results from FSl with th eone from Freesurfer: TRACULA or dt_recon method.
Please advise.
Many thanks,
Antonella
From: Anastasia Yendiki
To: Antonella Kis
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Friday, November 11, 2011 4:45 PM
Subject: Re: [Frees
Dear all:
Based on the DTI Basic Tutorial I understood that MRI data can be resampled &
registered in CVS space (by running mri_cvs_register), but alternatively can
be normalized in any other (for example, MNI or Talairach). Can you please let
me know how this can be done in MNI152 spac
s for your time and help.
Best regards,
Antonella
From: Lilla Zollei
To: Antonella Kis
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Monday, November 14, 2011 4:13 PM
Subject: Re: [Freesurfer] dt_recon registration
Hi Antonella,
> 1) I will be very g
his the equivalent file to fa-masked.ANAT+CVS-to-avg35.mgz (if I use the
CVS space)? In this case I don't need to run the last mri_vol2vol command?
Sorry for asking so many questions but it is very confusing the online material.
Many thanks!
Antonella
From: Lilla Zollei
To: Antonella Ki
;lzol...@nmr.mgh.harvard.edu"
To: Antonella Kis
Cc: Lilla Zollei
Sent: Friday, November 18, 2011 2:11 PM
Subject: Re: cvs_avg35
Hi Antonella,
> I know that mri_vol2vol just applies the transform. --no-save-reg just
> tells the
> command not to save a copy of the inverse transform th
;lzol...@nmr.mgh.harvard.edu"
To: Antonella Kis
Cc: Lilla Zollei
Sent: Friday, November 18, 2011 2:11 PM
Subject: Re: cvs_avg35
Hi Antonella,
> I know that mri_vol2vol just applies the transform. --no-save-reg just
> tells the
> command not to save a copy of the inverse transform th
;lzol...@nmr.mgh.harvard.edu"
To: Antonella Kis
Cc: Lilla Zollei
Sent: Friday, November 18, 2011 2:11 PM
Subject: Re: cvs_avg35
Hi Antonella,
> I know that mri_vol2vol just applies the transform. --no-save-reg just
> tells the
> command not to save a copy of the inverse transform th
Dear Lilla,
1) I will be very grateful if you let
me know what data I should use for my fsgd when I run the GLM group
analysis: the dti data after running the dtrecon (for example for my first
control I called this directory C01_dti or the FS data after running recon-all
on the structural data i
Dear Lilla,
Sorry I am bother you one more time with a question: I was trying to display
the dtrecon result smore exactly the GLM group analysis results.
After I did the
mri_concat */fa-tal.nii --o group-fa-tal.nii
I created a mask:
mri_concat */mask-tal.nii --o group-masksum-tal.nii --mean
Dear experts,
I would appreciate if you can provide me with the
TAL-to-avg35 template.
Thank you very much!
ANtonella
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The inform
Dear FS experts,
1) From dt_recon --help I found that:
Registration of lowb to same-subject anatomical using FSLs flirt creates
mask.nii and register.dat
I would appreciate if you can let me know if mask.nii is theresampled image of
any of my diffusion related files in the structural space.
Player
To: Antonella Kis
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Wednesday, November 30, 2011 5:11 PM
Subject: Re: [Freesurfer] resampled image of the diffusion data to structural
data
Antonella,
Please refer to this website for help with group analysis:
https://surfer.nmr.mgh.h
Dear all:
I am doing an FA group study (controls vs. patients without any
covariant so my C = +1.0 -1.0) and I want to see if there are
any clusters that survives by multiple comparison so I ran:
mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\
--fsgd DTI_group_analysis.fsg
-White-Matter
I am not sure if I am doing something wrong but is there a way that I can
visualize this clusters with Freeview?
Many thanks,
Antonella
From: Douglas N Greve
To: Antonella Kis
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Monday, December
Dear All,
I was trying to find an explanation of the color map: min, Mid, MAx and Offset
values in Freeview. Can someone please explain me if I have the color map set
it up as HEAT what is the meaning of this values if for example I am viewing
the existing clusters after multiple comparison for
Dear All,
1) On the FS Diffusion Tutorial webpage I found for the Group Analysis the
following scrip: GroupAnalysis.csh with the following instruction:
# Assemble input for group analysis
set type = CVS-to-avg35# alternatively could be 'TAL-to-avg35' or
'MNI-to-avg35'
Can you please e
Dear All:
I was using dtrecon on my DTI data and by default it will register my
diffusion data (fa) on the TAL space so i got the fa-tal.nii file and the
fa-tal-nii.reg the file which encodes the transformation while registering to
the TAL space.
Can you please advise me what is the best way
much!
Antonella
From: Lilla Zollei
To: Antonella Kis
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Tuesday, December 6, 2011 5:01 PM
Subject: Re: [Freesurfer] Diffusion Tutorial and GroupAnalysis.csh
Hi Antonella,
> 1) On the FS Diffusion
Dear All:
I would like to know if to check my DTI's data registration on the anatomical
data having the registration encoded in the registration.dat by tkmedit as
below:
tkregister2 --mov /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51_dti.nii.gz --s
/media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51
Dear Lilla,
I was running the mri_cvs_register with the flag --noaseg and no argument for
my target template so as I understood the registration was done on the cvs
template as you can see below:
mri_cvs_register--mov P01 --noaseg
After registration I got 4 files:
combined_tocvs_avg35_elre
Dear All:
I am trying to resample my DTI data in the CVS space and seems that after I ran
the mri_cvs_register with the flag --noaseg and no argument for my target
template (so the registration was done on the cvs template) I got the following
error:
ERROR: cannot find or read
/media/1Tra/A
Dear Lilla,
I will appreciate a lot if you can help me understand what is the meaning of
the results after running after running mri_cvs_register and the GLM group
analysis.
More exactly, I followed all the instructions from the webpage:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diff
from the
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion (I don't see
anymore the image with red and blue clusters posted on this website. Is
something going on?)
Thank you very much!
Antonella
From: Lilla Zollei
To: Antonella Kis
Hi,
I am doing a DTI group analysis study more exactly I am interested to see any
changes in the FA values within two groups: controls versus patients (children
with epilepsy). I introduced a white matter mask that will ensure that I am
only considering diffusion values in the white matter
Dear experts,
I was running the mri_cvs_register for a few times for a subject and I am
getting an error. The registration will not bwe completed but I got most of the
files so I wonder if I need to re-run the whole registration steps or there is
a way to just re-run the registration from the s
Dear Lilla,
I solved the problem with my registration so now is working well but I will be
very grateful if you can help me with the following questions:
For the DTI group analysis study I am interested to see any changes in the FA
values within two groups: controls versus patients (children
Hi,
I have a problem with mri_cvs_register. I am getthing the following error and I
will be very grateful if you can help me to fix it (I am don't understand what
means this errors).
Also, after running a group analysis with mri_glmfit-sim and using the option
--grf (so I have the survining
Dear Lilla,
I wonder if I can use my results from the mri_cvs_register to do a non_FA group
study analysis, more exactly I am interested on the mean diffusivity (adc.nii
from dt_recon).
I hope I don't need to run again the registration again.
Since from the significant map I can only find/ tell
Dear FS team,
I wonder if I can use my results from the mri_cvs_register to do a non_FA group
analysis, more exactly I am interested on the mean diffusivity (adc.nii from
dt_recon).
I hope I don't need to run again the registration again.
Since from the significant map I can only find/ tells
Dear FS team,
Can use my results from the mri_cvs_register to do a non_FA group analysis,
more exactly I am interested on the mean diffusivity (adc.nii from dt_recon).
Since from the significant map I can only find the p values how can I see if
there is an increase or decrease of the FA va
or decrease of the FA values for controls versus patients?
Many thanks,
Antonella
From: Bruce Fischl
To: Antonella Kis
Cc: "freesurfer@nmr.mgh.harvard.edu" ;
"lzol...@nmr.mgh.harvard.edu"
Sent: Wednesday, January 11, 2012 11:13 AM
Subj
trols group versus patients group.
Please advise me.
Thank you.
Antonella
From: Bruce Fischl
To: Antonella Kis
Sent: Wednesday, January 11, 2012 11:40 AM
Subject: Re: [Freesurfer] Non_FA Group study
Hi Antonella,
can you post this type of question t
Dear Bruce,
Once again many thanks for helping.I am not using tracula. I used the dt_recon
and I have done the registration for my FA data on the cvs space using the
mri_cvs_register. I used the GLM group analysis method after I concatenate FA
from individuals into one file and used
mr
Dear Bruce,
Once again many thanks for helping.I am not using tracula. I used the dt_recon
and I have done the registration for my FA data on the cvs space using the
mri_cvs_register. I used the GLM group analysis method after I concatenate FA
from individuals into one file and used
mri
Dear Doug,
I need some help regarding my FA and non-FA group analysis study. I am not
using tracula. I used the dt_recon and I have done the
registration for my FA data on the cvs space using the
mri_cvs_register. I used the GLM group analysis method after I concatenate FA
from individuals i
From: Douglas N Greve
To: Antonella Kis ; freesurfer
Sent: Friday, January 13, 2012 2:13 PM
Subject: Re: Fw: [Freesurfer] FA and non_FA group analysis
Look at the original sig map. This will be signed (blue and red/yellow), with
blue being neg, red/yellow being
Dear all,
I am trying to convert my DTI image which was previous resampled to CVS space
from an .mgz format to a .nii.gz format. When I resampled to CVS space I used
the nearest interpolation.
I used for converting this .mgz image to .nii.gz the mri_convert as you can see
below:
mri_convert -
Dear all,
I wonder why when I am using the mri_convert to convert my mgz image which is
very little tilted to the left into a nii.gz image which appears very little
tilted to the right instead to keep the same direction to the left.
I was using:
mri_convert
/media/2Tra/Antonella_2011/DTI_F
Dear all,
On the FS Tutorial/Diffusion the FA masked is defined as:
mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \
$SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
$TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgzand when it follows the resampling on
the CVS space I see:
mri_vol2vol --targ $FREESURFER_HOME/
Hi,
I would like to do a Group Analysis for my FA data.
For all my subjects (controls + patients) I have all the
fa-masked.ANAT+CVS-to-avg35.mgz (the resampled registered image to CVS space).
I am not sure if my steps for the Group Analysis are the right one:
1) Concatenate FA from individuals
sis.glmdir \
--grf 3 neg \
--cwpvalthresh .05 \
--overwrite
Thank you.
Antonella
From: Douglas N Greve
To: Antonella Kis
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Monday, January 23, 2012 4:50 PM
Subject: Re: [Freesurfer] mri_glm with grf over CVS
Dear all,
I would like to know if while doing a group analysis for my FA data and I do
the correction by multiple comparisons for the clusters:
mri_glmfit-sim \
--glmdir Group_Analysis.glmdir \
--grf 3 neg \
--cwpvalthresh .05 \
--overwrite
what exactly is defined the cwpvalthresh. I m
Hi Doug,
Sorry I forgot to ask one more question: after I am getting my clusters for my
FA group study should I use the fsaverage (which is not on the CVS space) or
the concatenated file GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz (registered
over the CVS space) or I should use the CVS space
las N Greve
To: Antonella Kis
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Thursday, January 26, 2012 3:17 PM
Subject: Re: How to visualize the group results after corrections by multiple
comparison
Use cvs_avg35 instead of fsaverage
doug
Antonella Kis wrote:
> Hi Doug,
>
&g
Hi,
I was trying to run for my FA group study the following:
mri_glmfit-sim \
--glmdir Group_Analysis.glmdir \
--sim neg perm 1 3 permcsd\
--cwpvalthresh .05
but I got an error: Flag permcsd unrecognized and then is asking me agout --sim
sign.
Can you please help?
THANK YOU!
Antonella
__
Hi Doug,
I wonder how many hours it can take the mri_glmfit-sim with perm option. This
is what I was running yesterday from 2 pm and is still not completed.
It can take so long or there may be something wrong? I did not get any error
but I have the same number of files as yesterday in my Group
dear All,
I would like to know if I am running the
mri_glmfit-sim \
--glmdir Group_Analysis.glmdir \
--sim perm 1 3 permcsd \
--sim-sign neg \
--cwpvalthresh .05
and I want to change the --sim-sign from neg to positive if I need to run again
the whole simulation or I can just run:
mri_glm
Dear all,
I was running the simulation:
mri_glmfit-sim \
--glmdir GroupAnalysis_abs.glmdir \
--sim perm 1000 3 permcsd \
--sim-sign abs \
--cwpvalthresh .05
and unfortunately I got the following error: mri_volcluster --in
GroupAnalysis_pos.glmdir/contrast/sig.mgh --mask
GroupAnalysis_pos.glm
Dear Doug,
I was running the
mri_glmfit-sim \
--glmdir GroupAnalysis_abs.glmdir \
--sim perm 1000 3 permcsd \
--sim-sign abs \
--cwpvalthresh .05
just to get an idea of how my FA Group Analysis data is looking and I got an
error before to get the permcsd.sig.cluster.summary file from the
mri
Dear All,
Can someone help me to find out what is the equivalent of the
fsaverage/mri.2mm/reg.2mm.dat when I use the cvs_avg35 template, I mean I
register my FA data over the CVS space?
I suppose I will need to repalce the fsaverage/mri.2mm/reg.2mm.dat in the
following command:
mri_volclust
clear!
Antonella
From: Douglas N Greve
To: Antonella Kis
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Wednesday, February 1, 2012 1:17 PM
Subject: Re: [Freesurfer] Error with mri_glmfit-sim -- sim perm
It is looking for the aparc+aseg.mgz so it can
Dear All,
How I can get the FA values in a table after running the GLM group analysis for
my FA data. I have GroupAnalysis-FA-MASKED.ANAT+CVS-to-avg35.mgz and the gmldir.
Thank you.
Antonella
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h
Dear all,
I use dt_recon to process my DTI data and get my fa.nii for the individual
subjects. I wonder if the FA values can be greater that one since for all my
subjects I got the FA max value graeter than one. Is something wrong with my
data or this is acceptable? I saw in most of the paper
Dear Experts,
I completed my FA group analysis and I expect my FA to be larger in controls
versus patients (based on the uncorrected results). I corrected by multiple
comparisons using:
mri_glmfit-sim \
--glmdir GroupAnalysis_pos.glmdir \
--sim perm 1000 3 permcsd \
--sim-sign pos \
--cwpvalth
Dear Experts,
I completed my FA group analysis and I expect my FA to be larger in controls
versus patients (based on the uncorrected results). I corrected by multiple
comparisons using:
mri_glmfit-sim \
--glmdir GroupAnalysis_pos.glmdir \
--sim perm 1000 3 permcsd \
--sim-sign pos \
--cwpval
Dear Doug,
When I run the:
mri_glmfit-sim \
--glmdir GroupAnalysis_pos.glmdir \
--sim perm 1 3 permcsd \
--sim-sign pos \
--cwpvalthresh .05
I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters
summary so as you recommended I am running the
mri_volcluster --in Grou
Dear Doug,
When I run the:
mri_glmfit-sim \
--glmdir GroupAnalysis_pos.glmdir \
--sim perm 1 3 permcsd \
--sim-sign pos \
--cwpvalthresh .05
I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters
summary so as you recommended I am running the
mri_volcluster --in G
Dear Experts,
I completed my FA group analysis and I expect my FA to be larger in controls
versus patients (based on the uncorrected results). I corrected by multiple
comparisons using:
mri_glmfit-sim \
--glmdir GroupAnalysis_pos.glmdir \
--sim perm 1000 3 permcsd \
--sim-sign pos \
--cwpv
: Douglas N Greve
To: Antonella Kis
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Wednesday, February 8, 2012 11:37 AM
Subject: Re: Reposting: Clusters by Multiple comparison
Hi Antonella, the right way to do it is to figure out what is going wrong with
mri_glmfit-sim. Did it obvious
Dear All,
I would like to know how I can get the RD radial diffusivity and AD axial
diffusivity after I was running dt_recon. I can see my mean diffusivity adc.nii
and a file called radialdiff.nii but I am not sure which one is the AD and Rd.
Can you please tell me the name of this files AD and
Dear Doug,
Can I run the mri_volcluter without --reg ?
I am asking this because when I run:
mri_glmfit-sim \
--glmdir GroupAnalysis_ADC.glmdir \
--grf 3 neg \
--cwpvalthresh .05 \
--overwrite
gives me the following error (I also attached the log file):
Also, does neg
es.
Thanks for helping.
Antonella
From: Douglas N Greve
To: Antonella Kis ; freesurfer
Sent: Tuesday, February 14, 2012 1:18 PM
Subject: Re: [Freesurfer] Clusters locations
Antonella Kis wrote:
> Hi Doug,
>
> 1) I would like to report the MNI coordinates and also a more exactly
>
Dear Doug,
Can I run the mri_volcluter without --reg ?
I am asking this because when I run:
mri_glmfit-sim \
--glmdir GroupAnalysis_ADC.glmdir \
--grf 3 neg \
--cwpvalthresh .05 \
--overwrite
gives me the following error (I also attached the log file):
Also, does ne
Dear all,
I completed my DTI group analysis at subcortical level on the CVS space and
found clusters that survived by multiple comparisons. The results shows that FA
is decreasing in patients vs. controls.
I used then the same subject to do a structural group analysis to compare the
cortical
Dear all,
I completed my DTI group analysis at subcortical level on the CVS space and
found clusters that survived by multiple comparisons. The results shows that FA
is decreasing in patients vs. controls.
I used then the same subject to do a structural group analysis to compare the
cortica
Dear Doug,
Is possible to get more clusters if I correct by multiple comparisons so I run:
mri_glmfit-sim \
--glmdir lh.GroupAnalysis_Thickness_15.glmdir \
--cache 2 pos \
--cwpvalthresh .999 \
--overwrite
than the number of clusters in the sig.mgh so the uncorrected results?
cwpvalthresh .999
Dear All,
I was running dt_recon on my DTI data and one output file is the eigvals.nii --
maps of the eigenvalues. I know that the diffusivity along the principal axis,
λ1 represents the longitudinal diffusivity or the axial diffusivity (or even
the parallel diffusivity λ∥).Can you please advis
Hi,
I have few questions and I will appreciate if anyone can help:
1) Can I get more clusters after I correct for multiple comparison than the
number of clusters I have in the uncorrected results? Is this possible?
2)When I change the smoothing from fwhm 10 to fwhm 20 for example why I a
Dear Doug,
I wonder if you could get the chance to finish the work regarding the Nearest
Cortical Label (Annotation) for the CVS space.
Also, I have few questions and I will appreciate if anyone can help:
1) Can I get more clusters after I correct for multiple comparison than
the number of
Dear Doug,
I wonder if you could get the chance to finish the work regarding the Nearest
Cortical Label (Annotation) for the CVS space.
Also, I have few questions and I will appreciate if anyone can help:
1) Can I get more clusters after I correct for multiple comparison than
the number
Dear All,
Is there a way that I can open my rh.aparc.stats files (saved in stats after
recon-all) in MATLAB as a matrix? I would like to concatenate all the
rh.aparc.stats files from all my subjects.
Many thanks,
Antonella
___
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Dear All,
Is there a way that I can get my clusters location (segmentation and/or
annotation) inthe MNI space if I know the MNI coordinates?
Many thanks.
AK
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Dear All,
I would like to know what is the best way in catching the uncorrected clusters
results from the sig.mgh for a structural study:
Should I use the:
mri_glmfit-sim \
--glmdir lh.GroupAnalysis_Thickness_15.glmdir \
--cache 2 pos \
--cwpvalthresh .99 \
--overwrite
But in this case I am
Dear All,
1)I would like to know what is the best way in catching the uncorrected
clusters results from the sig.mgh for a structural study:
Should I use the:
mri_glmfit-sim \
--glmdir lh.GroupAnalysis_Thickness_15.glmdir \
--cache 2 pos \
--cwpvalthresh .99 \
--overwrite
But in this case I
Hi,
I am trying to find a way to get the segmentation/cortical label (to determine
corresponding brain structures) in MNI space for a cluster for which I know the
MNI coordinates. How can I do this?
Many thanks.
Antonella___
Freesurfer mailing list
Hi Doug,
Sorry to bother again and I hope I'm not becoming too annoying with my
questions. I will be very grateful if you can advise what to do for the
following:
1) I am still struggling to find a way to localize my clusters in other words
to get the nearest cortical label(annotation
Thanks Doug.
You mean by subject to define the subject in the fs_tal2surf which by default
is 'subj': FreeSurfer subject
% {default = 'fsaverage'} to be subj = cvs_avg35?
Thanks.
Antonella
From: Douglas N Greve
To: Antonella Kis
Dear All,
I am trying to understand what should be my -fthresh and -fmax or -fmin and
-fmax values while visualizing in tkmedit the significant map of uncorrected
results so I can see all the clusters in this map. Further,I want to see what
clusters from this map did not survived after correct
Dear FS experts,
I would like to know if for a Diffusion tensor imaging (DTI) tractography study
with TRACULA I can use my previous results from FSTutorial/Diffusion more
exactly my results after running dt_recon and registrations on the CVS space.
If not can you please advise me if for a DTI p
Dear FS experts,
I would like to know if for a Diffusion tensor imaging (DTI) tractography
study with TRACULA I can use my previous results from
FSTutorial/Diffusion more exactly my results after running dt_recon and
registrations on the CVS space. If not can you please advise me if for
a DTI prob
only statistics.
This is what I meant by my previous results.
Thank you for your time and help.
Antonella
From: Anastasia Yendiki
To: Antonella Kis
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Wednesday, March 28, 2012 2:07 PM
Subject: Re: [Fr
Hi,
I would like to know if for a probabilistic tractrography using TRACULA I can
use the CVS space as a common template to register the diffusion data instead
of MNI template.
How I should change for the CVS space the following:
set doregmni = 1 which is the default for the MNI space. If I wa
Dear All,
I would like to know if there is a way to eliminate from my significant
clusters (grf.th3.pos.sig.cluster.mgh) obtained after running mri_glmfit-sim
with grf option and using mri_volcluster the clusters with a size smaller than
50 mm^3 or in other words to keep only clusters with a v
Dear FS experts,
I was using FreeView to see all my FA's clusters position from my DTI data
that survived after correction by multiple comparisons. This clusters are
locate in different slices and I would like to know if there is a way to print
out in the same time different slices not only on
Dear FS experts,
I was using FreeView to see all my FA's clusters position from my DTI data
that survived after correction by multiple comparisons. This clusters are
locate in different slices and I would like to know if there is a way to print
out in the same time different slices not only
Hello,
I just received my confirmation for posting on the mailing list.
Original Message
Subject: Welcome to the "Freesurfer" mailing list (Digest mode)
From:freesurfer-requ...@nmr.mgh.harvard.edu
Date:Fri, June 17, 2011 4:25 pm
To
Hello,
I just started to use the FreeSurfer software and until now I used an old
version V. 5.0.0. I wonder if to install the new version I have first to
remove the old one or I can do just updates for the old version.
If I downloaded the new version V.5.1.0 what will be the next step, how I
can
Good afternoon,
It is for the first time I am using FreeSurfer and I used only a little
the old version V.5.0. For this version my environment variable was
FREESURFER_HOME. If I am still having my old version V. 5.0 and also I
downloawded the new realeased version how I can install my new versi
Can you please let me know how I can install on top of an old version the
new version FreeSurfer v.5.1.0?
Thank you.
Antonella
--
--
Dr.Antonella Kis, PhD
Sessional Lecturer
Life Sciences, Physics Department
University of Toronto at Scarborough
Clinical Research Pr
Hello,
Can you please let me know how I can install on top of an old version the
new version FreeSurfer v.5.1.0?
Thank you.
Antonella
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Hello Experts,
I apologise for the stupidity of this question, but I am not used to using
Linux, but I need to uninstall my Freesurfer from the Desktop and then
reinstall it,however, I have no idea how to uninstall in Linux.
I was trying to execute: rm -rf /desktop/freesurfer but is not doing
Dear All,
I just installed my new FS version (I saved my old version under
freesurfer_backup). I am getting an error when I am running recon-all on
my GNU/LINUX.Do I need a license file before running? What steps I need to
follow before running the new FS version?
Here is the outcome:
[elysa@
Dear experts of the Freesurfer,
I am just learning freesurfer software and I was running recon-all for a
subject in my directory. I can view the volumes and surfaces and I would
be very grateful if you can list the next steps to be followed.
Do I need to make a data correction(check my data)
Dear Freesurfer experts,
I am still a beginer in using Freesurfer v.5.1.0
I finished running the recon-all and I am trying to visualize the volumes
and surfaces but I got an error wile using tkmedit. I will appreciate any
help, suggestions.
This is from bugr:
FREESURFER_HOME: /usr/local/freesurf
Dear Freesurfer experts,
I am trying to visualize the volumes and surfaces but I got an error wile
using tkmedit.
I will appreciate any help, suggestions.
This is from bugr:
FREESURFER_HOME: /usr/local/freesurfer/
Build stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
RedHat release: Fedora
Hi,
I have some problems with tkmedit. The recon-all finished without
problems, but when using tkmedit the following error occured:
/usr/local/freesurfer//tktools/tkmedit.bin: error while loading shared
libraries: libXmu.so.6: cannot open shared object file: No such file or
directory
I was
Hello,
I have some problems with tkmedit. The recon-all finished without
problems, but when using tkmedit the following error occured:
/usr/local/freesurfer//tktools/tkmedit.bin: error while loading shared
libraries: libXmu.so.6: cannot open shared object file: No such file or
directory
T
--
Dr.Antonella Kis, PhD
Clinical Research Project Coordinator
The Hospital for Sick Children (SickKids)
Diagnostic Imaging Department
Neurosciences and Mental Health
Sessional Lecturer
Life Sciences, Physics Department
University of Toronto at Scarborough
Hello,
ith Tkmedit (Bruce Fischl)
--
Message: 1
Date: Wed, 29 Jun 2011 10:49:56 -0400 (EDT)
From: Bruce Fischl
Subject: Re: [Freesurfer] Error with Tkmedit
To: Antonella Kis
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
Content-Type: text/plain; charset=&q
!
Antonella
Hi Antonella,
those regions should be compiled in the stats/aparc.annot.ctab file that
should be easy to import into excel or other packages for analsys and
plotting.
cheers
Bruce
On Mon, 4 Jul 2011, Antonella Kis wrote:
>
>
> Good morning Bruce,
>
> I posted my
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