[Freesurfer] freesurfer 5.0 in ubuntu 10.04
Hi, there, I just downloaded and installed freesurfer 5.0 under Ubunto 10. The version I am downlaoded is freesurfer-Linux-centos4-stable-pub-v5.0.0.tar.gz I ran a subject, but it failed at the first step, the error message I got is: talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux guangzeng-desktop 2.6.32-24-generic-pae #41-Ubuntu SMP Thu Aug 19 02:43:57 UTC 2010 i686 GNU/Linux I checked the talairach_avi.log, and I found this: gauss_4dfp: error while loading shared libraries: libg2c.so.0: cannot open shared object file: No such file or directory ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=127 ERROR: mpr2mni305 execution aborted So, how can I fix this problem? Thanks a lot! Guang ___ 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] Notes on CUDA Acceleration
On Thu, 2010-08-26 at 23:23 +0200, Georg Homola wrote: allow me one additional remark that may be crucial for those considering to invest in new cards. Although the Fermi class cards make use of the same architecture (Geforce GTX 480 and Tesla C2050 for example), for consumer products (GTX 400 series), double precision performance has been limited to a quarter of that of the full Fermi architecture (Tesla C20xx). Error checking and correcting memory (ECC) is also disabled on consumer cards. I don't really know how important double precision is for the CUDA enabled Freesurfer tools, but this could mean you have to buy four GTX cards to catch up with the performance of one Tesla card. This is correct. At the moment, I don't think that I use double precision anywhere, hence we're experimenting with CUDA Capability 1.1. I may have to start using double precision, given the problems which have just been found with mri_em_register_cuda. However, I'm not sure what the performance impact of the degraded GeForce performance will be. I'm reasonably certain that most of the code is bandwidth bound, so if anything a GeForce will outpace a Tesla, even if it uses double precision. Of greater concern is the amount of memory available. The Tesla cards have quite a bit more RAM. This is likely to become important in the near future, as I work to get the rest of the mri_ca_register pipeline onto the GPU - the GCA structure is quite sparse, but for the initial port, I'll burn RAM instead of coming up with a cunning packing method. There will be enough to debug without worrying about optimisation. Regards, Richard ___ 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] Partial voluming - mri_segstats --pv
Hi, I'd like to learn more about how the mri_segstats -pv calculation is done. Could someone send me the source code for this algorithm? Thanks! Paula Wu Summer Intramural Research Training Assistant Laboratory of Brain and Cognition, Section on Functional Imaging Methods, NIMH/NIH/DHHS Building 10, Room 1D80 10 Center Dr MSC 1148 Bethesda MD 20892-1148 w...@mail.nih.gov ___ 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] Partial voluming - mri_segstats --pv
Hi Paula,
here's the relevant function. If you want the whole code base Nick can
point you in the right direction.
Bruce
On Fri, 27 Aug 2010, Wu, Paula (NIH/NIMH)
[F] wrote:
Hi,
I'd like to learn more about how the mri_segstats -pv calculation is done.
Could someone send me the source code for this algorithm?
Thanks!
Paula Wu
Summer Intramural Research Training Assistant
Laboratory of Brain and Cognition,
Section on Functional Imaging Methods,
NIMH/NIH/DHHS
Building 10, Room 1D80
10 Center Dr MSC 1148
Bethesda MD 20892-1148
w...@mail.nih.gov
float MRIvoxelsInLabelWithPartialVolumeEffects(MRI *mri, MRI *mri_vals,
int label,
MRI *mri_mixing_coef,
MRI *mri_nbr_labels)
{
float volume, vox_vol ;
int x, y, z, nbr_label_counts[2];
int label_counts[2], this_label, border;
int nbr_label, max_count, vox_label ;
MRI *mri_border ;
float label_means[2], pv, mean_label, mean_nbr, val ;
int maxlabels = 2;
// DNG 6/7/07 : had to use maxlabels instead of MAX_CMA_LABELS here
// so that segmentations with values MAX_CMA_LABELS can be
// accessed. This includes the cortical segmentations as well as
// white matter segs. Currently, the max seg no is 4181, but this
// could easily change.
// NJS 2/17/10 : Indeed, it did change... the Destrieux a2009s atlas has
// label values up to about 15000.
if(label = maxlabels){
printf(ERROR: MRIvoxelsInLabelWithPartialVolumeEffects()\n);
printf( label %d exceeds maximum label number %d\n,label,maxlabels);
return(-10);
}
vox_vol = mri-xsize*mri-ysize*mri-zsize ;
/* first find border voxels */
mri_border = MRImarkLabelBorderVoxels(mri, NULL, label, 1, 1) ;
if (DIAG_VERBOSE_ON (Gdiag DIAG_WRITE))
MRIwrite(mri_border, b.mgz) ;
volume = 0 ;
for (x = 0 ; x mri-width ; x++) {
for (y = 0 ; y mri-height ; y++){
for (z = 0 ; z mri-depth ; z++) {
if (x == Gx y == Gy z == Gz)
DiagBreak() ;
vox_label = MRIgetVoxVal(mri, x, y, z, 0) ;
border = MRIgetVoxVal(mri_border, x, y, z, 0) ;
if ((vox_label != label) (border == 0))
continue ;
if (border == 0) volume += vox_vol ;
else{ /* compute partial volume */
MRIcomputeLabelNbhd(mri, mri_vals, x, y, z,
nbr_label_counts, label_means, 1, maxlabels) ;
MRIcomputeLabelNbhd(mri, mri_vals, x, y, z,
label_counts, label_means, 7, maxlabels) ;
val = MRIgetVoxVal(mri_vals, x, y, z, 0) ; /* compute partial
volume based on
intensity */
mean_label = label_means[vox_label] ;
nbr_label = -1 ;
max_count = 0 ;
/* look for a label that is a nbr and is
on the other side of val from the label mean */
for (this_label = 0 ; this_label maxlabels; this_label++) {
if(this_label == vox_label)
continue ;
if(nbr_label_counts[this_label] == 0)
continue ; /* not a nbr */
if ((label_counts[this_label] max_count)
((label_means[this_label] - val) *
(mean_label - val) 0)){
max_count = label_means[this_label] ;
nbr_label = this_label ;
}
}
if (vox_label != label nbr_label != label)
continue ; // this struct not in voxel
if (max_count == 0)
{
volume += vox_vol ; // couldn't find an appropriate label
if (mri_nbr_labels) // find max nbr label anyway for caller
{
for (this_label = 0 ; this_label maxlabels; this_label++) {
if(this_label == vox_label)
continue ;
if(nbr_label_counts[this_label] == 0)
continue ; /* not a nbr */
if (label_counts[this_label] max_count)
{
max_count = label_means[this_label] ;
nbr_label = this_label ;
}
}
MRIsetVoxVal(mri_nbr_labels, x, y, z, 0, nbr_label) ;
if (mri_mixing_coef)
MRIsetVoxVal(mri_mixing_coef, x, y, z, 0, 1.0) ;
}
}
else{ // compute partial volume pct
mean_nbr = label_means[nbr_label] ;
pv = (val - mean_nbr) / (mean_label - mean_nbr) ;
if (pv 0 || pv 1)
DiagBreak() ;
if (pv 1)
pv = 1 ;
if (pv 0)
continue ; // shouldn't happen
if (vox_label != label)
pv = 1-pv ;
volume += vox_vol * pv ;
[Freesurfer] PALS-B12-based ROIs in fsaverage in v5.0.0
there is one new feature in the new v5.0.0 which was missing from the early release notes, but that which some people might have an interest. the Van Essen Lab created some ROIs on their PALS-B12 atlas, and then mapped them to the freesurfer fsaverage subject. some basic info is here: http://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12 it will take a bit of freesurfer expertise on your part to make use of these, as you would need to: 1) identify which labels (ROIs) are of interest to you (by viewing the .annot file on fsaverage) 2) use mri_annotation2label to extract the labels 3) use mri_label2label to map from fsaverage to your subject 3) optionally use mri_anatomical_stats to get stats about those labels n. ___ 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 5.0 in ubuntu 10.04
i've just uploaded a new freesurfer-Linux-centos4-stable-pub-v5.0.0.tar.gz (the 32b linux dist) which corrects this problem. the original one was inadvertently built against the shared libg2c (which is not found on most linux systems) instead of the static lib. the version number doesnt need to change because the i/o behavior is identical, and those who having a working version (ie, somehow they have a shared libg2c) dont need to re-download. n. On Fri, 2010-08-27 at 01:40 -0500, Guang Zeng wrote: Hi, there, I just downloaded and installed freesurfer 5.0 under Ubunto 10. The version I am downlaoded is freesurfer-Linux-centos4-stable-pub-v5.0.0.tar.gz I ran a subject, but it failed at the first step, the error message I got is: talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux guangzeng-desktop 2.6.32-24-generic-pae #41-Ubuntu SMP Thu Aug 19 02:43:57 UTC 2010 i686 GNU/Linux I checked the talairach_avi.log, and I found this: gauss_4dfp: error while loading shared libraries: libg2c.so.0: cannot open shared object file: No such file or directory ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=127 ERROR: mpr2mni305 execution aborted So, how can I fix this problem? Thanks a lot! Guang ___ 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.
Re: [Freesurfer] Notes on CUDA Acceleration
Richard, Nick, Pedro, the Freesurfers, I am looking at choice of the lower end fermi cards and I was wondering if you could comment of Freesurfer's ability to take advantage of some seldom used functions included in nVidia GTX 400 (including tesselation) that were stripped down from nVidia GF104 chipset. GeForce GTX 465 has the original nVidia GTX 400 chip and GeForce GTX 460 has the revised GF104 chipset. Some claim that the revision in the chipset is geared towards cheaper manufacturing. Unfortunately benchmarks for those cards are usually aimed at gaming performance that is not of my interest. http://www.gpureview.com/show_cards.php?card1=632card2=631 Greetings, Jacek ___ 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] iPhone and IPad FreeSurfer based atlas
Some weeks ago Bruce announced the first version of the free brain atlas app for IPhone using FreeSurfer aseg. Today we have a major upgrade and now the app has a native IPad interface. Also Bruce provided high resolution mri segmented so IPhone and IPod touch users will benefit too http://itunes.apple.com/br/app/isurf-brainview/id381072423?mt=8 Suggestions for the upcoming version ate welcome. Cheers Pedro Paulo Jr. -- via iPhone iOS4 ___ 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] iPhone and IPad FreeSurfer based atlas
Hi! Pedro, Do you plan to release the source code? I did write an iphone app last year for a lung cad product. We abandon the project at the end. The biggest problem we have is finger is not really great for point and click compared to stylus. It always stand in the way between your eyesight and the region you want to pick. Do you have any insight for how to solve that problem? Anyway, I finally got some free time to work on Osirix. I hope I can integrate freesufer pipeline and its visualization together at the end. Will tackle IO and visualization in next few weeks. if anyone is interested in joining some coding, please let me know. we can coordinate the effort. Gen 2010/8/27 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br: Some weeks ago Bruce announced the first version of the free brain atlas app for IPhone using FreeSurfer aseg. Today we have a major upgrade and now the app has a native IPad interface. Also Bruce provided high resolution mri segmented so IPhone and IPod touch users will benefit too http://itunes.apple.com/br/app/isurf-brainview/id381072423?mt=8 Suggestions for the upcoming version ate welcome. Cheers Pedro Paulo Jr. -- via iPhone iOS4 ___ 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
