External Email - Use Caution
Dear all,
We are looking for another new Postdoc to work in an interdisciplinary and
internationally competitive environment at Karolinska Institute, one of the
top medical universities in the world and the home for the Nobel Prize in
Medicine.
We com
External Email - Use Caution
Dear all,
We are looking for a Postdoc to work in an interdisciplinary and
internationally competitive environment at Karolinska Institute, one of the
top medical universities in the world and the home for the Nobel Prize in
Medicine.
We combine imagi
External Email - Use Caution
Dear all,
We are looking for a Postdoc to work in an interdisciplinary and
internationally competitive environment at Karolinska Institute, one of the
top medical universities in the world and the home for the Nobel Prize in
Medicine.
We combine imagi
External Email - Use Caution
Dear all,
We are looking for a Postdoc to work in an interdisciplinary and
internationally competitive environment at Karolinska Institute, one of the
top medical universities in the world and the home for the Nobel Prize in
Medicine.
We combine imagi
External Email - Use Caution
Dear all,
We are looking for a Postdoc to work in an interdisciplinary and
internationally competitive environment at Karolinska Institute, one of the
top medical universities in the world and the home for the Nobel Prize in
Medicine.
We combine imagi
External Email - Use Caution
Dear all,
We are looking for a PhD student to work in an interdisciplinary and
internationally competitive environment at Karolinska Institute, one of the
top medical universities in the world and the home for the Nobel Prize in
Medicine.
We combine i
External Email - Use Caution
Dear all,
We are looking for a Postdoc to work in an interdisciplinary and
internationally competitive environment at Karolinska Institute, one of the
top medical universities in the world and the home for the Nobel Prize in
Medicine.
We combine imagi
External Email - Use Caution
Dear all,
If you have earned a PhD degree in China in the last 3 years and would like
to do a Postdoc at Karolinska Institute in Sweden, please see the project
below:
*Dynamic Changes in Functional Brain Connectivity over the course of
Alzheimer’s Dis
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Dear all,
We are organizing the second edition of the conference “Emerging Topics in
Artificial Intelligence”, which will take place from 1-5 August 2021 in San
Diego, USA.
The aim of this conference is to bring together experts from different
fields
External Email - Use Caution
Dear all,
We are looking for a Postdoc to work in an interdisciplinary and
internationally competitive environment at Karolinska Institute, one of the
top medical universities in the world and the home for the Nobel Prize in
Medicine.
We combine imagi
External Email - Use Caution
Dear all,
We are organizing a conference on “Emerging Topics in Artificial
Intelligence”, which will take place from 23-27 August 2020 in San Diego,
USA.
The aim of this conference is to bring together experts from different
fields to discuss new appl
Fischl
> wrote:
> >
> > Hi Joana
> >
> > have you added $FREESUFER_HOME/bin to your path? Have you sourced
> > $FREESURFER_HOME/SetUpFreeSurfer.csh?
> >
> > cheers
> > Bruce
> >
> >
> > On Mon, 8 Jun 2015, Joana Braga Pereira w
Dear all,
I've downloaded freesurfer and installed it on mac (v 10.10.2).
After running the recon-all pipeline on a subject, I opened tkmedit subj001
brainmask.mgz -surfs and the following message came out: -bash: tkmedit:
command not found.
I can open the same subject with freeview without any
idea why this is happening? This does mean the GEMS tool
should not be applied in such young subjects?
Any help would be greatly appreciated!
Many thanks,
joana
2014-06-13 15:40 GMT+02:00 Joana Braga Pereira :
> Hi Koen,
>
> Thanks for such a prompt reply.
>
> I visualized
2014-06-13 15:23 GMT+02:00 Koen Van Leemput :
> Hi Joana,
>
> This looks like a visualization issue rather than a segmentation error to
> me. How did you visualize this?
>
> Koen
> On Jun 13, 2014 2:59 PM, "Joana Braga Pereira"
> wrote:
>
>> Dear all,
&g
fields
> Cheers,
> Eugenio
>
>
>
> On 11/06/2013 11:32 AM, Joana Braga Pereira wrote:
>
> Dear all,
>
> I'm interested in assessing the changes in the volumes of hippocampal
> subfields between 2 time points.
>
> Can I use the longitudinal pipeline of F
Dear all,
I'm interested in assessing the changes in the volumes of hippocampal
subfields between 2 time points.
Can I use the longitudinal pipeline of Freesurfer and add the
-hippo-subfields flag to the longitudinal runs of the 2 time points?
Thanks!
ectors again. It may be
> some other combination of swaps that needs to be done, but the x and y
> looks like the most likely to me. For sure the gradient table is wrong.
>
>
> On Thu, 5 Sep 2013, Joana Braga Pereira wrote:
>
> Thanks!
>> I've uploaded those files as w
ps://gate.nmr.mgh.harvard.edu/filedrop2/>
>
>
> On Thu, 5 Sep 2013, Joana Braga Pereira wrote:
>
> Hi Anastasia,
>> Thanks! I checked dtifit_FA and did the overlay with V1.
>>
>> They don't look ok to me (see attached picture). Any suggestions on how
>&g
ly good).
>
> Is this a noisy dataset or something?
>
> ____
> From: Joana Braga Pereira [jbragapere...@gmail.com]
> Sent: Thursday, September 05, 2013 9:32 AM
> To: Watson, Christopher
> Cc: Anastasia Yendiki; freesurfer@nmr.mgh.harvard.edu
&g
27;s actually really easy to set up, too.
>
> From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, September 02, 2013 3:46 PM
> To: Watson, Christopher
> Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu
> Subject:
Dear Anastasia and FreeSurfers,
I was preprocessing some data using tracula and found this error after
running trac-all -bedp -c dmrirc:
INFO: SUBJECTS_DIR is /data-02/joana/Last
INFO: Diffusion root is /data-02/joana/tracula/
Actual FREESURFER_HOME /usr/local/freesurfer-5.3
WARN: Running FSL's
Dear FreeSurfers,
I tried using FreeSurfer 5.3 with the new T2 flags and I got the following
error:
INFO: Reading transformation from file
/tmp/1b2003d0-08c9-4e48-9e9d-622f29f0ff44/mri/transforms/T2raw.lta...
Reading transform with LTAreadEx()
No such file or directory
ERROR: Reading transform fr
Brad Dickerson who know
> more about this.
>
> Hope this helps,
>
> Koen
>
>
> On Thu, Jan 26, 2012 at 9:54 AM, JOANA BRAGA PEREIRA
> wrote:
> > Dear Koen & Freesurfers,
> >
> > I've been working with the GEMS tool for hippocampal subfields
> &
Dear Koen & Freesurfers,
I've been working with the GEMS tool for hippocampal subfields
segmentation and have a question I would like to ask you all.
I've noticed that the CA1 sector appears to be quite small compared to
other subfields (CA2-3 seems to be the largest), while previous
studie
Dear Van Leemput & Freesurfers,
I've been working with the GEMS tool for hippocampal subfields segmentation
and have a question I would like to ask you.
I've noticed that the CA1 sector appears to be quite small compared to
other subfields (CA2-3 seems to be the largest), while previous studies
s
Dear Van Leemput & Freesurfers,
I've been working with the GEMS tool for hippocampal subfields segmentation
and have a question I would like to ask you.
I've noticed that the CA1 sector appears to be quite small compared to
other subfields (CA2-3 seems to be the largest), while previous studies
s
Dear Doug and Freesurfers,
I have a structural MRI and DTI set of images that i've corregistered
(individually) using bbregister.
My mincost files show a value that varies between 0.1 and 0.2 for all
subjects.
I read the paper by Grieve et al., 2009 Neuroimage and was wondering
whether it is cor
Thanks Doug! It worked!
Joana
2011/10/17 Douglas N Greve
> No, use the register.dat that you manually created as the input to
> bbregister with the --init-reg. You could move your register.dat to
> regidster.man.dat and set the output to be register.dat.
>
> doug
>
> Joan
> range to expect for well-registered subjects. You should be able to use the
> registrations you created as input to bbregister (with the --init-reg
> option), and bbregister should do fine after that.
> doug
>
> Joana Braga Pereira wrote:
>
>> Hi Doug,
>>
>>
Dear Lilla and Ed,
Thanks a lot for your suggestions, they were really really helpful!
I did the analyses as you suggested. After bbregister i checked the results
with tkregister2 and saw that most subjects were well coregistered.
However in a few of them my lowb images were out of place with res
created in
bbregister and do mri_label2vol but i'm not sure how to do it.
Thanks,
Joana
2011/10/13 Bruce Fischl
> Hi Joana,
>
> try bbregister.
>
> cheers
> Bruce
>
> On Thu, 13 Oct 2011, Joana Braga Pereira wrote:
>
> Dear FreeSurfers,
>> I'm trying to c
Dear FreeSurfers,
I'm trying to coregister FA images pre-processed with FSL to Freesurfer,
however i'm having a few problems and was wondering if someone could help me
out.
These are the steps that i carried out:
mri_convert subj_01/mri/brain.mgz brain.nii.gz
fslswapdim brain.nii.gz x z -y brai
Dear Knut,
Here it is: setenv LC_ALL en_US
Good luck, Joana
2011/10/1 Knut J Bjuland
> Dear Joana
>
> Could you please send me proposed line to the .tcshrc file. You got from Priti
> and Anastasia.
>
>
> Best regards
>
> Knut J
>
>
>
> On 01. okt
please send your dmrirc file too?
>
> Thanks,
> a.y
>
>
> On Fri, 30 Sep 2011, Joana Braga Pereira wrote:
>
> Dear Freesurfers,
>>
>> I'm pre-processing my DTI data with Tracula and i found the following
>> error
>> while running trac-all -prep
Dear Freesurfers,
I'm pre-processing my DTI data with Tracula and i found the following error
while running trac-all -prep -c dmrirc_H_P01:
dtifit -k /home/joana/FIU/H_P01/dmri/dwi.nii.gz -m
/home/joana/FIU/H_P01/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r
/home/joana/FIU/H_P01/dmri/bvecs -b /home/
ouglas N Greve wrote:
> > This is actually something that you cannot currently do in QDEC. Try
> > doing a search for "paired" on our wiki for instructions on how to do
> > this type of analysis.
> > doug
> >
> > Joana Braga Pereira wrote:
> > > Dear
Dear Freesurfers,
I'm doing a longitudinal analysis of cortical thickness using the newest
version of Freesurfer and there is something i would like to ask you all.
I have two time points and only one group of patients.
I've finished the pre-processing and am now searching for differences
betwee
Dear all,
I have a question regarding smoothing in qdec.
>From what i've understood from previous emails, for monte carlo simulations
qdec calculates the best smoothing for your data set, saving it in the file
fwhm.dat.
How does it calculate this smoothing?
Many thanks,
Joana
_
consider the clusters that have statistically
different mean thickness between groups?
Many thanks
2010/8/3 Douglas N Greve
> It might be, it depends on how you defined the sign of the voxel-wise
> threshold. If you used "abs", then it is certainly possible.
>
> doyug
>
&g
Dear all,
I would like to ask you whether there should be an exact correspondence
between vertex-wise thickness and mean thickness of clusters.
I'll explain you my problem.
I did an analysis with 2 groups and 2 covariates.
Then i run the mri_glmfit script and found clusters of greater thickness i
Dear Freesurfer experts,
I've just finished running a qdec analysis of a comparison of cortical
thickness between controls and patients with 2 covariates and found a
strange result.
When i set the threshold at FDR some clusters appear in red which are the
corrected results from my analysis.
Howev
Dear all,
I'm running the mri_glmfit script that has been automatically generated in
qdec:
mri_glmfit-sim \
--glmdir /home/joana/subjects/qdec/results_2sample \
--sim mc-z 1 2 mc-z.abs.2 \
--sim-sign abs \
--overwrite
Because i want to get the clusters, area size and hopefully z or p va
Dear Freesurfers,
I'm a new/inexperienced user. I've just run a thickness comparison between
two groups with qdec and got several differences throughout the brain.
I would like to get the coordinates, mean thickness, z or t values of my
results. Would someone tell me how to do this or kindly dire
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