External Email - Use Caution
Hi list!
I was reading the documentation on mris_pmake (by the way, it is outdated,
the documentation still asks for --surface00, at least in 7.3.2), and I
would like to have a valid options.txt file to make it work with dsh (a
valid example .dsh*.yml
External Email - Use Caution
Hi!
Is there any way to write freeview screenshots when running Freeview as
part of a Docker container?
thanks!
Gari
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Thanks! Don't worry, I used it in Linux.
On Thu, 19 Jan 2017 at 18:40, wrote:
> The new version wont work in the FS5.3 framework. Its needs to be packaged
> within the development version for it to work.
>
> Whats the error? And does it only happen with one subject
Hi list,
mri_mcsim on FS5.3 is giving a strange error in osx 10.11, in the wiki a
newer Linux version is available and indicates to ask for other versions.
Is it possible to have the last osx version?
thanks!
Gari
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Freesurfer mailing list
Hi list,
is it possible to have multiple --meas files in mri_glmfit?
For example, for a group of 40 subjects, to check in every vertex if there
is a relation between CT and the t of a fMRI contrast.
Thanks!
Gari
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Freesurfer mailing list
t;
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_pmake
>
>
>
> On 11/28/2016 05:22 PM, Garikoitz Lerma-Usabiaga wrote:
> > Hi,
> > I am using the 2011 of mris_pmake and I've seen in the list that there
> > are newer versions.
> > I am using b
Hi,
I am using the 2011 of mris_pmake and I've seen in the list that there are
newer versions.
I am using both linux and mac.
It's giving several errors when computing distances in fsaverage (just in
some of the pairs), so I hope that the new version will be able to solve
them.
Thank you very
andards). Not sure
> that one is better than the other, but #2 is probably more like what is
> in the liturature.
>
>
> On 11/16/2016 04:53 PM, Garikoitz Lerma-Usabiaga wrote:
> > Hi all,
> > I have fMRI data in individual space, converted to individual surface
> > usin
Hi all,
I have fMRI data in individual space, converted to individual surface using
vol2surf and to fsaverage surface using surf2surf (commands [1] and [2]
below). With Matlab, I obtain the vertex with the maximum value: max_Vtx
and max_Vtx305. If I would like to obtain the MNI152 coordinate of
$ freeview
-Zeke
On May 9, 2015, at 3:09 AM, Garikoitz Lerma-Usabiaga gariko...@gmail.com
wrote:
Hi Nick!
just testing it in Yosemite and gives me this error, is there any
dependency I should consider?
Screen Shot 2015-05-09 at 09.05.53.png
On Fri, May 8, 2015 at 8:06 PM Nick Schmansky
Hi,
I have some volume ROIs in diffusion space (1-s and 0-s). I would like to
obtain, for example, the average FA values in that ROI.
I tried using mri_segstats, but it gives me an error, it needs a
segmentation volume.
mri_segstats --i dmri/dtifit_FA.nii.gz --mask
/2014 12:51 PM, Garikoitz Lerma-Usabiaga wrote:
Hi,
I have some volume ROIs in diffusion space (1-s and 0-s). I would like
to obtain, for example, the average FA values in that ROI.
I tried using mri_segstats, but it gives me an error, it needs a
segmentation volume.
mri_segstats --i dmri
space, the just run mri_label2vol to bring aseg
into the dti space.
doug
On 02/02/2014 05:24 AM, Garikoitz Lerma-Usabiaga wrote:
Hi Doug,
I've been reading the list and I ended with 4 steps to move from a
label to a mask in diffusion space (below). Is this correct? Is there
any other
Hi Doug,
I've been reading the list and I ended with 4 steps to move from a label to
a mask in diffusion space (below). Is this correct? Is there any other more
straightforward way? It should end with a binary mask in diffusion space (I
am using the anatorig2diff.bbr.dat created in the Tracula
/hippo_subfield_in_diffusion_space.nii
dmri.bedpostX/merged
dmri.bedpostX/nodif_brain_mask
If these all come from the output of tracula, aren't these all
in LAS orientation?
a.y
On Thu, 9 Jan 2014, Garikoitz Lerma-Usabiaga wrote:
Hi
dmri.bedpostX/nodif_brain_mask
If these all come from the output of tracula, aren't these all in LAS
orientation?
a.y
On Thu, 9 Jan 2014, Garikoitz Lerma-Usabiaga wrote:
Hi Anastasia,I want to use a hippocampal subfield as a seed in FSL. I am
having problems understanding how
Hi,
sorry to jump in, but maybe this solves your problem. What I've been doing
is:
1.- Convert the .mgz ROI in Freesurfer to .nii format in FSL: mri_convert
--in_type mgz --out_type nii --out_orientation RAS roi.mgz roi.nii
2.- Open the new roi.nii in mricron: mricron nu.nii -o roi.nii . Select
Hi Rujing,
About tksurfer visualization, we had the same problem, it was because the
graphic card in the server, you cannot do anything about it (well, install
a different one).
If I remember correctly, you need a graphic card that supports OpenGL.
Regards,
Gari
On Friday, December 20, 2013,
. Which build of freesurfer 5.3 and which build of the tracula
update do you have? Using our Centos 6 build, I was not able to replicate
your error.
a.y
On Wed, 11 Dec 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Anastasia,
I've got this error when running -prep Tracula step.
/usr/local
Hi list,
I am trying to visualize a .nii ROI coming from MEG, which is in Colin27
space.
I can visualize it perfectly in mricron and tkmedit with the following
command:
tkmedit -f path/to/spm8/canonical/single_subj_T1.nii -overlay MEG_ROI.nii
-fthresh 0.5
(single_subj_T1.nii is Colin27)
but when
...@nmr.mgh.harvard.eduwrote:
Try registering path/to/spm8/canonical/single_subj_T1.nii to Colin with
bbregister
doug
On 12/13/2013 11:09 AM, Garikoitz Lerma-Usabiaga wrote:
Hi list,
I am trying to visualize a .nii ROI coming from MEG, which is in
Colin27 space.
I can visualize it perfectly
...@nmr.mgh.harvard.eduwrote:
Try registering path/to/spm8/canonical/single_subj_T1.nii to Colin with
bbregister
doug
On 12/13/2013 11:09 AM, Garikoitz Lerma-Usabiaga wrote:
Hi list,
I am trying to visualize a .nii ROI coming from MEG, which is in
Colin27 space.
I can visualize it perfectly
Mikel_SingleSubject_to_Colin.dat -om
final.reg.dat
Then use final.reg.dat
doug
On 12/13/2013 11:56 AM, Garikoitz Lerma-Usabiaga wrote:
Hi Doug,
this is what I did. This system worked in other occasions. Could it be
the problem how the volume MEG_ROI.nii was created? My colleague had a
Matlab matrix
Hi Anastasia,
I've got this error when running -prep Tracula step.
/usr/local/freesurfer/bin/dmri_motion: error while loading shared
libraries: libnetcdf.so.6: cannot open shared object file: No such file or
directory
We have RedHat 6 (I tried in 2 different machines). Do you think it is some
Hi list,
I obtained cortical thickness and volumetric results before and after
correcting them for defects.
I just did some wm edits and mostly controls points in the top of the head
(some subjects had less signal so I put control points in order to allow
for a good surface reconstructions).
I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any
reason to not use this version in your CentOS 6, if you have some other
requirements maybe Nick or Zeke could help you better, I am just an user :)
On Wed, Nov 20, 2013 at 6:47 PM, pablo najt pablon...@hotmail.com wrote:
Hi,
I had a subject already run through recon-all.
After making recon-all -s ID -hippo-subfields
or
recon-all -s ID -hippo-subfields -make all
it is failing.
It is the first subject ever failing with the hippo-subfields. The rest of
the subjects are ok. This subject is properly segmented
Hi Anastasia,
could explain a little bit more what do you check exactly here?
What I usually look at is dlabel/diff/aparc+aseg.bbr.nii.gz, overlaid
on dmri/dtifit_FA.nii.gz.
Which would be the freeview command to visualize it?
Thanks!
Gari
On Mon, Oct 14, 2013 at 11:12 PM, Anastasia Yendiki
Hi,
Did you try changing the folder name?
tutorial/data/dti/a226A/226A/
Maybe that's what it has to start with a letter?
Just guessing. ..
On Oct 13, 2013 12:02 AM, Michael Datko mikeda...@gmail.com wrote:
Hello,
I have been trying to set up a working Tracula configuration file and I
keep
longitudinal fasciculus.
a.y
On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Anastasia,
I was testing just with one subject and it finished the -prep part with
error.
Please find attached the trac-all.log file.
As this is a test user you will see some other invocations of trac-all
. The centos6 build uses a newer version of gcc
which has optimization options not available on the version gcc for the
centos4 build, and that makes for run-time differences in recon-all.
-Zeke
On 09/26/2013 08:19 AM, Garikoitz Lerma-Usabiaga wrote:
Hi,
I have two identical Red Hat 6 boxes
Hi,
I have two identical Red Hat 6 boxes, to run recon-all-s.
I just realized that in one of those I had freesurfer 5.3 for CentOS4 and
in the other one I had freesurfer 5.3 for CentOS6.
I have one experiment were subjects used boxes indistinctly.
According to how the software is built, should
Hi Anastasia,
I am setting up the dmrirc file to run Tracula. I am using Siemens Dicoms,
so I did not specify any setting for bval and bvec, but when trac-all -prep
starts running it gives the following error: mv: cannot stat
'paths.../SubjectID/dmri/dwi_orig_flip.mghdti.bvecs': No such file or
Hi Doug,
just a very naive question about coordinate change: why do we need the
fourth component? I mean, shouldn't be the transformation matrix 3x3
instead of 4x4 for a coordinate change in 3D space?
thanks!
Gari
On Wed, Sep 11, 2013 at 12:52 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
Hi Daniel,
you can use mri_surfcluster.
br,
Gari
On Mon, Sep 9, 2013 at 8:25 PM, Yang, Daniel yung-jui.y...@yale.edu wrote:
Dear all,
Is there a way to convert .mgh to .label? My .mgh is a ROI file from
qdec-based group analysis and I don't want to draw the ROIs manually.
Thanks!
, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
Hi Gari, you can use mri_annotation2label
doug
On 8/14/13 3:00 PM, Garikoitz Lerma-Usabiaga wrote:
Hi list,
we have a cluster that survived the Monte Carlo simulation for thickness,
and we would like to obtain more data from that exact cluster
is too trivial!
Gari
On Thu, Aug 15, 2013 at 7:32 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Give it the annotation (.annot) file
On 08/15/2013 01:26 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks Doug!
Could you give me an example please? I cannot get it to work, with this
command
Hi list,
we have a cluster that survived the Monte Carlo simulation for thickness,
and we would like to obtain more data from that exact cluster (volume for
example), is it possible to automatically create a label from that cluster?
If I use mri_binarize or mri_cor2label is not working (I
)
doug
On 7/1/13 2:45 PM, Garikoitz Lerma-Usabiaga wrote:
Hi,
I want to obtain volume statistics from a ROI in fsaverage.
I have register.dat and a .nii file (the ROI), but I don't now how to get
to the .label.
The last try has been:
mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/label
Hi,
I want to obtain volume statistics from a ROI in fsaverage.
I have register.dat and a .nii file (the ROI), but I don't now how to get
to the .label.
The last try has been:
mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/label/ROI.nii
--o $SUBJECTS_DIR/fsaverage/label/ROI.mgh
--reg
Hi again,
is it possible to use mri_convert with a register.dat to create a .mgh
volume in the registered space?
any help would be appreciated...
thanks!
Gari
On Mon, Jul 1, 2013 at 8:45 PM, Garikoitz Lerma-Usabiaga
gariko...@gmail.com wrote:
Hi,
I want to obtain volume statistics from
Hi list,
is it possible to create a ROI in an inflated surface within freeview or do
I have to use tksurfer?
It seems that I only can edit volume files.
After exploratory mri_glmfit, I want to outline a ROI in fsaverage inflated
surface and afterwards create a label to obtain CT averages per
Hi list,
I am interested in a Cortical Thickness analysis in the Visual Word Form
Area.
I have been suggested to use a MNI152 coordinate and make an sphere (circle
in this case) of 5mm around it.
Has anybody got any experience or any recommendation on how to establish
the visual word form area
of control points in the WM up there should help a lot.
cheers
Bruce
On Thu, 6 Jun 2013, Garikoitz Lerma-Usabiaga wrote:
Hi list,we have some subjects with acquisition problems.
Do you think it is possible to save this two subjects, and if so, how?
They have been run with:
recon-all -i
/glerma/freesurfer/subjects
solved the problem.
Do you think this is a problem with fs resolving sym links? We haven't
found any problem with matlab or fsl.
thanks again!
Gari
On Sat, May 11, 2013 at 12:46 AM, Garikoitz Lerma-Usabiaga
gariko...@gmail.com wrote:
Yes,
first two lines
with sym links, but what you have is
definitely confusing! Is there any reason you have it that way? As a rule
of thumb, i'd keep things as simple as possible.
From: Garikoitz Lerma-Usabiaga [gariko...@gmail.com]
Sent: Saturday, June 01, 2013 4:21 PM
=L.mgz -cam azimuth 180
Let me know if this helps.
Cheers,
E
On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote:
There is a screenshot option -ss from the command-line. Run 'freeview
-h' will show you all the available options.
Ruopeng
On May 31, 2013, at 6:16 AM, Garikoitz Lerma
.
Ender
On 05/31/2013 11:05 AM, Garikoitz Lerma-Usabiaga wrote:
Thanks!
I can visualize the 3D renders of interest with different colors, but
from freeview -h I couldn't get the following: is it possible to
automatize the File Save movie frames option?
Thanks again!
Gari
On Fri
Hi,
Has anybody got problems using FS with NFS v4?
We cannot write subjects if the SUBJECTS_DIR is in a NFS v4 system.
Many thanks,
Gari
-- Forwarded message --
From: Garikoitz Lerma-Usabiaga gariko...@gmail.com
Date: Tue, May 7, 2013 at 5:25 PM
Subject: NFS v4 on CentOS 5.4
-- Forwarded message --
From: Garikoitz Lerma-Usabiaga gariko...@gmail.com
Date: Tue, May 7, 2013 at 5:25 PM
Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2
To: Freesurfer freesurfer@nmr.mgh.harvard.edu
Hi FS experts,
we have changed our file systems to NFS v4
?
We cannot write subjects if the SUBJECTS_DIR is in a NFS v4 system.
Many thanks,
Gari
-- Forwarded message --
From: Garikoitz Lerma-Usabiaga gariko...@gmail.com
Date: Tue, May 7, 2013 at 5:25 PM
Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2
To: Freesurfer
?
Can you output
# ls -l $SUBJECTS_DIR
I assume that since you say other programs can write to the filesystem, it
is mounted properly, but can you show what is in /etc/fstab? i.e. make sure
you see rw instead of ro.
On 05/10/2013 05:55 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks
you paste the output of ls -l $SUBJECTS_DIR, so we can see what
the permissions are? You may also want to paste the output of the parent
directory as well.
On 05/10/2013 06:18 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks Chris,
ls -l $SUBJECTS_DIR: it works
This is the output of the command
Hi FS experts,
we have changed our file systems to NFS v4 and we found that FS cannot
write to it (I mean, FS installed in an app server and subjects in the file
system is not working).
Last new I have is that FS in CentOS could read but not write and in Red
Hat could not write or read.
Is it a
Hi Priyanka,
You can download it from the Surfrend web page and then recon-all it with
the version you want (don`t use the -i, just the -s with the subject name
you choose).
Regards,
Gari
On May 7, 2013 10:56 PM, Priyanka bme.priya...@gmail.com wrote:
Hello FreeSurferusers,
Has anyone
the Surfrend, and found there
was no entry for input of register file during the processing.
Looking forward to your reply.
Best wishes.
zhiliang
At 2013-03-27 13:29:01,Garikoitz Lerma-Usabiaga gariko...@gmail.com
wrote:
Hi,
In my case transformation to fsaverage did not work very well. What I did
Hi,
In my case transformation to fsaverage did not work very well. What I did
was:
- from Surfrend page download Colin 27 subject and transform it to the
latest version (now 5.2)
- with bbregister obtain register.dat between this Colin 27 subject and
SPM-s single subject t1.nii, which is the 2mm
Regarding the -mprage tag, we read in the recon-all help that:
-mprage : assume scan parameters are MGH MP-RAGE protocol
-washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol.
both mprage flags affect mri_normalize and mri_segment,
and assumes a
of a subject to MNI305 space. You would
reverse that to go from MNI305 space to another subject's RAS space thus
allowing a RAS-RAS transform. If you have a surface overlay for a subject,
you can use mri_surf2surf to transfer it to another subject.
doug
On 3/12/13 11:54 PM, Garikoitz Lerma-Usabiaga
to transfer it to another subject.
doug
On 3/12/13 11:54 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks Doug,
I've seen the page, but I understand that everything is within the same
subject. I want to find the equivalencies between subjects. I mean, the
plane y = 30 in fsaverage, will correspond
/qdec_snowleopard
-Zeke
Update: tkmedit 5.1 is working with Xquartz installed in Snow Leopard,
tkmedit 5.2 is not working again.
Any suggestion?
thanks,
Gari
On Tue, Mar 12, 2013 at 1:16 PM, Garikoitz Lerma-Usabiaga
gariko...@gmail.com wrote:
Hi FS experts,
I just installed 5.2 for Snow
Hi FS experts,
I just installed 5.2 for Snow Leopard in a machine who already had 5.1.
When running tkmedit in 5.1 X11 works well, but when running it from 5.2 it
gives the following error:
BRODMANN80:~ glerma$ tkmedit bert T1.mgz
dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib
Update: tkmedit 5.1 is working with Xquartz installed in Snow Leopard,
tkmedit 5.2 is not working again.
Any suggestion?
thanks,
Gari
On Tue, Mar 12, 2013 at 1:16 PM, Garikoitz Lerma-Usabiaga
gariko...@gmail.com wrote:
Hi FS experts,
I just installed 5.2 for Snow Leopard in a machine who
Hi!
how can I translate a coordinate in talairach space of one subject
(Colin27), to every subject in a study? For example, I would like to know
where is the coordinate Y = +30 Talairach of Colin27 in Subject_00,
Subject_01, etc.
Should I use vol2vol to create a volume for every subject? Is there
...@nmr.mgh.harvard.edu wrote:
Hi Gary, check out this wiki page and let me know if you still have
questions
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
doug
On 3/12/13 8:04 PM, Garikoitz Lerma-Usabiaga wrote:
Hi!
how can I translate a coordinate in talairach space of one subject
(Colin27
Hi Bruce,
is there any recommended protocol for T2 acquisition to be used in the 5.2
recon-all stream?
Should we used the same voxel size as the T1? (we are using 1 mm3 right
now).
If it is going to improve the skull striping and pial surface creation, we
might acquire specific T2 images just
=FreeSurfer_Suggested_Morphometry_Protocols.pdf
Hi Gari
we use a bandwidth and readout matched (to our multi-echo mprage)
T2-SPACE
with a FLAIR inversion pulse. Andre (ccd) can give you the details
cheers
Bruce
On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Bruce,is there any
at 9:48 AM, Garikoitz Lerma-Usabiaga
gariko...@gmail.com wrote:
Thanks Juan Eugenio,we have visually inspected the segmentations,
and we observe that the volume differences between aseg and
hippo-subfields are constants among subjects, and consistent in
both left and right
Hi fs experts,
I have this error every time I try tu run aparcstats2table :
File /home/glerma/fs/52/freesurfer/bin/aparcstats2table, line 221
with open(o.qdec, 'rb') as f:
^
SyntaxError: invalid syntax
it appears each time I run aparcstats2table, even when I write:
Hi Nick!
this is the version:
Centos 4 32b or 64b (x86_64)
(Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64
x86_64 x86_64 GNU/Linux)
and the python version is:
Python 2.4.3 (#1, Feb 22 2012, 16:05:45)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2
(python --version
Thanks Nick!!
is it a solution to run 5.2 aparcstats2table (Snow Leopard) in another
machine, accessing the data from a network drive?
or is it a solution to run the aparcstats2table provided in 5.1 in the same
machine, but accessing the data created by the 5.2 version?
many thanks again for
$FREESURFER_HOME/bin
tar xf stats2tab.tar
Thanks again,
Nick
On Mon, 2013-02-11 at 17:06 +0100, Garikoitz Lerma-Usabiaga wrote:
Thanks Nick!!
is it a solution to run 5.2 aparcstats2table (Snow Leopard) in another
machine, accessing the data from a network drive?
or is it a solution to run
Hi all,
is this tool going to be available to download with the 5.2? I am
interested in it too.
thanks!
Gari
On Thu, Feb 7, 2013 at 3:09 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Luisa
yes, Mert Sabuncu and Koen Van Leemput have developed a MVPA algorithm
called RvoxM that I
Hi FS experts,
I just downloaded the latest version again today:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0.tar.gz(
4.2 GB 1/28/13 9:47:00 PM, fsaverage has been copied to /subjects/myproject
location)
When running this
Hello Anastasia and Stefano,
Maybe is of little help but I wanted to let you know that I've
experienced the same problem.
Using exactly the same data, and using 5.1 in both cases, and having
the locale set up as specified according to a solution in the mailing
list:
- in cent os 4 it is working
-
Hi FS experts,
I read that the current dev version for recon-all is going to be the same
to the 5.2 version, so I started a new project with the dev version (in
CentOS 4).
I have this very strange error that I am unable to interpret, when running
mpr2mni305 in one case the target is specified as
at 7:37 AM, Garikoitz Lerma-Usabiaga
gariko...@gmail.com wrote:
Hi Donald and everybody,
I created AAL .mgh and .label-s in FS Colin27 space, if anybody is
interested please drop me a line.
best regards!
Gari
On Thu, Jul 12, 2012 at 11:12 PM, MCLAREN, Donald
mclaren.don
Hi Donald and everybody,
I created AAL .mgh and .label-s in FS Colin27 space, if anybody is
interested please drop me a line.
best regards!
Gari
On Thu, Jul 12, 2012 at 11:12 PM, MCLAREN, Donald
mclaren.don...@gmail.comwrote:
Has anyone created an AAL label file for Freesurfer? I've done some
looking across
different methods. the size of the effect is very small, about 1.5%. Do you
see this as a problem?
doug
On 09/28/2012 05:14 AM, Garikoitz Lerma-Usabiaga wrote:
Hi Doug,
I think that the differences are significant enough, but just in case
please find attached an excel file
processing streams correctly? If so, what is
the other processing stream (given in this kind of detail)?
doug
On 09/25/2012 04:43 PM, Garikoitz Lerma-Usabiaga wrote:
I have both. In origin, the ROI-s are 2mm volume based .nii that I convert
to FS .mgh with register.dat I obtained with bbregister
into it and why?
doug
On 09/19/2012 06:15 PM, Garikoitz Lerma-Usabiaga (Gari) wrote:
Dear Freesurfers,
We've been comparing 2 different methods to obtain CT averages for 4
Volume ROI-s (volume ROI-s were in Colin27 space).
We've used the 40 buckner subjects for the comparisons.
METHOD
average CT intensities over them? Are the ROIs
volume-based or surface-based?
doug
On 09/25/2012 05:09 AM, Garikoitz Lerma-Usabiaga wrote:
Hi Doug,
many thanks for your answer, I try to detail it more:
1.- bbregister is registering two Colin27 brains. First one is a 2mm
found in spm
Dear Freesurfers,
We've been comparing 2 different methods to obtain CT averages for 4 Volume
ROI-s (volume ROI-s were in Colin27 space).
We've used the 40 buckner subjects for the comparisons.
METHOD L2L:bbregister mri_vol2surf (mgh) mri_binarize (mgh)
mri_cor2label (label)
Hi Li,
there you go,
Gari
https://docs.google.com/open?id=0Byf71TWfovledFhJYWN2cGtHV00
On 2012-09-15, at 19:38, Kong, Li li.k...@med.uni-heidelberg.de wrote:
Hi Gari,
I saw your email to Alex about your method obtaining statistics from multiple
subjects with Python script. Could you
Hi Alex,
I am using the same method, I created a Python script to automate it for
multiple users.
Basically, if you give it a file with all the subject ID-s, it maps labels with
mri_label2label, obtains statistics with mris_anatomical_stats and writes all
the stats in a single file.
You
, but it will make a difference
in your second call below.
doug
On 09/09/2012 06:13 PM, Garikoitz Lerma Usabiaga wrote:
Dear freesurfers,
I am trying to create .mgh labels in order to obtain CT averages from
several subjects.
I register the ROI-s with bbregister and I get the .nii which renders
Dear freesurfers,
I am trying to create .mgh labels in order to obtain CT averages from several
subjects.
I register the ROI-s with bbregister and I get the .nii which renders nicely in
tksurfer:
tksurfer Surfrend_Colin127 lh inflated -overlay
correction. Certainly it failed
in this case.
cheers
Bruce
On Fri, 10 Aug 2012, Garikoitz Lerma Usabiaga wrote:
Thanks for the answer Bruce,
it is still running, so I killed the process.
When using two individual structural images separately, the recon-all
process was OK. When I
overlap.
cheers
Bruce
On Mon, 6 Aug 2012, Garikoitz Lerma Usabiaga wrote:
Hi Bruce,
thanks for your answer.
I am mapping a volume ROI (BA45) from SPM in MNI 152 space to fsaverage
(the result is the red ROI). The problem is that:
- when I load the BA45.label from FS in order
by FreeSurfer, or mapping them from MNI space? In either
case you can get overlap unless you pick the most probably label at each
point.
cheers
Bruce
On Mon, 6 Aug 2012, Garikoitz Lerma Usabiaga wrote:
Hi freesurfers experts,
this is (please check attached image) the best I got when trying
Hi FS experts,
I've run recon-all -i file -s subject -qcache -measure thickness -all to:
- 18 subjects, session 1 T1
- same 18 subjects, session 2 T1
and everything went well.
Then I copied the subject_id_session/mri/orig/001.mgz-s to
subject_id/mri/orig/001.mgz and 002.mgz, and run the same
Hi freesurfer experts,
I want to use a volume based MNI152 ROI in Freesurfer, when I check it over
fsaverage with the following command the ROI is not in the correct position...:
tkmedit fsaverage T1.mgz -overlay ROI45.nii -overlay-reg
$FREESURFER_HOME/average/mni152.register.dat
And I have
and 305?
thanks!
Gari
On 2012-07-17, at 19:43, Douglas N Greve wrote:
Hi Gari,
Does it appear in the right place if you run
tkmedit -f $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz -overlay ROI45.nii
doug
On 07/17/2012 01:20 PM, Garikoitz Lerma Usabiaga wrote:
Hi freesurfer experts,
I
image (select:
avg152T1.nii) Save it (name: ROI45.nii)
2.- I follow exactly the same steps as the tutorial, but in step 3) when I
check the ROI in the inflated surface, it is clearly out of place...
Thank you very much in advance,
Gari
Garikoitz Lerma Usabiaga
Predoctoral Researcher
www.bcbl.eu
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