Freesurfer

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30064 discussions

PETsurf and mri_compute_volume_fractions
by Victor Montal Blancafort 29 Sep '17

29 Sep '17

Dear FreeSurfer experts, I am trying to obtain partial volume fractions of a DTI volume. When using the PETsurf framework (mri_gtmpvc), I obtain a pvf.nii.gz volume with GM, WM, subcortical, CSF and Skull tissue % values. However, when running the mri_compute_volume_fraction, the output diffears. Could you please tell me which are the parameters used (internally) in mri_gtmpvc when computing pvc, in order to replicate the same output when using mris_compute_volume_fractions?? Thank you in advance for your help! Victor M

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Re: [Freesurfer] recon-all -localGI problem / mris_compute_lgi problem
by Michael Leibbrand 28 Sep '17

28 Sep '17

I think I have fixed it myself. The input for the 'lh.pial' wasn't coming through correctly. I edited the find_corresponding_center_FSformat.m to take in not only 'lh.pial' but the entire path leading to 'lh.pial'. I did this for make_roi_paths.m and compute_lgi.m as well as added an input argument in /freesufer/bin/mris_compute_lgi to take in the current working directory ($PWD) and changed the acceslocation of the pial surface into [pial_dir '/' pial]. So, matlab: function find_corresponding_center_FSformat (pial, outersmoothed, stepsize, outdir, flagfile, pial_dir) [...] [mesh_total.vertices, mesh_total.faces]=freesurfer_read_surf([pial_dir '/' pial]); and bin file: set MLF = /tmp/mrc"_$$_".m set arg1 = ${input} set arg2 = ${input}-outer-smoothed set arg3 = ${stepsize} set arg4 = ${tmpdir} set arg5 = ${MLF} set arg6 = ${PWD} echo "find_corresponding_center_FSformat('${arg1}','${arg2}',$ {arg3},'${arg4}','${arg5}','${arg6}'); exit" > $MLF Just posting in case anybody needs this for future reference. Michael 2017-09-28 12:36 GMT-07:00 Michael Leibbrand <michael.leib7(a)gmail.com>: > Dear FreeSurfer team, > > I'm trying to calculate the local gyrification index for the test subject > Bert (or any of my own subjects for that matter) but I'm running into an > error when FS tries to read the lh.pial surface. > > I have the exact same error as Louise (see: https://mail.nmr.mgh. > harvard.edu/pipermail//freesurfer/2017-March/050593.html) but that > doesn't seemed to have been answered yet. > The error basicly takes place during the FS matlab command > freesurfer_read_surf, where it is unable to read the lh.pial (see the log). > This also causes the command find_corresponding_center_FSformat to fail > because there are no faces/vertices as input. > > ">> FREESURFER_READ_SURF [v 1.2 ] > Error using freesurfer_read_surf (line 90) > could not open surface file lh.pial. > > Error in find_corresponding_center_FSformat (line 26) > [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);" > > > If I run freesurfer_read_surf directly from matlab with the lh.pial as > input, it does return the faces/vertices to me in my matlab workspace. This > led me to think there might be a communication error between the FS toolbox > and matlab itself (or maybe the lh.pial is specified incorrectly?). > > Am I missing something here? > > FS versions used: nightly build and stable 6.0 > Matlab version: 2017a > OS: ubuntu 16.04 > uname -a: Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed > Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > Cheers, > > Michael >

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Adding control points to aparc+aseg
by Nicholas Goh 28 Sep '17

28 Sep '17

I am attempting to fix the aparc+aseg.mgz file for an image, and wanted to check to see if I am doing it correctly. What I was doing which seemed to be ineffective was 1)create a new point set of control points labelled control.dat 2)place control points along what should be white matter 3)save point set 4)run recon-all -autorecon2-cp -autorecon3 -subjid XXXX Is this the correct way to go about fixing aparc+aseg files that are missing chunks of the brain? Is there a better way to go about this? Thanks for the help, Nicholas Goh

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recon-all -localGI problem / mris_compute_lgi problem
by Michael Leibbrand 28 Sep '17

28 Sep '17

Dear FreeSurfer team, I'm trying to calculate the local gyrification index for the test subject Bert (or any of my own subjects for that matter) but I'm running into an error when FS tries to read the lh.pial surface. I have the exact same error as Louise (see: https://mail.nmr.mgh. harvard.edu/pipermail//freesurfer/2017-March/050593.html) but that doesn't seemed to have been answered yet. The error basicly takes place during the FS matlab command freesurfer_read_surf, where it is unable to read the lh.pial (see the log). This also causes the command find_corresponding_center_FSformat to fail because there are no faces/vertices as input. ">> FREESURFER_READ_SURF [v 1.2 ] Error using freesurfer_read_surf (line 90) could not open surface file lh.pial. Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);" If I run freesurfer_read_surf directly from matlab with the lh.pial as input, it does return the faces/vertices to me in my matlab workspace. This led me to think there might be a communication error between the FS toolbox and matlab itself (or maybe the lh.pial is specified incorrectly?). Am I missing something here? FS versions used: nightly build and stable 6.0 Matlab version: 2017a OS: ubuntu 16.04 uname -a: Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Cheers, Michael

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dev -FLAIRpial bug?
by Hibert, Matthew Louis 28 Sep '17

28 Sep '17

Hi FS Devs, We're running some reconstructions of 7T MPRAGEs with the -FLAIRpial flag turned on using the Martinos install of the dev version. Recently we encountered the error in the attached recon-all log in which it appears that recon-all is trying to use the aseg.mgz before it has been created. According to the dev table online, the mris_make_surfaces command as part of the -FLAIRpial processing should use aseg.presurf.mgz, but it crashes with an error that it was unable to open aseg.mgz. Thanks, Matt

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Compile problems
by Aziz Nanthaamornphong 28 Sep '17

28 Sep '17

Hi Freesurfer experts, I ran the commands to build Freesurfer (Yosemite based) by following this link https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page However, I got the error message when I ran *`make install'* command as follows: gunzip: can't stat: ../../distribution/average/cvs_avg35.tar.gz (../../distribution/average/cvs_avg35.tar.gz.gz): No such file or directory mv ../../distribution/average/cvs_avg35 \ /Users/azizn/fs_install_2/subjects mv: rename ../../distribution/average/cvs_avg35 to /Users/azizn/fs_install_2/subjects/cvs_avg35: No such file or directory make[2]: *** [install] Error 1 make[1]: *** [install-recursive] Error 1 make: *** [install-recursive] Error 1 Please let me know how to solve this problem. I need to compile the Freesurfer on my own Macbook. Best Wishes, Aziz

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Build Freeview on macOS
by Aziz Nanthaamornphong 28 Sep '17

28 Sep '17

Hi Freesurfer experts, Based on this link https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page, it mentions that "*As of the writing of this document (June 2016) freeview is unable to build on macOS 10.11 platforms and higher (El Capitan and higher)." * Could we build Freeview on macOS now? Best wishes, Aziz.

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freesurfer longitudinal pipeline
by miracle ozzoude 28 Sep '17

28 Sep '17

Hello Freesurfer, For the longitudinal pipeline, the website/ recon-all -help suggested that I calculate the different on the results from the longitudinal command (e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were named 1001_Baseline.long.longbase and 1001_Followup.long.longbase; is there a command i can use to preform this? Second question, i want to extract the output of the longitudinal pipeline using asegstats2table and aparcstats2table commands. what flag/s should i include in the original command to perform this? Thanks. Paul

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Re: [Freesurfer] bad midline cut
by Antonin Skoch 27 Sep '17

27 Sep '17

Bruce, Gabor, may I ask, does it ever matter where the midline surface lies? I thought that this does not affect anything in the analysis. Antonin hmmm, if you tar, gzip and upload the subject I'll take a look. Bruce On Tue, 26 Sep 2017, Gabor Perlaki wrote: > I've already corrected aseg.presurf.mgz and the left and right lateral ventricles are now correct in > the final aseg.mgz. However the pial surface is almost the same as earlier: > > https://mega.nz/#!XAZkWLZa!a6NgkEtiHzEqUkhZ6WimPgUKxytsGHKrgOLfyHdUuEM > > https://mega.nz/#!XRRHna7Q!vaeSLG5Cv-fGW-0xdEJlgFTNRPm7qGHOlShYh7y5z1g > >

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Freeview Versions
by Maksimovskiy, Arkadiy 27 Sep '17

27 Sep '17

Dear Freesurfer Experts, My apologies if I missed this information elsewhere on the website, but could not find any info. about it. There appear to be two Freeview versions, both from 2017 (released one day apart), for which the screenshots are attached. I was wondering if you could let me know what the difference is between the two. I do use one of them on the cluster and one locally- might that account for the difference in versions? If there are other processing differences that I should be aware of, please let me know. Thank you for all of your help and information. - Arkadiy [cid:image001.png@01D33153.34FF4EB0]

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