Dear Freesurfer experts,
I performed fMRI analysis using FSFast resulting in uncorrected significance
maps (fsig.nii.gz). For selxavg3-sess I did not use the -fwhm flag (I rerun
selxavg3-sess with -fwhm at moment).
How can I use simulations for native space hemispheres?. I tried to adapt
mri_
The link has been fixed. Thanks for letting us know.
-Zeke
On 11/13/2014 02:49 PM, Alex Spedding wrote:
> Hi,
>
> Sorry if this is the wrong place to put this - never used a mailing list
> before - but I've been watching the FreeSurfer lectures on Youtube. The
> link to download the slides in the
Hi Zeke,
Thanks for fixing it, I went through all the slides earlier today, and
2 more links are down:
TRACULA (includes the link on TRACULA Part 2)
https://www.youtube.com/watch?v=LpdYbe4pJK0
More Registration Techniques
https://www.youtube.com/watch?v=DQOmdLpf82k
I sent a message to the YouTu
Fixed both links. Thanks.
-Zeke
On 11/14/2014 10:39 AM, Alex Spedding wrote:
> Hi Zeke,
>
> Thanks for fixing it, I went through all the slides earlier today, and
> 2 more links are down:
>
> TRACULA (includes the link on TRACULA Part 2)
> https://www.youtube.com/watch?v=LpdYbe4pJK0
>
> More Regi
Hi Freesurfers,
I want to calculate the FA in a VOI 8 mm3 in the left and right prefrontal
white matter areas. My plan is to derive a mask for that area from aseg.mgz
then I will register this mask to the FA map to calculate the FA value. Is it
possible to derive like this mask from aseg.mgz and
Hi,
For one of my subjects, I have noticed a misalignment between sig.nii
and orig.mgz when I try to show the sig map using either tkmedit (as below):
cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Analysis
tkmedit-sess -s ../Subjects/auil2 -a OriExp_TR3_1p5mm_PR -c ANG_90_45
or tkmedit
Hi Mohamad
I would think you are better off using the wmseg for this.
cheers
Bruce
cheers
Bruce
On Fri, 14 Nov
2014, Alshikho, Mohamad J. wrote:
> Hi Freesurfers, I want to calculate the FA in a VOI 8 mm3 in the left and
> right
> prefrontal white matter areas. My plan is to derive a mask
I think Bruce is referring to the wmparc.mgz. Map the FA into the
anatomical space. Then use it with mri_segstats, probably with the erode
option.
doug
On 11/14/2014 11:41 AM, Bruce Fischl wrote:
> Hi Mohamad
>
> I would think you are better off using the wmseg for this.
>
> cheers
> Bruce
>
>
yes, sorry. That is what I meant
Bruce
On Fri, 14 Nov 2014, Douglas N Greve wrote:
> I think Bruce is referring to the wmparc.mgz. Map the FA into the
> anatomical space. Then use it with mri_segstats, probably with the erode
> option.
>
> doug
>
> On 11/14/2014 11:41 AM, Bruce Fischl wrote:
>> Hi
Doug an Bruce thanks a lot!!
I will do the following as I understood from your orientations and kindly
correct me if I am wrong:
first of all I will resample my FA map into the anatomical space as the
following command line :
mri_vol2vol --mov fa.nii --lta dti-analysis register.lta --fstarg --o
Dear all,
Is there a way to generate random or seed-based whole cortical (surface) or
brain (volumetric) parcellations in freesurfer or plugins, generating n
equal area (volume) scouts, where the user can select the n?
Thank you,
Octavian
___
Freesurfer
I think so, but I defer to Doug
Bruce
On Fri, 14 Nov 2014, Alshikho, Mohamad J.
wrote:
> Doug an Bruce thanks a lot!!
> I will do the following as I understood from your orientations and kindly
> correct me if I am wrong:
>
> first of all I will resample my FA map into the anatomical space as t
Hi Octavian
we do that on the surface (see e.g. mris_make_face_parcellation) but not in
the volume (although it would be a lot easier in the volume)
cheers
Bruce
On Fri, 14 Nov 2014, Octavian Lie wrote:
> Dear all,
>
> Is there a way to generate random or seed-based whole cortical (surface)
Yes, but you need to set the number of erodes. Each erode will be 1mm,
and you just need to erode enough to avoid partial voluming, so 2 is
probably fine. The more you erode, the smaller your ROI gets (and it can
disappear).
On 11/14/2014 02:05 PM, Bruce Fischl wrote:
> I think so, but I defe
Thanks!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, November 14, 2014 2:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Pref
Hello Freesurfers,
I am a beginner and have a question about the dicom file I need to select to
do the recon-all process.
I ran dcmunpack on the DICOM files I have with the following result
Institution RADIOLOGY ASSOCIATES-CDI
1 LOCALIZER3PLANE 5 20 40 0.546875 ROW 180
/home/freesurfer/D
That list gives you each acquisition and the protocol used to collect
it. You chose one (or more) and pass a single file to recon-all with -i;
recon-all will find the rest of the files in that series. As to which
series you need, it is hard to say since I did not collect the data :).
I'm guess
what is your SUBJECTS_DIR ?
On 11/14/2014 11:22 AM, SHAHIN NASR wrote:
> Hi,
> For one of my subjects, I have noticed a misalignment between
> sig.nii and orig.mgz when I try to show the sig map using either
> tkmedit (as below):
>
> cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Analysi
hi freesurfer folks,
when I try to run qdec or recon-all, they crash
recon-all -s MJ0001 -qcache
if: Expression Syntax.
qdec
cd: Too many arguments.
we have determined that because the subjects_directory name has spaces and
()'s in it, it is causing the two programs to crash
ech
I doubt any of them will work as they don't have enough slices/files,
meaning either the resolution is way too low or the FOV is not whole
brain. You typically need at least 128 slices in some T1-weighted volume
to get high enough resolution (e.g. <1.5mm or so)
cheers
Bruce
On Fri, 14 Nov 2014
The trick in the situation is to create a symbolic link. For example:
$> cd /Users/wieser/
$> ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\
Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001 MJ0001
$> recon-all -s MJ0001 -qcache
-Zeke
On 11/14/2014 02:53 PM, Jon Alan Wieser wrote:
> hi freesurfer folks,
I should have mentioned that in the example below, you will also want to
change your SUBJECTS_DIR.
$> export SUBJECTS_DIR=/Users/wieser
-Zeke
On 11/14/2014 03:13 PM, Z K wrote:
> The trick in the situation is to create a symbolic link. For example:
>
> $> cd /Users/wieser/
> $> ln -s /Users/wie
thanks Zeke,
I have created the symbolic link.
ln -s /Users/wieser/Dropbox\ \(UWM\ BraIN\ Lab\)/ImagingSuite/Blackbird/MJMRI
DROPBOX_MJMRI
I question is , when I cd into the symbolic link directory "DROPBOX_MJMRI"
(which contains all to my subjects), and use qdec and recon-all to cr
Yes, the directories and files will all exist under the Dropbox folder
and will thus be backed up by Dropbox. But I suggest you test this for
yourself and see.
-Zeke
On 11/14/2014 03:32 PM, Jon Alan Wieser wrote:
> thanks Zeke,
>
> I have created the symbolic link.
>
>
> ln -s /Users/wieser/Dro
yes, I will test it. i'm kind of new to symbolic links. thanks!
Jon
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Z K
Sent: Friday, November 14, 2014 2:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] qdec and recon-all crashes
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