Hi Jaiashre,
when switching scanners within a longitudinal study you will see effects that
are caused by the scanner (or a scanner / age, scanner /disease, scanner /
motion interaction). If the majority of your subjects is scanned on the same
scanner for most time points, then you may be able t
Hi Tamara,
in the base it is good the check the brain mask, as it is used for all time
points (it is fixed over time).
To check alignment accuracy, you could use either brain mask or norm. It should
not make a difference. It will be hard to find problems in that image (the
blurriness will be
Hi Matthieu,
to clarify, you can directly register to the long time point.
If, for some reason, the pet and MR (cross) are already very close in space, it
may make sense to first register to that, then concatenate that transform with
the one from cross to long and then map the PET there. Don’
Hi Antonin,
max does not constrain thickness. The location of the max is constrained to be
within 2*max for every iteration, so it will constrain how far outwards it
searches. But it will be done at each scale, so it can still deform a long way.
We initialize the surface processing in long wit
Hi Martin,
Thank you for clarifications !
1) What do you mean by "If, for some reason, the pet and MR (cross) are
already very close in space" ?
2) How could it be possible to directly register to the long time point ?
Since I use a rigid registration, the long time point T1 will not have been
d
And to add to this.
In a longitudinal study you search for small longitudinal changes. There you
should never switch versions or OS across time points, period.
(Also in a cross sectional study you should never do it, but often the effect
there, e.g. group differences, are much larger than proce
Dear FreeSurfer experts,
I am using HCP pipelines with my custom modifications of
FreeSurferHiResWhite.sh (especially to accomodate full-hires reconstruction) to
generate white and pial surfaces.
I tested the v6.0 beta mris_make_surfaces binary to hopefully fix some problems
with surfaces I f
Hi Antonin
I'm having trouble parsing your image. Could you:
1. Send the voxel coords of the location that you see overlap.
2. Send an image with *only* the two overlapping surfaces on, shown in
different colors?
thanks
Bruce
On Fri, 18
Nov 2016,
Antonin Skoch wrote:
Dear FreeSurfer expe
Dear Bruce,
see the screenshot in the attachment.
The coords (RAS) are: 2.2 -23.3 35.9.
The subject I have uploaded has this issue on multiple spots. The issue is
quite frequent, I have seen similar spots in several other subjects I have
checked so far.
Antonin
Hello,
So yes, this is expected. The just checked and the freesurfer VirtualBox
image is a 32bit operating system, and includes the 32bit version of
freesurfer. (I vaguely recall that when I set this up 3.5 years ago
there were no 64bit Ubuntu virtualbox images available.)
So the freesurfer v6
That is a very odd error and I havent seen anything like it that I can
recall.
My initial thoughts are that the nu_evaluate and nu_correct commands are
part of the mni tools shipped with freesurfer. The mni tools do a lot of
reading, writing and deleting of temporary files. (You can see how it
Pardon me for poking in here. I hope this is helpful.
It looks like the failure is on an lseek command which means the file isn't
there or was truncated, as Zeke suggests.
When you deploy your jobs to the cloud cluster, perhaps there's a directive
which can be tweaked to give you a bigger plaype
Those commands look right, though I would do the smoothing before
computing the standard dev. Also, I don't know whether your overall
method is valid.
On 11/15/2016 05:48 PM, Elijah Mak wrote:
> Hi Freesurfer Team,
>
> We would like to compare Z-scored surface maps between different
> modaliti
What was your exact mri_segstats command?
On 11/15/2016 05:59 PM, Elijah Mak wrote:
> Hi Doug,
>
> I am not sure if this is the correct way to reply to the thread. I
> thought that adding a "RE:" in front of the subject would
> automatically link the email to its orginal thread.
> I hope this w
Doug,
Any update on this?
Thanks,
Eli
On 11/10/2016 12:52 PM, Eli wrote:
> (2005,100e) for MRI (Philips)
> (0028,1053) for PET (Philips)
>
> I understand the PET may not be intended to work, but it doesn't seem
> to be copying over or applying the scale for either modality.
>
> On 11/10/2016 12
Thanks for your reply, Doug. Registering both LH and RH to fsaverage_sym worked
great.
As a preliminary step I am performing a group analyses with images reregistered
to the regular fsaverage using mris_apply_reg.
However, at the group level it is recognizing that the analyses were carried
out
Try converting the PET after setting this env var
setenv FS_SLICE_LIN_SCALE 1
This causes mri_convert to read 28,1052 (intercept) and 28,1053 (slope).
the output value should be
dicomvalue*slope + intercept
Is 2005,100e accompanied by an intercept ?
On 11/18/2016 11:25 AM, Rockers, Elijah D
Sorry, what are you trying to do? What did you do before you ran
isxconcat? What was your isxconcat command line?
On 11/18/2016 11:34 AM, James Roe wrote:
> Thanks for your reply, Doug. Registering both LH and RH to fsaverage_sym
> worked great.
>
> As a preliminary step I am performing a group
Hi Gari, those look correct (make sure that your indices are not off by
1 (ie, FS uses 0-based indexing, and matlab uses 1-based). I would not
expect them to be the same since #1 includes a non-linear transform, and
they are only off by about 1.5cm (not bad by affine standards). Not sure
that o
Hi Erik, I don't entirely follow what you are doing. It is not
appropriate to run mri_glmfit-sim on an fdr corrected map. Why not
analyze your functional data on fsaverage5?
On 11/15/2016 12:59 AM, ERIK JAHNER wrote:
> Dear free surfer experts,
>
>
> I was wondering if someone could give me som
Yes, (2005,100d) is the philips MRI intercept tag. it is zero in all of
our scans unfortunately they are using private tags for philips MR.
the 28,1052/1053 are the public tags, which their PET thankfully uses...
but for the MR they are empty.
I'm using bash, so i did export FS_SLICE_LIN_SC
.edu&q=from:%22Douglas+N+Greve%22>
> Fri, 18 Nov 2016 08:19:47 -0800
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20161118>
>
> Those commands look right, though I would do the smoothing before
> computing the standard dev. Also, I don
il-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22>
> Fri, 18 Nov 2016 08:19:47 -0800
>
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20161118>
>
> Those commands look right, though I wou
Hi,
I’ve read previously on the archive that it is not possible to use AFNIs
alphasim with freesurfer surfaces, however, I’m wondering if it might be
possible to use 3dClustSim (recent version with fixed bug)? Thanks for your
help.
___
Freesurfer maili
We have our own tools for doing this. When you run mri_glmfit-sim with
the --cache option, it access precomputed simulation tables. If you need
to create your own tables, see here
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
Note that the AFNI alphasim bug was not responsib
Thanks for all the helpful info Doug!
On 11/18/16, 1:38 PM, "Douglas N Greve" wrote:
>We have our own tools for doing this. When you run mri_glmfit-sim with
>the --cache option, it access precomputed simulation tables. If you need
>to create your own tables, see here
>
>https://surfer.nmr.mgh.h
Hi ZK,
Thanks. It is great news! I would like to report the following.
asegstats2table seems to be acting strangely.
File "/Applications/freesurfer_b6/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
Even typing asegstats2table --help lead
what happens when you run asegstats2table --help
It does not fail for me. I wonder if it is a python version problem
On 11/18/2016 04:01 PM, Elijah Mak wrote:
> Hi ZK,
>
> Thanks. It is great news! I would like to report the following.
>
> asegstats2table seems to be acting strangely.
>
> File
Thanks Doug,
this answers the question. I will use the fsaverage data for between
subject comparison and literature comparison then. Thanks!
Gari
PS: yes, the +1 and the xy flipping thing are a real pita :)
On Fri, Nov 18, 2016 at 5:54 PM Douglas N Greve
wrote:
> Hi Gari, those look correct (mak
Hi there,
I’m having trouble running the script. Should I place the script in the
$FSFAST/bin directory? Any advice on how to run the this version of mri_glmfit
would be much appreciated.
Thanks,
Keji
> On Nov 17, 2016, at 6:48 PM, Morenikeji Adebayo
> wrote:
>
> Thanks, Doug!! I’ll give it
Hi,
I can't find in my freesurfer version the mri_decimate, and I tried to
download it from the links in the mailing list archive but they are down.
>From where could I download it?
Thanks
Dorothy
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard
Hi Freesurfer Team,
I came across the following error while running mri_glmfit-sim. What is
vwsigmax?
Thanks for your help again.
The full log is as follows:
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Sat Nov 19 02:00:45 GMT 2016
Darwin dhcp-10-240-201-24.cp.wireless.privat
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