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I was reading the documentation on mris_pmake (by the way, it is outdated,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 w
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@nmr.mgh.harvard.edu
https://mail.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 data, or all
> subjects?
>
> >
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
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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@nmr.
r.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 both linux and mac.
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 much
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
> > using vol2surf and to fsaverage surface us
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 thi
HOME/SetUpFreeSurfer.sh
> $> freeview
>
> -Zeke
>
>
> On May 9, 2015, at 3:09 AM, Garikoitz Lerma-Usabiaga
> wrote:
>
> Hi Nick!
> just testing it in Yosemite and gives me this error, is there any
> dependency I should consider?
>
>
>
>
>
>
&
> On 02/24/2014 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 n
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
FSL_waypoint2Hipplh.unc_AS_avg33
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 dif
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 proc
obtain the FA values in order to correlate with behavior.
Thanks again!
Gari
On Mon, Jan 13, 2014 at 7:55 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Gari - Yes, fslmaths should be able to do it, with -thrp 20.
>
> a.y
>
>
> On Mon, 13 Jan 201
umes.
>
> On Sat, 11 Jan 2014, Garikoitz Lerma-Usabiaga wrote:
>
> Hi Anastasia,the problem is with mri/hippo_subfield_in_
>> diffusion_space.nii,
>>
>> which originally is mri/hippo_subfield.mgz, the output of running
>> recon-all
>> -hippo-subfields. So as far
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 Anastasia,I want to use a hipp
--steplength=0.5 -P 5000 --opd
On Thu, Jan 9, 2014 at 6:48 PM, Douglas N Greve
wrote:
>
> On 01/09/2014 12:45 PM, Garikoitz Lerma-Usabiaga wrote:
> > Hi Anastasia,
> > I want to use a hippocampal subfield as a seed in FSL. I am having
> > problems understanding ho
Hi Anastasia,
I want to use a hippocampal subfield as a seed in FSL. I am having problems
understanding how to change spaces around...
1.- Is this command ok?
mri_vol2vol --mov dmri/dtifit_FA.nii.gz --targ
mri/hippo_subfield_in_anatomical_space.mgz --inv --interp nearest --o
mri/hippo_subfield_in_
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 i
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, Ruji
recently. 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 go
o_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
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.
> >
>
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.
> >
>
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
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
mi
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).
Whe
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 wrote:
> Dear Gari,
> Thank you
Hi Pablo,
you shouldn't mix different OS-s or software version in the same study
(Gronenschild,
E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N.,
van Os, J., & Marcelis, M. (2012). The effects of FreeSurfer version,
workstation type, and Macintosh operating system version on
Hi Marcos,
I don' t know if you are trying to the same as me, but I just divided the
hippocampus with matlab and then treat each segment as an individual file,
from lh_HPC.mgz to lh_head_HPC.mgz, lh_body_HPC.mgz and lh_tail_HPC.mgz.
You can threshold those files and binarize, or you can leave their
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 (tkmedit
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" wrote:
> Hello,
> I have been trying to set up a working Tracula configuration file and I
> keep getting an error:
6 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,
>>
corticospinal, uncinate, inferior 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
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 I
a.y
>
> On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
>
> 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
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
dir
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 wrote:
> Hi Yang, I've computed
Hi Daniel,
you can use mri_surfcluster.
br,
Gari
On Mon, Sep 9, 2013 at 8:25 PM, Yang, Daniel 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!
> Daniel
> --
> Yun
on is too trivial!
Gari
On Thu, Aug 15, 2013 at 7:32 PM, Douglas N Greve
wrote:
> 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
, Douglas Greve wrote:
>
> 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
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 understa
spec --fstarg (no arguments)
> 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.
>
&
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 sta
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
$SUBJECTS_DIR/fsav
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 ever
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 f
Hi list,
I've been creating control points and I got the following error:
MRIwriteControlPoints(/home/glerma/freesurfer/subjects/TNT/TNT_solosubs/S_11/tmp/control.dat):
could not open file
No such file or directory
I created the /tmp/ folder by hand and then it created the control.dat file
prope
? A
> couple 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 thi
er had any problems 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]
>
g-m/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,
>
shut that window the next freeview window pops up and I do the
> same.
>
> 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 cou
s up and I do the
> same.
>
> 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 pos
e command-line. Run 'freeview
> -h' will show you all the available options.
> >
> > Ruopeng
> >
> > On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga <
> gariko...@gmail.com> wrote:
> >
> > > Hi list,
> > > is it possib
Hi list,
is it possible to automate Freeview automation from the command line?
I want to automatically render 3D images of the hippocampus (I have a
separate volume, based on hippo-subfields) and have an image for all
subjects for quality checking.
thanks!
Gari
___
wrote:
> Can 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 $SU
? Is your user an NIS account?
>
> Can you output
> # ls -l $SUBJECTS_DIR
>
> I assume that since you say other programs can write to the filesystem, it
> is mounted properly, but can you show what is in /etc/fstab? i.e. make sure
> you see "rw" instead of "ro".
gt; >> Gari,
> >>
> >> At the NMR Center we use NFS v4 without problems with freesurfer. Is
> >> the
> >> SUBJECTS_DIR writable? Note that in the default freesurfer
> >> distribution,
> >> the freesurfer/subjects directory is not writabl
if the SUBJECTS_DIR is in a NFS v4 system.
> >
> > Many thanks,
> > Gari
> >
> > -- Forwarded message --
> > From: Garikoitz Lerma-Usabiaga
> > Date: Tue, May 7, 2013 at 5:25 PM
> > Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2
&
Hi,
Has anybody got problems using FS with NFS v4?
We cannot write subjects if the SUBJECTS_DIR is in a NFS v4 system.
Many thanks,
Gari
-- Forwarded message --
From: Garikoitz Lerma-Usabiaga
Date: Tue, May 7, 2013 at 5:25 PM
Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2
To
Hi Priyanka,
You can download it from the Surfrend web page and then recon-all it with
the version you want (don`t use the -i, just the -s with the subject name
you choose).
Regards,
Gari
On May 7, 2013 10:56 PM, "Priyanka" wrote:
> Hello FreeSurferusers,
>
>
> Has anyone processed ICBM or Coli
Hi FS experts,
we have changed our file systems to NFS v4 and we found that FS cannot
write to it (I mean, FS installed in an app server and subjects in the file
system is not working).
Last new I have is that FS in CentOS could read but not write and in Red
Hat could not write or read.
Is it a kn
Sorry about my previous email, it seems I downloaded it three times, it is
installing ok now...
On Sun, Apr 14, 2013 at 8:02 PM, Garikoitz Lerma-Usabiaga <
gariko...@gmail.com> wrote:
> I cannot download it, do you think the problem is on my side?
>
> Terminal paste:
>
>
I cannot download it, do you think the problem is on my side?
Terminal paste:
Last login: Wed Apr 10 22:01:36 on ttys000
iMacGari2:~ gari$ curl -O
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0/freesurfer-Darwin-lion-stable-pub-v5.2.0.dmg
% Total% Received % Xferd Average Spee
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"
wrote:
Hi,
In my case transformation to fsaverage did not work very well. What I did
was:
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 v
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 da
RAS 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
>
>
>
opard:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/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,
>> G
ansfer 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
rote:
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), to every sub
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
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
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
Referenced
er.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&do=get&target=FreeSurfer_Suggested_Morphometry_Protocols.pdf>
>>
>>
>> Hi Gari
>>>
>>> we use a bandwidth and readout matched (to our multi-echo mprage)
>>> T2-SPACE
>>>
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 to
Brain &
>> Department of Psychology
>> University of California, Davis
>> 530.747.3805
>>
>>
>> On Tue, Feb 26, 2013 at 9:48 AM, Garikoitz Lerma-Usabiaga <
>> gariko...@gmail.com> wrote:
>> Thanks Juan Eugenio,we have visually inspecte
Hi,
I am calculating hippocampus volumes with 5.2 in CentOS 4.
I compare volumes (the same apply for lh and for rh) when calculating as:
> Left.Hippocampus value in 1mm3 from aseg.stats
> I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and
obtain the nonPartialVolumeStatsLeft.txt,
REESURFER_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
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 your
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 i
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:
aparcstat
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 wrote:
> Hi Luisa
>
> yes, Mert Sabuncu and Koen Van Leemput have developed a MVPA algorithm
> called RvoxM that I believe is state-of-the-art
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
- 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 command
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
7
ly notify the sender via telephone at
> (773)
> 406-2464 or email.
>
>
> On Tue, Oct 23, 2012 at 7:37 AM, Garikoitz Lerma-Usabiaga
> wrote:
> > Hi Donald and everybody,
> > I created AAL .mgh and .label-s in FS Colin27 space, if anybody is
> > interested plea
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
wrote:
> Has anyone created an AAL label file for Freesurfer? I've done some
> ROI analysis using AAL
t 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
y? 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.
-- In the ca
sities 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 brai
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
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" wrote:
> Hi Gari,
> I saw your email to Alex about your method obtaining statistics from multiple
> subjects with Python script. Could you send the code to me?
>
> Th
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 also
t, 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 regi
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
/Applications/freesurfer/subjects/ROI10/BrocaOrb
n. 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 s
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