Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30083 discussions

Question on Z-scoring
by Nillo, Ryan Michael R 04 Oct '19

04 Oct '19

Hello FreeSurfer users/devs, I have a question on z-scoring. I would like to produce z-scored volume maps for each subject in my study. Is my process correct? 1) mri_surf2surf —srcsubject $sub —trgsubject $sub —sval $sub/surf/$h.volume —tval $sub/surf/$h.volume.mgh —sfmt curv (convert .volume file to .mgh file) 2) mris_preproc --hemi $h --fsgd 09172019.fsgd.txt --meas volume --mean --fwhm 0 --o $PWD/$h.volume.pop_mean.mgh (obtain mean population volume at each vertex) 3) mris_preproc --hemi $h --fsgd 09172019.fsgd.txt --meas volume —std --fwhm 0 --o $PWD/$h.volume.pop_std.mgh (obtain volume standard deviation volume at each vertex) 4) mri_surf2surf —srcsubject fsaverage —trgsubject $sub —sval $PWD/$h.volume.pop_mean.mgh —tval $sub/surf/$h.volume.pop_mean.mgh —hemi $h (map population mean to subject space) 5) mri_surf2surf —srcsubject fsaverage —trgsubject $sub —sval $PWD/$h.volume.pop_std.mgh —tval $sub/surf/$h.volume.pop_std.mgh —hemi $h (map population std to subject space) 6) fscalc $sub/surf/$h.volume.mgh sub $sub/surf/$h.volume.pop_mean.mgh div $sub/surf/$h.volume.pop_std.mgh -o $sub/surf/$h.volume_z.mgh 7) mri_surf2surf —srcsubject $sub —trgsubject $sub —sval $sub/surf/$h.volume_z.mgh —tval $sub/surf/$h.volume_z —tfmt curv (convert .mgh to curv file) After z-scoring each vertex, I want to do a group analysis between the two groups in my cohort. Instead of using raw volume as my measurement, I would be using z-scored volume. Thanks for the help, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging External Email - Use Caution

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Tracula
by Juan Rivas 04 Oct '19

04 Oct '19

External Email - Use Caution Hi, I am trying to make the recon with diffusion images for running tracula. I gave this command: set cmd = dt_recon set cmd = ($cmd --b $SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/31190669_bvals set cmd = ($cmd --b $SUBJECTS_DIR/esq-15 hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/31190669_bvecs) set cmd = ($cmd --i $SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/esq-15-hc_dwi.nii.gz) set cmd = ($cmd --s $SUBJECTS_DIR/esq-15-hc/) set cmd = ($cmd --o $SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing) echo $cmd $cmd But ir marks two kinds of error: can´t fin bvals.dat or Eddy/Motion correct and stops. Could yo help me? Thanks, JC.

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Re: [Freesurfer] Curvature estimation from Hessian
by LOSKE, PHILIPP (PGR) 04 Oct '19

04 Oct '19

External Email - Use Caution Hi Bruce, thank you for your explanation. I think I might have an idea, why the Hessian matrix works in this case, maybe you can confirm or correct me if I'm wrong. Usually, if you're having a 2d surface in space, the principle curvatures are the eigenvalues of the shape operator (which needs calculation of first and second fundamental form), not the Hessian. Only in the particular case of a vanishing gradient, the eigenvalues are the same as those of the Hessian. F.e. for a quadratic function, the gradient vanishes at the minimum (in 1d first derivative is zero). Since you're modelling a quadratic function in a local neighborhood around each vertex, its minimum lies at the vertex, is that correct? if this is so, then the gradient should vanish and Hessian matrix should be fine and my confusion is resolved :). In the literature I found just vague explanations, sometimes mentioning the shape operator, sometimes the Hessian. I just want to make sure I understand this process correctly. Cheers Philipp Date: Thu, 3 Oct 2019 10:03:52 -0400 (EDT) Hi Philipp the Hessian is estimated at each vertex by doing a quadratic fit to the local surface as the height function over the tangent plane of all the vertices in a 2-neighborhood of that vertex. I'm not sure what the gradient vanishing is about, but the curvatures are just the eigenvalues of the Hessian, so I don't think the gradient has anything to do with it. Not that we also have some discrete tools for computing curvature make sense? cheers Bruce On Thu, 3 Oct 2019, LOSKE, PHILIPP (PGR) wrote: > > ????????External Email - Use Caution???????? > > Hi, > > I am trying to understand how exactly FreeSurfer estimates the curvature > values from the white surface. From the mailing lists I understood that the > white surface is modeled by fitting a second-order polynomial function and > curvatures are estimated from the Hessian matrix at each vertex (thank you > Bruce). However, I still have trouble to understand how this works in > detail. First, as I understand it, curvature can only be derived from the > Hessian if the gradient vanishes (why is this the case?), and from > differential geometry, shouldn't instead the shape operator be calculated at > each vertex on the surface? Second, are the Gaussian and mean curvatures > then directly calculated from?Hessian/Shape operator or first principle > curvatures (and are they saved somewhere?). I tried to find a detailed > explanation in some of the FreeSurfer papers, but couldn't find anything > really. > > Thank you very much in advance! > > Cheers > Philipp The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.

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Exporting ROI segmentation in T1 DICOM header
by Correia de Aguiar, V.M. 04 Oct '19

04 Oct '19

External Email - Use Caution Dear Freesurfer developers, Is it possible to export the ROI segmentations that are stored in ?h.aparc.a2009s.annot or ?h.aparc.annot files into the header of the DICOM file? I would like to open those files with corresponding segmentations in RayStation. Many thanks for your time. Regards, Vânia de Aguiar, PhD Assistant Professor in Neurolinguistics University of Groningen Faculty of Arts Oude Kijk in 't Jatstraat 26 Room 1315.0408 9712 EK, Groningen The Netherlands

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Re: [Freesurfer] Freesurfer - issue after installation in Linux
by Tim Schäfer 03 Oct '19

03 Oct '19

External Email - Use Caution You need to install the tcsh shell: sudo apt-get install tcsh Best, Tim > On October 3, 2019 at 6:30 PM Tim Schäfer <tim(a)rcmd.org> wrote: > > > You need to install the tcsh shell: > > sudo apt-get install tcsh > > Best, > > Tim > > > On October 3, 2019 at 6:26 PM Theotonio Pauliquevis <theotonio(a)gmail.com> wrote: > > > > > > External Email - Use Caution > > > > Hi, > > > > I just installed freesurfer in Linux Ubuntu 14.04, and I got a critical > > (and strange) problem in the earlier tests of freesurfer (Example 2). Any > > help would be appreciated. Basically, when trying example 2 in instructions > > homepage I got the following error: > > > > theo@theo-Inspiron-5457:~$ recon-all -i sample-001.nii.gz -s bert -all > > bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No > > such file or directory > > > > But the fact is that recon-all is there and apparently it is well > > configured, because 1) the recon-all does exist, and 2) permissions are ok: > > > > theo@theo-Inspiron-5457:~$ ls -l /usr/local/freesurfer/bin/recon-all > > -rwxrwxr-x 1 8481 1590 327555 Jan 18 2017 > > /usr/local/freesurfer/bin/recon-all > > > > and the command is promptly recognized : > > > > theo@theo-Inspiron-5457:~$ which recon-all > > /usr/local/freesurfer/bin/recon-all/ > > > > Any ideas? Anybody got this issue before? It seems to be some (not obvious) > > permission problem. > > > > Below I type the whole procedure to install, so one can see that I followed > > all installation instructions. > > > > History: > > > > 1) Successfully downloaded and unzipped the files at /usr/loca/freesurfer > > > > 2) Successful set up of environment variables after including the following > > lines in .bashrc: > > > > ############################################## > > #Software FREESURFER - Enviroment variables > > # > > export FREESURFER_HOME=/usr/local/freesurfer > > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > export SUBJECTS_DIR=/home/theo/freesurfer/subjects > > ############################################## > > > > BTW, "theo" is my userID > > > > 3) File license.txt copied to /usr/local/freesurfer > > > > 4) message after open a terminal window confirms that Enviroment variables > > were correctly set: > > > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /usr/local/freesurfer > > FSFAST_HOME /usr/local/freesurfer/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /usr/local/freesurfer/subjects > > MNI_DIR /usr/local/freesurfer/mni > > (base) theo@theo-Inspiron-5457:~$ echo $SUBJECTS_DIR > > /home/theo/freesurfer/subjects > > (base) theo@theo-Inspiron-5457:~$ > > > > > > Any help is welcome > > Regards > > > > Theotonio > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Dr. Tim Schäfer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Freesurfer's last version installation
by Barletta, Valeria 03 Oct '19

03 Oct '19

Dear Freesurfers, We need to install the last version of Freesurfer, but we need to keep the wm edits that we made with version 5.3 How can this be done? Is there any specific command? Thanks a lot, Vale

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Freesurfer - issue after installation in Linux
by Theotonio Pauliquevis 03 Oct '19

03 Oct '19

External Email - Use Caution Hi, I just installed freesurfer in Linux Ubuntu 14.04, and I got a critical (and strange) problem in the earlier tests of freesurfer (Example 2). Any help would be appreciated. Basically, when trying example 2 in instructions homepage I got the following error: theo@theo-Inspiron-5457:~$ recon-all -i sample-001.nii.gz -s bert -all bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory But the fact is that recon-all is there and apparently it is well configured, because 1) the recon-all does exist, and 2) permissions are ok: theo@theo-Inspiron-5457:~$ ls -l /usr/local/freesurfer/bin/recon-all -rwxrwxr-x 1 8481 1590 327555 Jan 18 2017 /usr/local/freesurfer/bin/recon-all and the command is promptly recognized : theo@theo-Inspiron-5457:~$ which recon-all /usr/local/freesurfer/bin/recon-all/ Any ideas? Anybody got this issue before? It seems to be some (not obvious) permission problem. Below I type the whole procedure to install, so one can see that I followed all installation instructions. History: 1) Successfully downloaded and unzipped the files at /usr/loca/freesurfer 2) Successful set up of environment variables after including the following lines in .bashrc: ############################################## #Software FREESURFER - Enviroment variables # export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=/home/theo/freesurfer/subjects ############################################## BTW, "theo" is my userID 3) File license.txt copied to /usr/local/freesurfer 4) message after open a terminal window confirms that Enviroment variables were correctly set: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni (base) theo@theo-Inspiron-5457:~$ echo $SUBJECTS_DIR /home/theo/freesurfer/subjects (base) theo@theo-Inspiron-5457:~$ Any help is welcome Regards Theotonio

1 0

Curvature estimation from Hessian
by LOSKE, PHILIPP (PGR) 03 Oct '19

03 Oct '19

External Email - Use Caution Hi, I am trying to understand how exactly FreeSurfer estimates the curvature values from the white surface. From the mailing lists I understood that the white surface is modeled by fitting a second-order polynomial function and curvatures are estimated from the Hessian matrix at each vertex (thank you Bruce). However, I still have trouble to understand how this works in detail. First, as I understand it, curvature can only be derived from the Hessian if the gradient vanishes (why is this the case?), and from differential geometry, shouldn't instead the shape operator be calculated at each vertex on the surface? Second, are the Gaussian and mean curvatures then directly calculated from Hessian/Shape operator or first principle curvatures (and are they saved somewhere?). I tried to find a detailed explanation in some of the FreeSurfer papers, but couldn't find anything really. Thank you very much in advance! Cheers Philipp The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.

2 1

selxavg3-sess
by Sanati Monfared, Shamsi 02 Oct '19

02 Oct '19

External Email - Use Caution Hi all, I am running the functional analyses (selxavg3_sess) and stuck at the following error, which I have no idea what to do (apparently the analyses have been OK up until run 010 and the error happened in run 012). I received the same errors in my all subjects (at run 012) 'gunzip -c /Users/smonfared6/Desktop/WheelerChess_dcm/Chess_Functional/chess001/bold/010/fmcpr.up.sm5.fsaverage.lh.nii.gz > /var/folders/v3/yznj9t351dbgs1093rr12wrh010dv3/T/tp7da06091_16b6_41ba_8283_005c005b5dd3.load_nifti.m.nii' cmd = 'gunzip -c /Users/smonfared6/Desktop/WheelerChess_dcm/Chess_Functional/chess001/bold/012/fmcpr.up.sm5.fsaverage.lh.nii.gz > /var/folders/v3/yznj9t351dbgs1093rr12wrh010dv3/T/tpc5683b1b_4f0b_4593_ab5d_82233348f546.load_nifti.m.nii' ERROR: fast_st2fir: two or more presentations are simultaneous ERROR: creating FIR design matrix for Condition03 Dot indexing is not supported for variables of this type. Error in flac_customize (line 358) if(~isempty(flacnew.TFmtx)) Error in fast_selxavg3b (line 184) flac = flac_customize(flac); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Any advice would be highly appreciated! Thanks, -Shamsi --- [cid:fdf9e808-3a33-4fda-a4f9-de06f4fae657] Wheeler Lab<http://wheelerlab.gatech.edu/> | Center for Advanced Brain Imaging<http://wheelerlab.gatech.edu/> 831 Marietta St NW, Atlanta, GA 30318 Email: smonfared6(a)gatech.edu Phone: 205-607-1656

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Freesurfer three groups: group A vs C power.
by cody samth 02 Oct '19

02 Oct '19

External Email - Use Caution Hi I have a question regarding how freesurfer calculates the degrees of freedom when you have three groups in the FSGD/contrast files but are running analyses on group A vs C. For example I have an analysis with 3 groups and 2 covariates. My primary question is: is there a difference between any groups. Which I have the contrast: 1 -1 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 When I write a contrast for A vs C: (1 0 -1 0 0 0 0 0 0) Does freesurfer consider this model as 9 regressors? Or 6 regressors; which would be present in a typical group 1 vs group 2 analysis that could be modeled by (1 -1 0 0 0 0) if group B didn't exist?

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