[Freesurfer] tkmedit error
Hi, I got an error with tkmedit command "freeglut (/home/pom/freesurfer/freesurfer/bin/tkmedit.bin): Unable to create direct context rendering for window 'Medit: ' This may hurt performance. Xlib: extension "XFree86-DRI" missing on display ":0.0". The only DRI related file I have is called /usr/X11R6/lib/modules/dri/fglrx_dri.so My freesurfer version is "freesurfer-Linux-rh9-stable-pub-v3.0.5". I am wondering if I need to update my linux, currently it is a very old OpenSuse 10.0 version? thank you -- Pom ___ 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] Interpreting results from Qdec
Exporting ROI volumes/thickness values may not be significant because the analysis in qdec (glm) includes the whole cortical surface. But, I have a follow up question to this question. In the plotted graph the abscissa reports F values. Which basically mean that the significant ROI reflects the distribution of F values. So for example the older the person the greater the F value in that region for thickness/volume. But that doesn't mean that thickness/volume in that region actually varies with age, rather that relative to the rest of the surface the older the person this ROI is more likely it is to be associated with age. Correct? Thanks Ilana On 4/27/11 8:12 PM, "Gallen, Courtney (NIH/NIDA) [F]" wrote: >Hi Doug > >Have a follow up question regarding significance levels in Qdec related >to extracting means from ROIs, etc. I'm posting to the entire mailing >list in case anyone else has ideas. > >Basically, I extracted mean volumes (from my set of participants) of ROIs >for which Qdec reports an interaction between two variables. I want to >look at these mean volumes in something like SPSS to see what is driving >the interaction/generate figures, etc. > >I'm having an issue with one such ROI, in that when I extract the mean >volumes and look for this interaction in SPSS, it is not significant (p ~ >0.5, so really not significant at all). Is there any way that an ROI >could be significant in Qdec (p of 0.05, Monte Carlo sim), but not in >SPSS when I extract means for each participant? > >Let me know if this isn't clear. Any thoughts would be appreciated! >Courtney > > >Courtney Gallen >Post-baccalaureate IRTA >Neuroimaging Research Branch >National Institute on Drug Abuse (IRP) >251 Bayview Blvd >Suite 200 >Baltimore, MD 21224 >Tel: (443) 740-2631 > >-Original Message- >From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu] >Sent: Tuesday, April 26, 2011 1:06 PM >To: Gallen, Courtney (NIH/NIDA) [F] >Subject: Re: [Freesurfer] Interpreting results from Qdec > >Those are the values outside (first column) and inside (2nd col) the >ROI. You can add "--id 1" to only report the values inside the ROI. > >doug > >On 4/26/11 1:02 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: >> It worked! >> Now, last question. The txt file has two separate values (?averages). >>What do they each represent? >> >> -Original Message- >> From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu] >> Sent: Tuesday, April 26, 2011 12:53 PM >> To: Gallen, Courtney (NIH/NIDA) [F] >> Subject: Re: [Freesurfer] Interpreting results from Qdec >> >> try "--slabel fsaverage lh ROI-drawn-on-QDEC-brain.label" >> >> >> On 4/26/11 12:52 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: >>> Actually, I hope I'm wrong about what I thought below. If I specify >>>individual subject's label and run: >>> >>> mri_segstats --in >>>/prot/Mprot/CTQ/freesurferDone/8579/surf/lh.volume.fwhm10.fsaverage.mgh >>>--slabel 8579 lh >>>/prot/Mprot/CTQ/freesurferDone/8579/label/lh.SupTemp_CTQxBDNFctrls.label >>> --avgwf lhSupTempctrls.txt >>> >>> I still get the same error about dimension mismatch >>> >>> >>> -Original Message- >>> From: Gallen, Courtney (NIH/NIDA) [F] >>> Sent: Tuesday, April 26, 2011 12:43 PM >>> To: 'Douglas Greve' >>> Subject: RE: [Freesurfer] Interpreting results from Qdec >>> >>> Ah I think I see the problem now. >>> >>> The label I originally specified is the general label created from the >>>ROI drawing in Qdec. Instead, I should use the individual subject's >>>label (from 'Map Label to Subjects') instead, right? >>> >>> Thank you! >>> >>> -Original Message- >>> From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu] >>> Sent: Tuesday, April 26, 2011 12:38 PM >>> To: Gallen, Courtney (NIH/NIDA) [F] >>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>> >>> You have to use the subject that matches the input, fsaverage in this >>> case. How did you define your label? If you defined it on subject 123, >>> you can transfer it to fsaverage using mri_label2label. >>> doug >>> >>> On 4/26/11 12:28 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: Not a problem at all! If I use --in, I get an error saying that there is a dimension mismatch between input volume and seg. Any other thoughts? Thanks again! -Original Message- From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 26, 2011 11:40 AM To: Gallen, Courtney (NIH/NIDA) [F] Subject: Re: [Freesurfer] Interpreting results from Qdec Hi Courtney, sorry for the delay. If more than a few days go by without a response, feel free to repost -- I promise not to get annoyed! Sometimes, things get pushed up and out of my mail browser window, and I often don't get back to them. Sorry! To answer your question, try using --in where you have --seg. The "segmentation" is actually already specified because you've specified a label. do
Re: [Freesurfer] HELP: recon-all error
do you have permission to write to that directory? Is the partition full? On Thu, 28 Apr 2011, Yunjo Lee wrote: > Hi all, > > I sent an email a couple of days ago but didn't get any answer yet... > I recently installed FreeSurfer in a virtual machine (Ubuntu). > > I installed it according to the freesurfer website and another source. > http://mirko.windhoff.net/how_to/install_freesurfer_on_ubuntu > > When I ran recon-all, I kept getting the following error message (see below). > Is there anything else that I have to install?? > > Thanks in advance, > Yunjo > > *Here's the error message:* > > 0597: dt=0.056000, rms=0.417 (0.032%), neg=0, invalid=766 > 0598: dt=0.028000, rms=0.417 (-0.000%), neg=0, invalid=766 > gcamFindOptimalTimeStep: Complete in 22111.002 ms > 0599: dt=0.00, rms=0.417 (0.000%), neg=0, invalid=766 > GCAMwrite(transforms/talairach.m3z): gzip encountered error. > writing output transformation to transforms/talairach.m3z... > mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed > ERROR: mri_ca_register with non-zero status 252 > but continuing despite the error > #-- > #@# CA Reg Inv Tue Apr 26 16:21:09 EDT 2011 > /usr/local/freesurfer/subjects/YC7178/mri > > mri_ca_register -invert-and-save transforms/talairach.m3z > > Loading, Inverting, Saving, Exiting ... > Reading transforms/talairach.m3z > ERROR: cannot find or read transforms/talairach.m3z > ERROR: mri_ca_register with non-zero status 0 > Linux VMBronzeWing 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19 20:34:50 > UTC 2010 i686 GNU/Linux > > recon-all -s YC7178 exited with ERRORS at Tue Apr 26 16:21:14 EDT 2011 > > > ___ 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] HELP: recon-all error
Hi all, I sent an email a couple of days ago but didn't get any answer yet... I recently installed FreeSurfer in a virtual machine (Ubuntu). I installed it according to the freesurfer website and another source. http://mirko.windhoff.net/how_to/install_freesurfer_on_ubuntu When I ran recon-all, I kept getting the following error message (see below). Is there anything else that I have to install?? Thanks in advance, Yunjo *Here's the error message:* 0597: dt=0.056000, rms=0.417 (0.032%), neg=0, invalid=766 0598: dt=0.028000, rms=0.417 (-0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22111.002 ms 0599: dt=0.00, rms=0.417 (0.000%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-- #@# CA Reg Inv Tue Apr 26 16:21:09 EDT 2011 /usr/local/freesurfer/subjects/YC7178/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux VMBronzeWing 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19 20:34:50 UTC 2010 i686 GNU/Linux recon-all -s YC7178 exited with ERRORS at Tue Apr 26 16:21:14 EDT 2011 ___ 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] FreeSurfer movie generation recipe
you can use -w in most binaries, including mris_sphere
On Thu, 28 Apr 2011,
Pedro Paulo de Magalhães Oliveira Junior wrote:
easier.
Can you inflate until you get the sphere?
2011/4/28 Bruce Fischl
or you can save snapshots from mris_inflate with
mris_inflate -w 1 -scale 1 ...
then render each of the resulting surfaces.
cheers,
Bruce
On Thu, 28 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
Some months ago it was asked in this list how to make a Movie of he
process
of the inflation of the brain.
Some hints:
Create this tcl script and name it as script.tcl:
for {set x 0} {$x<120} {incr x} {
set r [expr (round(1.2*$x + 3))]
shrink $r
redraw
save_tiff ${x}-img.tif
}
exit
Then use the commands:
tksurfer bert lh pial -annotation aparc.annot -tcl script.tcl
ffmpeg -r 15 -b 2500 -sameq -i %d-img.tif videoOutput.mp4
You can check the results at:
http://www.youtube.com/watch?v=aj-d8PZMXt8
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Re: [Freesurfer] FreeSurfer movie generation recipe
easier.
Can you inflate until you get the sphere?
2011/4/28 Bruce Fischl
> or you can save snapshots from mris_inflate with
>
> mris_inflate -w 1 -scale 1 ...
>
> then render each of the resulting surfaces.
> cheers,
> Bruce
>
>
> On Thu, 28 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
>
> Some months ago it was asked in this list how to make a Movie of he
>> process
>> of the inflation of the brain.
>>
>> Some hints:
>>
>> Create this tcl script and name it as script.tcl:
>>
>> for {set x 0} {$x<120} {incr x} {
>> set r [expr (round(1.2*$x + 3))]
>> shrink $r
>> redraw
>> save_tiff ${x}-img.tif
>> }
>> exit
>>
>> Then use the commands:
>> tksurfer bert lh pial -annotation aparc.annot -tcl script.tcl
>> ffmpeg -r 15 -b 2500 -sameq -i %d-img.tif videoOutput.mp4
>>
>>
>> You can check the results at:
>> http://www.youtube.com/watch?v=aj-d8PZMXt8
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] FreeSurfer movie generation recipe
or you can save snapshots from mris_inflate with
mris_inflate -w 1 -scale 1 ...
then render each of the resulting surfaces.
cheers,
Bruce
On Thu, 28 Apr 2011, Pedro
Paulo de Magalhães Oliveira Junior wrote:
Some months ago it was asked in this list how to make a Movie of he process
of the inflation of the brain.
Some hints:
Create this tcl script and name it as script.tcl:
for {set x 0} {$x<120} {incr x} {
set r [expr (round(1.2*$x + 3))]
shrink $r
redraw
save_tiff ${x}-img.tif
}
exit
Then use the commands:
tksurfer bert lh pial -annotation aparc.annot -tcl script.tcl
ffmpeg -r 15 -b 2500 -sameq -i %d-img.tif videoOutput.mp4
You can check the results at:
http://www.youtube.com/watch?v=aj-d8PZMXt8
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] FreeSurfer movie generation recipe
Some months ago it was asked in this list how to make a Movie of he process
of the inflation of the brain.
Some hints:
Create this tcl script and name it as script.tcl:
for {set x 0} {$x<120} {incr x} {
set r [expr (round(1.2*$x + 3))]
shrink $r
redraw
save_tiff ${x}-img.tif
}
exit
Then use the commands:
tksurfer bert lh pial -annotation aparc.annot -tcl script.tcl
ffmpeg -r 15 -b 2500 -sameq -i %d-img.tif videoOutput.mp4
You can check the results at:
http://www.youtube.com/watch?v=aj-d8PZMXt8
___
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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
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Re: [Freesurfer] tksurfer tcl script
Hi Bruce,
Thanks for your suggestion. I actually solved the problem by creating a new
tcl script for each look.
Yang
On Tue, Apr 26, 2011 at 8:16 PM, Bruce Fischl wrote:
> the easiest way is probably to use an environment variable, which you can
> access in tcl with $env(VAR_NAME) I think
>
> cheers
> Bruce
>
>
>
> On Tue, 26 Apr 2011, Yang Liu wrote:
>
> Hi all,
>>
>> I want to save the tiffs of different views automatically. I am trying to
>> use tcl script to do it.
>> My problem is that I need to pass the file's name that is being displayed
>> in
>> the tksurfer window to the tiff file that I want to save to.
>>
>> For example,
>>
>> I am running
>>
>> tksurfer -f $surface_file -tcl my_script.tcl
>>
>> In my_script.tcl, I have the following command:
>>
>> save_tiff ${file_name}-lateral.tiff
>>
>>
>> How can I pass the $surface_file in my command to ${file_name} in
>> my_scripts.tcl?
>>
>>
>> Thanks.
>>
>> Yang
>>
>>
>
> 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.
>
>
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[Freesurfer] general question on use of optseq2
Hi all, I have a very general question and hope someone can help. I would like to use optseq2 to optimise my fMRI design. I will use a event-related parametric design. I will have 2 conditions with each 4 loads. Will I define only 2 conditions/events in optseq as I will investigate the load variation within these two conditions. Or is it better to define 8 events? Thanks in advance, Maya ___ 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.
