run it with -help to get docs and examples. Also look at the ROI
tutorial on line. We do not compute a thickness measure for amyg.
On 3/2/17 10:17 PM, Gwang-Won Kim wrote:
Hello FreeSurfer Developers,
I have a question.
I want to evaluate volume and thickness of the amygdala using
asegstats2t
Hello FreeSurfer Developers, I have a question. I want to evaluate volume and thickness of the amygdala using asegstats2table. How do I obtain volume and thickness of the amygdala using asegstats2table?
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Dear Paul,
yes, this is the modification of FREESURFER_HOME you need to do (using setenv
command if you are using tcsh).
Regards,
Antonin
Hey Antonin,
Thank you. hence, the right path should be "setenv FREESURFER_HOME
/opt/freesurfer-6.0.0/freesurfer "
Best,
Paul.
On Thu, Mar 2, 2017 at 5:41
Dear Eli,
I have looked at your data.
Due to the fact that the white matter does have intensity well below 110 in the
large portion of white matter area under your problematic spot, I think that
instead of editing wm.mgz the better way in your case would be to add some
control points to the wh
Hey Antonin,
Thank you. hence, the right path should be "setenv FREESURFER_HOME
/opt/freesurfer-6.0.0/freesurfer "
Best,
Paul.
On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch wrote:
> Dear Paul,
>
> the slash problem prevents to properly create symbolic link to fsaverage in
> your SUBJECTS_DIR.
Dear Paul,
the slash problem prevents to properly create symbolic link to fsaverage in
your SUBJECTS_DIR.
Then, the mri_label2label could not find the fsaverage label file since
symbolic link for fsaverage does not exist, hence produces the error.log you
are attaching.
Regards,
Antonin
Tha
Bruce,
Main problem area that I can see is at coordinates [104,42,124].
My first attempt, I don't think I had the recon editing box checked when
I was editing the white matter, but I used a brush value of 255. My
second attempt I painted over the same voxels but with the recon editing
box checked
Thanks Antonin. Also, I got this error.log file in my label folder. Do you
think it is due to the slash problem?
Best,
Paul
On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch wrote:
> Dear Paul,
>
> I suppose the clue is following messages from your recon-all.log file:
>
> FREESURFER_HOME /opt/freesu
Dear Paul,
I suppose the clue is following messages from your recon-all.log file:
FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
and
cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s
/opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
ln: failed to create symb
Hi Cristian,
Can you send me the original mri_cvs_register command? When I apply the
m3z transform to your moving volume the result is not registered to the
target.
set morph = combined_toColin27_elreg_aseg.m3z
set targ = N27orig.mgz
set mov = TS076CDorig.mgz
set out = ${mov:r}.2.${targ}
Hi Douglas,
Thank you for your help,
So I still can't convert my volumetric file to a surface file and I don't
know what I am doing wrong.
My nifti volumetric file looks like : 1. screenshot
As you said, i have first registered the volumetric file
using bbregister.
I have used this command lin
I have uploaded the files i am using.
After updating to Freesurfer 6.0, i was able to use fullCSVmorph.tm3d, but the
coordinates in the output file remain unchanged.
The other tm3d files in my csv folder return 1 1 1 for each point
in the input txt file.
Best,
Cristian
Dear Mel,
if your recon in 5.3 version finished without error, there must be files
lh.orig.nofix and rh.orig.nofix present in the subj_id/surf directory.
This type of error is most frequently due to incorrectly fixed topological
defect. The original wm.mgz and orig.nofix errors can be quite a la
Dear Randy,
from the log file you provided it seems that both of your jobs exited on the
insufficient RAM. You should check your available RAM resources.
brainstem-structures:
std::bad_alloc
hippocampal subfiels:
Out of memory.
Regards,
Antonin
Hello FreeSurfer Experts/Community,
I a
Hello Bruce,
Thank you so much.
I will try later.
Xiuyi
On 2 March 2017 at 17:11, Douglas N Greve wrote:
> Click the button that says to show the annotation in outline (since you
> could not load it in outline mode
>
>
> On 03/02/2017 11:50 AM, Xiuyi Wang wrote:
> > Hi Bruce,
> >
> > Sorry fo
That was just a informational message and it can be ignored. Try check “Show
Outline only” on the GUI, since it should be invoked from the command-line in
V6.
> On Mar 2, 2017, at 11:50 AM, Xiuyi Wang wrote:
>
> Hi Bruce,
>
> Sorry for the misunderstanding.
>
> After showing the message "Did
Click the button that says to show the annotation in outline (since you
could not load it in outline mode
On 03/02/2017 11:50 AM, Xiuyi Wang wrote:
> Hi Bruce,
>
> Sorry for the misunderstanding.
>
> After showing the message "Did not find any volume geometry
> information in the surface", the
Hi all,
I was just wondering if it was possible to do seed to seed resting state
analysis in freesurfer, rather than seed to voxel? I am wanting to examine
connectivity within specific Yeo networks, using a spherical ROI as a seed.
The spherical ROI will be generated from one of the peak areas of
Dear Doug,
I am using quite recent dev version built 8/2/2017.
mris_label2annot of this version is following:
$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve
Regards,
Antonin
what version are you using? I thought I fixed the missing-last-label
problem in v6
On 03/01/2017 06:42 PM,
Same as with any other input file type. See our tutorials
On 03/02/2017 11:30 AM, yusif Al-kheder wrote:
> Thank you,
> How would I go on about using the segmentation with nifti mri files.
>
> Youssif
>
>> On Mar 2, 2017, at 11:24 AM, Douglas N Greve
>> wrote:
>>
>>
>>
>>> On 03/02/2017 11:18 A
so are these on the surface or in the volume?
On 03/01/2017 07:03 PM, Julie Hall wrote:
> Hi Doug
>
> Thanks for your quick reply. It¹s a resting state FC data driven
> parcellation atlas (see
> https://academic.oup.com/cercor/article-lookup/doi/10.1093/cercor/bhu239
> and attached)
>
> Julie
>
when you say it stops, you mean it crashes and returns control to the
command line? Or that the GUI stays up but is unresponsive?
On 03/02/2017 11:29 AM, Xiuyi Wang wrote:
> Hello Bruce,
>
> The program stops after displaying this message.
>
> So I guess your solution is to use FreeSurfer 6 and
Hello Bruce,
Thank you for your reply.
I have tried to delete “:annot_outline=1: before and the command lines are:
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:o
verlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
-viewport 3d
But I rec
Thank you,
How would I go on about using the segmentation with nifti mri files.
Youssif
> On Mar 2, 2017, at 11:24 AM, Douglas N Greve
> wrote:
>
>
>
>> On 03/02/2017 11:18 AM, yusif Al-kheder wrote:
>> Hello,
>> Is it possible to segment the brain into these parts if possible using
>> fre
Hello Bruce,
The program stops after displaying this message.
So I guess your solution is to use FreeSurfer 6 and I am not able to view
the data using FreeSurfer 5.3.
Thanks.
Xiuyi
On 2 March 2017 at 16:26, Douglas N Greve wrote:
> That is not an error, the program should have run normally a
That does not make sense. Can you run this subject in v6? If the problem
goes away, then there is not much we can do about it in 5.3
On 02/28/2017 05:27 AM, Melanie Ganz wrote:
> Hi Doug,
>
> the orig looks fine and we cannot see a file orig.nofix in the subject
> dirs. We still use v5.3.
>
> B
That is not an error, the program should have run normally after that.
This has been fixed in v6.
On 03/02/2017 11:23 AM, Xiuyi Wang wrote:
> Hello Bruce,
>
> Thank you for your reply.
>
> I have tried to delete “:annot_outline=1: before andthe command lines are:
>
> freeview -f
> $SUBJECTS_DIR
On 03/02/2017 11:18 AM, yusif Al-kheder wrote:
> Hello,
> Is it possible to segment the brain into these parts if possible using
> freesurfer;
> Cerebellum -- yes
> Midbrain -- not really (something called ventral diencphalon that overlaps a
> little)
> Pons -- no, but it is a target we will h
Hello,
Is it possible to segment the brain into these parts if possible using
freesurfer; Cerebellum
Midbrain
Pons
Medulla Oblongata
Hippocampus
Thalamus
Hypothalamus
Anterior and Posterior Commissura
Corpus Callosum
Hypophysis
Dura Mater
Youssif
___
Just run it with -qcache only and it will only do qcache
On 03/01/2017 02:48 PM, West, John D. wrote:
> Hi Douglas.
>
> Thanks for the reply. Forgive me for not responding quickly.
>
> It turns out what we really want is the interim files that are saved during
> recon-all if you add the -qcache
When you were getting the error message, was the program continuing? It
should have continued normally (though it is not good practice to have
big ERROR messages scrolling across the screen:)
On 03/01/2017 02:58 PM, Gustav Mårtensson wrote:
>
> Hi,
>
> Yes, the buildstamp says
> freesurfer-Lin
is the gii file a surface file or volume file?
On 03/02/2017 08:58 AM, Flavia Arduini wrote:
> I have GIFTI (.gii) format fileresulting from segmentation with cat 12
> (toolbox of spm). How can I convert? with mris_convert function I can
> not convert them. can someone help me?
>
> Thanks
>
> F
v6 will recognize and use all the manual edits from previous versions. I
don't think you need to copy aseg.mgz to aseg.presurf.mgz
On 03/01/2017 11:32 PM, Chris Adamson wrote:
> Is it possible to run Freesurfer 6.0 recon-all -all on a subject
> previously processed with 5.3 and have 6 utilise t
You can use that command, just remove annot_outline=1:
On 03/02/2017 07:18 AM, Xiuyi Wang wrote:
> Hi,
>
> I am learning Group Analysis using FreeSurfer 5.3 on Linux system.
>
> I followed the detailed instruction on the tutorial website.
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/G
what version are you using? I thought I fixed the missing-last-label
problem in v6
On 03/01/2017 06:42 PM, Antonin Skoch wrote:
> Dear Doug,
>
> thank you, adding --no-unknown indeed fixed the global shuffling of
> the label names. However, last line of .ctab seems not to be read this
> time
Bruce,
Main problem area that I can see is at coordinates [104,42,124].
My first attempt, I don't think I had the recon editing box checked when
I was editing the white matter, but I used a brush value of 255. My
second attempt I painted over the same voxels but with the recon editing
box checked
Hello FreeSurfer Experts/Community,I am currently working with NITRC (as a novice user) to build and investigate the operability of FreeSurfer v6.0 in their Computational Environment (NITRC-CE).We have been able to get a "recon-all" run to work, but we are failing to get the sub-calls -hippocampal-
Yes, their is a known issue with your version of Suse Linux and the freesurfer
5.3 license checking scheme. The issue was fixed in the latest release. If you
need to keep 5.3 then I can converse offline for a potential workaround to
getting it working on the server running Suse Linux.
> On M
Hello FreeSurfer Developers,
We are attempting to install Freesurfer 5.3 on a server. We have an odd
problem. When we run any FS command from this server we get a license
error: Invalid FreeSurfer license key found in license file
/opt/Ngs_analysis/programs/freesurfer/5.3/freesurfer/.license
But
I have GIFTI (.gii) format file resulting from segmentation with cat 12 (
toolbox of spm). How can I convert? with mris_convert function I can
not convert
them. can someone help me?
Thanks
Flavia Arduini
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Hi,
I am learning Group Analysis using FreeSurfer 5.3 on Linux system.
I followed the detailed instruction on the tutorial website.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
These are the commands that I typed:
freeview -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=
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