Usually that is because the SUBJECTS_DIR is not set. I'm not sure how that
works on the Mac.
On Wed, 9 Nov 2011, nooshin n.zade wrote:
> Dear Freesurfer Expers
>
> I have installed FS on the new mini Mac today, it can open bert with
> tkmedit and tksurfer.
> Using tkmedit for seeing my subject i
You can try running just recon-all -skullstrip first, if that doesn't fix
the problem, you can try changing the wsthresh and removing the
-no-wsgcaatlas flag (or add the flag if you didn't include it). Sometimes
that makes a difference.
-Khoa
On Wed, 9 Nov 2011, Julia Hill wrote:
Hi,
You are correct. mri_gcut is automatically done in v5.0 and not v5.1. If
you want to run it using v5.1 you'll have to specify -gcut after
-skullstrip. You can also try using a more conservative watershed
threshold value to get rid of the extra dura if there's a lot of it.
-Khoa
Control points do a good job in fixing the problem for me. You just have
to put a string of control points (not too many) on the white matter
strips for every 2-3 slice.
-Khoa
On Thu, 3 Nov 2011, Louis Nicholas Vinke wrote:
Hi,
Some other potential explanations for poor surfaces in this
ed to make edits to the wm.mgz or add control
points. If your subject has improved after the control points and wm
edits but is not perfect, you can try adding more control points or look
for more topological defects to fix.
Hope that helps,
-Khoa
On Wed, 21 Sep 2011, Vy Dinh wrote:
>
pial edits, then run -autorecon-pial. Here's a wiki page of all the recon
steps. On there you can also find the OtherUsefulFlags page with different
flags you can use when running your recons.
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
-Khoa
On Wed, 21 Sep 2011, Vy Dinh wrote
Hi,
How is the intensity of the wm between the putamen and the
white surface? If it's lower than 110, you can place a string of control
points along the inside border of the white surface. That might help
extend the pial surf to include all the gm.
-Khoa
On Fri, 16 Sep 2011, Sin
points would help with extending the pial surf on the lh.
-Khoa
>
> Hi Bruce and Sita:
>
> Thanks for your relay. And Here are the images.
>
> Jing
>
>
>
> From: Jing Ming [mj_com...@hotmail.com]
>
> Sent: Thursday, September 15, 2011 7:31 PM
>
> To: Vy
Hi Daniel,
Usually when I get the FindFacePath error, the wm.mgz is very bad. You can
try placing control points on the wm and rerun -autorecon2 and
-autorecon3. That worked for me.
-Khoa
On Sat, 10 Sep 2011, Daniel Ferreira Padilla wrote:
> Dear Bruce and experts,
>
>
>
>
Hi Jacquie,
I'm not sure why gcut isn't working. If you want, you can compress one of
the subject dirs and upload it. I can take a look and also see which other
ways you can fix the problem.
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-Khoa
On Thu, 4 Aug 2011,
remove them. If you want, you can try just running
"recon-all -skullstrip -s subjid" again instead. That might improve it.
-Khoa
On Wed, 3 Aug 2011, Jacquelynn Nicosia Copeland wrote:
> Hi Freesurfers:
>
> I am trying to minimize the amount of skull stripping manual edits I
If you can compress the whole subject dir and load them here, that'd be
great.
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-Khoa
On Tue, 2 Aug 2011, _andre...@sapo.pt wrote:
> Hi,
>
> I'm not being able to solve the segmentation problem on in this
> su
://surfer.nmr.mgh.harvard.edu/fswiki/Edits
-Khoa
On Mon, 1 Aug 2011, Gonzalo Rojas Costa wrote:
> Hi:
>
> In the web page "FSTutorial/TroubleshootingData - Free Surfer Wiki"
> appears "Try using an xopts script first to change the intensity
> thresholds being u
base, then you
can either do -force or delete the folder or delete whichever file you
made edits on (if made edits on wm.mgz in cross, delete wm.mgz in base).
Martin, is that correct?
-Khoa
On Wed, 20 Jul 2011, Jeff Sadino wrote:
> Hello,
>
> I have a subject with three timepoints I am
d the surface.
The tutorial for wm edits is here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
-Khoa
On Tue, 19 Jul 2011, Carolina Valencia wrote:
> Dear FS experts,
>
> I'm trying to analyse a case of cortical dysplasia, but after recon-all I
> see
g.mgz).
-Khoa
On Tue, 19 Jul 2011, Antonella Kis wrote:
Hi Bruce,
Based on your last suggestion, after running the recon-all on my NPI001 subject:
recon-all -s NPI001 -i
/usr/local/freesurfer/subjects/june2011/_orig_/NPI001.nii.gz -qcache -all
and editing the wm, I saved all my edits (usin
ing -autorecon2 -autorecon3.
-Khoa
On Fri, 1 Jul 2011, Tetiana Dadakova wrote:
> Dear list,
>
> For one of my subjects the skull strip is bad, but it doesn't
> (visually) affect neither surfaces nor segmentation (see the image in
> the attachment).
> In this case, do I have
edrop/index.html
-Khoa
On Mon, 6 Jun 2011, Irene Altarelli wrote:
> Dear Freesurfers,
>
> we are processing a dataset of children through recon-all, applying
> manual corrections when needed.
>
> For one subject, after manual correction and running autorecon2-cp, we
> observe
You can follow instructions on this website.
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Tue, 31 May 2011, k...@rice.edu wrote:
> Sure thing -- where and how do you structure your uploading?
>
> Thank you,
> Kareem
>
> Quoting Bruce Fischl :
>
>> You can upload this subject and w
Hi Kareem,
Did you check the skullstrip to see if it's correct? Sometimes that can
cause problems with the surfaces. If you can send the subject over, I
can take a look.
-Khoa
On Tue, 31 May 2011, k...@rice.edu wrote:
> Hello all,
>
> I have a subject for whom I have been tryi
Got it. I'll look at it and get back to you.
On Tue, 19 Apr 2011, Allie Rosen wrote:
> Hi,
>
> http://dl.dropbox.com/u/14127241/C42.tar.gz
>
> Here is the link to the subject. I hope this works!!
>
> Allie
>
>
>
> On Tue, Apr 19, 2011 at 9:38 AM, Khoa Nguy
use apparently I don't have ftp access.
>
> Allie
>
>
>
> On Tue, Apr 19, 2011 at 8:37 AM, Khoa Nguyen wrote:
>
>> Are you from the center? If so you can just cd into /space/outgoing and
>> copy your file there. If not, you can follow the instructions in the box
Hi Allie,
Can you upload the subject? I'll take a look and see if I can figure out
what's wrong.
-Khoa
On Tue, 19 Apr 2011, Allie Rosen wrote:
> Hi,
>
> This (recon-all after wm.mgz and brainmask.mgz edits) didn't work. The part
> that wasn't included in the
gt;>> no
>>> aseg for that. I would love to be corrected on that point though.
>>>
>>> Best
>>>Sebastian
>>>
>>> >
>>> >
>>> >
>>> > On Jan 10, 2011, at 9:34 PM, Yang Liu <
>>> liu.yan...@gmai
Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the solution.
Control points are to fix intensity problem, but you can also add wm
voxels manually to fix any wm defects. In this case, adding that many control
points
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