Re: [Freesurfer] modeling thickness data at a given age

If you are using the Different Offset Different Slope (DODS) model, then, by default, it tests at age=0. If you want to test at age=8, just subtract 8 from all the ages On 09/26/2017 01:57 PM, Eryilmaz, H. Hamdi wrote: > Dear all, > > We are modeling changes in cortical thickness over time

Re: [Freesurfer] Freesurfer Digest, Vol 163, Issue 45

Subject: Brain MRI Data sets. Dear Experts, I am a student of final year engineering.I am working on the project for Brain tumour detection.for which i need Mri image datasets, can anyone help me out to get those MRI scans. Looking forward for your support in this field.Thanking you. Sincerely

Re: [Freesurfer] Automatic Topology Correction

Well i think there are some by making comparisons between surfaces( pial and white) and the segmentation before topology correction ( i could see some holes still existed) . I'm going to check the mris_euler_number to see the result. Thank you. On Tue, Sep 26, 2017 at 5:30 PM Bruce Fischl

[Freesurfer] modeling thickness data at a given age

Dear all, We are modeling changes in cortical thickness over time using a cross-sectional design. We have two groups of participants, age 8 to 18. In the cortical regions that interest us, there is generally a linear decline in thickness with age. Each group can be fitted to a best-fit

[Freesurfer] Saving individual labels from aseg

Dear Experts, Is it possible to convert aseg file to individual lables ( except the one introduced by Jared Tanner) ? Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] bad midline cut

If I accurately understand the recon-all script, then -noaseg sets UseAseg=0, but "autorecon2-noaseg" is a different flag, which only sets the following things. case "-autorecon2-cp": case "-autorecon2-noaseg": case "-autorecon2-wm": set DoNormalization2 = 1; set

Re: [Freesurfer] bad midline cut

Dear Bruce, >From the recon-all script it seems to me that autorecon2-noaseg, autorecon2-wm and autorecon2-cp are totally equivalent (the same flags are defined to be true in all three cases). Could you confirm this? Best regards, Gabor

Re: [Freesurfer] Saving individual labels from aseg

Try mri_cor2label On 09/26/2017 04:11 PM, Fereshte wrote: > Dear Experts, > Is it possible to convert aseg file to individual lables ( except the > one introduced by Jared Tanner) ? > Thank you! > > > ___ > Freesurfer mailing list >

Re: [Freesurfer] bad midline cut

oh, sorry, you are correct. I guess you need to edit the aseg.presurf.mgz since that is what mri_fill is given as a segmentation. Sorry for the mistake Bruce On Tue, 26 Sep 2017, Gabor Perlaki wrote: > If I accurately understand the recon-all script, then -noaseg sets UseAseg=0, > but >

Re: [Freesurfer] bad midline cut

Dear Bruce, Gabor, while reading this thread, I think that there is misunderstanding. -noaseg flag of recon-all indeed disables using aseg.presurf,  whereas -autorecon2-noaseg does the same thing as -autorecon2-cp (at least in dev version, looking at the recon-all code). Antonin Skoch Hi

Re: [Freesurfer] bad midline cut

I've already corrected aseg.presurf.mgz and the left and right lateral ventricles are now correct in the final aseg.mgz. However the pial surface is almost the same as earlier: https://mega.nz/#!XAZkWLZa!a6NgkEtiHzEqUkhZ6WimPgUKxytsGHKrgOLfyHdUuEM

Re: [Freesurfer] bad midline cut

hmmm, if you tar, gzip and upload the subject I'll take a look. Bruce On Tue, 26 Sep 2017, Gabor Perlaki wrote: > I've already corrected aseg.presurf.mgz and the left and right lateral > ventricles are now correct in > the final aseg.mgz. However the pial surface is almost the same as earlier:

[Freesurfer] Error in mris_anatomical_stats

Hi list,using FS-FAST I have obtained a map reporting - Red_positive cluster shows difference for FC of group A > FC of group B- Blue_negative cluster shows difference for FC of group B < FC of group A Because I would like to extract the value of cortical thickness from each cluster, I have

Re: [Freesurfer] bad midline cut

yes, Gabor already pointed this out to me :) thanks to both of you Bruce On Tue, 26 Sep 2017, Antonin Skoch wrote: Dear Bruce, Gabor, while reading this thread, I think that there is misunderstanding. -noaseg flag of recon-all indeed disables using aseg.presurf,  whereas

[Freesurfer] fwhm in area analysis

Hi FreeSurfer experts, When I specify fwhm=15 to analyze area, mri_surfcluster said that it cannot find fwhm31 in fsaverage/${hemi}/cortex/fwhm31/... This did not happen when I used FreeSurfer 5.3.0 I am wondering if FreeSurfer 6.0.0 pre-smooths the surface area? Thanks, Daniel

[Freesurfer] freesurfer longitudinal pipeline

Hello Freesurfer, For the longitudinal pipeline, the website/ recon-all -help suggested that I calculate the different on the results from the longitudinal command (e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were named 1001_Baseline.long.longbase and

Re: [Freesurfer] bad midline cut

Dear Bruce, I've corrected the lateral ventricles in the aseg.presurf.mgz and ran "recon-all -autorecon2-noaseg -autorecon3 -subjid". Although the labels in aseg.mgz is fine the surfaces (and midline cut) remained bad. Any other idea how to correct this type of error? Best Regards, Gabor

Re: [Freesurfer] Automatic Topology Correction

why do you think there are defects? If you have run recon-all there are pretty much guaranteed not wo be any. You can't really see this visually, but mris_euler_number will tell you if there are any cheers Bruce On Tue, 26 Sep 2017, Fereshte wrote: Dear Experts, I checked the topology

Re: [Freesurfer] bad midline cut

Hi Gabor you don't want to specify -noaseg. That tells recon-all not to use the aseg. I think autorecon2-cp and autorecon3 should do the trick cheers Bruce On Tue, 26 Sep 2017, Gabor Perlaki wrote: > Dear Bruce, > > I've corrected the lateral ventricles in the aseg.presurf.mgz and ran >

Re: [Freesurfer] Automatic Topology Correction

Dear Experts, I checked the topology corrected surfaces in recon-all pipeline however i found it didn't do well as still there are many topology defects in the pial surfaces. I know how to correct them manually in freeview but are there any commands to recorrect these topological defects with for

[Freesurfer] Volume Version of ?h.sphere.reg and method to read it

Dear Freesurfer Team, I am using your reconstruction pipeline for my study. Since I need to morph all my subjects to an average subject (using mne-python for this) for upcoming a Volume Source Analysis I deeply looked into the whole source-code of both software packages. Narowing down the