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Thank you very much!
-原始邮件-
发件人:"Fischl, Bruce R.,PHD"
发送时间:2022-10-22 23:12:37 (星期六)
收件人: "Freesurfer support list"
抄送:
主题: Re: [Freesurfer] mris_ca_label -l can not generate lh.BN_Atlas.annot
It looks like you
It looks like you have a space between “/usr/local/freesurfer/subjects/1268”
and “/label/lh.BN_Atlas.annot”
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ???
Sent: Saturday, October 22, 2022 11:06 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_ca_label -l can not
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Hi,
When I used "mris_ca_label -l
/usr/local/freesurfer/subjects/1268/label/lh.cortex.label 1268 lh
/usr/local/freesurfer/subjects/1268/surf/lh.sphere.reg
/usr/local/freesurfer/subjects/lh.BN_Atlas.gcs
/usr/local/freesurfer/subjects/1268 /label/lh.
are they currently labeled 0? Where did you get your color LUT from?
On Wed,
6 Mar 2019, Jörg Stadler wrote:
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Hi Bruce,
this did not change anything. But I tried the process of mris_ca_train,
mris_ca_label with lh.oasis.chubs.annot and this worked fine.
A c
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Got it :)
filling the unassigned vertices with 'unknown' using tksurfer solved my
problem.
cheers,
Joerg
> Hi Bruce,
> this did not change anything. But I tried the process of mris_ca_train,
> mris_ca_label with lh.oasis.chubs.annot and this work
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Hi Bruce,
this did not change anything. But I tried the process of mris_ca_train,
mris_ca_label with lh.oasis.chubs.annot and this worked fine.
A closer look to my source annot file from mris_seg2annot showed that
the label 'unknown' is missing.
How c
Hi Joerg
I'm not positive that I understand, but have you tried giving
mris_ca_label the switch:
mris_ca_label -l $SUBJECTS_DIR/$subject/label/$hemi.cortex.label ...
that should remove non-cortical regions from your output annot
cheers
Bruce
On Tue,
5 Mar 2019, Jörg Stadler wrote:
this order.
>>
>>
>>
>> best,
>>
>> Andrew
>>
>>
>>
>>
>>
>> From: on behalf of
>> Rosemary Nicholas
>> Reply-To: FS Help
>> Date: Monday, July 23, 2018 at 1:22 PM
>> To:
,
Andrew
From: on behalf of
Rosemary Nicholas
Reply-To: FS Help
Date: Monday, July 23, 2018 at 1:22 PM
To: FS Help
Subject: [Freesurfer] mris_ca_label seed
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Hello,
I am running a dataset
*Reply-To: *FS Help
> *Date: *Monday, July 23, 2018 at 1:22 PM
> *To: *FS Help
> *Subject: *[Freesurfer] mris_ca_label seed
>
>
>
> *External Email - Use Caution*
>
> Hello,
>
>
>
> I am running a dataset through version 6.0 of Freesurfer on Lin
vertices in a random order to help prevent any spatial ordering effects, so the
given seed will initialize this order.
best,
Andrew
From: on behalf of Rosemary Nicholas
Reply-To: FS Help
Date: Monday, July 23, 2018 at 1:22 PM
To: FS Help
Subject: [Freesurfer] mris_ca_label seed
External Email - Use Caution
Hello,
I am running a dataset through version 6.0 of Freesurfer on Linux,
extracting results for both the Desikan atlas and our own atlas. When
extracting the stats for our atlas, the results were varying considerably
(sometimes up to 10%) in test-re
External Email - Use Caution
Hello,
I am running a dataset through version 6.0 of Freesurfer on Linux,
extracting results for both the Desikan atlas and our own atlas. When
extracting the stats for our atlas, the results were varying considerably
(sometimes up to 10%) in test-ret
Thanks . Its working now.
___T_
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: 11 April 2017 16:48
To: Freesurfer support list
Subject: Re: [Freesurfer
when you run mris_ca_train use -t and it will embed it
in the .gcs file
On Tue, 11 Apr 2017, Das S. wrote:
> Hi,
> I have created a color table, an annot file and a .gcs file( attached with
> the mail).
> But when I am trying to execute mris_ca_label with my own .gcs file I am
> getting the e
Hi Bruce,
I want to check the results and do some edit if possible.
What is the possible reason?
Thanks,
Haitao
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Why don't you run recon-all -all instead?
On Aug 30, 2011, at 10:31 PM, Haitao Ge wrote:
> Hi all,
>
> I have run FS one step by one step. When i goto mris_ca_label, i got
> something error. I dont know which path should i goto to run this command.
>
> When i goto $SUBJECTS_DIR or $SUBJE
Hi all,
I have run FS one step by one step. When i goto mris_ca_label, i got something
error. I dont know which path should i goto to run this command.
When i goto $SUBJECTS_DIR or $SUBJECTS_DIR/subj/, i will get the following
information
MRISreadVertexPosition(lh.spere.reg): could not ope
yes, that's what -make all will do (it checks timestamps to see what needs
to be rerun)
On Mon, 15 Feb 2010, Alessandro D.
Gagliardi wrote:
I wanted to avoid using recon-all because it generally takes so much
time, but from your message it sounds like it will only redo the tasks
that need re
I wanted to avoid using recon-all because it generally takes so much
time, but from your message it sounds like it will only redo the tasks
that need redoing. Is that correct?
Thanks,
-Alessandro
On Sat, Feb 13, 2010 at 4:28 PM, Bruce Fischl
wrote:
> Hi Alessandro,
>
> usually that means that t
Hi Alessandro,
usually that means that the smoothwm is out of date with the sphere.reg.
You can run mris_euler_number on both to make sure they have the same
number of vertices, faces and edges. Or you can just run
recon-all -s $subject -make all
which will rebuild things if it needs to
cheer
Dear Freesurfers,
I just upgraded to the latest version of Freesurfer
(leopard-i686-stable-pub-v4.5.0) and I want to rerun mris_ca_label to
generate ?h.aparc.a2009s.annot files. I figured I would just run the
command described at
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable, namely:
Andy,
Possibly the colortable wasnt saved in the .gcs file. I've attached a
couple scripts we use to create our .gcs files. The first,
create_aparc_edited_annot, creates a .annot file from your labels. Note
that all labels are explicitly listed. Then, the script
build_desikan_killiany_gcs crea
send us your mris_ca_train command line. It should specify the location
of the color lookup table (e.g. surface_labels.txt) to include in the
.gcs file, which will then put it into the automated labeling files
(.annot) for tksurfer to read.
Bruce
On Tue, 26 May 2009 xfore...@ucla.edu wrote:
Dear Freesurfer Experts,
I was able to use mris_ca_train to produce a atlas (.gcs) file with all the
labels I am interested in, and I also modified the surface_labels.txt in the
freesurfer folder so only the labels I am interested are listed on the
txt file.
however, when I try to use mris_c
Hi Satra,
there is a random element to it. The GCSANclassify: could not find GCS
for node 0! was a bug that somehow got into the atlas, and has been fixed.
Do the outputs look pretty much the same?
cheers,
Bruce
On Wed, 16 Nov 2005, Satrajit Ghosh wrote:
I'm noticing some discrepancies bet
I'm noticing some discrepancies between the 64 bit and the 32 bit version of
mris_ca_label. I've shown the output from the 64 bit version and the 32 bit
version operating on the same subject. I'm using are the dev versions for
centos from the download site.
To note:
1. In the 64 bit version I get
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