Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Large cluster size significant clusters
by Azeez, Azeezat 16 Jan '19

16 Jan '19

External Email - Use Caution Hello , I have results for my mri_glmfit-sim. I find a significant results in my cache.th20abs.sig.cluster.summary. Yet, the cluster size of the significant cluster is almost the size of the total cortical surface area. I am not sure what to make of this any help would be helpful. # Total Cortical Surface Area 65416.6 (mm^2) # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -44.154 9733 55204.38 -4.9 -47.1 29.6 0.00020 0.00000 0.00040 108257 isthmuscingulate -- Azeezat Azeez

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using tkregister2 to check registration to custom atlas
by lindsay hanford 16 Jan '19

16 Jan '19

External Email - Use Caution Hello Freesurfer Community, I am interested in seeing how well my subject scan registered to a custom atlas after being run through recon-all. From Freesurfer Wiki, although it is possible to see this in freeview, tkregister2 seems to be the best method as manual edits can be made if the registration went badly. I am however running into issues trying to load the subject image, atlas image, and surfaces in the same space. If I understand correctly, when I ran my recon-all specifying a custom atlas (-custom-tal-atlas RLB700_atlas_as_orig) the transform files (talairach.xfm) are to the custom atlas rather than the talairach atlas. If I load: tkregister2 --s 180523_HTP02168_ANAT5_init2base --fstal --surfs the subject scan, talairach atlas and surfaces load just fine. It is clear the talairach atlas was not used. I have tried running multiple variations of the following, and in all cases, the atlas is in a different space. tkregister2 --mov RLB700.nii.gz --s 180523_HTP02168_ANAT5_init2base --regheader --reg 180523_HTP02168_ANAT5_init2base/mri/transforms/talairach.xfm --surfs Resources used: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview https://surfer.nmr.mgh.harvard.edu/fswiki/MulitModalIntegration Any suggestions? Thanks, Lindsay

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mni --> RAS T1
by Krieger, Donald N. 16 Jan '19

16 Jan '19

External Email - Use Caution Is there a 4x4 transformation somewhere to convert mni coordinates to RAS T1 coordinates, I.e. something comparable to the transforms provided by mri_info -tkrscanner Thanks - Don

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Re: [Freesurfer] Running TRACULA
by Yendiki, Anastasia 16 Jan '19

16 Jan '19

Have you checked the registration between the structural and diffusion? The concern here would be that some of your subjects' brains could look more like bert's brain than others, and the registration could be better for the former than the latter. You would have to ensure that this doesn't introduce biases between groups (or age/gender biases) in your specific study, and therefore does not induce false group differences or accentuate any real differences. On Jan 11, 2019 9:35 AM, Ainara Gomez <ainara.ggastiasoro(a)deusto.es> wrote: External Email - Use Caution Hi Anastasia, thank you for your rapid response. Since I do not have the T1 of my subjects, I have not run the recon-all. Instead of that, I have copy-pasted the "mri" folder (including the aparc+aseg.mgz file) located in $FREESURFER_HOME/freesurfer/subjects/bert/mri into each subject's folder ($SUBJECTS_DIR/$subjectid/) so TRACULA can find all the files from Freesurfer that are needed in trac-all prep step. Thanks a lot again, Ainara El vie., 11 ene. 2019 a las 14:49, Yendiki, Anastasia (<AYENDIKI(a)mgh.harvard.edu<mailto:AYENDIKI@mgh.harvard.edu>>) escribió: Hi Ainara - What do you mean by default freesurfer files? Can you describe how you created each subject's recon-all style directory under SUBJECTS_DIR? TRACULA looks for $SUBJECTS_DIR/$subjectid/mri/aparc+aseg.mgz for each subject ID. a.y On Jan 11, 2019 8:30 AM, Ainara Gomez <ainara.ggastiasoro(a)deusto.es<mailto:ainara.ggastiasoro@deusto.es>> wrote: External Email - Use Caution Dear Freesurfer experts, I am trying to run TRACULA as a complementary analysis on a patients and healthy controls sample. I have read in the tutorial that it is assumed that FreeSurfer has already been run on all the subjects' T1-weighted data because TRACULA will use the aparc+aseg.mgz from each subject's FreeSurfer reconstruction. However, T1s of my subjects are not available for this study and I only have the diffusion images. I have run the three steps of the trac-all separately (using the default freesurfer files: aseg+aparc.mgz...) and all the processes have ended without errors. Is this correct? Is it possible to use the default freesurfer files instead of each subject's recon-all files in order to run trac-all? Thank you very much in advance, Ainara -- Ainara Gómez Gastiasoro Dpt of Methods and Experimental Psychology Neuropsychology of Severe Medical Conditions research team Faculty of Psychology and Education University of Deusto neurolab.deusto.es<http://neurolab.deusto.es/> https://twitter.com/deustoneurolab Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3268) <tel:%2B34%20944139000> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Ainara Gómez Gastiasoro Dpt of Methods and Experimental Psychology Neuropsychology of Severe Medical Conditions research team Faculty of Psychology and Education University of Deusto neurolab.deusto.es<http://neurolab.deusto.es/> https://twitter.com/deustoneurolab Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3268) <tel:%2B34%20944139000>

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preproc-sess mask issue
by Dowling, Kevin Francis 15 Jan '19

15 Jan '19

Hello FreeSurfer Experts, I'm writing with a question about a potential problems that has come up in my functional analysis. I'm running FS version 5.3 on a Linux (at the Martinos Center - CentOS release 7.6.1810). I was recently running osgm WLS analyses with mri_glmfit and the --prune flag when I noticed that a large number of vertices in my surface based analysis were pruned out due to no signal (about 40% of the entire surface, see attached an example image of a group analysis that includes one of the bad subjects: pruning_issue.png). My first thought was that this result was potentially due to a poor functional/structural alignment for some subjects. However, I re-checked my functional and structural alignments, along with the quality of the recons, and they all look good. Upon further inspection, I observed similar erroneous pruning problems affecting voxels in the mni305 space (for an example see pruning_issue2.png). This issue stems from a modest number of subjects that have first level analyses with large amounts of no signal. Indeed, removing these problematic subjects from group surface based analyses resolves most of the excessive surface pruning problems. When I look at the fmcpr.siemens.nii.gz files for the runs in the problematic subjects' directories the processed functional data looks good, but when I visualize the fmcpr.siemens.sm5.mni305.nii.gz (and ...fsaverage.lh.nii.gz / ...fsaverage.rh.nii.gz) files it is clear that an inappropriate number of voxels (/vertices) have been masked out. When I look at the brain.mni305.nii.gz, brain.fsaverage.rh.nii.gz, and brain.fsaverage.lh.nii.gz masks I can see they are missing a large number of voxels/vertices that should be in the masks, which leads me to think that something may be going wrong in the lh/rh/mni305 masking/mask generation step (though brain.nii.gz and brain.e3.nii.gz masks look fine to me). I've looked through the archives and wasn't able find a similar issue discussed previously. I was therefore wondering what might be causing this mask issue (given the alignments appear to be good) and what might be the best way to go about correcting this error. Would I need to manually edit all of these masks to include the missing voxels/vertices if the automatic generation failed or is there a better solution someone might be able to suggest? My preprocessing command is: preproc-sess -s SubjectID01 -surface fsaverage lhrh -mni305 -d $SUBJECTS_DIR -fsd bold -stc siemens -fwhm 5 -per-run I would be happy to send along mask files/other files should they be of help. Thank you in advance for any suggestions you might be able to provide! Best wishes, Kevin Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.3215 He / Him / His

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QDEC - command not found
by Alba Castells Sánchez 15 Jan '19

15 Jan '19

External Email - Use Caution Dear freesurfer experts, we installed the last version of freesurfer dev in a centos7 system (8th january 2019) and the matlab runtime to run segmentHA_T1.sh. We could obtain all the files without problems. However, today we tried to open qdec typing qdec like we used to do with other versions without problem and the answer is "command not found". We are really surprised, we haven't found any other comment on internet and the mailing list with this same problem. We have installed the same last version in a mac and we had the same problem. qdec doesn't exist. We have checked the files .sh in Freesurfersetup and similar files in the freesurfer direcotry looking for qdec without success. HOwever, there is a direcotry called Qdec in freesurfer/matlab/lme We don't know where is our mistake. We are also considering that maybe the issue is related with the version. Is this possible? Could you help us, please? Thousand thanks

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Pial and WM edits around the temporal lobes
by Stephanie Otto 14 Jan '19

14 Jan '19

External Email - Use Caution Greetings Freesurfer Team, We are working on quality checking reconstructions and there seems to be a common problem area around the temporal lobes where the white matter surface extends beyond the pial surface, or the pial surface just looks off. We know this is a difficult area to reconstruct and we aren't entirely sure how to correct for this. We want to avoid interfering with the resulting data. Can you instruct us on how we should proceed with this kind of correction (i.e. control points vs fill voxels, etc.)? If we are looking at temporal lobe structures, how much are these areas affected (or something like the grey matter volume)? Is there a standard protocol for dealing with issues such as these? Thanks for all your help and support! Best, Stephanie Otto Academic Advisor, Department of Psychology Graduate Student, Cognitive and Brain Sciences Program Mack Social Science, Room 414 University of Nevada, Reno sotto(a)nevada.unr.edu

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Re: [Freesurfer] -qcache error
by Peters, Douglas G 14 Jan '19

14 Jan '19

External Email - Use Caution I am new to FS, and I am having the same error that Krishna had last year. I don't see a link to the 'lh.white.k' file in my surf folder. Has anyone resolved this problem? I can side step the error with '-qcache -measure thickness' to only process thickness files, but I'd like to be able to process all the files in my subject folders. Thanks, Doug Command line input: recon-all -s <subject> -qcache Command line output: #@# Qdec Cache preproc lh white.K fsaverage /surf mris_preproc --s <subject> --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh nsubjects = 1 ERROR: cannot find /lh.white.K recon-all -s <subject> exited with ERRORS Re: [Freesurfer] -qcache error<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj…> Douglas Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Fri, 09 Mar 2018 08:18:34 -0800<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> It was deleted but then it was created as a link. Does the link exist? ________________________________ On 3/7/18 1:33 PM, Krishna Patel wrote: Hi - I would like to do group analysis on freesurfer data that is processed with verson 6. However when I try to run recon-all -s subjid -qcache I get following error after it runs for some time and generates some of the files. ERROR: cannot find surf/lh.white.K When I look at the log file - I see that this file was deleted. See following. total integrated curvature = -1.022*4pi (-12.846) --> 2 handles ICI = 169.4, FI = 1785.3, variation=28139.036 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K Does anyone have any idea of what might be the issue here? Thanks, -Krishna ________________________________ From: Peters, Douglas G Sent: Thursday, January 10, 2019 4:55:31 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: -qcache error I am new to FS, and I am having the same error that Krishna had last year. I don't see a link to the 'lh.white.k' file in my surf folder. Has anyone resolved this problem? I can side step the error with '-qcache -measure thickness' to only process thickness files, but I'd like to be able to process all the files in my subject folders. Thanks, Doug Command line input: recon-all -s <subject> -qcache Command line output: #@# Qdec Cache preproc lh white.K fsaverage /surf mris_preproc --s <subject> --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh nsubjects = 1 ERROR: cannot find /lh.white.K recon-all -s <subject> exited with ERRORS Re: [Freesurfer] -qcache error<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj…> Douglas Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Fri, 09 Mar 2018 08:18:34 -0800<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> It was deleted but then it was created as a link. Does the link exist? ________________________________ ________________________________ On 3/7/18 1:33 PM, Krishna Patel wrote: Hi - I would like to do group analysis on freesurfer data that is processed with verson 6. However when I try to run recon-all -s subjid -qcache I get following error after it runs for some time and generates some of the files. ERROR: cannot find surf/lh.white.K When I look at the log file - I see that this file was deleted. See following. total integrated curvature = -1.022*4pi (-12.846) --> 2 handles ICI = 169.4, FI = 1785.3, variation=28139.036 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K Does anyone have any idea of what might be the issue here? Thanks, -Krishna

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Tksurfer and Freeview label visualizations look different
by Anna Mynick 14 Jan '19

14 Jan '19

External Email - Use Caution Hi, I drew a collection of surface labels by hand in Tksurfer, but when I open them in Freeview to visualize them, they look incorrect. In particular, the labels in Tksurfer were drawn without any holes, but the labels in Freeview somehow got odd unintended holes (see attached images). Has anyone else run into this? For what it's worth, I drew the labels with an overlay loaded in Tksurfer, though I didn't think this would have an effect on the labels I saved. Thanks for any help, Anna tksurfer label originally drawn (purple) [cid:775863A3-49CB-4361-A9D7-B5B0745225CE@mit.edu] freeview (below, yellow) [cid:E1BB51C1-561F-4290-9AF9-DA755DAAF3ED@mit.edu]

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mris_apply_reg failing for area/volume
by James Michael Roe 14 Jan '19

14 Jan '19

External Email - Use Caution ? Dear freesurfer experts I'm running the following commands to register RH area and volume files per sub to both hemispheres of a symmetrical template following Xhemi routines. The commands have already worked for many subs, but are failing to write the target file for a number of others (and all run fine without the --jac flag) #right to left mris_apply_reg \ --src $SUBJECTS_DIR/$sub/surf/rh.area \ --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \ --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \ --jac #right to right mris_apply_reg \ --src $SUBJECTS_DIR/$sub/surf/rh.area \ --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \ --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \ --jac The error is not template-specific as the output is the same using fsaverage_sym Attached is the log file. Thanks in advance! ?- James

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