Hello Experts,
We used the brainstem segmentation that is built into FS 6.0, to interrogate
midbrain volumes. My question was: the way FS segments the midbrain, does it
include the cerebral peduncles?
cheers,Cat___
Freesurfer mailing list
Freesurfer@nm
no, seems to be plenty left.. 240 TB
On Wednesday, August 26, 2015 12:23 PM, Bruce Fischl
wrote:
they are empty (zero size). Maybe your disk filled up?
On Wed, 26 Aug 2015, Cat Chong wrote:
> Hi Bruce,
>
> Yes, they exist.
> but this seems strange...
> -rwx--
PM, Bruce Fischl
wrote:
Hi Cat
do those file exist? What does ls -l tell you for them?
Bruce
On Wed, 26 Aug 2015, Cat Chong wrote:
> Dear Experts,
>
> I am trying to use Freeview to view volumes using the command listed on the
> website: http://freesurfer.net/fswik
Dear Experts, I am trying to use Freeview to view volumes using the command
listed on the website:
http://freesurfer.net/fswiki/FsTutorial/OutputData_freeview but the only volume
that loads is the aseg. I am not able to load the T1, wm, or brainmask mgz’s .
either from the terminal or through
Dear Tracula Team,
Quick question: Is Tracula able to to process diffusion kurtosis data, and
yield, let's say, 'mean kurtosis' parameters for specific fiber
tracts?cheers,Cat___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mg
Dear Anastasia,
I am trying to visualize the tract p-values along one pathway as shown in the
tutorial.http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
I have implemented the p-values into a text file but I am uncertain of what the
settings for the heat scale thresholds ough
for where to find the output.
a.y
On Mon, 21 Jul 2014, Cat Chong wrote:
> Hello Anastasia,
>
> I ran Tracula on Freesurfer 5.3 but without the 2013 Tracula updates. Now,
> I would like to use the command "dwi_motion" on my data. I have installed
> the updates, but
Hello Anastasia,
I ran Tracula on Freesurfer 5.3 but without the 2013 Tracula updates. Now, I
would like to use the command "dwi_motion" on my data. I have installed the
updates, but will I have to completely reprocess my data inducing steps
trac-all -prep, trace-all -bedp, and trac-all path i
Thanks Chris,
I will try that right now!
> On Jul 18, 2014, at 2:37 PM, Chris Watson
> wrote:
>
> Do you have the latest version of Tracula? There was an update posted after
> FS 5.3 came out.
>
>> On 07/18/2014 04:48 PM, Cat Chong wrote:
>> Hello Anastasia
Dear Anastasia,
Another quick question:
We found significant differences in two subject groups for the AD_AVG as well
as the AD_AVG_Weight, which is stated as the "weighted average over the entire
path distribution'. Could you tell me how the average weight is calculated and
why it would be be
Hello Anastasia,
I have just converted pathstas.overall.txt files to a table for group analyses.
Now, I am trying to convert pathstats.byvoxel.txt files to a table for group
analyses using the command:
trac-all -stat -c
I am receiving the error message: ERROR: flag -stat unrecognized
I am work
Dear Experts,
I was wondering if you could possibly help me with a
reviewer-related question:
We conducted a between-group-analysis estimating the
interaction between cortical thickness and age.
In summary, we wanted
to investigate whether the interaction between cortical thickness and age is
Dear Doug,
Thank you for your instantaneous response!
Correcting for disease burden was actually a reviewer
comment.
We calculated mean
cortical thickness estimates for regions that showed vertex-wise age-related
cortical thickness differences between groups (using qdec) and then graphed out
Dear FreeSurfer Experts,
We are trying to run a between group analysis (1 patient
group 1 control group) within qdec. We are interested in investigating
age-related
thickness differences between groups. Our fixed factors are ‘group’ and our
continuous covariate is ‘age’. We
would like to contr
Dear Experts,
I was hoping you could help me with the following problem.
Tracula failed when I attempted to use Siemens (Skyra) dicoms as input for the
configuration file, so I converted the dicoms to niftii format using dcm2nii.
I used the gradient information of the bvec file created by dcm2
Dear Experts,
I am able to to initiate recon-all but it fails at various stages during the
recon-all process even though I should have plenty memory available to run the
process.
This is the error message I am getting and below is the log file. I am using
the freesurfer-Darwin-lion-stable-pub
1002.mgz
mri_convert: extra arguments ("1002/IM-0001-0001.dcm" and following)
type mri_convert -u for usage
I am not quite sure where I am making an error.
Cat
From: Douglas N Greve
To: Cat Chong ; "Freesurfer@nmr.mgh.harvard.edu"
Sen
Hello Experts,
I am trying to run the mri_convert command prior to the
recon-all command on Siemens T1 dicoms (as suggested in the archives). I am
using freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0, Mac OS X
Lion 10.7.5
I am using the command below:
mri_convert -it siemens_dico
Hello Experts,
Please forgive another question.
I have run 59 people through the recon-all freesurfer longitudinal stream with
2 timepoints (tp1id, tp2id).
I want to run these subjects through "tracula" next, since the same people also
received repeated Tensor imaging.
To process everybody t
Hello Experts,
Unfortunately I am currently only able to run tracula on a personal computer,
System Version: Mac OS X 10.6.7 (10J869)
Kernel Version: Darwin 10.7.0.
I have no problem running a single subject on the dmrirc_single subject
configuration file. When I try to run several sub
Hello Experts,
I am running bedpost x through fsl on
the dmri directory (as advised in a previous post). I receive the fsl
error message: “child process exited abnormally”. The command
line error states:
switching from
/8000_tracula/8000_tracula_out/8005_DTI/dmri to
/8000_tracula/8000_tracula_o
Hello Experts
I am still at the first pre-proc step
for Tracula and although the script is running, it seems to have
difficulty initializing the first pathway (1 out of 18)
Please see below script excerpt:
Is that normal that it takes this many
trials to initiate a pathway?
Cheers,
Catherine
WA
Hello Experts:
I am running the first pre-processing
step in Tracula and come across the error:
set: Variable name must begin with a
letter.
Below is an excerpt of the script which
seems to be running fine. Did I make a mistake in my
dmrirc_single_subject file?
Cheers,
Catherine
fmris-mac
Thank you for the almost immediate reply.
Yes, it seems to be otherwise working,
cheers,
Cat
From: Nick Schmansky
To: Cat Chong
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Wednesday, August 29, 2012 2:35 PM
Subject: Re: [Freesurfer] freeview tra
Dear Experts:
I have worked my way through Tracula and
things seem to work fine, but when I try to view my tractography
outputs I get the following persistent error using freeview (copied
below).
I am using a Mac OS X 10.6.7.
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Could this
Hello Experts,
Just a quick question: Do the Tracula updates(dmri_mergepaths, etc) for
snow_leopard replace the 'old' ones in freesurfer's "bin" directory?
cheers,
Cat
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https://mail.nmr.mgh.har
Hello Experts,
I get the following error when running trac-all:
*** set a breakpoint in malloc_error_break to debug
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 13th slice
I am using the update for trac-all that was recommended, but it still isn't
working.
I would be gratefu
Dear Experts,
I am occasionally noticing some 'pinching' on the inflated brain surfaces
around the temporal lobe pole. When I check the brainmask.mgz files, the raised
areas are due to a 'bubble' of pial surface forming on top of pial surface.
Upon checking white matter and grey matter boundari
Dear Freesurfers,
I would like to show several ROI labels that we created on top of an an
average brain which demonstrates the group results of cortical thinning with
advancing age. In qdec, when I go into File>Load Label, I can only view one
label at a time. Is there a way to show severa
Hello Freesurfers,
I have created an ROI label for 80
subjects in qdec. My question is the following: Is there a command
that will create a .stats file for all my subjects rather than using
the below command on each person individually?
mris_anatomical_stats -l rh.ento.label \ -t rh.thickness -b
Dear Freesurfers:
We have a large group of subjects (for which we have two time-points)
that were run through the
recon-all stream using 5.0. We
have done no manual editing yet.
We would like to do a longitudinal analysis of these
subjects using 5.1 by comparing both time-points for each su
Dear Freesurfers:
I am comparing two groups in qdec. I am looking at the scatter plot function
for a specific vertex for thickness to age correlation. If I "click" on a dot
on the scatter plot, it will provide me the thickness values for that vertex
for a specific person in the scatter plot fu
Hi Doug,
I spoke too soon. I tried to follow your advice and run either command:
In a terminal, cd to the GLM directory inside qdec directory and then cd to the
folder of the contrast of interest and run
mri_segstats --id 1 --slabel fsaverage lh yourlabel --i gamma.mgh --sum
yourlabel.sum
t
Hello Experts,
I am analyzing cortical thickness of two groups (APOE 4carries vs. noncarriers)
in freesurfer with age as a co-variate.
I am uncertain about the statistical differences behind:
1)Does the correlation between thickness and age accounting for APOE, differ
from 0?
in contrast to
Hello Experts,
I apologize for the basic question. I am currently examining the cortical
thickness differences between two groups, contolling for age. On the
scatterplot, I thought there was a way to view slopes and intercepts (between
groups)? I can't however, figure out a way to get these tre
Hello Experts:
In qdec, I would like to analyze if the thickness- entorhinal volume
correlation differs between APOE positive and negative subjects accounting for
age.
I have chosen age as a nuisance variable and entorhinal volume as a covartiate.
( hope this is correct)
Results show me several
eers,
catherine
From: Bruce Fischl
To: Cat Chong
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Friday, January 6, 2012 9:11 AM
Subject: Re: [Freesurfer] SPGR compressed files
Hi Catherine
can you explain what you mean by compression?
Bruce
On Fri, 6 Jan 2012, Cat Chong
wrote:
>
Hi Experts,
We wanted to run clinical scans that underwent some compression at the scanner
through freesurfer.
I just wanted to seek confirmation that SPGR sequences that have undergone
slight compression can not be run through freesurfer, is that correct?
thank you,
catherine
Hi Experts:
Sorry, I forgot to attach the following error message I get when I attempt to
generate stats data tables:
I would be grateful if you tell me what I am doing wrong,
catherine
asegstats2table --common-segs --meas volume --tablefile
/5000_series/5000_series/qdec/stats_tables/aseg.volu
Hello Experts:
Is is possible to run 3D SPGR's with contrast (gadolineum) through freesurfer?
Also, in a separate dataset, we have 3D SPGR's that have unfortunately been
compressed. Can they still be run?
Thanks,
catherine___
Freesurfer mailing list
F
HI Experts:
Using Qdec, I have tried to generate Stats Data Tables, but below is the error
message I received. .I get this error message for all subjects but the
aseg.stats files are there and seem ok...
any ideas of what I am doing wrong?
cheers,
catherine
asegstats2table --common-segs --mea
Hi all,
Just checking.. is the Freesurfer course in New Zealand this May the only
course offered this year, or are there others?
would love to go but New Zealand may be a stretch...
cheers,
catherine
___
Freesurfer mailing list
Freesurfer@nmr.mgh.h
Dear Experts,
I am sorry for the basic question but we have a dataset of subjects we like to
analyze for which we have different slice thicknesses and orientations in
dicom format. All T1's collected were SPGR volumes with the same scanner
parameters.
My question was: Do you advice to re-ori
Hello Experts,
I would like to be able to get measurements of the anterior portion of the
corona radiata using tracula. Is this a possibility? I did not see it as an
"option" in paths to reconstruct.
thank you very much for your help,
catherine___
Free
Another basic question:
Could you tell me what is the best way of putting the
?h.entorhinal_exvivo.stats into a spreadsheet for all subjects? Is there a way
to achieve a textfile output for all subjects similar in concept to
kvlQuantifyHippocampalSubfieldSegmentations.sh ?
catherine_
Hello experts,
I am very new to freesurfer so please excuse my basic question:
We want to get measurements of entorhinal cortex volumes on a group of people.
I found these results listed in ?h.aparc.stats.
I also noticed another ?h.entorhinal_exvivo.stats, with different results.
Which shou
Hello Experts:
I am new to Freesurfer. Does the SPGR data have to be of axial LPI orientation
in order to run through recon all?
thank you,
cat
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