Freesurfer March 2017

freesurfer@nmr.mgh.harvard.edu

148 participants
263 discussions

mri_vol2surf
by Redwan Maatoug 14 Mar '17

14 Mar '17

Hi experts, I try to convert my volumetric nifti file to surface files. My nifti volumetric file looks like : 1. screenshot I have first registered the volumetric file using bbregister with this command line : *bbregister --s fsaverage --mov segment_7.nii --reg segment_7.dat --t1 --init-coreg* then I have used the following command line and the file looks like screenshot 1 attached : *tkregister2 --mov segment_7.nii --reg register7.dat --surf* And after that, I have tried to convert my volumetric file to surface file with this command line : *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o ./segment_7-lh.nii --float2int round* But with this command when I load the file with freeview it does not work and with tkregister the file is empty. Or this one : *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o ./segment_7-lh.w --out_type paint --float2int tkregister* But with this command I have this warning : Warning: all vertex values are zero Could you please help me to convert my volumetric files because I am probably doing someting wrong. All my files come from an Atlas and I just need to convert them to surfaces files. Thank you for your help, Redwan

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Re: [Freesurfer] incorrect surfaces and aseg labeling in subject with large occipital horns of lateral ventricle
by Antonin Skoch 14 Mar '17

14 Mar '17

Dear Doug, I have uploaded them as tar.gzipped file occipital_horn_ventricle_aseg_and_surf_error.tar.gz to anonymous(a)surfer.nmr.mgh.harvard.edu/transfer/incoming I have uploaded it again in case the transfer failed. I also appologize to forgot to attach the screenshots. Sending them this time. Regards, Antonin Hi Antonin, where did you upload them to? On 03/13/2017 05:51 PM, Antonin Skoch wrote: > Dear experts, > > in my longitudinal study with 2 timepoints I encountered issue with > aseg.presurf labeling and white/pial surface estimation of one subject > in region of occipital horns of lateral ventricle. The voxels in horns > are mislabeled as either white or gray matter or contain zero values. > I am still in the stage 1 of longitudinal stream, so this is classical > cross-sectional recon-all stream. > > I tried to reprocess this subject by using recon-all -s subj > -bigventricles -FLAIRpial (despite the fact that the subject does not > have generally enlarged ventricles I thought that this could help > nonlinear registration by mri_ca_register ). In case of timepoint 2 > this helped to correctly label left occipital horn and corrected error > with surfaces, but right occipital horn remained labeled as white matter. > > In contrast, in case of timepoint 1 the -bigventricles did not help to > label left occipital horn and additionally new massive error with > white surface placement appeared in the region of occipital horn of > left lateral ventricle. See the attached screenshots to ilustrate this > issue: > > tp1_nobigventricles_surface_OK > tp1_bigventricles_surface_error > tp2_nobigventricles_surface_error > tp2_bigventricles_surface_OK > > I have uploaded file > occipital_horn_ventricle_aseg_and_surf_error.tar.gz containing 4 > recons (timepoint 1 and 2 with and withoug -bigventricles) to your server. > > I suppose that the root of the problem is incorrect nonlinear > registration. Could you please advise how to diagnose and solve the error? > > I am using development version from beginning of february 2017. > > Regards, > > Antonin Skoch

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Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?
by Antonin Skoch 14 Mar '17

14 Mar '17

Dear experts, can also be the difference between v5.3 and v6.0 behavior in HCP pipeline and possible sub-optimal behavior of v6.0 with HCP pipeline given by different in image input to mris_make_surfaces in HCP pipeline (FreeSurferHiResWhite.sh) ? For white surface estimation the recon-all input is brain.finalsurfs, which is very aggressively filtered so that the white matter voxels have typically values 110 and the SNR in deep white matter areas approach infinity. In contrast, for HCP pipeline the input T1w_hires_masked_norm image is filtered no to such an extent. Therefore there is much lower contrast-to-noise ratio in the region of GM-WM interface for mris_make_surfaces in FreSurferHiResWhite.sh. This maybe renders mris_make_surface more vulnerable to local deviations in intensity in GM-WM interface. My observation (without any thorougful tests) is that with v6.0 in HCP pipeline I had very often to edit wm.mgz in the region of GM-WM interface in the areas of (physiological) perivascular subcortical T1 hypointensities due to the ?h.white "leak" to these areas. And also, as I wrote in some of my previous (unanswered) posts: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51414.html the change of -first_wm_peak behaviour in v6.0 in fact worsened white surface estimation in my data I tested with HCP pipelines. I could upload some example subjects if you are interested and have time to dig in. In any case, it is probably hard to compare performance between standard recon-all and HCP pipeline and different versions of FreeSurfer due to different input to mris_make_surfaces and different flags used. The HCP pipeline, as it currently stands, would probably need different optimization of code or different command line options due to the different input used. Regards, Antonin Skoch Hi Bruce, I don¹t think the hires T1w and T2w stuff are as accurate as 5.3 in the HCP 0.7mm data that I have looked at (and as I recall at least one other user had some similar issues, as did one of my collaborators), but that was all I meant to refer to. Sorry if my reply came across more general than that, as of course we want to move to using FreeSurfer V6+ in the future. It is the highres T1w and T2w stuff that my pipelines are designed to exploit, however. Also there are some changes I have to make to the HCP Pipelines for FreeSurfer V6+ because of differing file names, etc.Best, Matt. On 3/13/17, 9:40 PM, "Bruce Fischl" <freesurfer-boun...(a)nmr.mgh.harvard.edu on behalf of fis...(a)nmr.mgh.harvard.edu> wrote: >Hi Matt > >To state without qualification that "6.0 has some regressions as far as >surface placement" is incorrect. We quantified its test-retest >reliability, >accuracy and power to detect disease effects and all were improved >relative >to 5.3. We tested V6 on hundreds of datasets across an array of >pathologies >and different MR sequences, field strengths and scanners. We visually >inspected dozens of brains multiple times in the process of improving >accuracy and robustness. I can believe that on Wash U HCP data there >could >be some specific issues, but to imply that V6 is generally less accurate >is >simply incorrect. > >cheers >Bruce > > >On Mon, 13 Mar 2017, Matt Glasser wrote: > >> Not yet. We are hoping FreeSurfer 6.1 will work nicely with the HCP >> Pipelines. For now version 6.0 has some regressions as far as surface >> placement goes and there are also some adaptations we need to make to >>the >> pipelines. >> >> Peace, >> >> Matt. >> >> From: <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of CAGNA >>Bastien >> <bastien.ca...(a)univ-amu.fr> >> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> Date: Monday, March 13, 2017 at 7:21 AM >> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >> Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome >> project's pipeline ? >> >> Dear freesurfer experts, >> >> >> I'm wondering if it's possible to run the human connetome project's >>minimal >> processing pipeline using freesurfer 6 ? >> >> >> Does it require some update of the pipeline or is there anybody that >>have >> already enjoyed the new freesurfer version with this pipeline ? >> >> >> Thank you for your attention and your help, >> >> Bastien Cagna >>

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Adjust bbregister affine to target raw T1
by Christopher Markiewicz 14 Mar '17

14 Mar '17

Hi all, Suppose you have a sub-pipeline: $ recon-all -s $SUBJ -i $T1 -all $ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat --fslmat fsl.mat Now `bbreg.dat`/`fsl.mat` is registered to `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to $T1? I've tried: $ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1 --fslregout adjusted.mat And that's clearly wrong, but I'm kind of stuck on where to go from here. Anybody see where I'm going wrong? Thanks, Chris

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Re: [Freesurfer] Intensity normalization in longitudinal processing
by Jaiashre Sridhar 14 Mar '17

14 Mar '17

Bruce, We had previously addressed an issue with creating the bases from 5 timepoints in v5.1 where mri_robust_register failed. We were advised by Dr. Martin Reuter to either replace mri_robust_register & mri_robust_template binary with the ones from v5.3 or to run all the bases and longs in v5.3. We chose to run the longitudinal stream in v6.0 as it was released by then. If it is not safe to mix versions (cross in v5.1; base-long in v6.0), could you clarify if it is alright to just use the binaries from v5.3/v6.0? Thank you very much, Jaiashre.

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R: Re: Whole preprocessing with FAST without to perform a seed based analysis
by stdp82＠virgilio.it 14 Mar '17

14 Mar '17

Thanks.1- By using only preproc-sess, how can I perform "band pass filtering"?2- And how can I take in account the nuisance variables: the CSF from which the top 5 principle components, the white matter from which the top 5 principle components, motion correction parameters (-mcextreg), 5th order polynomial. How can I eliminate the first 4 time points?RegardsStefano ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 14-mar-2017 16.14 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Whole preprocessing with FAST without to perform a seed based analysis just use preproc-sess On 3/14/17 10:45 AM, stdp82(a)virgilio.it wrote: Hi list, in FS-FAST, on rs-fMRI data, is possible to run selxavg3-sess without -a option? I would use whole the FS-FAST to preprocess my data. I would include the mkanalysis-sess step but I would not perform a seed-based analysis. Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?
by CAGNA Bastien 14 Mar '17

14 Mar '17

Hi everyone, Thanks for all your answers Bruce, Matt and Antonin. Matt, may I ask you when do you think that a freesurfer6-compliant version of the pipeline will be available ? Best regards, Bastien On 3/13/17, 9:40 PM, "Bruce Fischl" <freesurfer-boun...(a)nmr.mgh.harvard.edu on behalf of fis...(a)nmr.mgh.harvard.edu> wrote: >Hi Matt > >To state without qualification that "6.0 has some regressions as far as >surface placement" is incorrect. We quantified its test-retest >reliability, >accuracy and power to detect disease effects and all were improved >relative >to 5.3. We tested V6 on hundreds of datasets across an array of >pathologies >and different MR sequences, field strengths and scanners. We visually >inspected dozens of brains multiple times in the process of improving >accuracy and robustness. I can believe that on Wash U HCP data there >could >be some specific issues, but to imply that V6 is generally less accurate >is >simply incorrect. > >cheers >Bruce > > >On Mon, 13 Mar 2017, Matt Glasser wrote: > >> Not yet. We are hoping FreeSurfer 6.1 will work nicely with the HCP >> Pipelines. For now version 6.0 has some regressions as far as surface >> placement goes and there are also some adaptations we need to make to >>the >> pipelines. >> >> Peace, >> >> Matt. >> >> From: <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of CAGNA >>Bastien >> <bastien.ca...(a)univ-amu.fr> >> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> Date: Monday, March 13, 2017 at 7:21 AM >> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >> Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome >> project's pipeline ? >> >> Dear freesurfer experts, >> >> >> I'm wondering if it's possible to run the human connetome project's >>minimal >> processing pipeline using freesurfer 6 ? >> >> >> Does it require some update of the pipeline or is there anybody that >>have >> already enjoyed the new freesurfer version with this pipeline ? >> >> >> Thank you for your attention and your help, >> >> Bastien Cagna >> >> >> >> _______________________________________________ Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The >>information >> in this e-mail is intended only for the person to whom it is addressed. >>If >> you believe this e-mail was sent to you in error and the e-mail contains >> patient information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >>in >> error but does not contain patient information, please contact the >>sender >> and properly dispose of the e-mail. >>_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom it >is >addressed. If you believe this e-mail was sent to you in error and the >e-mail >contains patient information, please contact the Partners Compliance >HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in >error >but does not contain patient information, please contact the sender and >properly >dispose of the e-mail.

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Whole preprocessing with FAST without to perform a seed based analysis
by stdp82＠virgilio.it 14 Mar '17

14 Mar '17

Hi list,in FS-FAST, on rs-fMRI data, is possible to run selxavg3-sess without -a option?I would use whole the FS-FAST to preprocess my data. I would include the mkanalysis-sess step but I would not perform a seed-based analysis. ThanksStefano

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fsgd 4 groups, continuous dependent variable, 2 covariates
by Donna Cosgrove 14 Mar '17

14 Mar '17

Hi Freesurfer experts, I am looking at the effect of a genetic risk score (GRS) on cortical surface/thickness. I have two groups: patients, controls (male and female). GroupDescriptorFile 1 Title GRS_all_lh_surf_fwhm10 MeasurementName thickness Class SexFemaleControl Class SexMaleControl Class SexFemalePatient Class SexMalePatient I want to include total brain volume and age as covariates. Is this possible using an fsgd file? Is there an example you could give? Any advice would be great. Thanking you in advance Donna

2 1

tkmedit error
by Veronica Munoz 14 Mar '17

14 Mar '17

Dear all, I'm trying to use tkmedit to verify my recon-all results but I get these messages rather than the visualization of my volumes. Am I missing a library ? I've been using freeview and it works just fine but I would like to solve my problem. Thank you in advance. Best regards, Veronica M.R.

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Freesurfer March 2017