fied in
expert.opts ?...
Sincerely,
Gonzalo Rojas Costa
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Hi:
Which is the optimal parameters for a morphometric sequence in a 1.5
T MR OPTIMA 450w GE MRI equipment ?...
Sincerely,
Gonzalo Rojas Costa
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Hi Carolina:
And did you tested the tksurfer command ?...
for example: tksurfer CORBIC_vol01 rh pial
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Clinica Las Condes
Santiago
Chile
> Message: 4
> Date: Sun, 18 Sep 2011 10:25:26 -0400 (EDT)
> From: Bruce Fischl
>
Hi Carolina:
Is it possible, but in my case when the hard disk is full at the
moment of the processing, I got a fatal error from recon-all command...
Sincerely,
Gonzalo Rojas Costa
El 19-09-2011 9:53, Carolina Valencia escribió:
> Thanks for the answers.
> I think the problem w
Hi:
How can I get the volume of the different lobes of the brain
(occipital, parietal, temporal, etc) ?... White matter and gray
matter?... Labels ?...
Sincerely,
Gonzalo Rojas Costa
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Hi Douglas:
The solution that you sent me runs only in freesurfer 5... Do you
have ay solution for freesurfer 4.5.0 to compute GM+WM volume for each
lobule ?...
Sincerely,
Gonzalo Rojas Costa
On Mon, Sep 26, 2011 at 11:01 AM, Douglas N Greve
wrote:
> You can run mri_annotation2la
Hi:
There exist any paper related to the subcortical volume in children
(below 15 years old)?... any image database ?...
Sincerely,
Gonzalo Rojas Costa
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tration took 15 minutes and 1 seconds.
Abort"...
How can I correct it ?...
Sincerely
Gonzalo Rojas Costa
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The information in thi
Hi:
In rh.aparc.a2009s.stats file, appears the average cortical thickness
(ThickAvg) value for frontal middle gyrus (G_front_middle): how can I
get the values of the cortical thickness in that gyrus (for example),
not the average value ?...
Sincerely,
Gonzalo Rojas Costa
Hi:
In aseg.stats the WM hypointensities is included in left-cerebral
(right-cerebral) white matter volume ?...
Sincerely,
Gonzalo Rojas Costa
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Hi:
For example, if I execute the mri_cc command with "-t 2", mri_cc
shows me "setting callosum thickness to 5 mm"... Why ?... What exactly
specify the -t option ?...
Sincerely,
Gonzalo Rojas Costa
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Hi:
Any reference about how freesurfer divides the corpus callosum in
CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior,
CC_Anterior ?...
Sincerely,
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Hi:
How can I do a decimation to 1 polygons aprox to the pial surface ?...
Sincerely,
--
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
Dear Pedro Paulo:
I need to continue the freesurfer professing from a specific stage of
autorecon2 (careginv; stage 4 of autorecon2 in
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllStableTablev4)..
Which is the command line to do it ?...
Sincerely,
Gonzalo Rojas Costa
42:44 UTC 2008 i686 GNU/Linux
recon-all exited with ERRORS at Fri Jul 24 04:47:15 CLT 2009"
Which is the problem ?... How can install libtiff.so.3 ?..
Sincerely,
Gonzalo Rojas Costa
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idea ?...
SIncerely,
Gonzalo Rojas Costa
Krish Subramaniam escribió:
> Hi
>
> On Ubuntu, you will need to do the following:
> cd /usr/lib
> sudo ln -s libtiff.so.4 libtiff.so.3
> ( from http://surfer.nmr.mgh.harvard.edu/fswiki/Download )
>
> The second command only work
Dear Douglas:
And how can I view (render) in 3D the hippocampus that I got frok aseg.mgz
with the mri_binarize command ?...
Sincerely,
Gonzalo Rojas Costa
> mri_binarize with --match 17 or --match 53 will do it
>
> doug
>
> Guang Zeng wrote:
>> Hi, there,
>>
/Linux
How can I correct it ?...
Sincerely,
Gonzalo Rojas Costa
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How can I correct it ?... I have a PC with 2.5 GB RAM, and iit is the first
processing that fails with an error related to memory... Why ?... Is it
really a memory problem ?... There is a tip and trick that allows me to
correct it ?...
Sincerely,
Gonzalo Rojas Costa
page...
Sincerely,
Gonzalo Rojas Costa
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... Or the segmentation and
cortical thickness are computed in a independent way ?...
Sincerely,
Gonzalo Rojas Costa
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Hi:
bbregister is for 6 or 12 DOF corregistration ?...
Sincerely,
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Hi:
I want to modify the color palette that tksurfer uses to display overlay
data... How can i modify it ?... the same question for tkmedit...
Sincerely,
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Hi:
I will write my question in another way: in which file could I find the
palette that tksurfer and tkmedit uses to display overlay data ?... because
I want to create other palettes...
Sincerely,
Gonzalo Rojas Costa
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Hi:
I have three MRIs of the same patient took during different months... I need
to compare the hippocampus volume fof the three exams (for example), the
cortical thickness, etc... How can I do such computation ?...
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Hi:
How can I get the volume of each lobe ?.. each hemisphere ?...
Sincerely,
Gonzalo Rojas Costa
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Hi:
There exist any tool that could show me the structures that differ between
each hemisphere more than a given percentage (volume) ?...
Sincerely,
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Hi:
There exist any tool that could show me the structures that differ between
each hemisphere more than a given percentage (volume) ?... For example: the
hippocampus...
Sincerely,
Gonzalo Rojas Costa
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Hi:
I was processing a longitudinal processing (previous the 8.8 earthquake)
using a command line like:
recon-all -base -tp -tp ... -all
but it couldn't finished because the power cut... How can I continue the
processing without starting again from the beginning ?...
Sincerely,
Go
nning ?...
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Santiago
Chile
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The information in this e-ma
?...
Sincerely,
Gonzalo Rojas Costa
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The information in this e-mail is intended only for the person to whom it is
addressed. If you
thickness less
than 1 mm?... How you can measure it ?...
Sincerely,
Gonzalo Rojas Costa
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The information in this e-mail is
al Volume" (IntraCranialVol, ICV) ?...
The cerebelum is included in the ICV ?...
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Clínica Las Condes
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Hi Andreas:
As far as I know, the complete command is:
recon-all -s subjid -skullstrip -no-wsgcaatlas -wsthresh 35 -clean-bm
Sincerely,
Gonzalo Rojas Costa
Laboratory of Medical Imaging Processing
Department of Radiology
Clínica Las Condes
Santiago
Chile
> Date: Fri, 26 Mar 2010 11
Hi:
I need to know which is the normal value of BrainSegVolNotVent (Brain
Segmentation Volume Without Ventricles) of patients with 70 years aprox ?...
Any paper ?...
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Clinica Las Condes
Santiago
Chile
Hi:
I need to know which is the normal value of BrainSegVolNotVent (Brain
Segmentation Volume Without Ventricles) of patients with 70 years aprox ?...
Any paper ?...
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Clinica Las Condes
Santiago
Chile
Hi:
I need to know which is the value of BrainSegVolNotVent (Brain
Segmentation Volume Without Ventricles) of healthy volunteers at different
ages... Any paper ?...
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Clinica Las Condes
Santiago
Chile
d OASIS dataset ?...
Sincerely,
Gonzalo Rojas Costa
Bruce Fischl escribió:
> Hi Gonzalo,
>
> I think the OASIS dataset is distributed with asegs on them, so you could
download that and calculate it yourself, although of course it will be
age-dependent.
> cheers
> Bruce
>
>
&g
Hi:
Freeview only has grayscale, heat and jet in the color maps for a volume...
How can I specify another color map ?...
Sincerely,
Gonzalo Rojas Costa
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Hi Bruce:
The patient has 3 years old... The parameters of the sequence, are: TI =
1100 ms, TR=1870 ms, TE=3.25 ms, Number of averages=1, FOV 256x256, Avanto
1.5 T...
Sincerely
Gonzalo Rojas Costa
Bruce Fischl escribió:
> Hi Gonzalo,
>
> what age is this subject? And what type o
Hi:
If we want to compare the hippocampus volume between different patients,
which other volume could I use to normalize it ?... the ICV ?... the volume
of each hemisphere ?... And, if I want to compare the amygdala, for example
?...
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
I solve it ?
Sincerely,
Gonzalo Rojas Costa
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External Email - Use Caution
Hi:
How can install freesurfer 7.0.0 in a virtual machine ?
Sincerely,
Gonzalo Rojas Costa
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Hi:
No... I don't have any specific issue... I have a previous freesurfer
version installed that I want to continue using. So I want to install
version freesurfer 7.0 on a virtual machine...
Sincerely,
Gonzalo Rojas Costa
> Message:
system in both cases...
I reviewed the coregistration to MNI305 and it is reasonably good in both
cases...
The case was reviewed by an expert neuroradiologist, and she does not
consider that there is a significant visual difference between both sizes.
Sincerely
Gonzalo Rojas Costa
reprocess ?
Other question... what do you mean with " You might be comparing dewarped
vs not dewarped"
Sincerely,
Gonzalo Rojas Costa
>Message: 6
>Date: Thu, 10 Sep 2020 12:42:41 -0400
>From: "Douglas N. Greve"
>Subject: Re: [Freesurfer] big difference betwe
External Email - Use Caution
Hi:
Where can I find the virtual disk image of freesurfer 7.1.1 ?
Sincerely,
Gonzalo Rojas Costa
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Hi:
Which is the best library or software to create the hippocampus mesh from
aseg segmentation?
Sincerely
Gonzalo Rojas Costa
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? Especially hippocampal segmentation.
Sincerely,
Gonzalo Rojas Costa
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%2Farticles%2F10.3389%2Ffnins.2018.00235%2Ffull
How to convert that MNI coordinates to vertex in the pial surface ?
Sincerely
Gonzalo Rojas Costa
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
http://secure
External Email - Use Caution
Hi:
"Vertex Talairach" in tksurfer: how does it relate to MNI coordinates?
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-9777
External Email - Use Caution
Hi:
I tried to use mri_synthseg and mri_synthsr commands, but I got the
error message "Illegal instruction (core dumped)". Any solution? I
have the March 31st, 2022 version.
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
C
gMyCGFELAc-ReX5c6q891gCUl35SRXIWZUO0yvLGMBLAKZQpvywUwHckAUlf5_8SQ9ch05XQW5ockkLH0E_yaqNOGE5DPhCDJRX5qjywx1yF5JcMkcPbiNNbEc34hoNaOpP1Y0xmpNNirDZiIGlgBoFYRkmonGJsbGHxJHNnN8Vok295ZKv2AcDxmDMdvWQZIyAINNHpr5ixKNj5750wSN4LPTZHn8/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Ftrac-all,
but It was not
clear to me how to solve the problem.
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
C
External Email - Use Caution
Hi:
Is it possible to use input diffusion files in MOSAIC IMA Siemens
file format directly? Or is it necessary to convert to nifti file
format first?
Sincerely,
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of
External Email - Use Caution
Hi:
I coregistered a PET file to a freesurfer data using mri_coreg
command. I imported the freesurfer-generated data to 3D Slicer. How
can I import the PET.reg.lta file in 3D Slicer?
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
External Email - Use Caution
Hi:
How can I convert a .reg.lta linear transform to an ITK transform
for 3DSlicer?
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
(old),
3900.0 (new), etc... Why ?...
Sincerely,
Gonzalo Rojas Costa
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Hi:
No green line appears in tkregister2 over the fuzzy volume... Why ?...
Sincerely,
Gonzalo Rojas Costa
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The information
Hi Bruce:
It is "tkregister2 --mgz --s patient --fstal"
Sincerely,
Gonzalo Rojas Costa
Bruce Fischl escribió:
> what was your command line?
> On Wed, 19 May 2010, Gonzalo Rojas Costa wrote:
>
>> Hi:
>>
>> No green line appears in tkr
Hi:
I deleted the aseg.stats file by mistake (only that file)... How can I
regenerate that file ?... I have the complete processing of that patient...
Sincerely,
Gonzalo Rojas Costa
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Hi:
How can I display an overlay in such a manner that only values between "min"
and "max" are displayed in a color palette, and values less than "min" and
values greater than "max" are displayed in gray
Dear Doug:
But, I need the volume of each lobe including GM and WM... such as the one
that we can got from aseg.stats...
Sincerely,
Gonzalo Rojas Costa
Douglas N Greve escribió:
> There's one for drawing labels, but what you will want to do is to use
> mri_annotation2labe
Sincerely,
Gonzalo Rojas Costa
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe t
Hi:
I used the command:
"recon-all -subject OAS1_0153_MR1 -all -legacy"
but I got the error: "ERROR: you have specified -legacy, but this does not
look like a legacy analysis."
Sincerely,
Gonzalo Rojas Costa
___
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Hi Bruce:
Because, I want to use to control points defined in the original
processing, etc, etc... for that reason I want to use legacy option...
Sincerely,
Gonzalo Rojas Costa
Bruce Fischl escribió:
> try it without the -legacy
> On Sat, 17 Jul 2010, Gonzalo Rojas Costa wrote:
&
Hi Bruce:
Ok...
Sincerely,
Gonzalo Rojas Costa
Bruce Fischl escribió:
> You shouldn't need legacy for that. It will always keep all edits unless you
> explicitly tell it not to
>
>
>
> On Jul 17, 2010, at 10:33 PM, "Gonzalo Rojas Costa" wrote:
>
>
Hi:
How can I get more thinner parcelation borders ?... Or could I specify a
transparency factor ?...
Sincerely,
Gonzalo Rojas Costa
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Hi:
I change the color palette of the parcelation borders to white... But, I
need thinner parcelation borders... can I change that parameter ?... Or
could I specify a transparency factor for the borders ?...
Sincerely,
Gonzalo Rojas Costa
Hi:
I segmented a T1 volume of a patient with a tumor... in the aparc+aseg and
aparc.2009s segmentation,that tumor appears as "none"... How can I got the
volume of the tumor ?...
Sincerely,
Gonzalo Rojas Costa
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Hi:
How can I create an image such as the "Be happy" one that appeared in the
last slide of "Surface-based Analysis: Intersubject Registration and
Smoothing" PPT?...
Sincerely,
Gonzalo Rojas Costa
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Hi:
Can I install freesurfer v5.0.0 without erasing v.4.5.0 ?... Because I want
to test some new features but I need to continue using v.4.5.0... I
installed v.4.5.0 in /usr/local/freesurfer...
Sincerely,
Gonzalo Rojas Costa
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6
GNU/Linux
recon-all -s ingrid exited with ERRORS at Thu Aug 19 10:05:03 CLT 2010"
How can I solve the problem ?...
Sincerely,
Gonzalo Rojas Costa
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Dear Pedro:
Yes... I installed the NVIDIA drivers... I have driver version 180.44 and my
graphic card is Quadro FX 580...
Sincerely,
Gonzalo Rojas Costa
Pedro Paulo de Magalhães Oliveira Junior escribió:
> In Ubuntu you must install NVidia Native drivers in order to use CUDA:
>
Hi:
Any solution for the 32 bit version ?...
Sincerely,
Gonzalo Rojas Costa
> Message: 6
> Date: Fri, 20 Aug 2010 15:55:39 -0400
> From: Nick Schmansky
> Subject: Re: [Freesurfer] CUDA Error - all CUDA-capable devices are
> busyor unavailable
> To: Dan
se tell me how can I correct the problem ?...
Sincerely,
Gonzalo Rojas Costa
Nick Schmansky escribió:
> i've just posted the file 'fscudabins-linux-centos4.tgz' here:
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4/
>
> note that we h
quot;
Could you please tell me how can I correct the problem ?...
Sincerely,
Gonzalo Rojas Costa
Nick Schmansky escribió:
> i've just posted the file 'fscudabins-linux-centos4.tgz' here:
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4/
&
A Error in file 'devicemanagement.cu' on line 46 : unspecified driver error.
Linux image 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686
GNU/Linux
recon-all -s ingrid exited with ERRORS at Tue Aug 24 11:46:20 CLT 2010"
How can I find a solution to that problem ?...
Hi:
What it means the "nframes" parameter ?... Which is the difference between a
001 mgz file that has "dimensions: 256 x 256 x 176" and another that has
"dimensions: 256 x 256 x 176 x 2" ?...
Sincerely,
Gonzalo Rojas Costa
Hi Bruce:
And how can I get only one frame ?... I don't know why the medical
technologist got the two frames...
Sincerely,
Gonzalo Rojas Costa
Bruce Fischl escribió:
> the 2nd one is a 4D volume with 2 frames (each of which is 256x256x176)
>
> cheers
> Bruce
> O
Hi:
I am quantifying the brain volume of some MS patients
(BrainSegVol-ventricles-cerebelum-brain_stem)... There exist any paper that
shows normal brain volume ?... There exisst any other way to compute the
brain volume ?...
Sincerely,
Gonzalo Rojas Costa
Hi:
There could be an error in the computation of BrainSegVol (aseg.stats) ?...
How can I check it ?...
Sincerely,
Gonzalo Rojas Costa
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Hi:
How can I do a comparisson between the volumetry of the same patient but
with MRI of different dates (longitudinal study) ?...
Sincerely,
Gonzalo Rojas Costa
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Dear Dr. Wang:
I got the message:
"mris_info zstat3_rh.w
nquads=8321536, nvertices=2
ERROR: MRISread: file 'zstat3_rh.w' has many more faces than vertices!
Probably trying to use a scalar data file as a surface!
No such file or directory"
Sincerely,
Gonzalo Rojas
Hi:
How can I get the volume of pons, middle cerebellar pedunclues,
superior cerebellar peduncles ?... And, there exist any PSP-Freesurfer
related paper ?...
Sincerely,
--
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Las Condes Clinic
Lo
Hi:
I am currently configuring Freesurfer 5 in a new workstation that we
received... That workstation has Ubuntu 10.10, and a NVIDIA Quadro FX
1800 graphics card... Could you please send me the detailed steps
necessary to install and configure CUDA support ?...
Sincerely,
--
Gonzalo
Hi:
I am currently configuring Freesurfer 5 in a new workstation that we
received... That workstation has Ubuntu 10.10, and a NVIDIA Quadro FX
1800 graphics card... Could you please send me the steps necessary to
install and configure CUDA support ?...
Sincerely,
--
Gonzalo Rojas
,
Gonzalo Rojas Costa
El 04-02-2011 11:41, Mykol Larvie escribió:
> Hello,
>
> While the segmentation is not so good, the T1 coronal image that you
> sent suggests that the right medial temporal lobe may not be so
> normal. I think an underlying abnormality in the temporal lobe is
>
Hi Bruce:
And which freesurfer tool must I use to manually correct it ?... And,
how can I generate the aseg.stats file after the manual correction ?...
Sincerely,
Gonzalo Rojas Costa
El 04-02-2011 14:59, Bruce Fischl escribió:
> you may need to manually correct it. There's
Hi Bruce:
But, I must edit the wm.mgz file ?...
Sincerely,
Gonzalo Rojas Costa
El 04-02-2011 15:11, Bruce Fischl escribió:
> either tkmedit or freeview, then run autorecon2 and 3 to regenerate the
> surfaces.
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Hi Bruce:
But, I must edit the wm.mgz file ?...
Sincerely,
Gonzalo Rojas Costa
El 04-02-2011 15:11, Bruce Fischl escribió:
> either tkmedit or freeview, then run autorecon2 and 3 to regenerate the
> surfaces.
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Hi:
I want to do a longitudinal comparison of the aseg volumetry of the
same patient with two MRI in different dates... How can I do it ?... any
freesurfer tool ?... qdec ?...
Sincerely,
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
-all
iii) recon-all -long -all
Sincerely,
Gonzalo Rojas Costa
El 03-03-2011 13:03, Martin Reuter escribió:
> Hi Gonzalo,
>
> you should run your data with the longitudinal stream (if you use fs 5.0
> update mri_robust_template and recon-all first), see
Hi:
I tried to install CUDA to use with freesurfer, but I got some errors
that I sent to freesurfer list sometime ago... Could you please send how
can I install CUDA and freesurfer in a Ubuntu platform ?...
Sincerely,
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image
or (for
example) in the case that the patient is slightly rotated (freesurfer
segments only one section of the CC as CC and the other as WM)...
Sincerely,
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Con
Hi Bruce:
Thanks you very much for your answer... And, how can I get the volume
of the new segmentation of the CC that I got with mri_cc command ?...
Sincerely,
Gonzalo Rojas Costa
El 15-03-2011 21:27, Bruce Fischl escribió:
> I mean that if the volume is rotated in any 2d slice
Hi:
The CC volume in aseg.mgz is computed using two slices to the left
and two sagital slices to the right the midline ?...
Sincerely,
--
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes
Hi:
How can I change the font size used in the tksurfer dialogs ?... such
as "Configure Overlay Display" dialog ?... Because I changed the font
size in Ubuntu GNOME, but it didn't changed the font size used in
tksurfer...
Sincerely,
Gonz
rlay Display" didn't
appears the "Apply", "Close", and "Help" buttons, and I think that it
could be for the font size in the GUI, or the screen resolution...
Sincerely,
Gonzalo Rojas Costa
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Hi:
I want to re-process some OASIS-BRAINS database images using FS 5.
Must I use an recon-all option (because I want that FS use the CP
specified) ?...
Sincerely,
--
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica Las Condes
Lo
?...
Sincerely,
--
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
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