[Freesurfer] Pial in the thalamus

Dear all, We have this issue around the thalamus that is recurring in several of our scans and there does not seem to be a problem with the white matter mask in that area. Is it a problem? Does anyone have an idea how to fix this? We are using Freesurfer v5.3. Thanks. Yann

[Freesurfer] Tracula: anatomical priors

Dear FreeSurfers, Where can I find the anatomical ROIs from the aparc/aseg (end and begin points) that are being used to reconstruct the tracts in Tracula? Many thanks Heidi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] MEG time series to surface overlay

Can you send us the full command you ran and the full screen output? Thanks Bruce > On Mar 14, 2017, at 9:33 PM, Dorothy Sincasto wrote: > > Hi, > > I have MEG time series for every vertex in a decimated surface (~6000 > vertices). I want to create a file (i think is

[Freesurfer] MEG time series to surface overlay

Hi, I have MEG time series for every vertex in a decimated surface (~6000 vertices). I want to create a file (i think is called overlay) in which the timeseries are saved, like an fMRI mgz overlay. How can I do that with matlab? I have tried read_surf for reading the midthickness surface file,

Re: [Freesurfer] mri_vol2surf

Thank you very much Douglas, You made my day ! Have a good day, Redwan On 14 March 2017 at 10:48, Douglas Greve wrote: > Yes, I see a spot on the medial wall. You can also look at it in the > volume with > > tkmeditfv fsaverage orig.mgz -surfs -fminmax .5 1 -overlay

Re: [Freesurfer] incorrect surfaces and aseg labeling in subject with large occipital horns of lateral ventricle

I have the data, it might take a few days to get back to you on my conclusions ... On 3/13/17 6:30 PM, Antonin Skoch wrote: Dear Doug, I have uploaded them as tar.gzipped file occipital_horn_ventricle_aseg_and_surf_error.tar.gz to anonym...@surfer.nmr.mgh.harvard.edu

Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

Hi Antonin, can you upload that subject? In one case using 700um, the white surface looked fine, and I did not see much of a difference with the 1mm scan. On 3/14/17 5:39 AM, Antonin Skoch wrote: Dear experts, can also be the difference between v5.3 and v6.0 behavior in HCP pipeline and

Re: [Freesurfer] mri_vol2surf

Yes, I see a spot on the medial wall. You can also look at it in the volume with tkmeditfv fsaverage orig.mgz -surfs -fminmax .5 1 -overlay multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat On 3/14/17 1:45 PM, Redwan Maatoug wrote: Hi Bruce, Yes, I did. Do you see something ? Thank you,

Re: [Freesurfer] mri_vol2surf

Hi Bruce, Yes, I did. Do you see something ? Thank you, Redwan On 14 March 2017 at 09:19, Douglas Greve wrote: > did you look at the medial wall? > > On 3/13/17 8:48 PM, Redwan Maatoug wrote: > > Thank you very much Douglas, > > I think that I probably miss

Re: [Freesurfer] Adjust bbregister affine to target raw T1

There is no way to set a hard and fast threshold. I would recommend running a set of them (20ish), checking them manually to assure that they are correct, then compute the mean and stddev of the mincost. For a new data set, you can compute a z-score of the mincost and then pick a threshold

Re: [Freesurfer] Adjust bbregister affine to target raw T1

Hi Doug, As an update, --init-coreg produced essentially the same result as --init-fsl; however, that was on EPIs we've discovered were LR flipped during reconstruction, so I've switched to a different test subject for now. Now, for --init-fsl and --init-coreg, respectively, we get: MinCost:

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

Hi David, first I think it makes sense to - replicate the problem in the regular (cross sectional) stream - then fix it there (if it exists) or look for it in long. So you see the problem in the S02_t1 and S02_t2 also, right? Best, Martin > On 13 Mar 2017, at 16:55, David Semanek

Re: [Freesurfer] Intensity normalization in longitudinal processing

Hi Jaiashre, generally we advise against mixing version. It may work, but it may also fail. We do not test these combinations. I know for example that people did run 5.3 base and long on top of 5.1 cross successfully (at least they claim). I don’t know how mixing with 6.0 behaves. I am

Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

With FreeSurfer V6.1. Peace, Matt. From: on behalf of CAGNA Bastien Reply-To: Freesurfer support list Date: Tuesday, March 14, 2017 at 11:32 AM To: "freesurfer@nmr.mgh.harvard.edu"

Re: [Freesurfer] R: Re: Whole preprocessing with FAST without to perform a seed based analysis

You can't on either occasion just using preproc-sess. You can create an analysis with those components, then run selxavg3-sess with the -svres option. This will create a folder called eres with volumes that have had all the nuisance variables and low freqeuncies regressed out On 3/14/17

Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

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] R: Re: Whole preprocessing with FAST without to perform a seed based analysis

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

Re: [Freesurfer] mri_vol2surf

did you look at the medial wall? On 3/13/17 8:48 PM, Redwan Maatoug wrote: Thank you very much Douglas, I think that I probably miss something. There is no error in the terminal but when i launch tksurfer, I have the following screenshot (screen1). The overlay is loaded but the coordinates

Re: [Freesurfer] Whole preprocessing with FAST without to perform a seed based analysis

just use preproc-sess On 3/14/17 10:45 AM, std...@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

Re: [Freesurfer] fsgd 4 groups, continuous dependent variable, 2 covariates

See if one of these examples works for you http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples having two covariates is a straight forward extension of one On 3/14/17 7:47 AM, Donna Cosgrove wrote: ​Hi Freesurfer experts, I am looking at the effect of a genetic risk score (GRS) on

Re: [Freesurfer] Ventricles not filled

Hi Manuel yes, you can either fill them in the wm or edit the aseg cheers Bruce On Tue, 14 Mar 2017, Manuel Delgado wrote: > Dear Freesurfer list, > Does anybody know how to deal with the parts of the ventricles that have not > been filled in yellow when editing the white matter mask? (see

Re: [Freesurfer] tkmedit error

Hi Veronica if freeview works for you then you should just use it. We have deprecated tkmedit and are trying not to invest any time or energy in it any longer. cheers Bruce On Tue, 14 Mar 2017, Veronica Munoz wrote: > Dear all, > > I'm trying to use tkmedit to verify my recon-all results but

Re: [Freesurfer] Faulty alignment to standard surface

HI Daan wow, that is a pretty unusual folding pattern, which I'm sure is the source of the issue. Are you sure which one is the central sulcus? If so, draw it (I guess using tksurfer as the current version of freeview doesn't have extensive surface drawing tools yet), probably by just "custom

Re: [Freesurfer] Brain to skull distance

Hi Youssif you can save BEM surfaces with the -surf option to mri_watershed, but you would probably get more accurate measures if you have a T2 (or PD) scan. cheers Bruce On Tue, 14 Mar 2017, yusif Al-kheder wrote: Hello, Is it possible to use freesurfer to determine the distance

[Freesurfer] Whole preprocessing with FAST without to perform a seed based analysis

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___

[Freesurfer] fsgd 4 groups, continuous dependent variable, 2 covariates

​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

Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

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

Re: [Freesurfer] Faulty alignment to standard surface

Dear Douglas, Thank you for your response. The surface placement on the individual seems correct (see https://ibb.co/f4aeAa ). However, if I load the annotation files, the labels are wrong. In this screenshot (https://ibb.co/cycFiv ), I've loaded the BA annotation outlines and BA3a in yellow on