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
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
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 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
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
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
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 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 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
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 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
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 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
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:
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.
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
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
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...
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
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
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 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
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 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
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