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 f
Hello,
what is the correct way to cite freeview in a papar for a manual rois
segmentation task?
Thanks,
Luigi.
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The information in thi
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.
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
is
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
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
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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
bo
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.
>
>
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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 mat
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 what might be a potential solut
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 th
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 aseg.d
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 a
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:
$ bbregis
with 5.2 and beyond "SubcorticalGray" does not include cerebellum GM. See
http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
On 03/10/2017 05:27 AM, elisa ferrari wrote:
>
> Hello,
>
> I examined data from a public database (ABIDE) processed both with
> freesurfer 5.1 and freesurfer 6.0
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 br
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 behalf of CAGNA Bastien
Reply-To: Freesurfe
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
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 label
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 13:
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 co
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
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 ventr
I don't see why not, although we haven't tested it yet.
cheers
Bruce
On Mon, 13 Mar 2017,
CAGNA Bastien wrote:
>
> 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
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, 2
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?
dou
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 o
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 genera
Hello,
Is it possible to use freesurfer to determine the distance between the skull
and brain?
Youssif
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