Hi Paras,
The tcsh warning is ok, but see this link for more info and a fix:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg28980.html
The unrecognized flag error is because you have a space between the dash
and subjid, just delete that space.
-Louis
On Thu, 3 Jul 2014, Paras Pa
Dear Freesurfer team
I am sorry to bore you again with my problems, but I need your help (or
opinion) about which is the best solution in my situation.
Is there any way to make xhemireg and surfreg (--xhemi) work in my
Freesurfer version (5.0)? Or do I need to use the 5.3 version?
I would prefer t
Hello Angela,
Have you tried just running the specific commands to get the output file
you need?
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
Anthony
On 7/7/14, 10:52 AM, angela.fav...@unipd.it wrote:
> Dear Freesurfer team
> I am sorry to bore you again with my problems, but I n
Dear FreeSurfer Experts,
We are collecting a 0.9mm isotropic FSPGR sequence on a GE MR750 3T
scanner. We're observing, in many subjects, a problem mentioned in previous
posts to the list where the pial surface does not follow the cortex
properly in the anterior temporal lobe region (and also in s
Hi Las
can you send us a couple of images of the problems you are seeing?
cheers
Bruce
On Mon, 7
Jul 2014, Las Blawimo wrote:
> Dear FreeSurfer Experts,
>
>
> We are collecting a 0.9mm isotropic FSPGR sequence on a GE MR750 3T scanner.
> We're observing, in many subjects, a problem mentioned
Yea, that is actually a feature in the new version
On 07/02/2014 02:17 PM, Joshua S wrote:
> Hi all,
> I was following the group analysis tutorial when I got an error when
> trying to view the uncorrected significance map with freeview. I used
> the command "freeview -f
> $SUBJECTS_DIR/fsaver
when you run mri_vol2surf you also pass a registration file with it.
This allows vol2surf to compute the col, row, slice in the volume that
maps to a given vertex.
doug
On 07/03/2014 06:05 PM, Paul Quigley wrote:
> Hi Bruce,
>
> This will help me move in the right direction. I still need to fi
On 07/03/2014 08:01 PM, June k. wrote:
> Dear Douglas,
>
> Thank you for your advice.
> It works like magic.
> I have one more question.
> In qdec gui, I found some small areas in two-group comparision with
> two discrete variables (diagnosis and gender) and two nuisance
> variables (ICV, age).
If you just run bet2 (ie, /usr/lib/fsl/5.0/bin/bet2) outside of FS, do
you still get the error? Can you use any of the other FSL commands?
On 07/04/2014 06:26 AM, Alan Lee wrote:
> Hello freesurferers,
>
> I ran this command (3 is my subject name):
>
> selxavg3-sess -a Retinotopy.3.lh -s
both the polar angle and eccen will have angle.nii.gz files sampled on
the surface. You can load these into matlab with
angle = MRIread('angle.nii.gz');
angle.vol will be a vector of length equal to the number of vertices
You can load the label with read_label
label = read_label('', labelfile);
l
Not using qdec. You will have to use the "command-line" stream with
mris_preproc, mri_surf2surf, mri_glmfit, and mri_glmfit-sim. There is a
tutorial and slides available
doug
On 07/02/2014 10:46 AM, Isotalus, Hanna wrote:
>
> Dear Freesurfer experts,
>
>
> I am doing an analysis on a large dat
The name of which label?
On 07/02/2014 02:00 PM, Corinna Bauer wrote:
> Whereby the label name is derived from which, the GM labels? i.e.
> lh.rostralmiddlefrontal_div3
>
>
> On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> yes, or mri_binarize -
Hi Anthony,
I am not sure I understood what you are saying, but I had no problems with
recon-all commands (I already performed surface, curvature and
gyrification analyses comparing cases and controls, etc...) until I tried
to perform interhemispheric registration.
I had the same problem (see attac
the new white matter divided labels. I was not able to extract the labels
using the matching grey matter names, but was able to do so using the label
number seen in the tools from tkmedit. Seeing as there are over 100 labels,
is there a more efficient way?
On Mon, Jul 7, 2014 at 12:08 PM, Douglas
Hi Mike,
try running the command by itself and look at why it does not work,
maybe one of the files is missing or the path is wrong?
Best, Martin
On 06/21/2014 02:11 PM, Michael Kranz wrote:
Hi,
I'm having trouble figuring out following problem:
For one subject (out of 200), I get the foll
Hi Alfred,
using FS longitudinal will increase reliability of measurements and is
always the right tool for longitudinal studies. However, images will
look consistently different across the two scanners. You will never know
if the differences that you find are caused by the scanner change or b
Hi Wang,
this is only a warning. Usually it is a bad idea to input two different
images into the longitudinal pipeline. It would be good to find out why
your inputs have different geometries. You should find the answers to
these questions in order to know what you are working with: Has someone
The problem is probably that your slice thickness is 5.2mm. This will
certainly never work for getting surfaces, though I don't quite
understand why nu is failing
doug
On 06/30/2014 03:51 PM, Remy Wahnoun wrote:
> Thanks Douglas,
> orig.mgz looks fine to me. Do you know if there is any detail
hmmm, hard to say. Is it possible that you ran out of memory? Maybe
something else was running on the machine? Try rerunning and see if it is
ok, and also monitor memory usage. It died right in the middle of
mri_ca_label which I can't remember seeing before
On Mon, 7 Jul 2014, Emad Ahmadi wro
Right, this is going to be a problem. One of the things you can do is to
use the --ctab option of mri_annotation2label to create a colortable,
something like
mri_annotation2label --ctab new.lh.ctab --s subject --hemi lh
--annotation newannot --outdir junk
You can do this for both hemis, t
great, thanks! I'll give that a try and let you know how it goes.
On Mon, Jul 7, 2014 at 12:50 PM, Douglas N Greve
wrote:
>
> Right, this is going to be a problem. One of the things you can do is to
> use the --ctab option of mri_annotation2label to create a colortable,
> something like
>
> m
Hi Doug,
By new version, do you mean v5.3.0?
Qijing
On Mon, Jul 7, 2014 at 11:31 AM, Douglas N Greve
wrote:
>
> Yea, that is actually a feature in the new version
>
>
> On 07/02/2014 02:17 PM, Joshua S wrote:
> > Hi all,
> > I was following the group analysis tutorial when I got an error when
No, the one that will replace 5.3. I think the new version of freeview
is available here
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/
On 07/07/2014 01:05 PM, Qijing Yu wrote:
> Hi Doug,
>
> By new version, do you mean v5.3.0?
>
> Qijing
>
>
> On Mon, Jul 7, 2014 at 11:31 AM, D
Hi,
I have followed the steps in the longitudinal qdec tutorial (
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), but
when I try to analyze longitudinal features such as long.thickness-rate I
get an error:
Error in analyze: Couldn't open
/SUBJECTS_DIR/SUBJECT_ID/surf/lh.long
I have been able to replicate the error with the patch in 5.1 and I'm
working on a fix.
doug
On 07/07/2014 10:52 AM, angela.fav...@unipd.it wrote:
> Dear Freesurfer team
> I am sorry to bore you again with my problems, but I need your help (or
> opinion) about which is the best solution in my si
Hi Sal,
so you processed some data using the longitudinal stream (recon-all,
recon-all -base and recon-all -long). Then you ran long_mris_slopes?
Can you send the command that gives the error and the freesurfer version
you are using?
Also check if the file
/SUBJECTS_DIR/SUBJECT_ID/surf/lh.
Hi Doug,
thank you very much!
Angela
>
> I have been able to replicate the error with the patch in 5.1 and I'm
> working on a fix.
> doug
>
> On 07/07/2014 10:52 AM, angela.fav...@unipd.it wrote:
>> Dear Freesurfer team
>> I am sorry to bore you again with my problems, but I need your help (or
>>
Doug, that worked very well, thanks.
mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown
--volmask --wmparc-dmax 2 --o ${subj_dir}/mri/wmdivided.nii --annot
aparc.split
mri_annotation2label --ctab new.rh.ctab --subject ${subject} --hemi rh
--annotation aparc.split --outdir ${subj_di
Several months ago someone mentioned the possibility of a neonatal processing
stream.
Is this in development, and if so is there an approximate time frame for
release.
Thanks
Jim
The materials in this email are private and may contain Protected Health
Information. If you are not the intende
OK, I have updated
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi
with new versions of mri_surf2surf and xhemireg. Copy those into
$FREESURFER_HOME/bin (after making backups of what is already there)
doug
On 07/07/2014 03:24 PM, angela.fav...@unipd.it wrote:
> Hi Doug,
>
I've attached a file that describes the rules we use to determine the
coordinates. The c_ras is the center of the volume. This is computed
from the geometry in the dicom; there is no dicom field for it
doug
On 07/07/2014 05:49 PM, Fan, Qiuyun wrote:
Dear Freesurfer experts,
I used EicomE
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