Freesurfer

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QDEC results and stats
by carolina.mr 26 Sep '11

26 Sep '11

5 5

using isxconcat for partial correlation coefficient map
by SHAHIN NASR 26 Sep '11

26 Sep '11

Hi, Would you tell me how can I use isxconcat-sess to calculate group averaged "partial correlation coefficient map"? I have already generated pcc.nii files for each individual subject. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

1 0

volume of different lobes of the brain....
by Gonzalo Rojas Costa 26 Sep '11

26 Sep '11

Hi: How can I get the volume of the different lobes of the brain (occipital, parietal, temporal, etc) ?... White matter and gray matter?... Labels ?... Sincerely, Gonzalo Rojas Costa

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Tracula references
by Shanqing Cai 26 Sep '11

26 Sep '11

Hi, I am using Tracula in my diffusion data analysis and am interested in finding out what would be the best citations or references for this tool. A quick Internet search brings me to two conference papers, one in ISMRM and one in an IEEE conference. Are there any journal articles that have been published on Tracula? I need the information for better understanding of the tool and possible citations in future publications. Thank you. Best regards, Shanqing Cai

2 1

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

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Freesurfer