[Freesurfer] binarize white matter mask

Dear experts, I need a binarized wm mask for my analysis. The wm.mgz volume includes subcortical structures so I would like to use the aseg.mgz volume. I was hoping someone could give me instructions (command-line) on how to binarize aseg.mgz so that the wm=1 and everything else is 0. Thank you i

[Freesurfer] Antwort: Re: use manually defined talairach.xfm

Hi Antonin Thank you for your reply. Here is what I did: 1. tkregister2 --mgz --s x140214_b02_0917040_3_1_wipmp2rage0p8mmsenseV42_reOrient --fstal 2. manual registration (see attached file “before_recon-all_talairach.xfm”) 3. re-run recon-all, which is: recon-all -s x140214_b

[Freesurfer] Longitudinal spatiotemporal LME vs. V-LME

Dear freesurfer experts, I have a mixed 2x2 design with group (approx. 18 subjects per group) and timepoint (t0, t1) as factors. I analyzed the thickness data with the longitudinal stream and the spatiotemporal LME as a random intercept model, age as covariate. However, the model does not conv

Re: [Freesurfer] Antwort: Re: use manually defined talairach.xfm

Dear Clemens, I am almost out of ideas, since the behaviour is contrary to my expectations. I would expect that if you run your recon by recon-all -s subject_id -all the files you named before_recon-all_talairach.xfm and after_recon-all_alairach.xfm should be identical. Could you assure th

[Freesurfer] Curvature in FreeSurfer

Dear FreeSurfer, We have been discussing the mean curvature provided by FreeSurfer software. As i understand the mean curvature is measured as 1/r and has a unit of 1/mm. But a) What is the curvature an expression of? Is it the degree of folding of the brain and is it the white matter surface

Re: [Freesurfer] Antwort: Re: use manually defined talairach.xfm

Dear Clemens, I now see where is the problem: The current implementation of recon-all -talairach step is quite complicated, as far as I understand: The -talairach registration step produces talairach.auto.xfm. If the talairach.xfm exists, it is not overwritten by talairach.auto.xfm (unless -c

Re: [Freesurfer] Freesurfer Contrast Issues

Hi Mackenzie if you upload a couple of subjects (their entire subject dir, tarred and gzipped) to our ftp site (directions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange) I'll see what I can do cheers Bruce On Tue, 15 Aug 2017, Leavitt, Mackenzie wrote: Hello, Our instit

Re: [Freesurfer] AD cortical thickness signature

HI Hyon-Ah if your question is how to you compute the mean thickness for an ROI, if you have it in .label format you can simply call mris_anatomical_stats -l cheers Bruce On Wed, 16 Aug 2017, Yi, Hyon-Ah wrote: Dear FS experts I’m wondering whether there are ways of getting the sing

Re: [Freesurfer] binarize white matter mask

Hi Elizabeth check out the help of mri_binarize. I think something like: mri_binarize --all-wm --i aseg.mgz --o aseg.wm.mgz should do the trick cheers Bruce On Wed, 16 Aug 2017, Elizabeth Dao wrote: > Dear experts, > I need a binarized wm mask for my analysis. The wm.mgz volume includes > su

Re: [Freesurfer] Curvature in FreeSurfer

Hi Kaspar if you mean the values we store in the ?h.curv files, those are the spatially smoothed mean curvature (average of the two principal curvatures). a). it is of the white surface, but you can use mris_curvature to compute the curv of the pial if you want b) an increase in the curva

Re: [Freesurfer] Help with hippocampal subfield alignment

Hi Bruce, I've uploaded the subject through FileDrop. Thanks for your help. -Elizabeth On Tue, Aug 15, 2017 at 6:00 PM, Bruce Fischl wrote: > HI Elizabeth > > that should definitely not happen. Something must have gone pretty > dramatically wrong. If you upload the subject I'll take a look > >

Re: [Freesurfer] Curvature in FreeSurfer

Curvature does not really connect simply to folding, although they are of course related. Nonetheless, one cannot make universal statements like "A curvature means an in folding". Consider for example a pathology like poly-microgryria where numerous small "bumps" might appear on a brain surf

Re: [Freesurfer] Mean diffusivity on cortex?

Hi Dr Greve, On a similar note, can I use the Petsurfer on PET data that have already been averaged into a single frame 3D volume instead of 4D? Example, SUVR and BPND data. Thanks for your help again. On Tuesday, August 15, 2017, 9:09:33 AM GMT+1, Shane Schofield wrote: Hello Dr Greve, I hav

Re: [Freesurfer] Mean diffusivity on cortex?

SUVR you can. BP is a little trickier because BP estimation is a nonlinear operation that can be biased by noise. Probably it comes out similarly. On 08/16/2017 02:50 PM, Shane Schofield wrote: > Hi Dr Greve, > > On a similar note, can I use the Petsurfer on PET data that have > already been a

[Freesurfer] Segmentation of WM hypointensities

Hello, The Freesurfer segmentation for hypointensities is very good, but misses on some subjects, i.e. it does not include large chunks of hypointense regions in some subjects. It does fantastic picking up the periventricular hypointensities, but appears to fail on some deep WM regions. I just

Re: [Freesurfer] Matrix ill-conditioned error for dods thickness mri_glmfit analysis

posting the response to the list: The problem is that femalezero and femaletwo only have 4 and 3 subjects, respectively. As you are trying to estimate 4 slopes + an intercept, you will need at least 5 subjects per group. doug On 08/16/2017 03:27 PM, Sullivan, Danielle Renee wrote: > > Hi Do

Re: [Freesurfer] FS-FAST outputs is X.mat used? {Disarmed}

It has the design matrix plus a lot of other stuff in it. For parametric modulation, have you seen this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation On 08/15/2017 09:52 PM, Kevin Aquino wrote: > Dear all, > > I have a question regarding the output from selxavg3-sess.

Re: [Freesurfer] Recon-all error

That means that the surfaces are out of sync. the -make-all only works in certain circumstances. You can delete everything in the surf folder (it should all be recreated anyway with -autorecon2-cp) On 08/15/2017 10:04 PM, Bronwyn Overs wrote: > Dear mailing list, > > I am trying to batch a seri

Re: [Freesurfer] AD cortical thickness signature

not that I know of. You can merge the desired labels into one (mri_merge_labels) and then compute the mean in the merged label On 08/15/2017 11:56 PM, Yi, Hyon-Ah wrote: > Dear FS experts > > > I’m wondering whether there are ways of getting the single value of ROIs. > > I mean to get the value

Re: [Freesurfer] Antwort: Re: use manually defined talairach.xfm

That is the automatic failure detection for the talairach registration that is throwing the error. This checks the reg matrix against a sample of normal data. If the subject is in at a funny angle, then this can fail even if the registration is ok. You can just turn it off with -no-talcheck O

Re: [Freesurfer] Mean diffusivity on cortex?

Okay I understand. So  I ideally would like to do the PetSurfer before actually working on the BPND but I already got them in the BPND format as well as the raw dynamic images. I tried to obtain the BPND data out from PetSurfer myself, but then I realise I don't any time.dat with me.mri_glmfit

Re: [Freesurfer] FS-FAST outputs is X.mat used? {Disarmed}

Thanks for that Doug, [I was hoping i could do the parametric modulation in the contrast weights -- SPM style of doing this after the betas were fit]. Regarding the X.mat question, sorry I wasn't clear. I can see it has the nuisance regressors and constant terms, but is that x.mat used to estimat

Re: [Freesurfer] Recon-all error

Hi Douglas, Thanks for your reply. I followed your suggestion and deleted everything in the surf folder for each subject. I am not getting the following error: Reading source surface reg /workingdata/ID_001/surf/lh.sphere.reg No such file or directory mri_surf2surf: could not read surface /worki

[Freesurfer] Error with recon-all long

Dear freesurfer mailing list, I have been running the recon-all -long command and received the following errors: # #@# Surf Reg lh Wed Aug 16 18:07:26 AEST 2017 /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/TPID_001.long.BASEID_001/scripts

Re: [Freesurfer] Error with recon-all long

Hi again list, Sorry I made a mistake. The lh.sphere.reg and lh.smoothwm are both in the base image directory, but I’m still receiving the mismatch error. Partial ls -l displayed below: [b.overs@katana surf]$ ls -l $SUBJECTS_DIR/BASEID_001/surf total 120260 ... -rw-rw-r-- 1 b.overs GroupID 4554

Re: [Freesurfer] AD cortical thickness signature

Dear Doug ,, thanks for your suggestion .. I have more questions. 1. If then, I can get merged label using mir_mergelabels, As it is ' . label file', so I should run mris_label2annot and mis_anatomical_stats ? 2. is it possible to get the merged value of rh & lh ? Regards, Hyon-Ah ..