[Freesurfer] Speeding Freesurfer
Dear Freesurfer experts, I've been using Freesurfer on Mac computers for some years with great satisfaction. I just bought a monster computer, a Mac Pro with 12-core Xeon E5, 64 Gb RAM, GPU AMD FirePro D700. This is, out of doubt, a marvellous machine to compute many subjects simultaneously, but quite often we need to run one single subject as fast as possible. What can I do? OpenMP optimization is available only for CentOS, isn't it? What about CentOS in a VM, will it be able to exploit multithreading, or is it necessary to configure a multiboot machine with BootCamp? Any suggestions to do that? Moreover, what about CUDA and GPU acceleration? Is it available for FirePro graphic cards? Any other suggestions? Anything really new in the field with the next version of Freesurfer? Thanks a lot Francesco Cardinale, MD Neurosurgeon Claudio Munari Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia phone 0039 02 64442917 fax 0039 02 64442868 e-mail francesco.cardin...@ospedaleniguarda.it___ 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] A question of preproc-sess -fsd
Dear Freesurfer experts, Could you please give me more detail of -fsd? It is asked to specify a functional subdirectory with -fsd when i preprocess the functional data. If, for example, the current directory is /home/Proj, the f.nii is in /home/Proj/sess01/bold/002/ and /home/Proj/sess01/bold/003/, what the -fsd should be? Thanks. Mingxia ___ 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] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch
Hi Satra, that was really helpful... I patched 5.3.0, made a full run of recon-all with strace and wrote a little tool that checks which files must actually be part of the archive. I can confirm your file list, but there is a problem with fsaverage (you have already expressed your concerns) because some files are missing. Have a look to my subsequent list. I post here the minimum content of the freesurfer archive for getting recon-all -all running. I am currently testing the version in my cloud using Ubuntu 14.04 (x86_64) and Ubuntu 14.10 (x86_64). freesurfer_linux_x86_64_5.3.1_pipeline.tar: freesurfer/ freesurfer/lib/ freesurfer/lib/bem/ freesurfer/lib/bem/ic4.tri freesurfer/lib/bem/ic5.tri freesurfer/lib/bem/ic7.tri freesurfer/SetUpFreeSurfer.sh freesurfer/FreeSurferEnv.csh freesurfer/bin/ freesurfer/bin/mri_and freesurfer/bin/compute_vox2vox freesurfer/bin/mris_curvature freesurfer/bin/mrisp_paint freesurfer/bin/mri_label2label freesurfer/bin/mri_add_xform_to_header freesurfer/bin/analyzeto4dfp freesurfer/bin/mri_info freesurfer/bin/mris_inflate freesurfer/bin/mris_ca_train freesurfer/bin/mri_convert freesurfer/bin/mri_pretess freesurfer/bin/talairach_afd freesurfer/bin/mri_normalize freesurfer/bin/mri_fill freesurfer/bin/mri_fuse_segmentations freesurfer/bin/mris_jacobian freesurfer/bin/mris_curvature_stats freesurfer/bin/mri_aparc2aseg freesurfer/bin/mri_cc freesurfer/bin/extract_talairach_avi_QA.awk freesurfer/bin/mri_robust_register freesurfer/bin/mris_ca_label freesurfer/bin/mri_watershed freesurfer/bin/mris_calc freesurfer/bin/mri_remove_neck freesurfer/bin/mris_make_surfaces freesurfer/bin/mri_ca_label freesurfer/bin/mri_vol2surf freesurfer/bin/mri_gcut freesurfer/bin/pctsurfcon freesurfer/bin/mris_remove_intersection freesurfer/bin/mri_nu_correct.mni freesurfer/bin/imgreg_4dfp freesurfer/bin/mri_motion_correct.fsl freesurfer/bin/mris_smooth freesurfer/bin/mris_sphere freesurfer/bin/mri_or freesurfer/bin/mri_binarize freesurfer/bin/fsr-getxopts freesurfer/bin/mris_euler_number freesurfer/bin/mpr2mni305 freesurfer/bin/mris_anatomical_stats freesurfer/bin/mri_segstats freesurfer/bin/mri_robust_template freesurfer/bin/mri_edit_wm_with_aseg freesurfer/bin/mri_ca_register freesurfer/bin/tkregister2_cmdl freesurfer/bin/mris_spherical_average freesurfer/bin/mri_concatenate_lta freesurfer/bin/recon-all freesurfer/bin/mri_make_uchar freesurfer/bin/mri_em_register freesurfer/bin/gauss_4dfp freesurfer/bin/mri_matrix_multiply freesurfer/bin/freesurfer freesurfer/bin/mris_volmask freesurfer/bin/talairach_avi freesurfer/bin/mris_extract_main_component freesurfer/bin/mris_label2annot freesurfer/bin/mri_segment freesurfer/bin/mris_fix_topology freesurfer/bin/mri_concat freesurfer/bin/mris_topo_fixer freesurfer/bin/avi2talxfm freesurfer/bin/ifh2hdr freesurfer/bin/flirt.fsl freesurfer/bin/mris_register freesurfer/bin/mri_normalize_tp2 freesurfer/bin/mri_mask freesurfer/bin/mri_tessellate freesurfer/bin/mri_ca_normalize freesurfer/fsafd/ freesurfer/fsafd/TalairachingProbas.adf freesurfer/fsafd/TalairachingCovariance.adf freesurfer/fsafd/TalairachingMean.adf freesurfer/fsfast/ freesurfer/FreeSurferEnv.sh freesurfer/WMParcStatsLUT.txt freesurfer/SetUpFreeSurfer.csh freesurfer/build-stamp.txt freesurfer/average/ freesurfer/average/RB_all_withskull_2008-03-26.gca freesurfer/average/rigidly_aligned_brain_template.tif freesurfer/average/colortable_BA.txt freesurfer/average/lh.average.curvature.filled.buckner40.tif freesurfer/average/711-2C_as_mni_average_305.4dfp.img freesurfer/average/lh.destrieux.simple.2009-07-29.gcs freesurfer/average/711-2C_as_mni_average_305.4dfp.ifh freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs freesurfer/average/rh.destrieux.simple.2009-07-29.gcs freesurfer/average/RB_all_2008-03-26.gca freesurfer/average/rh.DKTatlas40.gcs freesurfer/average/lh.DKTatlas40.gcs freesurfer/average/mni305.cor.mgz freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs freesurfer/average/rh.average.curvature.filled.buckner40.tif freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.ifh freesurfer/subjects/ freesurfer/subjects/rh.EC_average/ freesurfer/subjects/rh.EC_average/label/ freesurfer/subjects/rh.EC_average/label/rh.entorhinal.label freesurfer/subjects/rh.EC_average/surf/ freesurfer/subjects/rh.EC_average/surf/rh.white freesurfer/subjects/rh.EC_average/surf/rh.sphere.reg freesurfer/subjects/fsaverage/ freesurfer/subjects/fsaverage/label/ freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label freesurfer/subjects/fsaverage/label/rh.V1.label freesurfer/subjects/fsaverage/label/rh.BA4a.thresh.label freesurfer/subjects/fsaverage/label/lh.V2.thresh.label freesurfer/subjects/fsaverage/label/lh.BA45.thresh.label freesurfer/subjects/fsaverage/label/rh.BA1.thresh.label freesurfer/subjects/fsaverage/label/rh.BA3a.label freesurfer/subjects/fsaverage/label/rh.BA3b.label
Re: [Freesurfer] Fwd: Fwd: Eccentric lesions
Hi Octavian You should try it and see. It's hard to predict how it will do Cheers Bruce On Nov 26, 2014, at 4:43 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi, Could you use a colormap for your aseg? It is really hard to see the different ROIs on a grayscale image. Thanks, Lilla On Wed, 26 Nov 2014, Octavian Lie wrote: Dear Lilla, Here is a snapshot of the aseg volume, which rescues some gray matter not included in the pia. I am not sure if the aseg is ok, as the portion extending in the lesion is labeled gray matter (intensity 42). I guess this is not a problem. If I generate a surface from aseg as you suggested: a. I would need to generate a surface for each of the two hemispheres; b. If a is doable, is there a way to make it 'pial' in the sense that it gets registered with sphere and gets to be applied the DK atlas? A corrolary would be whether I can trick FS by labeling the new surface as smth.pial during the recon pipeline and further complete the rest of the processing steps to generate a true pia. Thank you for your assist, Octavian ___ 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] Fwd: Fwd: Eccentric lesions
I tried, here is the command: mris_make_surfaces -cover_seg mri/aseg.mgz subjid lh and the last 5 lines of the run: ... smoothing surface for 5 iterations... repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 creating distance transform volume from segmentation ERROR: mris_make_surfaces-MRIcheckVolDims: volume1 height=256 != volume2 height=1. If this is it and not working, I wonder that editing the aseg to exclude the nonlesional GM outside the pia, but leaving/ adding lesional GM of interest, either under the GM label or a custom label would allow create a 'proper' volume, followed by surface generation. I known this is doable, the question is whether the generated surface can be registered to sphere and whether DK atlas can be applied (this is a more general question, whether any surface generated outside the default recon-all pathway can be registered to sphere and in effect become pia or another classical boundary surface?) example after labeling the lesion as 'o' (other): % generate mask from aseg cd /usr/local/fs5.3/freesurfer/subjects/subjid mris_fill -c -r 0.1 surf/rh.pial mri/rh.pial.filled.mgz \ mris_fill -c -r 0.1 surf/lh.pial mri/lh.pial.filled.mgz \ mri_concat --combine --i mri/rh.pial.filled.mgz --i mri/lh.pial.filled.mgz --o mri/pial.filled.mgz \ cd ./mri \ mri_binarize --i aseg.mgz --match o --o lesion.mask.mgz \ fscalc pial.filled.mgz add lesion.mask.mgz -o pialmask.mgz \ mri_convert brain.mgz brain.float.mgz -odt float \ mri_mask brain.float.mgz pialmask.mgz pialbrain.mgz % generate new 'pial' surface: mri_tessellate mri/pialbrain.mgz -a surf/lh.pialbrain.pial Please advise, Octavian ___ 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] Freeview - Vector and Spline information for Sufaces
Dear all, I'm currently trying to view face and/or vertex normals in freeview (of an existing surface). I've seen the option to load vector display data, but I do not know the format of such a file. Can someone help me with that issue? Regards, Daniel Universitätsklinikum Jena - Bachstrasse 18 - D-07743 Jena Die gesetzlichen Pflichtangaben finden Sie unter http://www.uniklinikum-jena.de/Pflichtangaben.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] mri_vol2surf --prodist measuring from pial surface
Hi, I was wondering if it's possible to sample x mm from the pial surface using mri_vol2surf (or another tool!). The point is that I'd like to be agnostic about exactly where the grey/white matter boundary lies. I've had a look through the help for mri_vol2surf and nothing's jumping out at me, is there an obvious option I'm missing?! Thank you! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com ___ 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.
