where did they come from? Did you try telling mri_conver that they are
dicom with -it dicom?
On Thu, 2 Sep 2010, Gabriel Go.Es. wrote:
>
>
>
> Hello FreeSurfers
>
> I'm trying to convert some dicom images, but some of them apparentely FS just
> does not recognize them as dicom images, even when
'dcm2nii' would be another DICOM to nifti converter to try.
good luck,
-MH
On Thu, 2010-09-02 at 17:54 -0400, Douglas N Greve wrote:
> Sorry, I don't have an easy solution. I think philips does something
> that breaks our 3rd party dicom reader, so there's not an easy way for
> me to fix it. T
Hi Doug and all,
In the output summary of optseq2, does the absolute value of the efficiency of
nominal ideal XtX matter when evaluating your design? Specifically, I'm
experimenting with different TR durations, and it looks like shorter TRs give
me lower efficiency values, but these values are
Sorry, I don't have an easy solution. I think philips does something
that breaks our 3rd party dicom reader, so there's not an easy way for
me to fix it. There are other converters out there (one called
MRIconvert). You can convert to nifti and just pass that to recon-all
instead of the dicom.
Mmm, now I just have a problem...
that dicom is from an structural MRI and still does not work... do you think
that can i solve it anyother way???
Gabriel
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The name/extension should not matter. I have had problems with
functional data from philips. Structurals seem to always work.
doug
Gabriel Go.Es. wrote:
> Thank for answering Doug
> Yes, they are from a philips scanner, and actually not with all
> series, there are some of them wich does not ha
Thank for answering Doug
Yes, they are from a philips scanner, and actually not with all series, there
are some of them wich does not have extension, and with those series FS works
perfectly, but not at all with the ones like the one i've send.
And i remmember that some day we have convert some
I had a couple questions relating to how to perform retinotopic analysis and
view the results in the new Freesurfer 5.0 distribution (bear with me,
previous I was using Freesurfer 4.0.2, so there's probably a bunch of
changes that are confusing me).
1. I was able to create a new analysis with mka
This is from a philips scanner, most of the time I think our tools work
on philips data. Does this happen with all of your philips data or just
this one series?
doug
Gabriel Go.Es. wrote:
>
>
> Hello FreeSurfers
>
> I'm trying to convert some dicom images, but some of them apparentely
> FS ju
On Sep 2, 2010, at 2:49 PM, corinna bauer wrote:
> Thank you, that seems to have done the trick.
>
> On Thu, Sep 2, 2010 at 2:13 PM, Krish Subramaniam > wrote:
> Hi Corinna
>
> I think most likely it's the division operator ( / ) you used in the
> line
>
>
> gwratio.vol = gray.vol/white.vol;
>
It could be that the input files (eg, mghrh.white.projfrac.pos35) were
created, then the subject was edited (which would change the number of
vertices), but the input files were not re-created. Check the creation
dates on the files.
doug
corinna bauer wrote:
> Do you have any idea as to what m
Hi Danny, sorry, that is the tutorial for the version 4.5 FSFAST. I
still need to post the version 5 tutorial.
doug
Danny Kim wrote:
> Hello all,
>
> I've recently downloaded Freesurfer 5 and was going through the FSFAST
> tutorial.
> I keep on getting an error saying when I run "preproc-sess -
Hi Corinna
I think most likely it's the division operator ( / ) you used in the
line
gwratio.vol = gray.vol/white.vol;
Element-wise division in MATLAB is achieved by a ./ . I think the line
should be
gwratio.vol = gray.vol./white.vol
You could debug it by placing a
size(gwratio.vol)
imme
Hello all,
I've recently downloaded Freesurfer 5 and was going through the FSFAST
tutorial.
I keep on getting an error saying when I run "preproc-sess -s mgh-101.1
-fwhm 5 -per-run":
--
preproc-sess logfile is log/preproc-sess.log
--
Do you have any idea as to what may have gone wrong? Both files that went
into creating the ratio have dimensions: 151243 x 1 x 1.
In matlab I did this:
rootdir = '/home/freesurfer4.4.0/subjects/corinna/ADNI';
paths=dir([rootdir,'/*']);
num=numel(paths)
for ii=428:num
fprintf('- Processin
that should be ok, but of course somewhat less accurate
Bruce
On Thu, 2 Sep 2010,
Muhammad Ayaz wrote:
> Does the data has to be isotropic to process it with freesrufer for cortical
> measurements? I have MPRAGES with resolution 1x1x1.5 which I want to run
> through recon-all.
>
> Ayaz
>
> __
Does the data has to be isotropic to process it with freesrufer for cortical
measurements? I have MPRAGES with resolution 1x1x1.5 which I want to run
through recon-all.
Ayaz
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Hi Doug et al,
I'm trying to import the polar and eccentricity maps resulting from a
retinotopy analysis into Matlab for some additional manipulation.
Specifically, what I'd like is to get something like the output from:
surf-sess -s sessid -a rtopy -retinotopy polar/eccen -flat
as polar an
Hi to all,
thanks for your help, we could solve the autorecon2 problem!
there is another problem with autorecon1...
ncid 4: No space left on device
mivarput1: MINC package entry point
nu_evaluate: crashed while running mincresample (termination status=768)
nu_correct: crashed while running nu_e
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