Hi everyone,
I have a couple of questions regarding the contents of
the summary file
generated by mri_surfcluster, and would be happy to get some help.
1) The Max value column, does it represent the SPM{t} value, SPM{z} value
or -log(p)[base 10].
2) Can the Tal{x,y,z}, if adj
Works. Thank you !
Flavio.
--- On Tue, 5/26/09, Nick Schmansky wrote:
From: Nick Schmansky
Subject: Re: [Freesurfer] Re: Transform orig.mgz image to native space
To: "Flavio Seixas"
Cc: "Bruce Fischl" , "Freesurfer Mailing List"
, t...@nmr.mgh.harvard.edu, "Doug Greve"
Date: Tuesday, May 2
try:
mri_convert orig.mgz -rl rawavg.mgz orig.nii
On Tue, 2009-05-26 at 18:10 -0700, Flavio Seixas wrote:
> The native data has (0.449219, 0.449219, 0.45) mm size and (512, 512,
> 356) voxels. The orig.mgz has (256, 256, 256) voxels. I would like to
> transform orig.mgz back to native data coord
I see. It's in scanner coords, but not the same voxel dimensions. Nick's
solution should do the trick
On Tue, 26 May 2009, Flavio Seixas wrote:
The native data has (0.449219, 0.449219, 0.45) mm size and (512, 512, 356)
voxels. The orig.mgz has (256, 256, 256) voxels. I would like to transform
The native data has (0.449219, 0.449219, 0.45) mm size and (512, 512, 356)
voxels. The orig.mgz has (256, 256, 256) voxels. I would like to transform
orig.mgz back to native data coordinates.
Best Regards,
Flavio.
--- On Tue, 5/26/09, Bruce Fischl wrote:
From: Bruce Fischl
Subject: Re: Tran
the data should already be in the native space, not talairach.
cheers,
Bruce
On Tue, 26 May 2009, Flavio Seixas wrote:
Hi Hii,
I'm beginner Freesurfer user. I segmented brain subcortical structures using Freesurfer
(recon-all). The process was concluded ok. How could I convert aseg.mgz and o
Hi Hii,
I'm beginner Freesurfer user. I segmented brain subcortical structures using
Freesurfer (recon-all). The process was concluded ok. How could I convert
aseg.mgz and orig.mgz back to native space? I've tried "mri_convert orig.mgz
orig.nii -ot nii --apply_inverse_transform transforms/talai
maybe it is really finished?
On Tue, 26 May 2009, Paula Diniz wrote:
I don`t have success!
[MacPro:~/trabalho_2_breno/CCl] paula% recon-all -s therezinha_maria -make
all
Subject Stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.2.0
Current Stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.2.0
I don`t have success!
[MacPro:~/trabalho_2_breno/CCl] paula% recon-all -s therezinha_maria -make
all
Subject Stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.2.0
Current Stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.2.0
Subject 'therezinha_maria': make all
make: Nothing to be done for `al
recon-all -s subjid -make all
Enviado do meu celular Nokia
-Msg original-
De: Paula Diniz
Enviada: 26/05/2009 17:47:04
Para: Freesurfer@nmr.mgh.harvard.edu
Assunto: [Freesurfer] when recon-all stoped
Hi
I was running recon-all -all when the computer was turned off. I can restart
the re
recon-all -s subj -make all
On Tue, 2009-05-26 at 17:47 -0300, Paula Diniz wrote:
> Hi
>
> I was running recon-all -all when the computer was turned off. I can
> restart the recon-all in the point that it stopped?How?
>
> Thanks
>
> 2009/5/15 Paula Diniz
> Hello!
>
> I
Hi
I was running recon-all -all when the computer was turned off. I can restart
the recon-all in the point that it stopped?How?
Thanks
2009/5/15 Paula Diniz
> Hello!
>
> I have to convert the aseg.mgz file to a minc file, but I lost the
> structure values reference.
> Where I can find a conver
Hi Doug,
I fixed the problem. i had given the path ../stats when I should have used
./stats.
Now it works:
[jdr...@trumpet mri]$ mris_anatomical_stats -mgz -f ./stats/lh.aparc.stats
-b -a ../label/lh.aparc.annot -cf ../label/aparc.annot.ctab convertedfile
lh
INFO: assuming MGZ format for
volumes
Hi Doug,
./stats/lh.aparc.stats does NOT exist, but it still seg faulted when I have
chmod'd -R 777 the mri directory recursively.
john
On Tue, May 26, 2009 at 3:43 PM, Douglas N Greve
wrote:
> Does ../stats/lh.aparc.stats exist and do you have write perms to the file
> and directory?
>
> John
Hi Doug,
It is writing to the trumpet directory which is not full.
It does write out the output file aparc.annot.ctab, but seg faults at the
end.
Here is the df -h output for the trumpet directory (775Gb are available):
[jdr...@trumpet label]$ df -h
FilesystemSize Used Avail Use% Mo
Does ../stats/lh.aparc.stats exist and do you have write perms to the
file and directory?
John Drozd wrote:
Hi Doug,
It is writing to the trumpet directory which is not full.
It does write out the output file aparc.annot.ctab, but seg faults at
the end.
Here is the df -h output for the trum
Hi Doug,
Thank you for your clarification. I checked Randy Buckner's paper, and it
did include the CSF based on my interpretation of the paper's Fig. 3 images
of the manual tracings in atlas space.
john
On Tue, May 26, 2009 at 3:08 PM, Douglas N Greve
wrote:
>
> The eTIV we report is not based
Can you verify that the disk it is writing to is not full?
Is this an average subject?
doug
John Drozd wrote:
Hello again,
Sorry, I forgot to include the required info:
john
FREESURFER_HOME: /trumpet/downloads/FreeSurfer/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4
The eTIV we report is not based on counting voxels inside the skull.
Instead, it is based on a statistical relationship between the TIV
computed from a manual segmentation and the talairach transfrom (see
Randy Buckner's paper). I don't know whether the original manual segs
included CSF (I as
Hello again,
Sorry, I forgot to include the required info:
john
FREESURFER_HOME: /trumpet/downloads/FreeSurfer/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0
RedHat release: Fedora release 10 (Cambridge)
Kernel info: Linux 2.6.27.21-170.2.56.fc10.x86_64 x86_64
Hello,
I have a question about the eTIV intracranial volume calculation.
My question is:
Does the eTIV intracranial volume include everything interior to the outer
pial surface
(excluding the skull, eyes, neck and dura), and does it also include the
CSF?
That's all.
Thank you for your time.
jo
tkmedit is crashing when I try to load a particular subject's
inner_skull.surf or outer_skull.surf surfaces. These files were created by
the MNE software, so my apologies if this question would be better suited
to mne_support. If I load from the command line I get the messages below
in the terminal
Hello,
I am running the reconall steps individually for a firts try.
I noticed that I get a segmentation fault when I run mris_anatomical_stats
as whown below:
[jdr...@trumpet mri]$ mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats
-b -a ../label/lh.aparc.annot -cf ../label/aparc.annot.ctab
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
In the article section of FreeSurfer wiki there is a paper about cortical
thickness in PMG. In that study we also analyzed, but still not published,
cortical dysplasia cases.
In some cases we made manual interventions (look at FreeSurfer wiki on
recon-all process.) to fix small segmentation err
Hi,
I've run the standard recon-all processing stream on a subject with a
fairly large (~ few cms) focal cortical dysplasia near the central
sulcus. On the MR scan the intensity's somewhere between gm & wm,
although it is clearly visible. The wm surface has pretty much missed
the whole thing
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