[Freesurfer] Brain to skull distance

Hello, Is it possible to use freesurfer to determine the distance between the skull and brain? Youssif ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

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

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

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

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

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

To augment Matt's comment, the v6.0 T1-only stream is more accurate and sensitive to than 5.3 according to our tests (both cortically and subcortically). I think Matt has found some examples where the T1+T2 stream has some inaccurate placement. Matt, weren't you going to send me examples?

Re: [Freesurfer] Error viewing corrected results

Hi Antonin, This makes a good sense now. Now, my results are making more sense with clustere_tstat_fwep.mgz, where the cluster is very close to higher PCC values. Thank you so very much Antonin all your help, patience and time in figuring out all these issues :). Thanks, Sahil On Fri, Mar 10,

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

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

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

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.

Re: [Freesurfer] mri_vol2surf

The file you created is not a label so don't try to load it with -label. Instead use -overlay file.mgh -fminmax .5 1 On 03/13/2017 05:40 PM, Redwan Maatoug wrote: > Hi Douglas, > > Sorry to bother you, again. > Actually, my command was t1 and not t2 but even with t1 nothing works. > So if my

Re: [Freesurfer] mri_vol2surf

Hi Douglas, Sorry to bother you, again. Actually, my command was t1 and not t2 but even with t1 nothing works. So if my command line is exact, do you think it is a problem with my files ? Thank you, Redwan Maatoug Resident in psychiatry Stanford University Amit Etkin lab On 13 March 2017 at

Re: [Freesurfer] mri_surfcluster to obtain ROI (label) centroid MNI coordinates

It turns out that setting --min to 0 causes a problem. Try setting it to something close to 0, eg 1e-6 On 03/09/2017 03:10 AM, Ladan Shahshahani wrote: > Hi, > > Following previous discussions on the mailing list, I am using > mri_surfcluster to extract MNI (or Talairach) coordinates of a

Re: [Freesurfer] BUG: bbregister --init-best needs to unset InitCoreg

just use mri_coreg -- that is the best! On 03/13/2017 04:27 PM, Christopher Markiewicz wrote: > Hi all, > > bbregister --init-best always produces "ERROR: cannot spec an init > method with --init-best", because InitCoreg is defined as 1 by > default, and never set to 0 by --init-best. (Setting

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

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: on

Re: [Freesurfer] mri_vol2surf

Use --t1 (I assume the --tw was supposed to be --t2, which is wrong for that mni152 volume) On 03/09/2017 08:58 PM, Redwan Maatoug wrote: > Hi Douglas, > > Indeed you have already helped me ! > Thank you for your help and for your time. > > I have tried to do, as you said. > I have used the

[Freesurfer] BUG: bbregister --init-best needs to unset InitCoreg

Hi all, bbregister --init-best always produces "ERROR: cannot spec an init method with --init-best", because InitCoreg is defined as 1 by default, and never set to 0 by --init-best. (Setting something else that unsets InitCoreg will trigger the same error.) Example, given SUBJ and EPI: $

Re: [Freesurfer] Qdec effect sizes, correlation coefficient

if you use the version 6 of mri_glmfit, it will automatically output the pcc.mgh file. If you want a cohen's D, then you can cd glmdir/contrast fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh On 03/13/2017 01:45 PM, Juan Baldermann wrote: > Dear all, > > I did a correlation analysis in qdec

Re: [Freesurfer] Report indicating aseg edits

It does not, but you could make one easily enough, eg, cd $SUBJCTS_DIR/subject/mri fscalc aseg.auto.mgz sub aseg.manual.mgz -o aseg.diff.mgz mri_binarize --i aseg.diff.mgz --min 0.5 --o aseg.diff.bin.mgz mri_segstats --i aseg.diff.bin.mgz --accumulate --seg aseg.mgz --ctab-default --sum

Re: [Freesurfer] Extract the cortical thickness

You can use aparcstats2table to report the thickness, surface area, and volume as a table from a group of subjects. Is that what you want? On 03/13/2017 02:01 AM, Duy Nguyen wrote: > Dear FreeSurfer expert > > I wonder that whether I can use the command aparc2statstable to get > the cortical

Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding

Hello, Sorry for the late reply. I did try re-running it and it did work this time! Thank you. Daniela On Mon, Mar 6, 2017 at 12:15 AM, wrote: > Hello Daniela, > > Ive been looking into this error, and although I am unable to replicate it > on my Mac, I do have

[Freesurfer] Qdec effect sizes, correlation coefficient

Dear all, I did a correlation analysis in qdec and now I want to report effect sizes of my significant clustes. How can I extract a correlation coefficient for this type of analyis? Or any other effect size? I saw that i can derive them from the pcc.mgh file, but this somehow didn't work in

Re: [Freesurfer] How to cite freeview

I guess just cite the "FreeSurfer" paper On Mon, 13 Mar 2017, Luigi Antelmi wrote: > Hello, > what is the correct way to cite freeview in a papar for a manual rois > segmentation task? > Thanks, > Luigi. > > ___ Freesurfer mailing list

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

Thanks, I have uploaded the cross and long stream processing from one subject which requires numerous white matter edits to correct defects in the white matter surfaces; the file is on the ftp server as dsemanek.zip. Both of the cross subject folders, s02_t1 and s02_t2 have had edits done to

[Freesurfer] Report indicating aseg edits

Hello, I am currently checking and editing the aseg outputs in my longitudinal data. I was wondering whether Freesurfer offers a report indicating the edits I have made to aseg output. Thank you, Tamara ___ Freesurfer mailing list

Re: [Freesurfer] Intensity normalization in longitudinal processing

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

Re: [Freesurfer] WM/pial edits

Dear All, Please advise. Some of the dural enclosure defects involve both wm and pia surfaces (wm/pia extending to dura), so in those cases, correcting pia will also touch the wm. Editing wm in wm.mgz and running recon-all -autorecon2-wm -autorecon3 ameliorates but does not solve the wm defect

Re: [Freesurfer] Error recon-all program quits at mri_nu_correct

Freesurfer v5.3 will fail at the mri_nu_correct.mni command on newer Linux distributions (that come with perl version 5.22 and higher) due to an incompatibility with the mni tools shipped with FreeSurfer and newer versions of perl. The issue has been fixed in the latest release of freesurfer.

[Freesurfer] How to cite freeview

Hello, what is the correct way to cite freeview in a papar for a manual rois segmentation task? Thanks, Luigi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

[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

[Freesurfer] Extract the cortical thickness

Dear FreeSurfer expert I wonder that whether I can use the command aparc2statstable to get the cortical thickness or is it better to get the cortical thickness of a volume defined ROI or is there the easy way to get the most accurate cortical thickness from ROI I am following the pipeline