Hallo,
first of all: Sorry to be a little bit clingy, but I have some problems in
understanding regarding the DIAG option in FreeSurfer. As suggested by Bruce, I
have set DIAG to 0x and DIAG_VERBOSE to 1. I am getting a lot of output
now and a very large recon-all.log.
Unfortunately, I
Dear Freesurfer experts:
Recently, I have update my OS to Ubutnu 16.04. Afterwards, I tried to
re-run some analysis using Qdec 1.4 (stable 5.1) and Qdec 1.5 (stable 6.0).
However, I am not able to input any threshold via my keyboard (neither the
Subjects or Display tab).
This issue also happens wh
Hi Duy
ls -l
Will show you permissions, but I think you will need to do a unix tutorial or
get some local help
Cheers
Bruce
> On May 30, 2017, at 8:06 PM, Duy Nguyen wrote:
>
> Dear Bruce
>
> Thanks for your response. Would you please showing me how to check the Unix
> permission? And furt
Yes I updated those and renamed them so that they'd be in the locations TRACULA
expects.
Lauren
El may. 30, 2017, a las 8:12 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> escribió:
Yes, this is what I suspected. The outputs of bbregister are
anatorig2diff.bbr.dat and anatorig2dif
Yes, this is what I suspected. The outputs of bbregister are
anatorig2diff.bbr.dat and anatorig2diff.bbr.mat. Are these the ones that you
updated? The other ones are generated by trac-all -intra.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@n
Dear Bruce
Thanks for your response. Would you please showing me how to check the Unix
permission? And further that when I tried with the tutorial subject data,
it was fine.
Please let me know if you have any more inquiries
Thank you and warmest regards,
Duy
On Sat, May 27, 2017 at 9:16 PM Bruce
Hi Anastasia,
It looks as though some but now all have updated -
[franklin:xfms] (nmr-dev-env) ls -l
total 152
-rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat
-rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat~
-rw-rw-r-- 1 lo941 megclin83 May 30 15:07 anat2anator
Hi Lauren - Can you run "ls -l" in this subject's dmri/xfms/ and check the
creation dates of the files to see if they were updated?
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren
[lostro
you mean not to generate surfaces/parcellations/thickness? I guess you
could run -autorecon1 -autorecon2. That would do the start of the surface
stuff, but not much (and not long)
cheers
Bruce
On Tue, 30 May 2017, Becker, Valerie
wrote:
Hi all,
Forgive me, as I' new at this, but I cant s
lme_mass_FDR, fast_fdrthresh, and MRISfdr2vwth should give basically the
same result if the mask is the same. Note that there is mri_fdr which
should also give the same result. One place where they might give
different results is if no vertex survives, but that does not look like
the case. My g
you can run it with -autorecon1 -autorecon2
On 05/30/2017 04:00 PM, Becker, Valerie wrote:
>
> Hi all,
>
>
> Forgive me, as I' new at this, but I cant seem to quite make heads or
> tails of the Recon-all page with instructions on how to divide it the
> commands. We're just trying to run indivi
Hi all,
Forgive me, as I' new at this, but I cant seem to quite make heads or tails of
the Recon-all page with instructions on how to divide it the commands. We're
just trying to run individual volumetric analyses at the moment. Is there a way
to do that with a recon- proc? So as to shorten pr
Dear FreeSurfers,
I have a ROI that I want to correct with FDR. I found that FreeSurfer has
different implementations of FDR correction and all of them give different
results.
My ROI has 4205 vertices with p values between -5.0366 and 1.1673.
When I set FDR in tksurfer (MRISfdr2vwth), I get p th
Hi Anastasia,
I just re-ran the trac-preproc script with the bbregister command set to 0 in
the configuration file, and I'm afraid I got the same erroneous result. Do you
have any other ideas as to where the problem could be coming from?
Lauren
From: freesurfe
I don't think there is an 6 for the sym. To get it on to the normal sym,
run recon-all on the mni152, then treat it like a subject (ie, run
xhemireg, etc)
On 05/30/2017 11:00 AM, Meiling Li wrote:
> Dear freesurfer experts
> I have processed resting state fMRI data in MNI space , for example:
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister
registration file. That's because the -intra step in TRACULA doesn't just run
bbregister, but also does a bunch of other things with the output of
bbregister, like transform, invert, and compose a bunch of registration fil
Hi Stefano
mris_anatomical_stats -l ROI_mask.label ...
should do the trick
cheers
Bruce
On Tue, 30 May 2017,
std...@virgilio.it wrote:
> Hi list,
> is possible to calculate the thickness of a ROI_mask.label which I have drawn
> using tksurf?
> Please could you suggest a command line?
> Thanks
there might be. The problem with having all one group from one scanner
and all other other group from another scanner is that you cannot tell
what is due to scanner and what is due to group.
On 05/30/2017 11:50 AM, Dr Sampada Sinha wrote:
> Thanks Dr Greve for your reply. I understand it can be
Hi list,is possible to calculate the thickness of a ROI_mask.label which I have
drawn using tksurf?Please could you suggest a command line?ThanksStefano___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/li
Thanks Dr Greve for your reply. I understand it can be taken into account
if study group is the same and different scanner is used on the same group.
So does it mean there is a differential change in volume depending on the
field strength?
Appreciate your help.
Kind regards,
Sam
On Tuesday, May
Dear Freesurfer team,
We are analyzing the gray matter volume of some customized labels, using
mris_anatomical_stats.
We are wondering about some characteristics of the obtained volume.
Is the volume of a label (as calculated by mris_anatomical_stats) the sum of
the volume elements of each v
Dear freesurfer experts
I have processed resting state fMRI data in MNI space , for example: Data:
91*109*91*240, 240 was the time frames number. How could i project the data in
MNI space to the symmetric surface(eg lrsym_fsaverage6) ?
Thanks in advance!
Meiling __
I don't think there are clear answers to this kind of question. The
optimal smoothing kernel size depends on the size of the effect you are
looking for, not the modality that you are using. The actual amount of
smoothing will be more for PET because of the inherent smoothing, but
that smoothing
You do need to take it into account, but you cannot if one group is 1.5T
and the other is 3T.
On 5/28/17 10:41 AM, Dr Sampada Sinha wrote:
Dear freesurfer experts,
I am presently trying to calculate hippocampal volume for two
different study groups. One study group images (MDD) was acquired
Dear FS experts,
I've been working with the proposed pipeline, but I still have a doubt
regarding the degree of smooth to be applied to the final surfaces prior to the
analyses.
The first question is that, given a "standard" PET scanner, with a PSF between
5-8mm, what size smooth would you app
Hi,
sorry to dig up this old email (just came across it).
We have stopped with the gcut, because in some cases it cropped brain.
Also passing a T2 via the -T2 flag (which is supposed to remove dura)
sometimes crops cortex.
It should be made clear that at the stage of the brainmask this should
Hi Clara,
more likely there is a problem with your sever (e.g. disk IO problems).
The label intersection works like this:
For each subject it copies the of the first time point to
rh.cortex.label
to the base directory as:
rh.long.cortex.label
it then intersect the label with the one from the
Hi Emory,
Lots of publicly available Datasets have controls
OASIS, ADNI, MIRIAD
the problem is that these images were scanned on different scanners with
different protocols, so the measurements are not comparable to your
patients.
Best, Martin
On 05/24/2017 12:10 AM, shi yao wang wrote:
We
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