Re: [Freesurfer] new GPU binaries
Hi Nick, Richard, Freesurfanados and GPU fans, I've downloaded the latest _cuda binaries from the tarball you have posted, but when I try to run the recon-all on the mri_ca_register_cuda it appears: * #...@# CA Reg Mon Oct 25 10:33:15 CEST 2010 /home/neuro/proc/OutPBS_GPU/AAG_106/mri mri_ca_register_cuda -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/neuro/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z Acquiring CUDA device Using default device CUDA Error in file 'devicemanagement.cu' on line 46 : no CUDA-capable device is detected. ERROR: mri_ca_register with non-zero status 1 but continuing despite the error #-- #...@# CA Reg Inv Mon Oct 25 10:33:15 CEST 2010 /home/neuro/proc/OutPBS_GPU/AAG_106/mri mri_ca_register_cuda -invert-and-save transforms/talairach.m3z Acquiring CUDA device Using default device CUDA Error in file 'devicemanagement.cu' on line 46 : no CUDA-capable device is detected. ERROR: mri_ca_register with non-zero status 0 Linux ww-neuro04 2.6.18-194.17.1.el5 #1 SMP Wed Sep 29 12:50:31 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s AAG_106 exited with ERRORS at Mon Oct 25 10:33:15 CEST 2010* I think that error was solved in a previous releases of de _cuda binaries, maybe with the new compilation with cuda 3.1 it has been appeared again... I'm running cuda on a NVIDIA GEFORCE 9800 GT with cuda toolkit 3.2.9... Thank you!! /Jordi. 2010/10/25 Nick Schmansky > Freesurfanados and GPU fans, > > We (namely Richard) have fixed some of the problems with the existing > freesurfer gpu binaries, which were the result of building against cuda > 3.0 on our build platforms, which seemed to be incompatible with 3.1. > We've built against 3.1, although now i see nvidia has come out with > 3.2, but i've tested against that and they seem to work. > > So you can get the binary tarball here: > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/fscudabins-linux-centos4_x86_64.tgz > > and here for the 32b linux: > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/fscudabins-linux-centos4.tgz > > copy the extracted contents of those tarball into your freesurfer/bin > dir. > > The binaries are: > > mri_ca_register_cuda > mri_em_register_cuda > mris_fix_topology_cuda > mris_flatten_cuda > mris_inflate_cuda > mris_sphere_cuda > mri_vol2vol_cuda > > No doubt people will encounter problems, so let us know. But hopefully > you will see a dramatic reduction in the runtime of the subcortical > segmentation stage (mri_ca_register). > > Also, to remind people, Richard is targeting our gpu development for the > Fermi class of gpu card, which has better memory management which leads > to better performance of some algorithms, so if you're buying new > hardware, be sure to spec that class of card (see nvidia site). > > Nick > > > ___ > 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. > > -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ 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] new GPU binaries
what does the freesurfer utility 'cudadetect' return when you run it? can you try rebooting your machine, then try running 'mri_em_register_cuda' (with no args) to see if it gives the same message or returns help text? if it returns help text, then that means it found a device. n. On Mon, 2010-10-25 at 10:45 +0200, Jordi Delgado wrote: > Hi Nick, Richard, Freesurfanados and GPU fans, > > I've downloaded the latest _cuda binaries from the tarball you have > posted, but when I try to run the recon-all on the > mri_ca_register_cuda it appears: > > #...@# CA Reg Mon Oct 25 10:33:15 CEST 2010 > /home/neuro/proc/OutPBS_GPU/AAG_106/mri > > mri_ca_register_cuda -nobigventricles -T transforms/talairach.lta > -align-after -mask brainmask.mgz > norm.mgz /home/neuro/freesurfer/average/RB_all_2008-03-26.gca > transforms/talairach.m3z > > Acquiring CUDA device > Using default device > CUDA Error in file 'devicemanagement.cu' on line 46 : no CUDA-capable > device is detected. > ERROR: mri_ca_register with non-zero status 1 > but continuing despite the error > #-- > #...@# CA Reg Inv Mon Oct 25 10:33:15 CEST 2010 > /home/neuro/proc/OutPBS_GPU/AAG_106/mri > > mri_ca_register_cuda -invert-and-save transforms/talairach.m3z > > Acquiring CUDA device > Using default device > CUDA Error in file 'devicemanagement.cu' on line 46 : no CUDA-capable > device is detected. > ERROR: mri_ca_register with non-zero status 0 > Linux ww-neuro04 2.6.18-194.17.1.el5 #1 SMP Wed Sep 29 12:50:31 EDT > 2010 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s AAG_106 exited with ERRORS at Mon Oct 25 10:33:15 CEST > 2010 > > I think that error was solved in a previous releases of de _cuda > binaries, maybe with the new compilation with cuda 3.1 it has been > appeared again... > > I'm running cuda on a NVIDIA GEFORCE 9800 GT with cuda toolkit > 3.2.9... > > Thank you!! > /Jordi. > > 2010/10/25 Nick Schmansky > Freesurfanados and GPU fans, > > We (namely Richard) have fixed some of the problems with the > existing > freesurfer gpu binaries, which were the result of building > against cuda > 3.0 on our build platforms, which seemed to be incompatible > with 3.1. > We've built against 3.1, although now i see nvidia has come > out with > 3.2, but i've tested against that and they seem to work. > > So you can get the binary tarball here: > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/fscudabins-linux-centos4_x86_64.tgz > > and here for the 32b linux: > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/fscudabins-linux-centos4.tgz > > copy the extracted contents of those tarball into your > freesurfer/bin > dir. > > The binaries are: > > mri_ca_register_cuda > mri_em_register_cuda > mris_fix_topology_cuda > mris_flatten_cuda > mris_inflate_cuda > mris_sphere_cuda > mri_vol2vol_cuda > > No doubt people will encounter problems, so let us know. But > hopefully > you will see a dramatic reduction in the runtime of the > subcortical > segmentation stage (mri_ca_register). > > Also, to remind people, Richard is targeting our gpu > development for the > Fermi class of gpu card, which has better memory management > which leads > to better performance of some algorithms, so if you're buying > new > hardware, be sure to spec that class of card (see nvidia > site). > > Nick > > > ___ > 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. > > > > > -- > Jordi Delgado Mengual > PIC (Port d'Informació Científica) > Campus UAB, Edifici D > E-08193 Bellaterra, Barcelona > Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 > http://www.pic.es > Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mai
[Freesurfer] average p-value from an ROI
Dear all,
I have a follow-up question to the previous discussion ("correction for
behavioral varialbles in qdec" Tue, 04 Aug 2009.
Is there an option to extract the average p-value from a ROI? After a group
analysis I specified ROIs at p < 0.001 and extracted the mean cortical
thickness, the peak p-value, and mean ROI size. Now, I would like to report
not the peak, but the average p-value of an ROI in the fsaverage space. Is
there any flag to obtain this information? I did not use the mri_surfcluster
command, but a matlab script to extract the information form the output of
the mri_segstats command.
Thanks for help!
Cheers,
Aga
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Re: [Freesurfer] data not Surving FDR
FDR adjusts the threshold on a case-by-case basis, so it's not surprising that you see different thresholds for different data sets. The actual threshold is set based on the search space and the amount of activation. If you have a large search space, and not very much activation, then it is going to give you a high threshold. See the Genovese, Lazar, and Nichols 2002 paper for more details. Also see the Chumbley and Friston 2009 paper on the limitations of FDR. doug Mira Michelle Raman wrote: > Hi, > I have a dataset that seems to have some very nice group differences > (please see the graph and qdec image), but they never seem to survive FDR. I > noticed when I run the "Set Using FDR", it generates a very high threshold > above 5; where as, with some of my other datasets FDR is set much lower > (often in the 2's and 3's). Can you please give me some insight into why the > threshold is being set so high? Is it solely linked to the small sample size, > or is there something additional we can do in the processing, so that regions > with such large group differences will survive correction? > > Thank you, > Mira > > > > > ___ > 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 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] average p-value from an ROI
You can load in the sig.mgh file instead of the ces.mgh file. Convert
the sig to p with p = 10.^(-abs(sig)). It is fairly unusual to report
the average p-value in an ROI, you might want to double check that this
is really what you want to do.
doug
Agnieszka Burzynska wrote:
> Dear all,
> I have a follow-up question to the previous discussion ("correction for
> behavioral varialbles in qdec" Tue, 04 Aug 2009.
>
>
> Is there an option to extract the average p-value from a ROI? After a group
> analysis I specified ROIs at p < 0.001 and extracted the mean cortical
> thickness, the peak p-value, and mean ROI size. Now, I would like to report
> not the peak, but the average p-value of an ROI in the fsaverage space. Is
> there any flag to obtain this information? I did not use the mri_surfcluster
> command, but a matlab script to extract the information form the output of
> the mri_segstats command.
>
> Thanks for help!
> Cheers,
> Aga
>
>
> ___
> 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
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Re: [Freesurfer] mni coordinates to volume index
Yes, but you'll need to create the matrix to do it. See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.ppt for more info. doug Yigal Agam wrote: > Hi, > > Is it possible in matlab to get the volume index coordinates > corresponding to specific MNI coordiates? > > Thanks, > Yigal > ___ > 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 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] average p-value from an ROI
Hi Aga,
maybe you want to compute the average thickness in the roi and then the
(single) p value for that?
Best, Martin
On Mon, 2010-10-25 at 16:21 +0200, Agnieszka Burzynska wrote:
> Dear all,
> I have a follow-up question to the previous discussion ("correction for
> behavioral varialbles in qdec" Tue, 04 Aug 2009.
>
>
> Is there an option to extract the average p-value from a ROI? After a group
> analysis I specified ROIs at p < 0.001 and extracted the mean cortical
> thickness, the peak p-value, and mean ROI size. Now, I would like to report
> not the peak, but the average p-value of an ROI in the fsaverage space. Is
> there any flag to obtain this information? I did not use the mri_surfcluster
> command, but a matlab script to extract the information form the output of
> the mri_segstats command.
>
> Thanks for help!
> Cheers,
> Aga
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
___
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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
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] Error with mri_segstats
Hi, I'm trying to use mri_segstats and get the following error: ERROR: could not open stats/aseg1.stats for writing The full command I gave was: mri_segstats --seg mri/aseg.mgz --sum stats/aseg1.stats --pv mri/ norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent -- subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity- units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab / Applications/freesurfer/ASegStatsLUT.txt --subject C001 The SUBJECTS_DIR was set to the directory containing the subject C001. I have full privileges to read/write to all folders. If I try to write to just aseg1.stats (so using option --sum aseg1.stats) I get the error message that aseg.mgz could not be opened. I'm on a Mac using FreeSurfer v5.0.0. Ed ___ 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] Error with mri_segstats
Are you in the C001 directory when you run the command? Can you send the terminal output? Ed Gronenschild wrote: > Hi, > > I'm trying to use mri_segstats and get the following error: > > ERROR: could not open stats/aseg1.stats for writing > > The full command I gave was: > > mri_segstats --seg mri/aseg.mgz --sum stats/aseg1.stats --pv mri/ > norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent -- > subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity- > units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab / > Applications/freesurfer/ASegStatsLUT.txt --subject C001 > > The SUBJECTS_DIR was set to the directory containing the subject C001. > I have full privileges to read/write to all folders. > > If I try to write to just aseg1.stats (so using option --sum > aseg1.stats) I get the > error message that aseg.mgz could not be opened. > > I'm on a Mac using FreeSurfer v5.0.0. > > Ed > > ___ > 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 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] Total GM and WM volumes
Hi, In the v5.0.0 aseg.stats file I can find the following volumes: - left/right cortical gray matter - subcortical gray matter - total cortical gray matter - total gray matter volume and - left/right cortical white matter - total cortical white matter How can I derive the total white matter volume? Ed ___ 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] How to transform the thickness per vertex to another space?
Dear FS experts, I 've question concerning the thickness per vertex. Here is what I want to do: I have a data series which entered the FS pipeline. Afterwards, I transformed the aparc+aseg file to another space. Is it somehow possible to transform the thickness per vertex to this space using the same transformation matrix? Thanks, Mo ___ 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] How to transform the thickness per vertex to another space?
Hi Mo, You can sample them into the volume with mri_surf2vol, then transform that volume. cheers Bruce On Tue, 26 Oct 2010, Mohammed el Morabit wrote: > > Dear FS experts, > > I 've question concerning the thickness per vertex. Here is what I want to do: > > I have a data series which entered the FS pipeline. Afterwards, I transformed > the aparc+aseg file to another space. Is it somehow possible to transform the > thickness per vertex to this space using the same transformation matrix? > > Thanks, > Mo > ___ 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.
