Hi Gary, you would use the MNI305 space as the common space. Eg, Case 2
shows you how to go from RAS of a subject to MNI305 space. You would
reverse that to go from MNI305 space to another subject's RAS space thus
allowing a RAS-RAS transform. If you have a surface overlay for a
subject, you ca
Hey All,
I am trying to turn my long.qdec.table.dat into a cross.qdec.table.dat
using the following command:
long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out
./qdec/cross.qdec.table.dat
However, when I try and load it into QDEC afterwards I get the following
error:
Loading data
Thanks Doug,
the problem is that I have a volume overlay.
When I register avg305T1.nii with Colin27 I have a different register
matrix than when using single_subject_T1.nii.
Do you think that this procedure will work (scripted for every subject)?
- *bbregister --s Colin27 --mov S_01 --init-spm -
Gari,
This is definitely an XQuartz issue. Have you rebooted your system since
installing XQuartz? Does /opt/X11/lib/libGLU.1.dylib exist? In my
experience, installing XQuartz can be a finicky process that sometimes
requires at least one reboot and a logout/login. If rebooting doesn't
solve your i
Many thanks for your answer Zeke,
We tried everything, install, delete, install again, with complete
reboots... At the end 5.1 is working in both X11 and Xquartz and 5.2
is not working in any of them (the first error is the one you describe
in your wiki and the second one is Bus Error (described in
Hi all,
I have a hard time relating the boundaries of the insula defined by Freesurfer
(Destrieux a2009s) with what is out there in the literature. Most of what is
out there is described in terms of anterior and posterior insula, and I'm not
sure if most of them match well with what is describe
Hi Nassim
I would say :
> Anterior insula = "G_insular_short"
> Posterior insula = "G_Ins_lg_and_S_cent_ins"
I wouldn't add the circular sulcus of the insula which limits it from the
surrounding frontal, parietal and temporal opercula
cheers
>
--
Christophe Destrieux,
Directeur du Dépa
Hi Folks,
Based on the tutorials, we normally run full recon-all pipeline; then add
control points if required and then
run -autorecon2-cp and -autorecon3 again.
Recently, I was looking at the process flow table:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
and I have two questions:
ps: just wanted to add a clarification to my question. The two scenarios
are:
Scenario A:
1. recon-all -s -autorecon1 -autorecon2 -autorecon3
2. add control points
3. recon -all -s -autorecon2-cp -autorecon3
Scenario B:
1. recon-all -s -autorecon1 -autorecon2
2. add control points
3. recon -all
Mehul,
Scenerio B is permissible. And to address your question, the pial
surface is created in the autorecon3 stage, making use of the
parcellation data to refine it. I think a pial is generated during
make_final_surfaces as its normal output, but its overwritten in
autorecon3.
Nick
On Wed, 2
Hello,
I am trying to download these files for Surface-Based Interhemispheric R
egistration:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfregftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemiregftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mr
Hi Nick,
Thank you very much. I have two followup questions. Since Scenario B is
permissible, I believe the following two scenarios should also be allowed.
(Just wanted to confirm this:)
Scenario C (for white matter edits):
1. recon-all -s -autorecon1 -autorecon2
2. edit wm.mgz (
http://surfer.n
Mehul,
Correct, in both scenario C and D you do not need to include the
-autorecon3 flag prior to making edits. For D, the kind of edits to
brainmask necessary to fix the pial surface will be visible in the pial
produced in -autorecon2 (which recall is not the final one, but will
certainly expose
Dear Doug,
Can you please advise me of the correct location of the ftp
directories/files required to be installed for surface based
interhemispheric registration?
I'm trying to download and install the required files from the specified
path: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/
Hi Doug,
The brainmask.mgz does exists, and the full recon-all runs normally. The
problem seems to be in the -FLAIRpial sequence only for me. The
registration runs, but doesn't produce mri/FLAIR.mgz.
I have attached the FLAIRraw.dat.log file. Please let me know if you would
like me to upload the
Oh, sorry, those get periodically deleted. Are you using 5.2? If so they
are already in the distribution. If not, I'll copy them back over.
doug
On 3/13/13 10:33 PM, Negar Memarian wrote:
> Dear Doug,
> Can you please advise me of the correct location of the ftp
> directories/files required to
Dear fellow Surfers,
I am trying to overlay
FreeSurfer 5.1 MNI305 (=fsaverage) aparc+aseg.mgz 3D volumes (caudate,
putamen, pallidum, etc)
onto
FSL MNI152 2mm resolution volume.
I first extract the nuclei from MNI305 aparc+aseg.mgz, for example:
mri_extract_label $FREESURFER_HOME/subjects/fs
Hi Doug,
No, I'm using 5.1. I'd appreciate if you copy them back.
Thank you,
Negar
On Wed, Mar 13, 2013 at 2:50 PM, Douglas Greve wrote:
> Oh, sorry, those get periodically deleted. Are you using 5.2? If so they
> are already in the distribution. If not, I'll copy them back over.
> doug
>
>
>
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