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Did you already have the time to look at the logfile? Do you have any
suggestions how to proceed?
Thank you!
> Am 02.12.2019 um 19:18 schrieb Boris Rauchmann :
>
>
> In this example tried it with only the subcortical segmentations from my
>
I guess I would try adding control points to the wm in the region that is
darker
On Thu, 5 Dec 2019, Laurel Quinlan wrote:
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Thanks Bruce! I will chat with my supervisor about uploading the brain to the
ftp site, but for now, I
can see intensity
Hi Laurel
do you want to upload this subject to our ftp site and we can take a
look? Alternatively you can overlay the wm.mgz as a heatmap on top of the
brain.mgz with the ?h.orig surface overlaid so you can see where it is
missing stuff and why
Bruce
On
Thu, 5 Dec 2019, Laurel Quinlan
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Thanks for the help!
On Wed, Dec 4, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Yes, but threshold it first, eg
> mri_binarize --abs --i sig.cluster.mgh --min .01 --o newmask.mgh
>
> On 12/4/19 1:38 PM, cody samth
Hi Laurel
yes, the lh.orig.nofix is created using the control points and other
things, and so the number of holes in it will definitely change if the
placement of control points changes
cheers
Bruce
On Thu, 5 Dec 2019, Laurel Quinlan
wrote:
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Hi Doug,
Thank you! Yes, their control point edits were different. Are the number of
?h.orig.nofix defects calculated after reconstruction with control point edits?
-Laurel
From:
We currently do not have a mac build of mri_aparc2aseg, and we recommend
downloading the freesurfer dev release to resolve this issue.
On 12/5/19 1:00 PM, Joshi, Nandita wrote:
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>
> Thank you so much for that! The README file instructs to download
>
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Dear Dr. Douglas,
Thank you so much!
Best regards,
Ting
On Thu, Dec 5, 2019 at 11:45 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> I've attached a couple of papers
>
> On 12/3/19 9:24 PM, Ting Li wrote:
> >
> > External
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Thank you so much for that! The README file instructs to download
make_average_subject and platform specific mri_aparc2aseg. However, the mac
version of mri_aparc2aseg is missing in the patch. Could it be possible to
download it from elsewhere?
-
Yea, not sure. It could be that the uptake in WM near the NAcc is
somewhat less than average (GTM assumes constant throughout). If so,
then the GTM would subtract too much from the NAcc in an attempt to
remove the spill in from WM. This is more of a problem for amyoild and
tau ligands because
The same one that you would use with the T1 stream, just make sure to
include -T2pial
On 12/5/19 5:04 AM, Steve Petersen wrote:
>
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>
> Dear Freesurfer experts,
>
> I used t2 image as input in subjects that have already been processed
> without them
It does not create a file with a single voxel. Below, prv.mgz is meant
to represent the file that has all the voxels/vertices. Once you know
the vertex no you are interested in, you extract it with the pvrvtx line.
On 12/5/19 12:47 PM, Barletta, Valeria wrote:
> I did what you suggested in your
If your WM volume is not conformed, you will need to conform it with
mri_convert yourwm.mgz --conform wm.mgz
On 12/5/19 4:24 AM, Jordi Huguet wrote:
>
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>
> Hi Douglas,
>
> I have followed the suggested approach, however I get an error related
> to the
See the REAME file here
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
On 12/5/19 11:47 AM, Joshi, Nandita wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to make a study specific template based on the
> instructions at:
>
I did what you suggested in your previous email:
> That does not have the pvr in it. You can extract the pvr for that
> vertex and add it as a column to the X matrix with
> pvr = fast_vol2mat(MRIread('pvr.mgz'));
> pvrvtx = pvr(:,vertexno+1);
Which file shall I look like for the single voxel?
On 12/4/19 11:51 AM, Barletta, Valeria wrote:
> Ok I did it and did not get any .mgh file as a result.
Did what?
>
> At this point I wonder, what is the best model to check for
> correlation between my continuous outcome CME.mgh and the continuous
> variable ficvf.mgh?
> Shall I include
Use mri_label2label. Run it with --help to get examples
On 12/4/19 1:58 AM, 于倩倩 wrote:
>
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>
> Dear Freesurfer Expert:
> First, I got the lh.parsorbitalis.label according to the command:
> mri_annotation2label --subject fsaverage --hemi lh --outdir
>
Are you 100% sure that the DTI and the anatomical are the same subject?
Also, please send the bbregister log file
On 12/5/19 12:14 PM, VictorM - Gmail wrote:
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>
> Hi Freesurfer experts,
>
> I have been trying to run a registration between my DWi data and
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Hi Freesurfer experts,
I have been trying to run a registration between my DWi data and the T1.
I am struggling to obtain a good cortical matching, despite I have
previously run it withour problems in other datasets. The mincost for
most of the
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Hello,
I am trying to make a study specific template based on the instructions at:
https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
However, on running the first step:
make_average_subject --out newtemplate --subjects subj1 subj2
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Dear Freesurfer experts,
I used t2 image as input in subjects that have already been processed
without them following the instructions of the website. Although pial
surface segmentation has improved there is still some error. After edit the
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Hi Douglas,
I have followed the suggested approach, however I get an error related to
the dimensions of the WM volume (see log trace below).
...
Found wm edits: 23448857 deletes, 783317 fills
>
> cp wm.mgz wm.seg.mgz
>
>
> mri_segment -keep
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