below I meant you could run it only on the first two time points. Maybe
there is already enough power to see effects.
Best, Martin
Am 08.09.2017 um 09:13 schrieb Martin Reuter:
Hi Michelle,
when scanners (or even scanner hardware, like head coil or software
upgrades etc) change in a longit
Hi Douglas,
Thank you very much for that, I will try it!
Eva
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 05 September 2017 22:07
To: freesurfer@nmr.mgh.harvard.edu
Subject: EXT: Re: [F
On 09/10/2017 04:02 AM, Xianwei Che wrote:
> Dear experts,
>
> I am going to run a group analysis on thickness but limit the results
> to certain regions, say prefrontal cortex. l did find this thread but
> failed to make it work on my data
> (https://www.mail-archive.com/freesurfer@nmr.mgh.h
The tal_QC_AZS scripts expects the log file to have a specific format,
and it looks like something changes when you run it inside matlab.
sorry, the only idea I have is that the linux environments might be
different in bash vs matlab.
On 09/11/2017 08:25 AM, Giuseppe Cabras wrote:
> Dear fre
Hi list,I would like to perform longitudinal analysis with FS-FAST, fMRI
data.Please could you list, in summary, the processes that I should
done?ThanksRegardsStefano___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard
ps, you can run it with -no-talairach to turn off checking (soit will
run all the way through)
On 09/11/2017 08:25 AM, Giuseppe Cabras wrote:
> Dear freesurfer developers,
>
> I call recon-all -all from a matlab script using a system(cmd) which
> is (apparently) correctly executed, as shown in
there is nothing special about doing long analysis in FSFAST. You just
need to set up the group analysis appropriately.
On 09/11/2017 12:26 PM, std...@virgilio.it wrote:
> Hi list,
> I would like to perform longitudinal analysis with FS-FAST, fMRI data.
> Please could you list, in summary, the p
Hi Team,
Am getting segmentation error during the reconstruction process.
Please help in resolving the error.
I have attached log for reference.
Thanks,
Janani
::DISCLAIMER::
---
Hi,
We running FS 5.3 analyses on 2 cohorts (control vs. malnourished adolescents)
and I was wonderful what FS measure would be most accurate for normalizing the
volumes.
(i.e total GM, total WM, suparatentorial, etc). The eTIV measures are
significantly different between the cohorts.
Is eTIV
dear fs community,
as a kind of a freesurfer greenhorn i would kindly ask you to help me out with
identifying the different labels used by freesurfer.
after using mri segstats most of the labels seem to be describing thereselfs in
proper way.
what i don’t understand are for example the differen
Hello,
Hope this message finds you well.
I was beginning to run recon-all on a dataset and was encountering a
problem with the talairach registration. I've encountered this error before
here and there, but I've been receiving the same error for every scan that
I've been trying to run, and I'm not
I am trying to find the best way to identify likely duplicate subjects with in
a database of about 550 subjects. Some subjects where duel-consented for
studies and had multiple scans over a relatively short period of time. What is
the best way to tease these out?
John Sherrill
jtsherr...@uams.e
One way is to perform a 6DOF registration between each pair. It is a lot
of pairs, but I don't think you can avoid it. Pairs that come from the
same subject will have an abnormally high (or low) objective function.
You could use mri_coreg (use --no-smooth) . If you've already run all
550 throug
I have run recon-all on all of the files. So I should start with
asegstats2table ( https://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table ) ?
John Sherrill
jtsherr...@uams.edu
john_sherr...@me.com
(870) 761-0580
From: freesurfer-boun...@nmr.mgh.harvard
Yea, that's what I would do. You can run asegstats2table to get a list
of the volume for all ROIs (so this gives you a matrix of 550 by about
50). For each row (subject), compare the volumes to that of every other
row. You'll need to come up with a comparison function; maybe mean
percent diffe
Try running
unsetenv FS_LOAD_DWI
then re-running recon-all
On 09/11/2017 12:57 PM, M Janani wrote:
>
> Hi Team,
>
> Am getting segmentation error during the
> reconstruction process.
>
> Please help in resolving the error.
>
> I have attached log
You can look here for what stats are available
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
There is no one method that is considered the gold standard. Each will
represent a different hypothesis to test. Eg, if you use whole brain
volume, then you will be looking at changes with
Hello all!
I am looking for a automatic or semi-automatic segmentation tool for the
mammillary bodies. Any suggestions?
Many thanks!
Heidi
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On 09/11/2017 01:20 PM, Benjamin Luerweg wrote:
> dear fs community,
>
> as a kind of a freesurfer greenhorn i would kindly ask you to help me
> out with identifying the different labels used by freesurfer.
> after using mri segstats most of the labels seem to be describing
> thereselfs in prop
That means that geometry information (ie, what is left and right,
anterior or posterior) is not part of the nifti file. Without that
information, the anatomical analysis cannot be done. You will either
have to fix it yourself (ie, imbed that info into the file) or, better,
recreate the file wit
Sounds good. Unfortunately when I open many of my files that do not contain an
aseg file. Many only have a scripts directory and nothing else. Is there a way
to process the files to just get the aseg data without doing a recon-all?
John Sherrill
jtsherr...@uams.edu
john_sherr...@me.com
(870) 76
Ah, I see - how would I be able to do either of those? And would I have to
check the geometry of each scan individually? Not sure how that works, but
I have a substantially large dataset.
Thank you for your response!
On Mon, Sep 11, 2017 at 1:02 PM, Douglas N Greve
wrote:
> That means that geom
No, you at least have to run it through autorecon2
On 09/11/2017 04:06 PM, Sherrill, John T wrote:
> Sounds good. Unfortunately when I open many of my files that do not contain
> an aseg file. Many only have a scripts directory and nothing else. Is there
> a way to process the files to just ge
I don't know how you (or someone else) generated the nifti files in the
first place, so I can't help there. If you did not generate them, then
talk to the person who did. I do not really recommend trying to do it by
hand. You can get AP and SI correctly, but you'll never know whether
they are L
Ok - thank you! I will speak to the person who generated the files then.
On Mon, Sep 11, 2017 at 1:56 PM, Douglas N Greve
wrote:
> I don't know how you (or someone else) generated the nifti files in the
> first place, so I can't help there. If you did not generate them, then
> talk to the person
Dear Doug,
Thank you for the answer. I will try it out.
Regards
*-*
Mr Xianwei Che
PhD Candidate
Monash Alfred Psychiatry Research Centre (MAPrc)
Central Clinical School & the Alfred
Monash University
Level 4, 607 St Kilda Road, Melbourne 3004, Australia
On 12 September 2017 at 01:4
Dear Doug,
After some trial and error I am still not able to run group analysis in ROI
manner.
Here is my understanding: I need to define a label (mri_binarize ?) in
which my ROIs should be labeled as 1 with other regions being 0. Then I can
take this label to glm with --lable and then run correc
Hi all,
I have finished the command “recon -all” without error. But I get an error that
says:
“Received X error!
Error code :158
Request code : 148
Minor code: 2
Error text :’GLXBadLargeRequest’”
I am using the command “tksurfer sub lh inflated”.
Then clic
Hi Douglas,
We tried running this command. But command not found error.
Thanks,
Janani
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 12 September 2017 01:25
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