Re: [Freesurfer] Converting MNI152 coorindates to fsaverage space
External Email - Use Caution Hi Tim, Case #8 is transforming between MNI152 and MNI305 spaces. MNI305 is different from fsaverage: one is a volumetric space and one is a surface space. If you are indeed looking for a transformation between MNI152 volumetric space and fsaverage surface space, you can consider the following: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion Regards, Thomas On Sat, Feb 9, 2019 at 11:11 PM Tim Schäfer wrote: > External Email - Use Caution > > > Dear list, > > > > I have some points of interest (volume coordinates, e.g. '5.9, -27.7, > 49.7') in MNI152 space. I would like to transform them to fsaverage space. > > > > How should I do that? > > > > To answer my own question, this seems to be explained as use case #8 on > the following website (at the bottom): > > https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems > > To be precise, the website explains the transformation in the opposite > direction, so one should use the inverse of the matrix given on the website. > > -- > Tim > > ___ > 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
[Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output
External Email - Use Caution Dear Douglas, Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according your advice to obtain voxel-wise output rescaled without PVC correction, I have done sequentially the different steps to obtain this output. However, when comparing voxel-wise rescaled output (rbv.nii.gz) between the two methods, final values at each voxel are not the same… To obtain first rescaled voxel-wise output I have used sequentially these steps: 1. Concatenate transforms from PET space to gtmseg.mgz 2. Register native PET into gtmseg space (trilin. interpolation) 3. Compute mean PET inside reference regions (with regions masks from gtmseg.mgz) 4. Compute intensity normalized PET images in gtmseg space Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command use these same steps ? Best, Matthieu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Runtime of Freesurfer on Linux VM on Google Cloud Platform
yes, that is correct, we see those runtimes commonly with openmp. Someone else will have to answer the VM question though. Bruce On Sun, 10 Feb 2019, Yi-Fang Chuang wrote: External Email - Use Caution Thanks~ I was asking this because the release note of v6.0.0 said the recon-all -all runtime of new-ish workstation is just under 3 hours!!! That makes me wonder if I missed something or did not set up the VM right. Yi-Fang Bruce Fischl 於 2019年2月10日 週日 上午9:21寫道： yes, but -openmp N should give significant imrpovements up to about N=4 On Sat, 9 Feb 2019, Tim Schäfer wrote: > External Email - Use Caution > > I do not have experience with running on Google Cloud, but from what I know, the common way is to run FreeSurfer in parallel over many subjects instead of using openmp to speed up the process for a single subject. > > So your desktop should run 4 subjects in parallel, and the cloud instance 16. Not that bad. > > Tim > >> On February 9, 2019 at 4:33 PM Yi-Fang Chuang wrote: >> >> >> External Email - Use Caution >> >> Dear Freesurfer developers and users, >> >> Has anyone had experience running Freesurfer on Linux VM on Google Cloud >> Platform? >> I have a question about runtime of recon-all -all. >> The specs of VM on GCP as follows, >> Linux CentOS 6, 16 CPU(Intel(R) Xeon(R) @ 2.50GHz) with 60 G memory >> I installed Freesurfer v 6.0.0 and run recon-all -all -parallel -openmp num >> No matter what number I put (6,8,12,16 after openmp), the recon-all runtime >> of a single subject ranges 6-7 hours. >> It's just disappointing to compare to my own desktop. >> My own Desktop is Mac Pro (3.7 GHz quad-core intel xeon E5, 16G memory). >> The recon-all runtime (Freesurfer version 5.3.0, no parallel) for a single >> subject is usually 7~8 hours. >> Is this a reasonable runtime given the setting of VM? Only 1-2 hour >> shorter than my Mac Pro?? >> Or is there any configuration of VM I should pay attention to set up? >> >> Thanks, >> Yi-Fang Chuang >> ᐧ >> ᐧ >> ___ >> 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 > > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Yi-Fang Chuang (莊宜芳), M.D., Ph.D. Assistant Professor Institute of Public Health, National Yang-Ming University No. 155, Sec. 2, Linong Street, Taipei, 11221 Taiwan (R.O.C) +886-2-28267000#7981 chua...@ym.edu.tw Attending physician Department of Psychiatry, Far Eastern Memorial Hospital No.21, Sec. 2, Nanya S. Rd,. Banqiao Dist., New Taipei City 220, Taiwan (R.O.C) Special Volunteer NIA-Laboratory of Behavioral Neuroscience-Unit of Clinical and Translational Neuroscience BRC-Biomedical Research Center, 04C316 251 Bayview Blvd. Baltimore, MD chua...@mail.nih.gov [t?sender=aZ3JhY2UueWlmYW5nY2h1YW5nQGdtYWlsLmNvbQ%3D%3D=zerocontent=5cf2b1c3-2adc-4f8d-8d03-170b683d51a 5] ᐧ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_segstat: same output with two different label
External Email - Use Caution Thanks a lot for the reply! If I run mri_diff order/z.nii.gz disorder/z.nii.gz I indeed get zero. However, if I perform the contrast "order minus disorder" I get 0.1, so I should see some difference although very small, right? These are the outputs: francesca@francesca-desktop:/opt/freesurfer/fsfast/OrderDisorder/AB/bold/AB_OrderDisorder_lh$ mri_segstats --i order/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_order_avg --snr --sum lh.V2dorsal_AB_order_sum $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --i order/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_order_avg --snr --sum lh.V2dorsal_AB_order_sum sysname Linux hostname francesca-desktop machine x86_64 user francesca UseRobust 0 Constructing seg from label Loading order/z.nii.gz Vertex Area is 0.65781 mm^3 Generating list of segmentation ids Found 2 segmentations Computing statistics for each segmentation Reporting on 2 segmentations Using PrintSegStat Computing spatial average of each frame 0 1 Writing to lh.V2dorsal_AB_order_avg 0 -0.950279 1 1.31525 mri_segstats done francesca@francesca-desktop:/opt/freesurfer/fsfast/OrderDisorder/AB/bold/AB_OrderDisorder_lh$ mri_segstats --i disorder/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_disorder_avg --snr --sum lh.V2dorsal_AB_disorder_sum $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --i disorder/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_disorder_avg --snr --sum lh.V2dorsal_AB_disorder_sum sysname Linux hostname francesca-desktop machine x86_64 user francesca UseRobust 0 Constructing seg from label Loading disorder/z.nii.gz Vertex Area is 0.65781 mm^3 Generating list of segmentation ids Found 2 segmentations Computing statistics for each segmentation Reporting on 2 segmentations Using PrintSegStat Computing spatial average of each frame 0 1 Writing to lh.V2dorsal_AB_disorder_avg 0 -0.950279 1 1.31525 mri_segstats done mri_segstats --i order-vs-disorder/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_orderVsdisorder_avg --snr --sum lh.V2dorsal_AB_orderVsdisorder_sum $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --i order-vs-disorder/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_orderVsdisorder_avg --snr --sum lh.V2dorsal_AB_orderVsdisorder_sum sysname Linux hostname francesca-desktop machine x86_64 user francesca UseRobust 0 Constructing seg from label Loading order-vs-disorder/z.nii.gz Vertex Area is 0.65781 mm^3 Generating list of segmentation ids Found 2 segmentations Computing statistics for each segmentation Reporting on 2 segmentations Using PrintSegStat Computing spatial average of each frame 0 1 Writing to lh.V2dorsal_AB_orderVsdisorder_avg 0 0.119339 1 -1.93788 mri_segstats done Thanks again for the help! Best Francesca Il giorno mar 22 gen 2019 alle ore 20:55 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > I don't know what is happening. If the two z-maps are really different, > then it should have given different values. Run this > mri_diff order/z.nii.gz disorder/z.nii.gz > Does it indicate that there is a difference? If so, can you run your two > mri_segment commands and send me the terminal output of each? > As for the two mean intensity values, one (Seg0001) is from inside your > ROI and the other (Seg) is outside. You can have it exclude Seg > with --excludeid 0 > > > On 1/20/19 10:00 AM, Francesca Strappini wrote: > > > > External Email - Use Caution > > > > Dear Freesurfer's experts, > > > > I'm trying to run a ROIs mean intensity analysis using mri_segstat. > > I'm using as an input contrast maps created with mkcontrast-sess and > > selxavg3-sess (block-design experiment) and as masks, some labels > > created on the surface with a retinotopic analysis. > > > > I noticed that all my outputs with the same label have the same > > values, regardless of the contrast map that I'm giving as an input. > > However, if I plot the contrast maps on the surface I can clearly see > > that there are differences, so also the mean signal should be different. > > > > Maybe I'm not running the command correctly: > > > > mri_segstats --i z.nii.gz --slabel sub1 lh lh.V2dorsal_sub1.label > > --sfavg lh.V2dorsal_sub1_condition1_avg --snr --sum > > lh.V2dorsal_sub1_condition1_sum > > > > These are two outputs from the same regions but with two different z > > maps as inputs. > > I can also see that are indicated two different values as mean > > intensity, -0.95028 and 1.31525, what's the difference between them? > > > > # Title
