Hi Bronwyn,
sure, it should be easy to do in matlab. If the array is called pvals and
it is from the left hemi, you would do:
save_mgh(pvals, 'lh.pvals.mgz', eye(4), [0 0 0 0]);
cheers
Bruce
On Tue, 1 Dec 2015,
Bronwyn Overs wrote:
> Hi Freesurfer mailing list,
>
> Using an external softwar
Hi Freesurfer mailing list,
Using an external software package we have completed of analysis for the
vtx-wise thickness data extracted from freesurfer. We now have a p-value
array containing one value for each vtx, and we would like to map this
back onto the brain surface. Is there a way to cr
Hi all,
for the question below, is it correct this command?
probtrackx2 --network -x /dir/subj001/mask/masks.txt -V 1
--onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 50 --fibthresh=0.01
--distthresh=0.0 --sampvox=0.0 --forcedir --opd -s
/dir/subj001/bedpostX/merged -m /dir/subj001/bedpostX/no
Hello freesurfer users,
I am a new user of freesurfer. We are using FS to define ROIs for out PET
analysis. I looked at the FS color lookup table, and saw the following
ROIs.
8001 Thalamus-Anterior 74 130 181 0 8002 Thalamus-Ventral-anterior 242 241
240 0 8003 Thalamus-Lateral-dorsal 206 65 78 0
Hi Falk,
I used the command and got the following error:
Command: ris_topo_fixer -mgz -warning -seed 1234 ICBM lh
mris_topo_fixer -mgz -warning -seed 1234 ICBM lh
INFO: assuming .mgz format
setting seed for random number genererator to 1234
reading input surface
/home/imuser/Downloads/mni_icbm1
esurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for Biomedica
Dear Bruce,
I was wondering whether you received my transfer well. If you sent me an
email back already, my apologies. I accidentally switched of email service
from the support list for a day.
Thank you in advance,
Annelinde
2015-11-24 10:29 GMT-08:00 Annelinde Vandenbroucke <
vandenbroucke.w...
Hi - that's way too low, unfortunately. You need at least 4GB and more is
preferred.
See: https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements
On Mon, Nov 30, 2015 at 5:19 PM, salvatoreandrea...@libero.it <
salvatoreandrea...@libero.it> wrote:
> I have around 2 Gb of total RAM. Isn't th
that is just a warning, it is not a problem. the results should be fine
On 11/30/15 6:28 AM, Carme Uribe Codesal wrote:
Dear FreeSurfer users,
I am trying to add a per-vertex regressor in my general lineal model
(a cortical thickness analysis with the white matter-grey matter
contrast paramet
look in the glmfit output folder for a file called fwhm.dat
On 11/29/15 3:06 PM, Emma Thompson wrote:
Sorry for the repost of my last post, but I now realize that what I
need is the estimated filter width that was actually used in the qdec
analysis not the fwhm that I actually specified, i.e.
I have around 2 Gb of total RAM. Isn't that sufficient to run recon-all? If it
is not, do you know whether there is a way to split up the process?
Messaggio originale
Da: theni...@gmail.com
Data: 27-nov-2015 17.24
A: "salvatoreandrea...@libero.it", "Freesurfer
support list"
Ogg:
Hi Ajay
if you can use our ftp or file drop, both linked at:
https://surfer.nmr.mgh.harvard.edu/fswiki
then I'll take a look. And yes, uploading the entire subject dir will make
it easier.
cheers
Bruce
On Mon, 30 Nov
2015,
Ajay Kurani wrote:
Hi Falk,
Thank you very much for the sug
Hi Falk,
Thank you very much for the suggestion! I will give it a try.
Also Bruce I sent a separate email with a link to the original image for
you to download. I can also move all of my processed files for that
template there if you would like so you do not have to restart from
scratch?
Than
Hi Bruce,
I encountered this error once with 3 digit file names, but it is okay now, I
will take Martin's advice of reconstructing with the best image.
Thanks very much.
Best
Dong
-邮件原件-
发件人: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] 代表 Bruc
Dear FreeSurfer experts,
I'm trying to convert some retinotopic labels I created on the surface of
each individual subject to MNI305 space for FSL.
I run the following commands, but the output is not registered correctly.
It seems to be shifted downward.
mni152reg --s LG
mri_label2label --srcla
Hi Martin,
Thanks for your help, I think you are right, there is no need to average so
many MPRAGE images, I will simply select the best one to reconstruct.
Thank you very much for helping me.
Best
Dong
发件人: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.e
Hi Bishesh,
Disclaimer up front:
You probably know that adding time points without re-creating the base
is dangerous (as you bias you analysis, because not all time points are
treated the same).
Now here is why you see the error.
The way a new time points get added to an existing base is this
Hi Dong,
you should see in the scripts/recon-all.log file, what the exact command
is.
The list of all inputs gets created via:
set RunList = `ls $subjdir/mri/orig/[0-9][0-9][0-9].mgz`
so 4 digit file names are not supported. It should work with three, not
sure what it going on. Please post
Hi Dong
sorry, not sure I understand. Is it the case that recon-all finds 001.mgz
through 009,.mgz but fails to find 010.mgz, 011.mgz etc...?
cheers
Bruce
On Mon, 30 Nov 2015, Dong Haoming wrote:
Dear freesurfer exports,
I still have the problem to recon the surface with more than 10 in
hmmm, if either of you wants to upload a subject that is an example of
this we will track it down and fix it.
cheers
Bruce
On Mon, 30 Nov 2015, Falk Lüsebrink
wrote:
Hi Ajay,
I ran into the same error processing hires data a while ago using a nightly
build of centos 6 with the hires flag o
Dear FreeSurfer users,
I am trying to add a per-vertex regressor in my general lineal model (a
cortical thickness analysis with the white matter-grey matter contrast
parameter as regressor). I have no problems with the command line
mri_glmfit:
mri_glmfit --y rh.cth_corr_MMSE.mgh --fsgd cth_corr_M
Hello,
I had run a longitudinal run by creating a base template with a set of
time-point scans (tpts). I wanted to add a new tpt (say new1) without
recreating the base template, hence I used the option -addtp in the
recon-all -long run. Later on, I no longer needed the results of the long
run for n
Dear freesurfer exports,
I still have the problem to recon the surface with more than 10 inputs from
one person with following command:
“recon-all -s ${subjec} -autorecon1 �Cnotal-check -clean-bm -gcut
-no-isrunning -noappend”,
Is there a limit on the number of the inputs?
What is the algor
Hi Ajay,
I ran into the same error processing hires data a while ago using a nightly
build of centos 6 with the hires flag only. Disk space or alike wasn't an
issue. I ran mris_topo_fixer instead of mris_fix_topology to get working
surfaces.
Best,
Falk
-Ursprüngliche Nachricht-
Von: f
24 matches
Mail list logo
