Hi Gio
have you used a command line Unix before?
cheers
Bruce
On Fri, 17 Dec 2010, Giovanni
Rodriguez wrote:
> To Whom It May Concern:
>
> My name is Giovanni Rodriguez, I am a high school student working at
> the University of Miami in a research lab. My lab professor told me to work
> throug
To Whom It May Concern:
My name is Giovanni Rodriguez, I am a high school student working at
the University of Miami in a research lab. My lab professor told me to work
through the basics on my own and to download the tutorial and dataset. Is there
anyway that I could find a dumb proof, step by
How do they look in the volume? Can you send pics?
Elvira Fischer wrote:
>
> Dear freesurfer users,
>
> Maybe somebody could help me with the following problem:
>
> On my retinotopic map I observe extensive blobs with max. values
> (turquoise and yellow, heat color map), that rather look like no
Dear freesurfer users,
Maybe somebody could help me with the following problem:
On my retinotopic map I observe extensive blobs with max. values (turquoise and
yellow, heat color map), that rather look like noise. However these blobs
always appear in the same region, around the anterior portion
Yes, that's fine.
--
On Tue, 25 May 2010, [GB2312] Àîèª wrote:
Hi, all
Bruce has suggested that we can directly give recon-all dcm file as input.
However, I have done recon-all with mgz file as input. Is that input file
OK?
For example, sub1 has 128 dcm files, 001~128, I just ran a syntax:
mri
Hi, all
Bruce has suggested that we can directly give recon-all dcm file as input.
However, I have done recon-all with mgz file as input. Is that input file
OK?
For example, sub1 has 128 dcm files, 001~128, I just ran a syntax:
mri_convert 001 sub1.mgz
then the computer read 128 dcm files and conve
you don't need to reorient your data for FreeSurfer. Check the FSL
site/list to see what there orientation requirements are
doug
chenchunhuichina wrote:
> Hello FreeSurfer users,
> I may be asking a stupid question but it really troubled me a while.
>
> I converted dicom files to nift using dcm2n
if the directions are labeled properly then you aer probably ok. In
general you are better off just giving recon-all the dicom files as input
and not doing any conversions beforehand.
cheers
Bruce
On Tue, 4 May 2010,
chenchunhuichina wrote:
Hello FreeSurfer users,
I may be asking a stupid
Hello FreeSurfer users,
I may be asking a stupid question but it really troubled me a while.
I converted dicom files to nift using dcm2niigui (MRIcron). In fslview, it
displayed in RAS coordinates, but template of FSL are in LAS coordinates.
Should I filp L-R before doing any further analysis?
Hi Guang,
I think it probably does make a difference, but we haven't quantified how
much. The initial round of registrations are pretty rigid, so it may not be
that big an effect, but Thomas Yeo (ccd) may have a different opinion.
cheers
Bruce
On Tue, 1 Dec 2009, Guang Zeng wrote:
>
> Hi, the
Hi, there,
I have made our own template using 20 subjects follwoing the instruction in
FreeSurfer WIKI.
(http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates).
I have a quesition now,
Does the quality of the new template depends on the first subject I picked to
built the tempalte
Probably something wrong in your contrast files.
It's hard to tell just from this msg
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.2 www.Netfilter.com.br
--- Novo Netfilter Smal
What probably happened is that you ran QDEC a couple of times. The
currently distributed version does not clean up very well and leaves
files from old analyses around. You may need to delete the qdec
directory and re-run it.
doug
Dalwani, Manish wrote:
> Hi All,
>
> I am getting the following
Hi All,
I am getting the following error after running the simulation script generated
by QDEC.
ERROR: dimension mismatch between X and contrast
/usr/local/freesurfer/subjects/
qdec/Untitled/tmp.mri_glmfit-sim-15306/lh-Avg-Intercept-volume.mtx X has
2 cols, C has 6 cols
Kindly advise!
Hi All,
I am getting the following error after running the simulation script generated
by QDEC.
ERROR: dimension mismatch between X and contrast
/usr/local/freesurfer/subjects/
qdec/Untitled/tmp.mri_glmfit-sim-15306/lh-Avg-Intercept-volume.mtx X has
2 cols, C has 6 cols
Kindly advise!
you can load it in tkmedit from the file menu and probe it one voxel at a
time, or you can use
mri_convert atlas.gca#0 means.mgz
and
mri_convert atlas.gca#1 priors.mgz labels.mgz
to look at the most likely label and it's mean
cheers,
Bruce
On Thu, 29 Oct 2009, Guang Zeng
wrote:
>
> Hi, the
Hi, there,
I want to know how the FS GCA atlas looks like, is there a way to load the FS
GCA Atlas and view it using tkmedit or matlab?
Is it possible to replace FS Atlas with our own Atlas and use it for analysis?
Thanks a lot!
Guang
7:28 PM
To: Kim, Miyoung
Cc: Allison Stevens; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] (no subject)
Hi Miyoung,
you can always edit the aseg.mgz if you want. Do you find this happens
frequently? That hasn't been our experience.
Bruce
On Fri, 4 Sep 2009, Kim,
Miyoung wrote:
&
ge-
> From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu]
> Sent: Friday, September 04, 2009 12:06 PM
> To: Kim, Miyoung
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] (no subject)
>
> The parcellation is created using the surfaces and a cortical atla
bor Day weekend!
Miyoung
-Original Message-
From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu]
Sent: Friday, September 04, 2009 12:06 PM
To: Kim, Miyoung
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] (no subject)
The parcellation is created using the surfaces and a cortic
Hi Anthony,
mostly independent. The surface reconstruction itself is dependent on the
subcortical labeling, and we do use the subcortical information for
distinguishing callosum for cingulate and such, but otherwise they are
independent.
cheers,
Bruce
On Fri, 4 Sep 2009, Anthony Dick wrote:
>
So the segmentation and the cortical parcellation are completely
independent? Or does the cortical parcellation still use information
from the segmentation?
Bruce Fischl wrote:
> Hi Miyoung",
>
> it's based on the white (yellow line) and pial surfaces.
>
> cheers,
> Bruce
>
> On Fri, 4 Sep 2009,
Hi Miyoung",
it's based on the white (yellow line) and pial surfaces.
cheers,
Bruce
On Fri, 4 Sep 2009,
Kim, Miyoung wrote:
> Hi.
>
> Just a quick question - is cortical parcellation performed based on the pial
> line (red line) or the cortical segmentation (brown shade)? The reason for
> t
The parcellation is created using the surfaces and a cortical atlas so you
shouldn't have to worry about the subcortical segmentation overlabeling
like that. Take a look at the aparc+aseg.mgz in tkmedit.
--
On Fri, 4 Sep 2009, Kim, Miyoung wrote:
> Hi.
>
> Just a quick question - is cortical
rd.edu
> To: caoa...@hotmail.com
> CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] (no subject)
>
> Hi Aize,
>
> I think hippocampus will probably be the hardest since it shares so much
> of a border with dark things that will be
ll be appreciated for your answer.
With my best regards,
Aize
Date: Mon, 17 Aug 2009 17:01:40 -0400
From: fis...@nmr.mgh.harvard.edu
To: caoa...@hotmail.com
CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] (no subject)
Hi Aize,
I think the hippocampal
> CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] (no subject)
>
> Hi Aize,
>
> I think the hippocampal gray matter is so dark in your images that it is
> very difficult to distinguish from CSF. Do you have a lot of data collected
> with thes
xplain that the left side is bigger than the right side?
I hope your help. Thanks a lot.
Best Regards,
Aize
Date: Mon, 17 Aug 2009 13:51:26 -0400
From: fis...@nmr.mgh.harvard.edu
To: caoa...@hotmail.com
Subject: RE: [Freesurfer] (no subject)
wow, I don't think I've ever seen a
on, how can
we explain that the left side is bigger than the right side?
I hope your help. Thanks a lot.
Best Regards,
Aize
> Date: Mon, 17 Aug 2009 13:51:26 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: caoa...@hotmail.com
> Subject: RE: [Freesurfer] (no subject)
>
d.edu; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] (no subject)
Hi Aize,
you are using the CMA manual segmentation protocol? We have not found a
bias in volumes, and our DICE is usually close to .9 for hippocampus.
What acquisitions are you using?
cheers,
Bruce
On Sat, 15 Aug 2009, ca
m: fis...@nmr.mgh.harvard.edu
> To: caoa...@hotmail.com
> CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] (no subject)
>
> Hi Aize,
>
> you are using the CMA manual segmentation protocol? We have not found a
> bias in volumes, and our D
ation.
Aize
Subject: Re: [Freesurfer] (no subject)
From: ni...@nmr.mgh.harvard.edu
To: fis...@nmr.mgh.harvard.edu
CC: caoa...@hotmail.com; freesurfer@nmr.mgh.harvard.edu
Date: Fri, 14 Aug 2009 18:53:41 -0400
just to add a factoid, from the ADNI data set, 793 subjects processed by
freesurfer:
Volume
g the mean volume for auto is less than
manual segmentation.
Aize
> Subject: Re: [Freesurfer] (no subject)
> From: ni...@nmr.mgh.harvard.edu
> To: fis...@nmr.mgh.harvard.edu
> CC: caoa...@hotmail.com; freesurfer@nmr.mgh.harvard.edu
> Date: Fri, 14 Aug 2009 18:53:41 -0400
>
just to add a factoid, from the ADNI data set, 793 subjects processed by
freesurfer:
Volume Mean: StdDev:
--- - ---
Left-Hippocampus 3184.335 604.930
Righ
is your segmentation protocol the same as the one we base our automated
segmentation on? For example, are fimbria and alveus considered part of
the hippocampus?
As far as left/right switches go, do you have any fiducial markers (e.g.
vitamin E tablets) in the images?
cheers
Bruce
On Sat, 15
Hi, there,
I have some problem for the hippocampus segmentation results.
1. My structural data are originally in par-rec file. I used r2agui to
convert them into .nii format, then use recon-all -i to convert the .nii
data into freesurfer .mgz format. Based on these operations, I run
recon-all -
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Hi Elina,
what version are you running? Presumably this doesn't get fixed
correctly by the auto-topology-fixer? This defect is probably not visible
in any one slice. There is a trail of voxels that connect the temporal lobe
to the main body of the white matter. You'll need to erase some to rem
Hi freesurfer,
We would make a new LUT to create an annot file with personalized
names and colours..
How is it possible?
Thanks,
Martina Campanella
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please unsubscribe me from the list
many thanks,
aza...@liv.ac.uk
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a lot.
Hope this helps,
Regards,
Falk
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Elina Pitri
Sent: Wednesday, April 29, 2009 12:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] (no subject)
Hello
recon-all -all will take approximately 30 hours. It depends on the quality
of your data and how many errors need to be fixed.
Allison
--
On Wed, 29 Apr 2009, Elina Pitri wrote:
Hello Freesurfer Creators,
I am wondering how much time should Volume and Surface processing (using
recon-all comm
Hello,
Do you know how can I convert my images which are in ctf format to a freesurfer
compatible format?
thanks,
Elina___
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Hello Freesurfer Creators,
I am wondering how much time should Volume and Surface processing (using
recon-all commands) take.
thanks,
Elina___
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Thank you everyone for your answers. They have been very helpful.
Devdutta
On Tue, Feb 17, 2009 at 1:24 PM, Bruce Fischl wrote:
> I agree. The average looks fine, and the stuff at the bottom is because we
> don't automatically redraw the graphics window. You need to click redraw (or
> alt-r whe
I agree. The average looks fine, and the stuff at the bottom is because
we don't automatically redraw the graphics window. You need to click
redraw (or alt-r when the focus is in the graphics window) is you
obscure part of it.
cheers,
Bruce
On Tue, 17 Feb 2009 c...@nmr.mgh.harvard.edu wrote:
As far as the first, This happens sometimes when you make your own average
subject. You just need to inflate it more. I will try to dig up an old
email I have on the commands.
As for the second, just click the redraW BUTTON
CARL SCHWARTZ
On 2/17/09 12:44 PM, "Devdutta W" wrote:
Oops, forg
Hi Corey,
if the talairach transform has been computed (as it is in recon-all),
then loading one of the standard anatomicals will bring it up. Something
like:
tkmedit norm.mgz lh.pial -aux ct.anat.nii
where is the name you gave to recon-all .
cheers,
Bruce
On Fri, 13 Feb 2009, Keller, C
you have to give it the actual name of the subject (it has to have been
analyzed in freesurfer)
Keller, Corey J. wrote:
Hi Freesurfers,
We have an MRI coregistered with a CT scan using spmregister. I have converted
the CT to the anatomical volume using mri_vol2vol. We are then trying to view
Hi Freesurfers,
We have an MRI coregistered with a CT scan using spmregister. I have converted
the CT to the anatomical volume using mri_vol2vol. We are then trying to view
the anatomical ct in tkmedit and output talairach coordinates but as of now can
only see RAS coordinates. Is there a way to
Hi Ali,
do you want to send us a sample of the data. It's very hard to get
anything like uniform contrast over the whole brain at 7T due to
dielectric effects. We rarely use the 7T for this kind of thing as in our
experience the 3T is better (in contrast to say T2* weighting, which is
beautif
Dear FreeSurfer experts,
I did contact you before regarding the problem below ( Talairach Failure
Detection ) and one suggestion was to use lower resolution MPRAGE rather than
using .5mm one. ( Our MPRAGEs were acquired at 7T scanner with 0.5mm isotropic
resolution). I acquired a new MPRAGE at
first - wich is the command line for transform an *.img o *.mgh to *.label
second.
I have a program that gave a PET mask (*.img) with a specific region of
activation, I want to know wich are the vertex of that region, to take them to
FS and to create a label for making the thickness of that s
d how to make a label takin'
those parameters on FS
Date: Mon, 22 Dec 2008 14:35:19 -0500From: gr...@nmr.mgh.harvard.eduto:
gabriel...@hotmail.comcc: freesur...@nmr.mgh.harvard.edusubject: Re:
[Freesurfer] (no subject)how are you defining your ROI? Below is some info Im
putting toget
how are you defining your ROI? Below is some info Im putting together on
segmentations, parcellations, and labels. It's still pretty raw, but it
might be useful to you.
Segmentation
- each voxel has an index
- index into lookup table (LUT), eg FreeSurferColorLUT.txt
- only one index per vox
hello
in the case that i have a ROI and i don't know wich voxeles are in there, or
the coordenates of those voxeles, i want to create a specific label that only
contains those voxeles, how can i do that??'
_
Arrastrar y colo
A command 'mri_convert' can do that
See http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert
for a detailed description of the binary
Best
Krish
On Nov 17, 2008, at 5:57 PM, Al-Radaideh Ali wrote:
Dear FreeSurfer expert,
Any way that I can convert the mgz back to any analyze format so
tha
Dear FreeSurfer expert,
Any way that I can convert the mgz back to any analyze format so that different
softwares can open it?. if not, any software that can open the mgz other than
freesurfer?
Many thanks
Ali
This message has been checked for viruses but the contents of an attachment
may sti
it looks okay to me in the slices you sent, but it's hard to tell.
Basically you should check the ?h.white surface and see if it follows the
true boundary, and if not edit the wm.mgz to add/delete voxels
cheers,
Bruce
p.s. if you are still not sure, tar and gzip the subject and drop it on our
Hi Rysia,
I would look at wm.mgz loaded as auxiliary volume and switch to main volume
frequently to see, whether you have anything in wm.mgz, which needs to be
fixed. There is a tutorial on fixing wm.mgz on the followning web-page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatter
Dear Rudolph Pienaar,
could you please tell me if the Folding index and the sulc are in a way
correlated?
thank you
_
Hotmail to go! Hol' Dir Hotmail aufs Handy!
http://windowslivemobile.msn.com/BrowserServiceHotmail.aspx?lang=de-de_
Hello, Group,
I have a hard time to register the functional ROIs to the exact location
(x,y,z) on thickness map. I can't find articles that register the fsl result
onto freesurfer thickness map and then do the ROI analysis. Could someone
kindly list some references for me? I appreciate if anyo
Dear FreeSufer Experts,
I was running the recon-all autorecon-all -s bert step and I have got the
error message below. this is the first time I see this message although I have
analysed more than 7 MPRAGEs.
Any suggestions please?
Note: I usually call my subject as bert.
Thanks
Ali
[EMAIL
Christian,
I suspect that in example3-frontal and example2-frontal you have motion
artifacts causing increased intensity in the cortex. On the other,
example1-horizontal and example1-sagittal seem to have pretty low SNR,
specially in GM, but very good GM-WM contrast. I wonder, if they were not
hmmm, that's pretty bad ringing in your data. You could try editing the
wm to remove incorrect segmentations in these regions (if the orig surface
also extends out too far).
On Fri, 5
Sep 2008, Christian Scheel wrote:
Dear FS-Experts,
While checking the results of the autorecon2 process an
Hi Hong,
we've just rewritten the longitudinal stream to be significantly more
accurate. Unfortunately (for us) Nick is on vacation at the moment so
you're question will have to wait a few days for an answer. Repost next
week if you haven't heard before then.
Bruce
On Thu, 28 Aug 2008, Xie, H
Hello, group,
I am running longitudinal process step by step following the wiki page of
12 differences between longitudinal and recon-all process. But some needed
files are not generated by these 12 steps, for example, brain.mgz, wm.seg.mgz,
wm.asegedit.mgz, aseg.auto_noCCseg.mgz, wm.mgz
Hello, group,
I am running longitudinal process step by step following the wiki page of 12
differences between longitudinal and recon-all process. But some needed files
are not generated by these 12 steps, for example, brain.mgz, wm.seg.mgz,
wm.asegedit.mgz, aseg.auto_noCCseg.mgz, wm.mgz, fi
[EMAIL PROTECTED]
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There are two options:
1) You don't have libGLU installed.
Solution: Go to
http://rpm.pbone.net/index.php3/stat/3/srodzaj/1/search/libGLU.so.1()(64bit)
and install LibGLU
2) You have another version:
to find out run: find / -name "libGLU.so*" -print
Best Regards,
Pedro Paulo JR
2008/6/24 Damia
I think this may have been something that other people have figured out, and I
would be grateful to know how.
In the past week if I try to run autorecon-2 it fails. Running each individual
command that make up autorecon-2 it would seem that the error is with the final
stage (-cortribbon). The m
each subject should have one at:
$SUBJECTS_DIR/$subject/stats/aseg.stats
cheers,
Bruce
On Mon, 2 Jun 2008, Irene Mattisi wrote:
Hi Bruce!
yesterday I asked you if it is possible with the new FS version to obtain the
cerebellar cortical volume. You told me that it should be one of the entries
Hi Bruce!
yesterday I asked you if it is possible with the new FS version to obtain the
cerebellar cortical volume. You told me that it should be one of the entries in
the aseg.stats file (left and right cerebellar cortex). Now I'm not very good
with FS, so can you explain me where can I find
Hi Irene,
yes, it should be one of the entries in the aseg.stats file (left and
right cerebellar cortex).
cheers,
Bruce
On Sun, 1 Jun 2008, Irene Mattisi wrote:
Hi everybody,
I would like to know if with the new version of FS I can also obtain the
cerebellar cortical volume.
Thanks
Iren
Hi everybody,
I would like to know if with the new version of FS I can also obtain the
cerebellar cortical volume.
Thanks
Irene Mattisi
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And just to be clearer, qcache does not actually smooth the surfaces but
the thickness values on the surface. There is no need to smooth the
surfaces themselves.
doug
Nick Schmansky wrote:
The -qcache option performs smoothing at 5, 10, 15, 20 and 25mm FWHM
(plus 0mm, ie no smoothing). O
The -qcache option performs smoothing at 5, 10, 15, 20 and 25mm FWHM
(plus 0mm, ie no smoothing). On the design tab in Qdec, there are
selections for smoothing levels, and it will use the smoothed files
produced by -qcache.
On Mon, 2008-02-25 at 12:40 -0500, James Olkin wrote:
> Hello,
>I'm w
Hello,
I'm wondering if surfaces need to be smoothed (and if running "recon-all
-s SUBJECT -qcache" performs the smoothing) when analyzing data. Thank you.
-Ryan McGarry
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Hi Jon,
are the ventricles labeled properly in the aseg? Probably not. Try
running recon-all with -bigventricles and see if it improves.
cheers,
Bruce
On Mon, 7 Jan
2008 [EMAIL PROTECTED] wrote:
We are having trouble posteriorly with delineating the pial and white matter
surfaces in scans
Almost there Jessica. Just a few more comments on the "art of the bug
report". It is easiest for us if you put thing in a way that we can
just cut and paste from the email. Eg, if I were submitting this report
I would write:
ssh nexlin6
source /usr/local/freesurfer/nmr-std-env
setenv SUBJECTS
Hi Doug -
Does anyone know if there is an issue with mri_convert or unpacksdcmdir?
I ran mri_convert within unpacksdcmdir.
Here is what was typed at the command prompt:
unpacksdcmdir -src `/usr/pubsw/bin/findsession $subjName | grep PATH
| awk '{print $3}'` -targ ../ -cfg "$subjName"_unpack_fs
Dear All,
I have been trying to apply tkregister to our FEAT data as registration
using automatic FLIRT does not work accurately when only a couple of
functional slices are recorded. I use the option --fslregout to create a
FSL compatible transformation matrix, registering the example_funct to
the
Hi,I am wondering if part of this process can be turned into a script:I am
forming ROIs in freesurfer using tksurfer and a long list of talairach
coordinates. Here is my process:1) I use the "select_talairach_point x y z"
function, then I click the point that is highlighted on the brain from the
I think thiis was a bug that was fixed a while ago, but the fix might
not be in your version. I've put a linux version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_annotation2label
can you give it a try?
doug
Lisa Ronan wrote:
Hi All,
I am interested in crea
Hi All,
I am interested in creating a surface label for the temporal lobe. I have
tried running the mri_annotation2label calling the aparc.a2005s annotations,
then merging the appropriate labels. The process sees to work fine except no
label is made for S_temporal_superior. I understand from the -
hi ,I have solved the the probelm.Now, I have some new
question, just as belows:1 In the GUI interface, I can't type the
letters ,I don't know why?2 when I choose the volume in the
Morphometric-Measure, the Qdec runs error. how to solve it ? the screenshot
on the attachment.3 In the term
hi ,I have solved the the probelm.Now, I have some new
question, just as belows:1 In the GUI interface, I can't type the
letters ,I don't know why?2 when I choose the volume in the
Morphometric-Measure, the Qdec runs error. how to solve it ? the screenshot
on the attachment.3 In the term
QDEC has not been officially released yet -- soon!
[EMAIL PROTECTED] wrote:
> hi, when I run the qdec & command, the error show as below:
>
> [EMAIL PROTECTED]:~> qdec &
> [1] 10941
> [EMAIL PROTECTED]:~> qdec.bin: error while loading shared libraries:
> libexpat.so.0:
> cannot open shared object
hi, when I run the qdec & command, the error show as below:[EMAIL
PROTECTED]:~> qdec &[1] 10941[EMAIL PROTECTED]:~>
qdec.bin: error while loading shared libraries: libexpat.so.0: cannot
open shared object file: No such file or directory I do't
know how to deal with this problem. Could you tell
@nmr.mgh.harvard.edu
Subject: [Freesurfer] (no subject)
hi, when I run the recon-all -s wangrong -qcache command, It goes wrong, show
like that:
freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local
hi, when I run the recon-all -s wangrong -qcache
command, It goes wrong, show like that:
freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5 Setting up
environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME
/usr/local/freesurfer FSFAST_HOME
/usr/local/freesurfer/fs
Hi,
The instructions for this are on the wiki page you indicated previously,
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
When you run mris_preproc you specify thickness as the measure you are
looking at.
We have a new group analysis tool, with a GUI interface, that is n
FSGD file in the same
way that it is described on the wiki page.
Jenni
_
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED]
Sent: Monday, June 11, 2007 7:38 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] (no subject)
Thank you for
Thank you for previous help.Now I want to compare the cortical
thickness of the two groups. Mr Pacheco tells me to use the group analysis to
compare. When I read the manual of the group analysis (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis";>https://surfer.nmr.mgh.harvard
: freesurfer
Subject: [Freesurfer] (no subject)
hi,
I want to compare the occipital lobe's cortical thickness in 2 groups,but I
do't know how to do it? Athough I have seen some paper using FreeSurfer
software to compare the thickness, it has no detail procedure.
hanke
hi,
I want to compare the occipital lobe's cortical thickness in 2 groups,but I
do't know how to do it? Athough I have seen some paper using FreeSurfer
software to compare the thickness, it has no detail procedure.
[EMAIL PROTECTED]
2007-5-26
___
F
can you explain what you want to do? Compare the mean thickness of the
whole occipital lobe in 2 groups? Make a map of thickness?
On Sat, 26 May 2007, hankee wrote:
Hi, I have finished 3 demension data management by the Freesurfer software, but
I do¡¯t know how to compare the cortical thickne
Hi, I have finished 3 demension data management by the Freesurfer software, but
I do’t know how to compare the cortical thickness of the occipital lobe between
the patient group and the control group. Could you tell me the way to deal with
that? Thank you very much!
[EMAIL PROTECTED]
2007-5-2
Hi, I have finished 3 demension data management by the Freesurfer software, but
I do’t know how to compare the cortical thickness of the occipital lobe between
the patient group and the control group. Could you tell me the way to deal with
that? Thank you very much!
[EMAIL PROTECTED]
2007-5-
OK, thanks,
Francesca
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wednesday, May 16, 2007 2:36 PM
To: Bagnato, Francesca (NIH/NINDS) [E]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] (no subject)
I think by default we generate both parcellations
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