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Re: [Freesurfer] mri_glmfit and R
External Email - Use Caution
Firstly, yes. I was making that error, and many thanks for catching it!
Unfortunately, even after applying that fix, the problem remains, but it
does explain why some of my earlier attempts to figure things out on my own
failed. I will try to duplicate a simpler model and see if that works.
Follow up question.
If I have a 2-level factor that I want to include as a nuisance variable,
(e.g. gender), would I be able to define that as a numeric variable with
values 0 and 1, rather than splitting up my other categories?
Thank you for your help,
-Eric
On Thu, Aug 13, 2020 at 9:42 AM Douglas N. Greve
wrote:
> Do you have a 1-off error? Ie, FS starts counting at 0 and matlab starts
> counting at 1. So vertex 53263 is vertex 53264 in matlab.
>
> On 8/12/2020 5:31 PM, Eric Cunningham wrote:
>
> External Email - Use Caution
> Hello Freesurfer Experts,
>
> I am trying to plot the ${meas} values at the maximum vertex in a
> significant cluster found by the group analysis pipeline (mri_glmfit).
>
> I created an .mgh file with mris_preproc, rh.cbd7.area.10.mgh. I read
> this file into matlab using MRIread.
> (mgh=MRIread(${path}/rh.cbd7.area.10.mgh);) After running mri_glmfit and
> mri_glmfit-sim, I found a significant cluster with maximum at vertex
> 53263. I read the values at this vertex using matlab again
> (values=mgh.vol(1,53263,1,:)). I then tried to duplicate the p value that
> mri_glmfit gave me at that vertex in R, and was unsuccessful (the p values
> did not match, and were actually quite different).
>
> I had assumed that mri_glmfit ran a glm at every vertex of the smoothed
> mgh file created by mris_preproc, and that the p values of that glm were
> assembled into sig.mgh. Was this assumption wrong?
>
> Thanks,
> -Eric
>
> ___
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>
>
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Re: [Freesurfer] mri_glmfit and R
External Email - Use Caution
There's a minor bit of confusion with the code you sent.
[F p] = fast_fratio(beta,X,rvar,C); gives the error "inner error dimensions
must agree" on the line "ces= C*beta".
size(C) = [1 9]
size(beta) = [1 9]
should this be
[F p] = fast_fratio(beta',X,rvar,C); ?
when I run that, size(p) = [1 9], so I'm not sure if that's the intent.
Thanks
-E
On Thu, Aug 13, 2020 at 11:50 AM Douglas N. Greve
wrote:
> Probably your model in R is not the same as the model in FS. First, see if
> you can replicate using
>
> X = load('Xg.dat')
> C = load('contrast/C.dat');
> [beta rvar] = fast_glmfit(X,y); % y is the data at your vertex
> [F p] = fast_fratio(beta,X,rvar,C);
> p should be the same as in the .sig file
>
> Generally, gender should be separate groups. In some simple cases it works
> to simulate it as a covariate.
>
> On 8/13/2020 11:43 AM, Eric Cunningham wrote:
>
> External Email - Use Caution
> Firstly, yes. I was making that error, and many thanks for catching it!
> Unfortunately, even after applying that fix, the problem remains, but it
> does explain why some of my earlier attempts to figure things out on my own
> failed. I will try to duplicate a simpler model and see if that works.
>
> Follow up question.
> If I have a 2-level factor that I want to include as a nuisance variable,
> (e.g. gender), would I be able to define that as a numeric variable with
> values 0 and 1, rather than splitting up my other categories?
>
> Thank you for your help,
> -Eric
>
> On Thu, Aug 13, 2020 at 9:42 AM Douglas N. Greve
> wrote:
>
>> Do you have a 1-off error? Ie, FS starts counting at 0 and matlab starts
>> counting at 1. So vertex 53263 is vertex 53264 in matlab.
>>
>> On 8/12/2020 5:31 PM, Eric Cunningham wrote:
>>
>> External Email - Use Caution
>> Hello Freesurfer Experts,
>>
>> I am trying to plot the ${meas} values at the maximum vertex in a
>> significant cluster found by the group analysis pipeline (mri_glmfit).
>>
>> I created an .mgh file with mris_preproc, rh.cbd7.area.10.mgh. I read
>> this file into matlab using MRIread.
>> (mgh=MRIread(${path}/rh.cbd7.area.10.mgh);) After running mri_glmfit and
>> mri_glmfit-sim, I found a significant cluster with maximum at vertex
>> 53263. I read the values at this vertex using matlab again
>> (values=mgh.vol(1,53263,1,:)). I then tried to duplicate the p value that
>> mri_glmfit gave me at that vertex in R, and was unsuccessful (the p values
>> did not match, and were actually quite different).
>>
>> I had assumed that mri_glmfit ran a glm at every vertex of the smoothed
>> mgh file created by mris_preproc, and that the p values of that glm were
>> assembled into sig.mgh. Was this assumption wrong?
>>
>> Thanks,
>> -Eric
>>
>> ___
>> Freesurfer mailing
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>>
>>
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>
>
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>
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