Freesurfer

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Re: [Freesurfer] Errors running TRACULA (data attached) - valid frame numbers
by Mazzetti, C. (Cecilia) 06 Oct '19

06 Oct '19

External Email - Use Caution Hi Anastasia, Thank you for answering! I think you are right and the problem is there, when checking the number of slices in the dwindling file I get: dimensions: 104 x 104 x 72 Although the original dwindling data has: 104 x 104 x 72 x 111 voxel sizes: 2.019231, 2.019231, 2.000000 type: SHORT (4) fov: 210.000 dof: 0 xstart: -105.0, xend: 105.0 ystart: -105.0, yend: 105.0 zstart: -72.0, zend: 72.0 TR: 3670.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9897, y_r = 0.1290, z_r = -0.0618, c_r = -1.2731 : x_a = -0.1108, y_a = -0.9647, z_a = -0.2389, c_a = -22.2682 : x_s = -0.0904, y_s = -0.2296, z_s = 0.9691, c_s = 12.8890 Orientation : LPS Primary Slice Direction: axial voxel to ras transform: -1.9985 0.2605 -0.1236 93.5531 -0.2238 -1.9480 -0.4778 107.8607 -0.1826 -0.4636 1.9382 -23.2834 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 8.15459 ras to voxel transform: -0.4901 -0.0549 -0.0448 50.7312 0.0639 -0.4778 -0.1137 42.9079 -0.0309 -0.1194 0.4845 27.0558 0.0000 0.0000 0.0000 1.0000 I don't understand why, given those are outputs of recon-all .. Do you think you know what's happening? Thank you very much!? Best, Cecilia Cecilia Mazzetti - Ph.D. Researcher Donders Centre for Cognitive Neuroimaging, room 2.257 Kapittelweg 29 | 6525 EN Nijmegen

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Errors running TRACULA (data attached) - valid frame numbers
by Mazzetti, C. (Cecilia) 06 Oct '19

06 Oct '19

External Email - Use Caution Dear members, I've tried troubleshooting but can't wrap my head around this. Trying to run TRACULA after recon-all the subjects, but I keep getting: ################ [...] R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. (a bunch of these) TR=3670.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.989717, -0.110817, -0.0904434) j_ras = (-0.128995, 0.964706, 0.22957) k_ras = (-0.0618111, -0.238876, 0.969081) keeping frames 0 1 12 23 34 45 56 67 78 89 100 ERROR: valid frame numbers are between 0 and 0 trac-preproc exited with ERRORS ##### I checked the # of bvals and bvecs in the dorm folder compared to orig ones, same. I don't know what's wrong below config file: set subjlist = ( subject02_C ) set dcmlist = ( /myfolder/freesurfer/subject02_C/dmri/data.nii.gz ) set bveclist = ( /myfolder/freesurfer/subject02_C/dmri/bvecs ) set bvallist = ( /myfolder/freesurfer/subject02_C/dmri/bvals ) set doeddy = 1 set dorotbvecs = 1 set usemaskanat = 1 set thrbet = 0.3 set doregflt = 0 set doregbbr = 1 ?set doregmni = 1 set doregcvs = 0 set pathlist = ( lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) Please any sort of input/help is super appreciated. Let me know if I can give more information Cheers, Cecilia ?

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Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 7
by Juan Rivas 05 Oct '19

05 Oct '19

External Email - Use Caution Thank you for your answer, I pursued your recommendations, and now the warning is that it can open file....../COR-.info. What can I do? JC. El sáb., 5 oct. 2019 a las 12:00, <freesurfer-request(a)nmr.mgh.harvard.edu> escribió: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Curvature estimation from Hessian (LOSKE, PHILIPP (PGR)) > 2. Segmentation faule recon-all (Backhausen, Lea) > 3. Tracula (Juan Rivas) > 4. Re: Tracula (Yendiki, Anastasia) > 5. Question on Z-scoring (Nillo, Ryan Michael R) > 6. ERROR gtmseg (Marina Fern?ndez) > 7. Re: Question on Z-scoring (Greve, Douglas N.,Ph.D.) > 8. Re: ERROR gtmseg (Greve, Douglas N.,Ph.D.) > 9. Re: Segmentation faule recon-all (Greve, Douglas N.,Ph.D.) > 10. Vertex by Vertex Analysis (WON JONG CHWA) > 11. Re: question about aparcstats2table (Kiyotaka Nemoto) > 12. Brodmann area parcellation (sang ho shin) > 13. Errors running TRACULA (data attached) - valid frame numbers > (Mazzetti, C. (Cecilia)) > 14. Confidence interval for Cohen's d from gamma/rstd > (Caspar M. Schwiedrzik) > 15. Re: Errors running TRACULA (data attached) - valid frame > numbers (Yendiki, Anastasia) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 4 Oct 2019 16:27:51 +0000 > From: "LOSKE, PHILIPP (PGR)" <p.loske.18(a)abdn.ac.uk> > Subject: Re: [Freesurfer] Curvature estimation from Hessian > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > AM0PR0402MB36506BB2F6A775BE1ACFC1F9E89E0(a)AM0PR0402MB3650.eurprd04.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > 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 cl?raichte ann an Alba, ?ir. > SC013683. >

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Segmentation faule recon-all
by Backhausen, Lea 04 Oct '19

04 Oct '19

External Email - Use Caution Dear FreeSurfer experts, when running the recon -all -all command (I included the -3T flag) with FreeSurfer Version 6.0.0 I get this error for one of my subjects: MRInormalize: could not find any valid peaks. Make sure the Talairach alignment is correct! I added the recon-all log to this email. Is there a way to fix this? Thank you for any suggestion! Best, Lea Backhausen ---------------------------------------- Lea Backhausen PhD Student / Psychologist (M.Sc.) Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>

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ERROR gtmseg
by Marina Fernández 04 Oct '19

04 Oct '19

External Email - Use Caution Dear experts, The following error occurs with one subject when I am running gtmseg command: *Computing colortable* *ERROR: cannot find match for subcortical segid 229* *ERROR: mri_gtmseg -s qsm_04_year3 --usf 2 --o gtmseg.mgz --apas apas+head.mgz --no-subseg-wm --no-keep-cc --no-keep-hypo* *gtmseg existed with errors* *ans=1* Do you know what happened with this subject? What can I do to solve it? Thank you very much in advance. Marina.

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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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