Freesurfer September 2017

freesurfer@nmr.mgh.harvard.edu

109 participants
199 discussions

Cortical Parcellation Yeo2011
by Lorenzo Pini 29 Sep '17

29 Sep '17

Hi list, I have already run by recon-all -all all my subjects in order to run PetSurfer. Output stats is saved in gtm.stats.dat and values correspond to Desikan-Killiany Atlas, However, I am interested in calculating values using Yeo atlas of 7 networks. Do you have any suggestions to get Partial Volume Corrected values from Yeo atlas for each subject? Do I have to switch to Yao atlas during recon-all -all process or during gtmseg? Thank you Lorenzo

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Edits to aparc+aseg
by Jake Rieke 29 Sep '17

29 Sep '17

Hi FreeSurfers, I have a group of subjects with manual edits to the aparc+aseg volume. These edits were made to re-label unknown regions of cortex. I am wondering what recon-all flags I could use to implement the changes and re-generate cortical stats based on these edits. Thanks in advance. Best regards, Jake

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3D visualization
by John Anderson 29 Sep '17

29 Sep '17

Dear FS experts, Are there any tools in freesurfer for 3D visualization (e.g. glass brain)? Any recommendations are appreciated Thanks John

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Problem with mris_anatomical_stats on .label which is threshold under negative value on FS-FAST, using tksurfer
by stdp82＠virgilio.it 29 Sep '17

29 Sep '17

Hi list, aftermri_label2label --srcsubject Subj01 --srclabel ROI.label --trgsubject Subj01 --trglabel Subj01/label/ROI.label --hemi lh --regmethod surfaceandmris_anatomical_stats -l Subj01/label/ROI.label -b Subj01 I have run mris_anatomical_stats -l Subj01/ROI_neg.label -b Subj01 lh the following error has been produced: Subj01/mri/wm.mgz...reading input surface Subj01/surf/lh.white...Using TH3 vertex volume calcTotal face volume 211969Total vertex volume 209028 (mask=0)reading input pial surface Subj01/surf/lh.pial...reading input white surface Subj01/surf/lh.white...No such file or directorymris_anatomical_stats: could not open label file Subj01/label/ROI_neg.labelNo such file or directorySubj01: could not read label file Subj01/label/ROI_neg.label This error did not occur for another label (Red_positive.label) which is threshold over positive value. Please take in account that the Blue_negative.label is obtain from FS-FAST map using tksurfer.Blue_negative.label expresses the difference for FC of group B < FC of group A.Conversely, Red_positive cluster shows difference for FC of group A > FC of group BPlease also note that clusters were thresholded before to save the .label with tksurfer +at 1.3 for defining Red_positive.label and at for defining - 1.3. I do not know if this step could induce an error in label properties. Thanks Stefano

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failed -base processing with 1 tp
by Michelle VanTieghem 29 Sep '17

29 Sep '17

Hello, I am running the -base processing so that I can create a subject-specific template for the -long processing. I have some subjects with only 1 timepoint. According to the website, all versions 5.2 and higher can handle 1 time point when making the base. I am using freesurfer 5.3. However, when I run the -base commands, it's working fine for subjects with 2-3 scans but fails mid way through processing for subjects with only 1 scan. I cannot determine why this is happening, and it happens at *different stages* of processing. (e.g. fix topology or CA Reg) the recon-all.error log does not provide useful information. Is there an extra flag that i am missing: Here is an example command: recon-all -base SB017templatebaseline -tp SB017 -all -3T -mprage Here is a recon-all.error log: ------------------------------ SUBJECT SB014templatebaseline DATE Thu Sep 28 15:00:02 EDT 2017 USER mrv2115 HOST casablanca.cc.columbia.edu PROCESSOR x86_64 OS Linux Linux casablanca.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /vega/psych/app/freesurfer/bin/recon-all PWD /vega/psych/users/mrv2115/fsdata/processed/CLEAN/SB014templatebaseline/scripts CMD mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 SB014templatebaseline rh -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

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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

3 5

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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Freesurfer September 2017