Freesurfer October 2019

freesurfer@nmr.mgh.harvard.edu

111 participants
180 discussions

TRACULA prep gets stuck in -prior 'WARN: Could not find satisfactory control point fit - try 20784 Finding center streamline'
by Mazzetti, C. (Cecilia) 11 Oct '19

11 Oct '19

External Email - Use Caution Dear all, I am trying to understand what is going on in my subjects (same problem with 5 different ones). the outputs from the first steps of trac-all seems to work fine, so I am running: trac-all -prep -c config_01C.txt -nocorr -noqa -nointra -nointer -nomasks -notensor -no-isrunning but the process gets stuck (in the log file I read something like 'WARN: Could not find satisfactory control point fit - try 20784 Finding center streamline' ) which keeps going... The only outputs which seem to be created are for cst and Ilf, the others not. I am also trying to include just some tract by specifying in the configuration file: set pathlist = ( lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) but nothing seems to change.. Can I please have some assistance here? It has been days and I cannot seem to fix it.. also, I tried to run bedpost only but I receive an erro: trac-all -prep -c config_01C.txt -nocorr -noqa -nointra -nointer -nomasks -notensor -noprior -no-isrunning saying that I didn't specify any steps.. isn't bedpost a preprocessing step? also when tryingtrac-all -bedp -c config_02C.txt -no-isrunning? nothing works... is it because the -prior steps needs to be finished? Thanks to anyone willing to help! Best, Cecilia Cecilia Mazzetti - Ph.D. Researcher Donders Centre for Cognitive Neuroimaging, room 2.257 Kapittelweg 29 | 6525 EN Nijmegen

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Re: [Freesurfer] ERROR gtmseg
by Marina Fernández 11 Oct '19

11 Oct '19

External Email - Use Caution Dear Douglas, Thank you very much for the help. We could solve the problem with that subject but now we have a similar problem with another subject. In the previous case, we have only one problematic voxel in the skull, but now the label 75 (it shouldn't exist either) is taking a lot of voxels in the ventricles and the caudate. So, I think that we should use other solution to fix it. I know that this issue is weird. We use gtmseg command with more or less 500 subjects and we only have this type of problem with two subjects. Best regards, Marina. > Probably the easiest thing is just to edit that voxel to be one of the neighboring > segments. First, load the aseg and find that voxel. See which segment(s) are around > that voxel and get the segmentation id. Then run > mri_binarize --replaceonly 229 YourNewSegID --i aparc+aseg.mgz --o > aparc+aseg.mgz > then re-run gtmseg

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Re: [Freesurfer] ERROR gtmseg
by Marina Fernández 11 Oct '19

11 Oct '19

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Freesurfer using dof9 with preproc-sess
by Droppa, Kyle Salmon 11 Oct '19

11 Oct '19

Good evening, I am using freesurfer version 6 and I am having an issue with changing the degrees of freedom when I run preproc-sess. I ade some registrations that are 9 and 12 dof instead of the default 6, however when I try to run preproc-sess, it pulls the dof6 files instead. Is there a flag I can use that pulls the register.dof9.lta and register.dof12.lta files instead? Thank you and have a nice night! ___________________ Kyle Salmon Droppa, B.A. Clinical Research Coordinator Athinoula A. Martinos Center for Biomedical Imaging Magnetic Resonance - Physics & Instrumentation Group https://www.martinos.org/lab/mr-pig <https://www.massgeneral.org/nicc>

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using dof9 or dof12 in preproc-sess
by Droppa, Kyle Salmon 11 Oct '19

11 Oct '19

Hello, I posted this earlier and wasn't able to get a response. I am using freesurfer version 6 and I am having an issue with changing the degrees of freedom when I run preproc-sess. I made some registrations that are 9 and 12 dof instead of the default 6 using bbregister, however when I try to run preproc-sess, it pulls the dof6 files instead. Is there a flag I can use that makes preproc use the register.dof9.lta and register.dof12.lta files instead? Thank you and have a nice day!

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local Gyrification Index
by LOSKE, PHILIPP (PGR) 11 Oct '19

11 Oct '19

External Email - Use Caution Hello FreeSurfer Team, I am trying to compute the local Gyrification index on my subjects with recon-all -s <subj> -localGI. Running this under FS 6.0 runs without errors, with FS 5.3. I get: mesh_outer = struct with fields: vertices: [68598x3 double] faces: [137192x3 double] facesOfVertex: [68598x1 struct] preparing pial mesh structure ... ...searching for mesh edges...done (82.56 sec). ... creating path file for vertex 1 / 68598 area file for outer ROIs saved at 1 {Unable to perform assignment because the left and right sides have a different number of elements. Error in dsearchn (line 84) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); } >> ERROR: make_roi_paths did not complete successfully! Now I wonder why the computation works in version 6 but not in 5.3. My subjects are originally reconstructed with version 5.3., does the computation for local Gyrification Index differ between both versions or can I just run the command in FS6? 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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fsaverage label into functional space
by Lauri Tuominen 10 Oct '19

10 Oct '19

External Email - Use Caution Dear FreeSurfers! I would like to confirm something before I proceed with my analyses. I think I am just confused again. I am doing resting state analysis using fsfast. I am trying to use a label defined in the fsaverage space as a seed using the fcseed-config & fcseed-sess commands. Now these commands say that the label should be in fuctional space, which I gather is the space of the f.nii. So in order to move the label into functional space I say: mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label --o lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01 --hemi lh --temp ${projectdir}/${sessionj}/rest/001/f.nii --fill-ribbon --reg ${projectdir}/${session}/rest/register.dof6.lta To my surprise, the voxel size here corresponds to the anatomical (orig.mgz) but not the functional space (f.nii). To test this further I did: mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label --o lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01 --hemi lh --temp $SUBJECTS_DIR/$/${sessionj}/mri/orig.mgz --fill-ribbon --reg ${projectdir}/${session}/rest/register.dof6.lta And I get exactly the same ROI in the volume. So just to confirm, is this what I want for the fcseed -commands? Thank you so much again! Lauri Tuominen

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Brodmann area parcellation
by sang ho shin 10 Oct '19

10 Oct '19

External Email - Use Caution Dear Freesurfer Developers, I am trying to get the seed mask of premotor and motor cortex. Because I can't get it through 'recon-all -all', I tried to find brodmann area ('recon-all -s subjid -ba-labels') But I received ERROR message. Can you tell me how to get Brodmann area through recon-all or freesurfer parcellation? And I appreciate if you can help me to solve this error message as follows, ================================================================= sinsanghoui-MBP:~ shinsangho$ export SUBJECTS_DIR=~/freesurfer_subjects sinsanghoui-MBP:~ shinsangho$ echo $SUBJECTS_DIR *sinsanghoui-MBP:~ shinsangho$ recon-all -s NOR82_PJI -i ~/DTI_analysis/nor82_pji_t1/coT1.nii -ba-labels* Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /Users/shinsangho/freesurfer_subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin sinsanghoui-MBP 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64 /Users/shinsangho/freesurfer_subjects/NOR82_PJI \n mri_convert /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii /Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz \n mri_convert.bin /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii /Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii... TR=1670.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.000121244, -1, 0) j_ras = (-0.0235518, -2.85817e-06, 0.999723) k_ras = (0.999723, 0.000121211, 0.0235518) writing to /Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz... /Users/shinsangho/freesurfer_subjects/NOR82_PJI/label #-------------------------------------------- #@# BA_exvivo Labels lh Fri Oct 4 17:43:23 BST 2019 \n mri_label2label --srcsubject fsaverage --srclabel /Users/shinsangho/freesurfer_subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject NOR82_PJI --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface \n srclabel = /Users/shinsangho/freesurfer_subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = NOR82_PJI trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/shinsangho/freesurfer_subjects FREESURFER_HOME /Applications/freesurfer Loading source label. Found 4129 points in source label. MRISread(/Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /Users/shinsangho/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface * /Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white* *No such file or directory* *ERROR: could not read /Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white* Darwin sinsanghoui-MBP 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64 recon-all -s NOR82_PJI exited with ERRORS at Fri Oct 4 17:43:25 BST 2019 For more details, see the log file /Users/shinsangho/freesurfer_subjects/NOR82_PJI/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ================================================== Best wishes, Sangho ᐧ

3 6

Assign different number in FreeSurferColorLUT
by Gwang-Won Kim 10 Oct '19

10 Oct '19

2 1

Freesurfer 6 current state of submillimeter processing
by Daniel Westfall 10 Oct '19

10 Oct '19

External Email - Use Caution Hi Everyone, I just wanted to double check the current state of processing T3 submillimeter data with Freesurfer 6. We have two studies: one with 0.9 mm isotropic and the other with 0.8 mm isotropic. After doing some investigating, I found that there is either the option to run recon-all with the -hires flag ( https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon) or I found that on the release notes for Freesurfer 6 there is a patch ( https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/) I would guess that the patch method is the most recent version that I should use? Thank you for the assistance. Best, Daniel

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Freesurfer October 2019