Freesurfer

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problem fast_selxavg3b
by Desiree Thielemann 06 Oct '15

06 Oct '15

Dear freesurfer experts, I included the new function fast_selxavg3b but I got another problem: First error: /opt/freesurfer/bin/mris_fwhm --mask /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz --i /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz --o /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann /opt/freesurfer/bin/mris_fwhm: symbol lookup error: /opt/freesurfer/bin/mris_fwhm: undefined symbol: ncerr ERROR: /opt/freesurfer/bin/mris_fwhm --mask /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz --i /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz --o /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann ans = 127 Second error with another server running the analyses: /opt/freesurfer/bin/mris_fwhm: /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/freesurfer/bin/mris_fwhm) /opt/freesurfer/bin/mris_fwhm: /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /opt/freesurfer/bin/mris_fwhm) The problem seems to be the version of matlab. Which version would you suggest to use while using the function fast_selxavg3b? And why is there an undefined symbol? Do you have any suggestions how to solve the problem? Best regard, Desiree >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Zitat von Douglas Greve <greve(a)nmr.mgh.harvard.edu>: > oops, sorry, that did not make it into the distribution. You can get it here > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3… > > thanks > doug > > > On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote: >> Dear members of the freesurfer mailing list, >> >> I'm using freesurfer-Linux-centos7_x86_64-dev-20150728. I started to >> analyse mri data with fs-fast. I did the preprocessing and used the >> function mkanalysis-sess and mkcontrast-sess without any problems. I >> tried to run the function selxavg3-sess next and it stopped with the >> error message: >> >>>>>>>>>> /opt/freesurfer/fsfast/toolbox/fast_selxavg3.m >>>> /opt/freesurfer/fsfast/toolbox/fast_ldanaflac.m >>>> /opt/freesurfer/matlab/MRIread.m >>>>>>>> ??? Undefined function or method 'fast_selxavg3b' for input >>>> arguments of type >> 'char'. >> >>>> ------------------------------------------ >> ERROR: fast_selxavg3() failed\n >> >> I looked for the function fast_selxavg3b in matlab. Unfortunatly only >> the function fast_selxavg3 is included in the fsfast/toolbox. By >> trying to use the function fast_selxavg3, it recommand me to use >> fast_selxavg3b. I could not find the function in the internet. >> >> Do you have any suggestions what to do? >> >> Best regards, >> Desiree >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Lost toolbar in freeview
by Antonin Skoch 06 Oct '15

06 Oct '15

Dear Ruopeng, thank you, it worked! Only, just to let you know, this tiny popup menu item was completely blank in my case, without any inscription. When I left-clicked at it, the menu bar appeared, and on this popup menu item only checkmark newly appeared. Regards, Antonin

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Re: [Freesurfer] high area.pial values
by Andrews, Derek 06 Oct '15

06 Oct '15

Dear Bruce, Thank you for your response regarding high area values. I have indeed observed high values (I.e. >20) in both the white and pial surfaces of my subjects, albeit only at a few vertices. The vertices indices that contain the highest values in these surface appear around ~258,000-324,000. Would you consider this the end of the array? And if not, what could cause a value of ~80 in the ~258,000 vertex of a pial surface reconstruction? As a background to what I¹m hoping to accomplish: I am using Freesurfer features (arrays) as inputs for pattern classification, therefore I am interested in potential impact on my models due to these outliers. Smoothing reduces the effect of these outliers, however also raises the values of surrounding vertices. I am thinking of replacing these high values with an average area measure taken across all participants prior to smoothing. Again, thank you for your insights in this topic. Best, Derek ________________________________________ Derek Sayre Andrews, MSc PhD Candidate & IoPPN Student Forum Chair Department of Forensic and Neurodevelopmental Sciences & The Sackler Institute for Translational Neurodevelopment Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews(a)kcl.ac.uk On 25/09/2015 17:00, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >are they only high on the pial and not on the white? I would have guessed >that they would be high on both, and further that it is due to the >topology >correction and the quirks of the way we retesselate. One easy way to find >out if this is true is if the vertex index is near the end of the list >(i.e. close to the total number of vertices, since the vertices added >during the correction are at the end of the array) > >cheers >Bruce > >On Fri, 25 Sep 2015, Andrews, Derek wrote: > >> Dear FreeSurfer Support Team >> >> First of all, I must thank you for your excellent software! >> >> I have been looking at distributions of various free surfer features >> (histograms of the vertex wise measures). I have noticed some high >>values >> among the pial and white matter surfaces, these values range from 20-85. >> Again, this in only in a handful of vertices (out of millions of >>measures). >> I am wondering what could account for such a high value? >> >> Thank you for your help in clarifying this. >> >> Best, Derek >> >> >> >>_________________________________________________________________________ >>___ >> >> Derek Sayre Andrews, MSc >> PhD Candidate >> >> Department of Forensic and Neurodevelopmental Sciences & >> >> The Sackler Institute for Translational Neurodevelopment >> Institute of Psychiatry, Psychology & Neuroscience, King's College >>London >> >> Telephone: +44 (0)20 7848 5701 >> Email: Derek.Andrews(a)kcl.ac.uk >> >> >> >>_______________________________________________ >Freesurfer mailing list >Freesurfer(a)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.

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Re: [Freesurfer] Calculate the cortical thickness in patients with brain tumor
by Bruce Fischl 06 Oct '15

06 Oct '15

Hi Feng it depends on where the tumor is cheers Bruce On Wed, 30 Sep 2015, chenhf_uestc wrote: > Hi, freesurfer experts, > > If my data came from the patients with brain tumors, could I perform > recon-all analyses to calculate cortical thickness, surface area and so on. > If not, could I mask the brain region with tumor and then conduct such > analyses? I think the tumor might lead to the inaccuracy of cortical > reconstruction > > Best, > Feng > >

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Re: [Freesurfer] Lost toolbar in freeview
by Antonin Skoch 06 Oct '15

06 Oct '15

Dear Ruopeng, I am using Ubuntu 12.04. LTS 32bits. There is no directory ~/Library/Preferences in my home directory. There is only "GNUstep" directory containing subdirectories "Defaults" and "Library". "Library" dir is empty and "Defaults" contains .GNUstepDefaults file, which is very short file containing only NSGlobalDomain entry. Regards, Antonin

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mris_surf2vol
by Kevin Aquino 06 Oct '15

06 Oct '15

Hi all, I am trying to "voxelize" the cortical surfaces generated in freesurfer and I am a little stuck. I have been using mris_surf2vol with the --mask option however this generates a very speckled representation of the cortical surface on the voxels. What I would prefer would be the level sets of the cortical surface interpolated onto voxels, even if they are at a different resolution that could be enough. Is this possible with any of the available commands? I also went down the route of mris_volmask however, this generates the cortical ribbon, which is something that I don't need. Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Imaging Center, School of Physics & astronomy, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney. *E* Kevin.aquino(a)nottingham.ac.uk, aquino(a)physics.usyd.edu.au | *W* www.physics.usyd.edu.au/~aquino/ ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

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Re: [Freesurfer] Question about the volume conversion in freesurfer
by chenhf_uestc 05 Oct '15

05 Oct '15

Yes, my data have been normalized to the MNI space. So, in my case, what should I do if I want to use the mri_surf2vol function? Best, Feng 发件人：Douglas Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2015-09-29 00:00 主题：Re: [Freesurfer] Question about the volume conversion in freesurfer 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： This is not an easy thing to do. First of all, did you apply a nonlinear registration to get the fMRI to the normalized MNI space? If so, then you can not do what you want with the data you have pre-processed. On 9/24/15 2:26 AM, chenhf_uestc wrote: Dear freesurfer experts, I want to compute functional connectivity based on the region with significantly different cortical thickness of two groups. The fMRI data have been preprocessed by using SPM software and normalized to the MNI space. However, I do not how to use the function mri_surf2vol. The required flagged arguments include --surfva, --hemi and --volreg (i.e., volume registration file). How can I set up the --volreg argument? What is the third arguments --volreg? The online manual states that contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. The format of this file is that as output by tkregister2 and includes the name of the subject. It will be assumed that the input surface values are sampled on the surface of this subject. Where could I find the volume registration file? Any help would be greatly appreciately. Best, Feng _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] mri_vol2surf
by Douglas Greve 05 Oct '15

05 Oct '15

On 9/29/15 3:36 PM, Martin Tisdall wrote: > I am trying to produce a scalar overlay from PET data to overlay onto the pial surface. > I have coregistered the pet with T1.mgz and then used the transform from mri_info --scanner2tkr to co-localise with orig.mgz. What does that mean? You'll need to run bbregister to get the registration file > I then do: > mri_vol2surf --src <coregistered pet> --out <output file.w> --out_type paint --regheader <subject> --hemi lh --surf pial --projfrac 0.5. If you want it on the pial surface use --projfrac 0.0. The way you have it now, it will sample a distance of half the thickness beyond the pial surface. Also, I would recommend using .mgh as the output format as not many tools work the paint files. > > The output doesn't seem quite right as seems to be some areas of signal drop out. > Can anyone tell me if my options look right or am I missing something. > Thank you > Martin > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Re: [Freesurfer] problem fast_selxavg3b
by Douglas Greve 05 Oct '15

05 Oct '15

It is never good to mix versions, so I would re-do it. On 9/29/15 1:45 PM, Desiree Thielemann wrote: > Thanks Doug! > > I have another question: We did the fsfast analysis some time ago before > we updated freesurfer version with fast_selxavg3. Now we want to analyse > additional persons. Do you think it is comparable or is it better to > re-do the analysis for all persons with fast_selxavg3b instead of 13 > persons with fast_selxavg3 and 2 persons with fast_selxavg3b? > > Thanks in advance, > Desiree > > Am 29.09.2015 um 15:34 schrieb Douglas Greve: >> oops, sorry, that did not make it into the distribution. You can get it here >> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3… >> >> thanks >> doug >> >> >> On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote: >>> Dear members of the freesurfer mailing list, >>> >>> I'm using freesurfer-Linux-centos7_x86_64-dev-20150728. I started to >>> analyse mri data with fs-fast. I did the preprocessing and used the >>> function mkanalysis-sess and mkcontrast-sess without any problems. I >>> tried to run the function selxavg3-sess next and it stopped with the >>> error message: >>> >>>>>>>>>>> /opt/freesurfer/fsfast/toolbox/fast_selxavg3.m >>>>> /opt/freesurfer/fsfast/toolbox/fast_ldanaflac.m >>>>> /opt/freesurfer/matlab/MRIread.m >>>>>>>>> ??? Undefined function or method 'fast_selxavg3b' for input >>>>> arguments of type >>> 'char'. >>> >>>>> ------------------------------------------ >>> ERROR: fast_selxavg3() failed\n >>> >>> I looked for the function fast_selxavg3b in matlab. Unfortunatly only >>> the function fast_selxavg3 is included in the fsfast/toolbox. By >>> trying to use the function fast_selxavg3, it recommand me to use >>> fast_selxavg3b. I could not find the function in the internet. >>> >>> Do you have any suggestions what to do? >>> >>> Best regards, >>> Desiree >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Re: [Freesurfer] selxavg3-sess outputs
by Douglas Greve 05 Oct '15

05 Oct '15

Yes, they do. There is also a pcc.nii.gz which is the partial correlation coefficient. On 9/30/15 1:14 PM, Jiahe Zhang wrote: > Dear Freesurfer experts, > > The freesurfer command 'selxavg3-sess' outputs many files in the > contrast folder in addition to the three documented on the Wiki (ces, > cesvar, sig). Is there more detailed documentation on what each output > is and how they're computed? In particular, I was wondering if the > t.nii.gz and z.nii.gz maps contain standard t and standard z scores. > > Thanks, > Jiahe > > > -- > Jiahe Zhang > Ph.D. Candidate > Department of Psychology > Northeastern University > 617-373-4789 <tel:617-373-4789> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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