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
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
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
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
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 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
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
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
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
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
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
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
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)
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
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
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
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
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
>
>
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
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 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
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 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
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
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_
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