Hi Alex
Certainly, for such a simple design
matrix, only two repeated measures per subject with a small
inter-subject variability in between-scan time interval and a very small
number of subjects with a single time point the results from both
procedures should not be very different. Furthermore
If you can get good alignment between the EPI and the T1 images for
the 4 subjects with good T1 images, you might try the following:
(1) coregister each T1 to the corresponding EPI;
(2) normalize the coregistered T1 to the 112RM-SL atlas (see McLaren
et al. 2010 in Methods for your options)
(3) app
Thanks for your input, Donald. Unfortunately, I won't be able to acquire
the missing high quality anatomy.
Doug, I did not get from the documentation how to use preproc-sess to align
data to an NHP atlas in volume space (that is not in human MNI space).
Please advise.
Thanks!
Caspar
2013/2/12 MC
Dear Jorge,
For the statistical analysis of longitudinal data we used the "Two Stage
Model" (TSM) and the "Linear Mixed Effects".
Our intergroup LME results (2 groups, 2 time points) had many
similarities with TSM results. Then with TSM we analysed the intragroup
changes (one group, and 2 ti
The matrix that you have will fail because Col1+Col2=Col3 (and same for
the other columns). To do what you want, use the DODS that mri_glmfit
generates along with a contrast of [0 0 1 -1]. The constant term is
modelled by the first two columns.
doug
On 02/12/2013 03:19 PM, jm wrote:
> Hi fs ex
Hi Stefano - The order of the 3 trac-all steps is not inter-changeable.
You need to run bedpostx *before* you can run the path reconstruction.
a.y
On Wed, 13 Feb 2013, std...@virgilio.it wrote:
Thank you Anastasia. But I do not understand why I have the error in trac-all
-path. The configu
Thank you Anastasia. But I do not understand why I have the error in trac-all
-path. The configuration file that I have attached is good?
Stefano
Messaggio originale
Da: std...@virgilio.it
Data: 12-feb-2013 23.27
A:
Cc:
Ogg: [Freesurfer] R: Re: R: trac-all -path error
Hi Ana
Hi Stefano - All is well here, thank you. Yes, you can run bedpostx
directly on the dmri directory. If you search for bedpostx in the
freesurfer email list archives, you'll find the info you need since other
people have done this before.
a.y
On Tue, 12 Feb 2013, std...@virgilio.it wrote:
Hi Anastasia,
thanks! I hope that is all ok in Boston.
I'm attaching the configuration file that I'm using.
I'd like ask you if/how I can also run the second step of trac-all (bedpostx)
using FSL on other pc? May I directly run in FSL dmri folder? Do you think that
I should rename some files?
An
and yes, you'll need to run recon-all on your data before running tracula
cheers
Bruce
On
Tue, 12 Feb 2013, Anastasia Yendiki wrote:
>
> Hi Jon - You'll the aparc+aseg.mgz (cortical parcellation + subcortical
> segmentation). The basis of TRACULA is that it uses the underlying anatomy
> to recon
Hi Jon - You'll the aparc+aseg.mgz (cortical parcellation + subcortical
segmentation). The basis of TRACULA is that it uses the underlying anatomy
to reconstruct the tracts.
a.y
On Tue, 12 Feb 2013, Jon Wieser wrote:
> no i have not run recon-all yet on this dataset,
> do i need to run recon-
Hi Jon - Have you run freesurfer (recon-all) on your T1 data?
a.y
On Tue, 12 Feb 2013, Jon Wieser wrote:
i got past the problem with the bvesc, and bvals,
my current output has a new problem:
here's the last part of the output.
#@# Tensor fit Tue Feb 12 15:24:51 CST 2013
dtifit -k /Studi
I would recommend using the volume space initially until you can get
more surfaces to create your group surface. The one issue with the
112RM_SL is that there is no EPI template.
Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachus
Hi Doug,
the issue is that the 112RM atlas is only available as a volume; also, I do
not have a surface for one of my subjects. I could either make a surface
from the atlas volume and align to that surface for the group analysis, or
align the data to the atlas in volume space (if possible) and perf
in the release notes there is a link for a beta download if you want to give it
a try.
Nick
On Feb 12, 2013, at 4:09 PM, XJ Kang wrote:
> Hi FS Experts,
>
> I post an email one year ago about problem of the segmentation of GM/WM
> because of the duram layer. (See
> https://mail.nmr.mgh.harv
yes, using T2 or FLAIR is a better solution, or using multi-echo mprage so
you get the late echoes without sacrificing CNR
On Tue, 12 Feb 2013, XJ Kang wrote:
> Hi FS Experts,
>
> I post an email one year ago about problem of the segmentation of GM/WM
> because of the duram layer. (See
> https:
If you can create an average subject and register your individual
surfaces to that subject, then it can be done. By default, recon-all
will register to the human atlas to create ?h.sphere.reg
doug
On 02/12/2013 03:57 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> thank you very much.
> One more
Hi Doug,
thank you very much.
One more question: From the documentation, I wasn't really sure whether it
would also be possible to do the analysis of the functional data in a
common volume space (not MNI, as it is NHP data).
Thanks again, Caspar
2013/2/12 Douglas N Greve
> Hi Caspar, with 5.1 y
Hi fs experts,
I need to execute *mri_glmfit* with -X option to probe interactions
between Diagnosis and Age,
Statistic Software help suggest: The*homogeneity of slopes designs* can
be used to test whether the continuous and categorical predictors
interact in influencing responses, and thus, w
Hi Jon - This is the same issue. The reading from the dicom part will work
for the Siemens dicoms that we have here but is not guaranteed to work
with other dicoms. You'll have to define bvecfile, bvalfile, and nb0. (The
first two should be in columns, not rows.)
Let me know if you run into an
I see. So I will discriminate between what bedpostx requires from the more
inclusive bedpostx_seychelles script. Thank you for your help. I sincerely
appreciate it.
Best,
Susie Kuo
On Tue, Feb 12, 2013 at 1:56 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Everything that's in
Everything that's in bedpostx is also in bedpostx_seychelles. I've just
added to it. But if you want to run bedpostx directly on the command line
instead of going through trac-all -bedp, you can do that, too.
On Tue, 12 Feb 2013, Susie Kuo wrote:
> Thank you very much for your response. Is the
Thank you very much for your response. Is there a way to use bedpostx instead
of bedpostx_seychelles?
If not, no worries. I will look at your script and compose one of our own.
Best,
Susie Kuo
On Feb 12, 2013, at 11:56 AM, Anastasia Yendiki wrote:
>
> Hi Susie - FSL's bedpostx script work
Hi Gabriel
I would run recon-all and see whether the remaining non-brain is included
in the surfaces or cerebellum. If not you should be set. I would worry
about shaving of gray matter though, which can be difficult to see.
cheers
Bruce
On Tue, 12 Feb 2013, Gabriel Obregon wrote:
> Hi,
>
> I
look in the subject/scripts/build-stamp.txt
Note that if you set this environment variable
setenv REQUIRE_FS_MATCH 1
it will require that a re-running of recon-all use the same version as
previous runs
doug
On 02/12/2013 12:35 PM, krista kelly wrote:
> Hello,
>
> Is there any way to find out whic
Hello,
Is there any way to find out which Freesurfer version I used to process
data?
Thanks,
Krista
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The information in this e-mail
He should recon-all the anatomical data for the subject, register the
fMRI to the anatomical (bbregister), then use mri_vol2surf to map the
fMRI to the subject's anatomy. Then use mri_surf2surf to go to fsaverage
if needed (though why?). Also, the retinotopy results will look much
nicer if the
Hi FreeSurfer!
A colleague has retinotopic results that he would like to overlay on the FS
surface (most likely fsaverage).
The retinotopic data is in 2mm isotropic resolution.
What would be the best way to be able to overlay this data correctly?
Should he first warp the volume to the volume of f
Sorry, reading stuff from the dicom header will not work for all dicom
versions. It should work for Siemens dicoms though.
On Tue, 12 Feb 2013, Jon Wieser wrote:
> according to the
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
>
> nb0 does not need to be specified when using ori
Hi Susie - avscale is part of the FSL package. You have to make sure FSL
is installed and in your path.
a.y
On Wed, 6 Feb 2013, Susan Kuo wrote:
Hi FreeSurfer community, I am currently trying to troubleshoot my
preprocessing part of TRACULA with the
tutorial dataset (for Diff001 as the s
Hi Susie - FSL's bedpostx script works for parallelization on the type of
cluster they have at Oxford, and bedpostx_seychelles is a modified version
of it that also works on our cluster. Other than that, support for all
possible cluster setups at other centers is beyond the scope of our
resea
Hi Jon - My guess is you didn't define the nb0 variable in your
configuration file, see here:
http://www.freesurfer.net/fswiki/dmrirc
The new version, which will come out in a few days, will be able to figure
it out without you having to specify it but with the current version you
have
Hi Caspar, with 5.1 you would not use any of those programs (ie,
func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use FSFAST,
then see the tutorial for getting started. You'll need to set up the
directory structure properly, then run preproc-sess, mkanalysis-sess,
and selxavg3-sess.
Hi Stefano - There is no need to attach the trac-all script, I am quite
familiar with it. Perhaps you could attach the configuration file that you
set up?
Thanks,
a.y
On Mon, 11 Feb 2013, std...@virgilio.it wrote:
I'm attaching my trac-all file for check.Thanks,
Stefano
Messaggio ori
Hi Stefano - What are the contents of the bedpostX output directory? In
your case, that'd be this directory:
/Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX
a.y
On Mon, 11 Feb 2013, std...@virgilio.it wrote:
Hi list,
I'm running trac-all -path -c $FREESURFER/dmrirc_singl
Anyone know how to reset the LOCAL? Even if temporarily to see if this
is the problem?
doug
On 02/12/2013 08:23 AM, Richter, Julia wrote:
> It says the same even if I put 1.3 in quotes. :( Any other possibility to get
> access to the data?
>
>
> -Ursprüngliche Nachricht-
> Von: Douglas
Hi TRACULA Experts,
Is there a way of parallelizing BEDPOSTX on a cluster, not using the
bedpostx_seychelles option since I'm on a non-MGH cluster?
Thanks!
Susie Kuo
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Hi Joerg, see http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples and
look at the 2 group with 0 covariates.
doug
On 02/12/2013 10:51 AM, Jörg Pfannmöller wrote:
> Hello,
>
> I have two different results from a paired difference analysis lets call it A
> and B. How can I do a two sample t-test
Hi,
I'm using the -gcut flag for the first time and I've noticed that the skull
stripping process is still leaving small fragments of dura behind. Will this
affect my surfaces? Should I manually edit the brainmask volume to remove as
much of these fragments as I can?
Also, should I only be co
Hi Linn, make_average_subject does not compile statistics so this is normal.
doug
On 02/12/2013 11:14 AM, Bruce Fischl wrote:
> Hi Linn
> that sounds normal to me
>
> cheers
> Bruce
> On Tue, 12 Feb 2013, Linn Mittlestein wrote:
>
>> Dear freesurfer experts,
>>
>> i have a question regarding maki
Dear Bruce,
Thank you for your reply
Regards, Linn
On Tue, Feb 12, 2013 at 4:14 PM, Bruce Fischl wrote:
> Hi Linn
> that sounds normal to me
>
> cheers
> Bruce
>
> On Tue, 12 Feb 2013, Linn Mittlestein wrote:
>
> Dear freesurfer experts,
>>
>> i have a question regarding making my own average
Hi Linn
that sounds normal to me
cheers
Bruce
On Tue, 12 Feb 2013, Linn Mittlestein wrote:
> Dear freesurfer experts,
>
> i have a question regarding making my own average. I received this message
>
> Tue Feb 12 10:54:34 GMT 2013
> make_average_volume done
>
> However, the stats file in the av
Hello,
I have two different results from a paired difference analysis lets call it A
and B. How can I do a two sample t-test with those results (A-B)? Somehow I am
stuck in using isxconcat-sess on the group results A and B. Help is highly
appreciated.
Cheers Joerg
___
hello
i am trying to process the dti data with trac-all. I am new to tracula
my input images are 3300 dicoms, 60 slices and 55 dti diffusions
i have attached my dmrirc_single_subject file
i did the following command:
trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject
and got the re
Catherine,
Thats odd, can you email me your qdec.table.dat file? qdec parses
'discretes' if they're non-numerical, so maybe there is a stray character
thats messing it up.
Nick
> Sorry, just to clarify; it lists age as a discreet variable rather
> than continuous for some reason, not the other
Catherine,
Is your SUBJECTS_DIR enviro var setup properly prior to starting qdec?
That is, set to your own writable subjects directory? I noticed in the
error message that it looks like the subjects dir is the default one under
the /freesurfer dir, which is read-only.
One option is to put this
Sorry, just to clarify; it lists age as a discreet variable rather
than continuous for some reason, not the other way round as I
accidentally wrote=)
Regards
Quoting Catherine Bois on Tue, 12 Feb 2013
14:58:45 +:
>
> Dear all,
>
> I have a question;
>
> I am trying to load data into
Dear all,
I have a question;
I am trying to load data into qdec; the data table is loaded fine
(although it lists age as continuous for some region, rather than
discreet). However, When i try to generate the stats table, this error
comes up. Does this mean I somehow have to manually set th
Dear all,
I have a question;
I am trying to load data into qdec; the data table is loaded fine
(although it lists age as continuous for some region, rather than
discreet). However, When i try to generate the stats table, this error
comes up. Does this mean I somehow have to manually set the
Post-Doctoral applications are invited in the newly established Brain and
Language Lab at the Department of Clinical Neuroscience at the University of
Geneva, in collaboration with the Swiss Institute of Technology (EPFL) in
Lausanne, Switzerland. Projects will include the development of new
Dear Freesurfer experts,
I am trying to prepare some NHP functional data for a whole brain group
analysis, and I was wondering which sequence of steps you would recommend,
given that the data cannot be processed with recon-all.
I have surfaces from 4 subjects, but one subject for which I do not hav
Dear freesurfer experts,
i have a question regarding making my own average. I received this message
Tue Feb 12 10:54:34 GMT 2013
make_average_volume done
However, the stats file in the average subject is empty, and the tmp
folder, but the other folders are not empty. Is this "normal"? Does the
a
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