Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

26 Sep '11

Hello, I was wondering what orientation conventions are used when calculating the affine transformation matrix in register.dat. For an example, I'll use the data from subject 101 of the fsfast tutorial. According to mri_info, the functional volume is in LPS orientation, and the processed anatomical volume (T1.mgz) is in LIA orientation. Does the matrix in register.dat convert from the functional LPS orientation to the anatomical LIA orientation, or does the matrix assume these volumes are already transformed in some other way? Thanks, Clark

2 4

Talairach registration failes
by Martijn Steenwijk 26 Sep '11

26 Sep '11

Dear all, I have a problem running Freesurfer on images having a relatively tight FOV. While running talairach_afd, the registration of the template to the image fails. Checking the registration (as explained on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach) reveals that the template gets completely squeezed, so it's not a problem of a too sensitive registration quality detection, it's the registration which fails. Is there a way to make this registration more robust for these kind of images? With best regards, Martijn

1 0

Re: [Freesurfer] tksurfer can't rotate hemisphere -SOLVED
by Michelle Umali 25 Sep '11

25 Sep '11

Dear Bruce and the Freesurfers, I had to update my ATI graphics driver and set the doublebufferflag to 1. Everything is working just fine. Thanks for your help. Michelle On Sun, Sep 25, 2011 at 2:49 PM, Michelle Umali <mumali01(a)gmail.com> wrote: > Hi Bruce and the Freesurfers, > Sadly instead of .028 seconds, it takes ~60 second for a single 90 degree > rotation. > > Thanks for helping. > Michelle > > Here is the screen output: > > BOTANICA:~> tksurfer ld07 lh inflated > subject is ld07 > hemi is lh > surface is inflated > surfer: current subjects dir: /usr/local/freesurfer/subjects > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /home/michelle > checking for nofix files in 'inflated' > Reading image info (/usr/local/freesurfer/subjects/ld07) > Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz > surfer: Reading header info from > /usr/local/freesurfer/subjects/ld07/mri/orig.mgz > surfer: vertices=156145, faces=312286 > surfer: single buffered window > surfer: tkoInitWindow(ld07) > surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl > Reading /usr/local/freesurfer/tktools/tkm_common.tcl > Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl > Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl > Reading /usr/local/freesurfer/tktools/tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > % surfer: curvature read: min=-3.127128 max=2.364444 > > > > > > On Sun, Sep 25, 2011 at 2:35 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> Hi Michelle >> >> 28063 microseconds = 28milliseconds = 0.028 sec which is quite fast. Is >> that what you observe? Do you get any errors when you start tksurfer? Can >> you paste the screen output of tksurfer in an email? I'm not sure what's >> going on. When Nick/Krish/Ruopeng start reading email tomorrow, maybe they >> can help >> Bruce >> >> >> >> On Sun, 25 Sep 2011, Michelle Umali wrote: >> >> Hi Bruce, >>> Pressing return after entering the angle doesn't help :-) >>> >>> Still extremely slow: rotations, loading labels, and loading annotation. >>> >>> >>> Do you have any suggestions for a fix? >>> >>> Thanks. >>> Michelle >>> >>> >>> On Sun, Sep 25, 2011 at 1:59 PM, Bruce Fischl < >>> fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> When you type in a different angle make sure you hit return. Tk >>> is strange that way >>> >>> >>> >>> On Sep 25, 2011, at 1:50 PM, Michelle Umali <mumali01(a)gmail.com> >>> wrote: >>> >>> Hi Bruce, >>> I got 28063 microseconds per iteration. No, I'm not >>> running remotely. >>> Also, no matter what angle I choose, the rotation is >>> always by 90 degrees. >>> >>> Thanks. >>> Michelle >>> >>> On Sun, Sep 25, 2011 at 1:39 PM, Bruce Fischl >>> <fischl(a)nmr.mgh.harvard.edu> wrote: >>> Try typing >>> >>> time redraw >>> >>> At the tcl % prompt. Something sounds like it is very >>> wrong as it should be less than a second, not a minute. >>> You aren't running over vnc or something, are you? >>> >>> >>> >>> On Sep 25, 2011, at 1:28 PM, Michelle Umali >>> <mumali01(a)gmail.com> wrote: >>> >>> Dear Bruce and the Freesurfers, >>> >>> It turns out that the hemisphere does rotate, >>> but only if I press the same button again >>> after at least a minute or so. Then I have to >>> wait for a while before I can press another >>> rotation button. Do I maybe need to do any >>> display setup for using hardware acceleration >>> under Ubuntu? >>> >>> Thanks. >>> Michelle >>> >>> On Sun, Sep 25, 2011 at 1:16 PM, Bruce Fischl >>> <fischl(a)nmr.mgh.harvard.edu> wrote: >>> nope, nothing else should be >>> required. Did you push any >>> "rotate" buttons first? >>> >>> On Sun, 25 Sep 2011, Michelle Umali wrote: >>> >>> Dear Freesurfers, >>> I have recently installed >>> Freesurfer 5.1 and FSL 4.1.4 on a >>> linux machine. >>> When I run tksurfer, I can't >>> rotate the hemisphere. It will >>> show the >>> curvature, but the hemisphere just >>> won't turn. I was able to do this >>> through virtual box on my windows >>> laptop. >>> >>> Is there another software >>> package/toolbox that is needed? >>> Is either Matlab >>> or AFNI required as well? >>> >>> Thanks. >>> Michelle >>> >>> >>> >>> >>> >>> 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(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> >>> >

2 1

tksurfer rotation isssue
by Michelle Umali 25 Sep '11

25 Sep '11

Hi Bruce and the Freesurfers, Sadly instead of .028 seconds, it takes ~60 second for a single 90 degree rotation. Thanks for helping. Michelle Here is the screen output: BOTANICA:~> tksurfer ld07 lh inflated subject is ld07 hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/michelle checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/ld07) Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: vertices=156145, faces=312286 surfer: single buffered window surfer: tkoInitWindow(ld07) surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl Reading /usr/local/freesurfer/tktools/tkm_common.tcl Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % surfer: curvature read: min=-3.127128 max=2.364444 On Sun, Sep 25, 2011 at 2:35 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Michelle > > 28063 microseconds = 28milliseconds = 0.028 sec which is quite fast. Is > that what you observe? Do you get any errors when you start tksurfer? Can > you paste the screen output of tksurfer in an email? I'm not sure what's > going on. When Nick/Krish/Ruopeng start reading email tomorrow, maybe they > can help > Bruce > > > > On Sun, 25 Sep 2011, Michelle Umali wrote: > > Hi Bruce, >> Pressing return after entering the angle doesn't help :-) >> >> Still extremely slow: rotations, loading labels, and loading annotation. >> >> >> Do you have any suggestions for a fix? >> >> Thanks. >> Michelle >> >> >> On Sun, Sep 25, 2011 at 1:59 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> > >> wrote: >> When you type in a different angle make sure you hit return. Tk >> is strange that way >> >> >> >> On Sep 25, 2011, at 1:50 PM, Michelle Umali <mumali01(a)gmail.com> >> wrote: >> >> Hi Bruce, >> I got 28063 microseconds per iteration. No, I'm not >> running remotely. >> Also, no matter what angle I choose, the rotation is >> always by 90 degrees. >> >> Thanks. >> Michelle >> >> On Sun, Sep 25, 2011 at 1:39 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> Try typing >> >> time redraw >> >> At the tcl % prompt. Something sounds like it is very >> wrong as it should be less than a second, not a minute. >> You aren't running over vnc or something, are you? >> >> >> >> On Sep 25, 2011, at 1:28 PM, Michelle Umali >> <mumali01(a)gmail.com> wrote: >> >> Dear Bruce and the Freesurfers, >> >> It turns out that the hemisphere does rotate, >> but only if I press the same button again >> after at least a minute or so. Then I have to >> wait for a while before I can press another >> rotation button. Do I maybe need to do any >> display setup for using hardware acceleration >> under Ubuntu? >> >> Thanks. >> Michelle >> >> On Sun, Sep 25, 2011 at 1:16 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> nope, nothing else should be >> required. Did you push any >> "rotate" buttons first? >> >> On Sun, 25 Sep 2011, Michelle Umali wrote: >> >> Dear Freesurfers, >> I have recently installed >> Freesurfer 5.1 and FSL 4.1.4 on a >> linux machine. >> When I run tksurfer, I can't >> rotate the hemisphere. It will >> show the >> curvature, but the hemisphere just >> won't turn. I was able to do this >> through virtual box on my windows >> laptop. >> >> Is there another software >> package/toolbox that is needed? >> Is either Matlab >> or AFNI required as well? >> >> Thanks. >> Michelle >> >> >> >> >> >> 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(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >>

1 0

tksurfer can't rotate hemisphere
by Michelle Umali 25 Sep '11

25 Sep '11

Dear Freesurfers, I have recently installed Freesurfer 5.1 and FSL 4.1.4 on a linux machine. When I run tksurfer, I can't rotate the hemisphere. It will show the curvature, but the hemisphere just won't turn. I was able to do this through virtual box on my windows laptop. Is there another software package/toolbox that is needed? Is either Matlab or AFNI required as well? Thanks. Michelle

2 7

defining our own regions for tractography
by Ritobrato Datta 23 Sep '11

23 Sep '11

Hello All, I am a total newbee in dt-recon and tracula. So sorry if this is a very basic question. >From what I gathered so far- TRACULA uses the aparc+aseg.mgz from the FreeSurfer recon (T1-weighted volume) as ROIs to construct the tracts and also constructs a few tracts by default. Is there a way of defining our own ROIs and get tracts ? Thanks Ri

2 1

total wm volume calculation
by Zhang, Yuning 23 Sep '11

23 Sep '11

Dear FreeSurfer Expert, i am trying to generate the total wm volume using mris_wm_volume <subjid> <hemi> ,but this value is different from what i get using mirs_volume ?h.white, could you explain the differences between these two commands. and which is the best representation of the surface based total wm volume ? thanks yuning

2 1

QDEC and Cortical Thickenss
by Antonella Kis 23 Sep '11

23 Sep '11

Hi Doug, Many thanks for the valuable answer and help. I would appreciate a lot if you can advise me how I can get in a table from QDEC the clusters after I find the clusters and also the mean value for the cortical thickness within this clusters. I know in GLM the files are coming as an output but I cannot see in QDEC this files. The same question for the values after running FDR in QDEC. My last question is what should I do if for one case I get error when I do FDR and thresh is becoming 3.18 (instead of 2) and QDEC cannot run the statistics for the clusters. Also it is possible to get more clusters after running FDR in comparison with the no. of clusters when I set up the thresh 2? Thank you very much and have a great weekend! Antonella ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com>; freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Sent: Thursday, September 22, 2011 3:53 PM Subject: Re: [Freesurfer] Contrast Vector while eliminating age and gender If you want to "eliminate" age and gender, you have to include them in the model. In this case, they are called "nuisance" regressors. But this is just an arbitrary name. The model is constructed of regressors, some of which you care about and some you don't, but the GLM is run in the same way regardless. Where the difference comes is when you go to construct contrast vectors. If you want to treat some regressors as nuisance, then put a 0 in their column in the contrast vector. doug Antonella Kis wrote: > Hi Doug, > > Yes, I looked online but in all the examples I found age was included > in the study. The same thing for qdec all the examples I saw online > are related to a study (a comparison between two groups) but > considering age. > > I couldn't find any documentation for a study between two groups while > eliminating age and gender. > > Please advise and sorry for all this questions. > Regards, > Antonella > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Thursday, September 22, 2011 12:03 PM > *Subject:* Re: [Freesurfer] Contrast Vector while eliminating age and > gender > > Have you looked at the FSGD examples on the wiki? Do a search for FSGD. > doug > > Antonella Kis wrote: > > > > > > > > Dear All, > > > > What should be my contrast vector if I want to do a direct comparison > > between groups (patients vs. controls) after eliminating gender and > > age? Should this be [1 -1]? > > > > Should I change my FSGD in order to be able to compare between > > patients and controls accounting for age (I want to make sure that the > > age does not confound my results). Please see attached my FSGD file. > > > > Also, my question is how the clusters are created: the clusters > > formation is due to a similar value within cortical > > thickness(cortical thickness with similar values from patients and > > controls are grouped together in a cluster (e.g. cluster no.1) while > > other cortical thickness values are forming different clusters) or the > > clusters are formed based on age -age grouping (each subject belong to > > an age cluster)? > > > > Thank you, > > AK > > > > > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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(a)nmr.mgh.harvard.edu <mailto: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. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

tracula - if expression syntax
by Judit Haasz 23 Sep '11

23 Sep '11

Hi, I have been running tracula on a Linux machine, without a problem. Now I am trying to run tracula on a Mac-Pro machine (running Mac OS X version 10.7.1 - Lion). I followed the tutorial and set up the requested structure and configuration file. When I try running the preprocessing step (trac-all -prep -c ./scripts/dmrirc, both in bash and tcsh) I get the following message: If: expression syntax. Do u have some suggestions that i could try to overcome the problem? thanks, Judit

2 1

Re: [Freesurfer] Recon-all Error: _FindFacePath
by Louis Nicholas Vinke 23 Sep '11

23 Sep '11

Hi Daniel, Both of the cases you sent us had a fair amount of neck/spine remaining after the skullstrip step which caused mris_fix_topology to fail. I processed both cases again using the following command and recon-all finished without errors: recon-all -skullstrip -autorecon2 -autorecon3 -s [SubjID] Sometimes running the skullstrip step a second time can get rid of or reduce large portions of skull/dura which were not removed during the first pass. With those two cases there is still some skull/dura left which you could try to remove by playing with the skullstrip watershed parameters. See this wiki page for details: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix -Louis >> From: "Daniel Ferreira Padilla" <danifer(a)ull.es> >> Date: September 15, 2011 5:48:30 AM EDT >> To: <fischl(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Recon-all Error: _FindFacePath >> > >> Dear Bruce, >> >> >> >> Thank you very much. I have uploaded these two subjects to the file drop linked to your email (fischl(a)nmr.mgh.harvard.edu) It should be going to you. >> >> >> >> Thanks again >> >> >> >> Daniel Ferreira >

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Freesurfer