Dear Freesurfer Experts,
While performing the long_mris_slopes cmd, we receive an error:
---
SUBJECT pls_pd_base00 Running Within-Subject GLM
Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat ...
mri_glmfit --y
/Applications/freesurfer/subjects
Hello Everyone,
could someone please give us an advice about which method you consider
is the best for our study ?
we have two groups with MRI at Time 1. Each group received medication.
After this we performed another MRI at Time 2 after 2 weeks.
The best method for this study is a longitud
multiple scans/subject.
>
> cheers
> Bruce
> On Tue, 3 Jun 2014, Alexandru Hanganu wrote:
>
>> Hello Everyone,
>>
>> could someone please give us an advice about which method you consider is
>> the best for our study ?
>>
>> we have two groups wi
Dear FreeSurfer Experts,
How could the longitudinal analysis be performed in order to show
whether a parameter at time 1 is predictive of changes in cortical
thickness over time ? and can thecorresponding regions be shown in
FreeSurfer ?
In a statistical analysis, as we see it, we must perfo
, from an MRI,
PET, inflammation, morphopathology and genetics perspectives.
Early registration deadline: 1st March 2019.
more details at:
http://fourwav.es/neurosciences21-22mai2019
On behalf of the organizing committee,
Alexandru Hanganu
___
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Hello Martin,
I was wondering - how solved the "Unmatched" error ?
In our case, this error appears for both 5.3, 6.0 and dev, on 2 different
clusters.
All folders exist, are filled with data and reecon-all finished without
error, plus hippocampus and
end details?
>
> Best, Martin
>
> On Wed, 2019-08-07 at 08:31 -0400, Alexandru Hanganu wrote:
> > External Email - Use Caution
> > Hello Martin,
> >
> > I was wondering - how solved the "Unmatched" error ?
> >
> > In our case, this er
e send applications (Cover letter, CV, names of 3 references including
current supervisor and github repository) to:
Alexandru Hanganu: alexandru.hang...@umontreal.ca (Primary Supervisor) and
Oury Monchi: oury.mon...@ucalgary.ca (Co-Supervisor)
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Hello FreeSurfer Developers,
I attemting to run brainstem/ hippocampus/ thalamus segmentation with FS
7.1 and there seems to be a problem with environment variables. Based on
comments on other forums, I cannot install GlibC (if this is the case)
since
External Email - Use Caution
Hi,
I also had this error in the past. It would be reasonable to try and log
all the steps now, because I didn't manage to find out where that error was
coming from. In my case - I made adjustments to my own scripts.
I can take a look at your scripts,
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Hi,
In this case, there's a list of steps, written by Martin Reuter in one of
the previous answers:
check that folders exist, are filled with data and reecon-all finished
without error
check that all folders and readable: (chmod 777 -R)
check in the
and will benefit from collaborations with
Dr. Alexandru Hanganu at the Department of Psychology of the University of
Montreal. Other collaborators include Dr. Nils Forkert head of the Medical
Imaging Processing and Machine Learning laboratory. A special focus will be
given to the neural origins and
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Hi Freesurfer,
can't find if this was reported.
This refers to freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551.
seems that in the new 7.1.1 version the required license file is located at
FRESURFER_HOME/license.txt (instead of previous version
Dear Doug,
There´s a message in the list from Dec. 2008 about interhemispheric
comparison, and you said there wasn't any good way to do this. Is there some
new method included in FS 5.0 for right vs left hemisphere comparison ?
Thanks.
Sincerely,
Alex.
*
*
_
Dear Freesurfer experts,
1) How many simultaneous processing can be done on a cluster ? I did 20
analysis at the same time, and it worked. They all finished without error.
(didn't find this question on the list)
2) In order to adapt the previous subject analysing to the new FS-5.1, must
I use the
Dear Freesurfer experts,
In the QDEC plot there is the possibility to view cortical thickness for
each subject in a specific region. Is there a possibility to make an
automatic table of all these thickness data ?
In a previous question, the answer was to use a script:
===
0.9403-0.5673
5.00 5.5673
2 1 15731 15731.0 2.39290.7417 0.8352
4.45 3.6158
Sincerely,
Alex.
Von: Doug Greve
An: Alexandru Hanganu
CC: FS Mailing List
Gesendet: Montag, den 8. Dezember 2008, 19
negative.
Two questions:
- are the p-values actually t-values ?
- normally the X coordinates of the right hemisphere should be positive.
Any ideas why they are negative ?
Thank's a lot for any help.
Best regards,
Dr. Alexandru Hanganu
___
Departme
and we receive the Error:
– /usr/local/freesurfer/subjects/average/surf/lh.sphere.reg – could not open
file
Could you please tell us where might be the mistake ? What step is needed to
create the lh.sphere.reg file. Thank you very much for your help.
Best regards,
Dr. Alexandru Hanganu
Von: Doug Greve <[EMAIL PROTECTED]>
An: Alexandru Hanganu <[EMAIL PROTECTED]>
CC: FS Mailing List
Gesendet: Dienstag, den 18. November 2008, 19:39:04 Uhr
Betreff: Re: [Freesurfer] mri_surf2surf - Error
did you create a subject called "average"? This is d
goal ?
Thank you.
Best regards,
Dr. Alexandru Hanganu
___
Department of Neurology,
Schleswig-Holstein University Hospital, Kiel Campus
Arnold-Heller-Str. 3, building no. 41
D-24105 Kiel, Germany.
___
Freesurfer ma
Thank you Nick, and Doug for your answers. I used both "--reshape" flag and
"--noreshape" flag and the results after "mri_segstats" were in both cases:
.
.
.
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 2 segmentations
Computing statistics for each
of 3D to surface ?
Thank you for your help,
Alex.
Von: Doug Greve <[EMAIL PROTECTED]>
An: Alexandru Hanganu <[EMAIL PROTECTED]>
CC: FS Mailing List
Gesendet: Montag, den 8. Dezember 2008, 19:41:52 Uhr
Betreff: Re: [Freesurfer] Statistic analysin
Hello All,
Can you please tell me, when we get the results from
QDEC {$SUBJECTS_DIR/qdec/Untitled/lh-Avg-thickness-age-Cor/sig.mgh} how can we
threshold the image and include it as a seed into FSL tractography ? What
command line should I use ?
Thank you for your help,
Best regards,
Alexandru
Thank you Nick for your answer. We will try this method.
Von: Nick Schmansky
An: Alexandru Hanganu
CC: Freesurfer Mailing List
Gesendet: Donnerstag, den 11. Dezember 2008, 23:16:15 Uhr
Betreff: Re: [Freesurfer] QDEC data into FSL
Alexandru,
I can'
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