.x86_64 #1 SMP Tue Jun 20
01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Any idea what went wrong here?
Thank you!
Sincerely yours,
Lars M. Rimol, PhD
Senior Researcher
Norwegian Advisory Unit for Functional MRI
Department of Radiology
St. Olav's University Hospital
7006 Trondheim
Norway
bedpostx_mgh -n 2
/home/larsrim/lbkabel/tbi/morfometri_test/DWI/TRACULA/local/1001_c1/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 131:
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
Sincerely yours,
Lars M. Rimol, PhD
Senior Researcher
Norwegian Advisory Unit for Func
it crashes, and why does it add "?" to the subject name?
Thank you!
sincerely yours,
Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondhe
>control points in general, it depends on the specific case.
>BTW, if you change the number of control points, you don't need to use the
>reinit variable - that's only for rerunning with the same control points
>as before.
>
>Best,
>a.y
sincerely yours,
Lars M. Rimol, PhD
Senior
Hi,
Rerunning the tractography using reinit, is it an absolute requirement to
specify number of control points? It doesn't seem like I can just set
reinit = 1 and let the number of control points be the default.
Also, is there a trade-off in terms of number of control points? For
instance, when
+0200 2016
Where do I go next?
sincerely yours,
Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway
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rated look fine too?
a.y
On Sat, 2 Jul 2016, Lars M. Rimol wrote:
Hi,
Trying to run trac-all -c dmric_file -prep, I get an error message stating
that there are different numbers of entries in the bval and bvec files. I don't
understand why, since both have the same number of rows (64).
OS = U
/lmr2/subjects/DTI/tracula_2016_nativerows
set subjlist = (4_FS)
set dcmroot = /media/lmr2/subjects/DTI
set dcmlist = ( 4/5/1.dcm )
set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv
Thank you!
yours,
Lars M. Rimol, PhD
Senior
Hi,
Is it possible to overlay .mgh files with statistics (e.g. p-maps) directly
in FreeView, for purposes of visualizing the results, the same way you can
in tksurfer? When I try load an overlay in FreeView, it seems to be
expecting a volume file.
Thank you!
sincerely yours,
Lars M. Rimol
2002). The volumetric
registration matrix is then applied to the corresponding
surfaces."
Thank you!
sincerely yours,
Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondhe
' names individually. With over 100
subjects, however, that's not an option.
I'd be grateful for any suggestion on how to run asegstats2table with a
subjects list.
Thank you!
sincerely yours,
Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
S
t for one subject I asked
about in a previous e-mail) and there are no outliers in any of the
subjects (according to QAtools).
Any idea why I get this error message?
Thank you!
sincerely yours,
Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radi
M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway
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,
Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway
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: failed, trying double buffered window
Received X error!
Error code : 2
Request code : 154
Minor code : 3
Error text : 'BadValue (integer parameter out of range for operation)'
Can't create a context!
surfer: failed, no suitable display found
sincerely yours,
Lars M. R
nstant.
Error in load_mgh (line 158)
switch type
(PS! I've tried chancing the file name to just lh.mgh but get the same
error message. And the file(s) exist and the path is correct.)
sincerely yours,
Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Depa
,
Lars M. Rimol, PhD
Department of Medicine
John A. Burns School of Medicine
University of Hawai'i
1356 Lusitana Street, University Tower
Honolulu, HI 96813
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if
060027_S01_to_060027.lta is supposed to be there before mri_robust_template
starts? Is that the problem or is it something else?
Any help would be appreciated,
Thank you!
yours,
Lars M. Rimol, PhD
Norwegian University of Science and Technology (NTNU)
Trondheim,
Norway
to have a larger number of control points, except for the increase (I
assume) in processing time? Or will a larger number produce a worse result
for less curved tracts?
yours,
Lars M. Rimol, PhD
Norwegian University of Science and Technology (NTNU)
Trondheim,
Norway
.dcm 74.dcm 80.dcm 87.dcm 93.dcm 9.dcm
106.dcm 112.dcm 119.dcm 125.dcm 131.dcm 138.dcm 144.dcm 150.dcm
157.dcm 18.dcm 24.dcm 30.dcm 37.dcm 43.dcm 4.dcm 56.dcm 62.dcm
69.dcm 75.dcm 81.dcm 88.dcm 94.dcm
yours,
Lars M. Rimol, PhD
Norwegian University of Science
can drop from the
covariance model?
Have I understood you correctly?
Thank you!
yours,
Lars M. Rimol, PhD
Norwegian University of Science and Technology (NTNU)
Trondheim,
Norway
On Wed, Dec 17, 2014 at 5:00 PM, jorge luis jbernal0...@yahoo.es wrote:
Hi Lars
I'm not sure whether you
documented.)
Thank you!
yours,
Lars M. Rimol, PhD
Norwegian University of Science and Technology (NTNU)
Trondheim,
Norway
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Hi Martin,
Does that mean that one would expect to see reduced lgi (local gyrification
index) where this occurs?
Thank you!
LMR
yours,
Lars M. Rimol, PhD
Norwegian University of Science and Technology (NTNU)
Trondheim,
Norway
On Wed, Oct 29, 2014 at 3:39 PM, Martin Reuter mreu
distribution and it's unclear to me what the distribution of such ratios
are.
Thank you!
LMR
yours,
Lars M. Rimol, PhD
Norwegian University of Science and Technology (NTNU)
Trondheim,
Norway
Bruce Fischl
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:%22Bruce+Fischl
lh.pial_lgi
To perform a vertex-wise analysis in QDEC of the lgi surface data, first
sample the results to the average template subject 'fsaverage':
recon-all -s my_subject_id -qcache -measure pial_lgi
Do this for each of the subjects in your group
--
yours,
Lars M. Rimol, PhD
Norwegian University
)
No such file or directory
ERROR: reading curvature file
--
yours,
Lars M. Rimol, PhD
St. Olavs Hospital
Trondheim,
Norway
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this
Thank you!
--
yours,
Lars M. Rimol, PhD
St. Olavs Hospital
Trondheim,
Norway
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The information in this e-mail is intended only
to create fsaverage), or, probably better,
get an average area map for your cohort
doug
On 07/30/2014 08:38 AM, Lars M. Rimol wrote:
Hi Bruce,
I would like to be able to tell what proportion of a region of
interest (ROI), as defined in atlas space by e.g. Desikan-Killiany,
that shows
matter vertex locations...
On 07/15/2014 09:04 AM, Lars M. Rimol wrote:
Hi,
I go to File - Label - load label and there I pick
lh_binarymap_area_covar8.label and then I get the error message:
% 0 nonzero vertices found
label stat field
?
any help is greatly appreciated
thanks,
Chris
--
yours,
Lars M. Rimol, PhD
St. Olavs Hospital
Trondheim,
Norway
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:20140711
use mri_cor2label with the --surf option
On 07/11/2014 01:36 PM, Bruce Fischl wrote:
Hi Lars
this would be pretty simple to do in matlab, but I'm not sure if we
have anything do to it otherwise (Doug might)
cheers
Bruce
On Fri, 11 Jul 2014, Lars M. Rimol wrote:
Hi,
Is there a way
, but that seems to produce volumes and I'm not really sure what it
does anyway...
Thank you!
--
yours,
Lars M. Rimol, PhD
St. Olavs Hospital
Trondheim,
Norway
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to the coefficient of the time
covariate (the
second covariate) when the group covariate is zero (i.e for the
controls).
Hope this makes
sense.
Best
-Jorge
--
yours,
Lars M. Rimol, PhD
St. Olavs Hospital
Trondheim,
Norway
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Hi Anderson,
Thank you! How would you suggest I address this issue when I smooth these
images before statistical analysis? I normally use the smoothing algorithm
implemented in FreeSurfer (mri_surf2surf).
--
yours,
Lars M. Rimol, PhD
St. Olavs Hospital
Trondheim,
Norway
to the design matrix. Note: the
contrast matrices must include columns for these components.
Thank you!
--
yours,
Lars M. Rimol, PhD
Division of Mental Health and Addiction
Institute of Clinical Medicine
University of Oslo
P.O. Box 85 Vinderen,
0319 Oslo, Norway
. Is this correctly understood? Is
this also the case in the underlying C-code?
Thank you!
LMR
--
yours,
Dr. Lars M. Rimol
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--
yours,
Dr. Lars M. Rimol
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e
Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Lars
do you have write permission? Is the partition full? Try:
touch /home/lmr/test.mgh
and see if that works
cheers
Bruce
On Thu, 20 Jan
2011, Lars M. Rimol wrote:
Hi,
I got this error message when attempting to use mri_concat. Number
type 'limit'
what does it tell you?
On Thu, 20 Jan 2011,
Lars M. Rimol wrote:
Hi Bruce,
Yes I can create files. I was trying to run a script with almost 500
mgh files that I wanted to concatenate. I figured there was something
wrong with the script because I could run command lines
stacksize 10240 kbytes, sorry!
--
yours,
Dr. Lars M. Rimol
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The information in this e-mail is intended only for the person to whom
from the data recon'ed with v3.0.2?
Thank you!
yours,
Dr. Lars M. Rimol
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The information in this e-mail is intended only for the person
Hi,
What does it mean when mris_surf2surf produces the error message that the input
file cannot be read as type 3 ?
The file is an .mgh which I converted from an .mgz using mri_convert
(mri_convert oldfile.mgz newfile.mgh). I get the same error when I use the .mgz
file.
Thank
Yes, I can load it as an overlay in tksurfer.
Here's the mri_info output:
[...@localhost area]$ mri_info TOP_sm100_lh_cc2_11072009.mgh
Volume information for TOP_sm100_lh_cc2_11072009.mgh
type: MGH
dimensions: 163842 x 1 x 1 x 216
voxel sizes: 1., 1., 1.
type: FLOAT (3)
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cannot read file as type 3
Hi Lars,
can you send us the whole command line and output? I think type 3 is an
MGH/MGZ file. Does mri_info work on it properly?
cheers
Bruce
On Sat, 11 Jul 2009, Lars
M. Rimol wrote:
Hi,
What does
Hi,
I've used the fdr function in tksurfer and compared the results to Tom Nichol's
matlab function (http://www.sph.umich.edu/~nichols/FDR/). I use p =
10.^-abs(pfile), where pfile is 'sig.mgh'.
I find that the p-threshold (pID, assuming positive dependence) is usually
exactly the same
Hi,
Please disregard my previous mail. I was a little too trigger happy..., the
1.928 threshold set by tksurfer is too high for any vertex to survive so the
two methods DO concur. I should actually look at the maps and not just the
output...
The reason I asked is that I'm combining
Hi,
I have done an analysis involving three groups, so there are three pairwise
comparisons across two hemispheres = 6 p-maps. I want to adjust for multiple
comparisons (across the vertices), so I use FDR. But since FDR determines
the threshold basd on the actual p-values, I get 6 different
M. Rimol lari...@gmail.com wrote:
Hi,
I have done an analysis involving three groups, so there are three pairwise
comparisons across two hemispheres = 6 p-maps. I want to adjust for multiple
comparisons (across the vertices), so I use FDR. But since FDR determines the
threshold basd
Hi,
This is perhaps a tricky problem. I have created a lh STG label using
custom fill and the up to functional threshold option and retrieved
the data from those vertices. This label is just a minor portion of the
entire STG parcellation. Now I would like to compare to the homologous area
in the
: freesurfer@nmr.mgh.harvard.edu; destri...@med.univ-tours.fr;
ra...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Destrieux or Desikan/Ron Killiany
Hi Lars,
you need to send images of the folding patterns for Christophe and Rahul
to decide.
cheers,
Bruce
On Tue, 10 Mar 2009, Lars M
Hi Rahul,
Thanks for the input!
I'm afraid I don't see how the atlases agree with regard to the medial SFG,
since only a tiny portion of the area of interest is in SFG according to the
Destriuex annotation (SFG is the uppermost parcellation in the anterior half of
the hemisphere in that
Hi,
Is there a way to get the standard error of the adjusted means for each
group in a glm with a categorical predictor?
--
yours,
LMR
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Hi,
I have fitted a glm with three different groups, using mri_glmfit (FS
v4.0.3). I use the beta.mgh to get the adjusted means within an ROI,
for each group. I'd like to make a bar or box diagram with the adjusted
means/betas, but I'm not sure how to get the standard error of the betas so
I can
Hi,
I've done a glm model fit comparing cortical thickness between two
groups, and have certain areas (blobs) on the cortical surface that are
above sig. threshold. I'd like to get a list of the vertex numbers for each
of these significant areas, which do not correspond to the parcellations in
FS.
Hi,
In tksurfer, when I have loaded an overlay and then try to add a color bar,
I get this error message:
freeglut ERROR: Function glutBitmapCharacter called without first calling
'glutInit'
I'm using freeglut v 2.4.0. I don't know if this is caused by a bug in
freeglut (I think it's the latest
Hi,
I am experiencing similar problems to Jennifer and Glenn with tksurfer; the
(tksurfer) error message is:
surfer: ### redraw failed: no gl window open
and the display shows only a thin slice of the posterior of the surface.
The computer is a fresh install of RHEL 5 on a new machine, and my
Hi,
We have a dataset that was processed (by somebody else) with an old
freesurfer version and we need to find out exactly which version was used.
We have a freesurfer_3.0 directory (and a
freesurfer-Linux-centos4-stable-v3.0-full.tar.gz download) with a
build-stamp.txt that says:
Hi,
I'm just wondering what the dimensions of an mgh file generated by
mris_preproc with e.g. 300 subjects should be?
Should it be 163842x1 or 163842x300 ? I would assume that it should contain
a vector for each vertex, with the same length as number of subjects that
were listed in the fsgd file
Hi,
I'm wondering what the dimensions of an mgh file generated by mris_preproc
with e.g. 300 subjects should be? Should it be 163842x1 or 163842x300 ? I
would assume that it should contain
a vector for each vertex, with the same length as number of subjects that
were listed in the fsgd file used
Hi,
I downloaded the freesurfer-Linux-rh9-stable-pub-v4.0.3-full, and I followed
the instructions on your website (
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-platform-release-full.README.txt
):
1) extract to /usr/pubsw/packages/
2) place the license file in the resulting
Hi,
I ran mri_glmfit with a fsgdf looking (in principle) like this:
GroupDescriptorFile 1
Title MyTitle
Class Group1 plus blue
Class Group2 circle green
Variables ICV
Input subjid1 Group1 1
Input subjid2 Group22
Dependent variable iscortical thickness.
When I
Hi,
Please ignore my previous mail, I did not see that external on the y axis
means dependent variable (blame it on the early morning blues...)
--
yours,
LMR
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of the subjectsdir, and also write the output
to that dir? It seems if you give the full path, FS assumes that it should
be added to the path of the subjects dir.
Thank you!
Lars
Hi Lars,
it looks like no input subjects are defined.
Bruce
On Wed, 27 Jun 2007, Lars M.
Rimol wrote:
Hi,
Trying to run
Hi,
Trying to run make_average_subject but getting an error message. Any idea
what may be wrong?
Thank you!
Lars M. Rimol
make_average_surface --fsgd
/space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out
/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest
$Id: make_average_surface,v
Hi,
I have combined the Desikan parcellations into regions of interest, which I
would like to visualize. So I need to create an ad hoc color coding scheme.
In order to visualize the ROIs I would load a file equivalent to the
?h.aparca2005s.annot file, which would show the same color for those
Hi,
When I try to run mris_preproc wiht the nocleanup flag I get an error
message:
flag --nocleanup not recognized
Same thing happens for --cleanup (i.e., not recognized), and --tmpdir
tmpdir doesn't seem to work (it still does cleanup). But all these flags
are listed under the help function for
Hi,
I am wondering if it is possible to use some kind of a list of subjects to
specify input for mri_concat, like you can use --f filename, where filename
refers to a list of subjects, for mri_surf2surf ?
It seems that using e.g.: mri_concat subj*-lh.mgz --o allsubjs-lh.mgz
is an alternative
Hi,
Is the determinant of the Jacobian matrix for the sphere morph to atlas space saved vertex by vertex? If so, where is it saved?
-- yours,LMR
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Hi,
When one runs mris_preproc with e.g. -meas thickness, does it get the thickness information from the files in the stats directory within each subject's directory- or from the ?h.thickness files under the surf directories?
Thank you!-- yours,LMR
Hi,
I just ran make_average_subjects with increased swap (from 2G to 8G) on
178 subjects and now it worked, which would seem to indicate that it
may have been a memory issue? I did not crash with 3, 10 and 113
subjects with 2G swap.
yours,
LMR
Hmmm, I've run it on 100 subjects without trouble.
Hi, I have two questions on make_average_subject1) Why are two sets of surfaces created by the make_average_subjectscript? What is the difference between e.g. inflated and inflated_avg?Which one(s) should be used for visualization?
2) As far as I understand, make_average_subject is run for
Hi,
I am using FS v3.02. I am using the tutorial to figure out how to do
group analysis with the new FS version but there is one step that is
confusing. The tutorial says that I should first create a FSGDF (and
run make_average-subject), and then it says that running mris_glm will
create the
improves, that's why we've started using that. So we need to know how to proceed from there.(We use the recommended reconstruction, so we check the talairach and skullstrip after autorecon1.)
Thanks!
-- yours,Lars M. Rimol
depends why you needed to improve the talairach. If it's just forreporting
it's a question of what your goals are Lars.-- yours,Lars M. Rimol
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G, Agartz I. Smaller cerebellar vermis but not hemisphere volumes in chronic schizophrenia. Am J Psychiatry, 2003; 160:1614-7)-- yours,
Lars M. Rimol
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,Lars M. Rimol
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