Hello Sir,
I'm using FreeSurfer through Virtual Box. I tried the below command for
reslicing my volume according to a reference volume but the process gets
stuck at " reading volume".
*mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz*
A: Volume to be resampled / resliced
B: Reference Volume
e error message). They are free.
>
> cheers
> Bruce
> On Wed, 12 Nov 2014, Gunjan Gautam wrote:
>
>
>> Hello Sir,
>>
>> I'm using FreeSurfer through Virtual Box. I tried the below command for
>> reslicing my volume according to a reference volume
talled on the Desktop whereas the
> prepackaged version made by us is installed in /usr/local
>
> -Zeke
>
> On 11/12/2014 08:54 AM, Gunjan Gautam wrote:
> > Hello Sir,
> >
> > License file is present in the folder but with the name LICENSE. Should
> > I download
et a valid license file you will need to place it in your
> $FREESURFER_HOME directory (the same directory that contains
> build-stamp.txt) and give it the name .license or license.txt. Try both.
>
> -Zeke
>
> On 11/12/2014 01:29 PM, Gunjan Gautam wrote:
> > Sir earlier I wa
t; Bruce
>
>
>
> On Tue, 18 Nov 2014, Gunjan Gautam wrote:
>
> Hello Sir,
>>
>> I have place the "license.txt" in the same directory that contains
>> build-stamp.txt as there were no directory with name "FREESURFER_HOME".
>> free
ue, Nov 18, 2014 at 6:47 PM, Bruce Fischl
wrote:
> I think if the file existed you would have gotten a syntax error. Does it
> exist? If not, then either you didn't install FreeSurfer there or something
> went wrong with your installation
>
>
> cheers
> Bruce
>
> On Tue
omplain about
> libjpeg or libtiff:
>
> cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu distros)
> sudo ln -s libjpeg.so.8 libjpeg.so.62
> sudo ln -s libtiff.so.4 libtiff.so.3
> ***
>
> -Zeke
>
>
>
>
> On 11/18/2014 03:55 AM, Gunjan Gautam w
will do everything that we know how to do
> (including those steps)
>
> cheers
> Bruce
> On Wed, 19 Nov 2014, Gunjan Gautam wrote:
>
>
>> Ok, I try this tomorrow morning.
>>
>> I will be thankful if you could tell me about getting brain mask and
>> perf
Ok, I go through that.
Thanks,
Gunjan
On Nov 19, 2014 12:37 AM, "Bruce Fischl" wrote:
> Hi Gunjan,
>
> it's all on the wiki. You should go through our tutorials
>
> cheers
> Bruce
> On Wed, 19 Nov 2014, Gunjan Gautam wrote:
>
>
>> Thank you
&
easier than trying to ru individual
> steps
>
> chers
> Bruce
>
> On Wed, 19 Nov 2014, Gunjan Gautam wrote:
>
> Hi,
>>
>> I am facing few issues. I will be thankful if you can help me out.
>>
>> Query 1) I used "mri_convert a.nii a.resliced.nii
he subject id is one that you make up - it will be the name of the
> directory under which the results are stored. Also specify a SUBJECTS_DIR
> on the command line, which will be the root directory under which all the
> individual subject trees live (with -sd
>
> cheers
> Bruce
>
uce Fischl" wrote:
> no, because I don't know what the volume are that you are using
> On Wed, 19 Nov 2014, Gunjan Gautam wrote:
>
>
>> Ok I try this out.
>>
>> Did you answer my Query 1(related to cropped output of mri_convert
>> command ?
>>
trying to achieve?
cheers
Bruce
On Wed, 19 Nov 2014, Gunjan Gautam wrote:
> I have attached both the volumes (reference and input) with my mail.
> Its the last step of my work, I'm stuck at and not finding any solution. I
> read that FreeSurfer can solve my problem.
>
> I wi
Hi,
I used recon-all with all and its taking a lot of time. My main concern is
only to get the stripped brain.
I tried with autorecon1 as well but its also taking not less than 15min and
I need to deal with a huge data.
Last stage of autorecon1 is skull stripping which takes the NU corrected
input
> the failure rate would go up. We've tuned it to improve automaticity and
> reduce failures quite a bit.
>
> cheers
> Bruce
>
>
> On Sat, 22 Nov 2014, Gunjan Gautam wrote:
>
>
>> Hi,
>>
>> I used recon-all with all and its taking a lot of tim
Ok thank you Bruce
On Nov 23, 2014 10:37 PM, "Bruce Fischl" wrote:
> we don't have a binary one, but all voxels in brainmask.mgz that are >5
> are in brain and everything <5 is not in brain
>
> cheers
> Bruce
>
> On Sun, 23 Nov 2014, Gunjan Gautam wrot
Hi Bruce,
What about the voxels having value equal to 5 (if exists) ?
Gunjan
On Sun, Nov 23, 2014 at 10:39 PM, Gunjan Gautam
wrote:
> Ok thank you Bruce
> On Nov 23, 2014 10:37 PM, "Bruce Fischl"
> wrote:
>
>> we don't have a binary one, but all voxels in br
Hi FreeSurfers,
brainmask.mgz is generating 256 slides per volume. How can I have control
over it, in terms of generating less number of slides (say 181) per volume?
Gunjan
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>
>
> - Original Message -
> From: "Gunjan Gautam"
> To: "Freesurfer support list"
> Sent: Monday, December 1, 2014 2:23:12 PM
> Subject: [Freesurfer] Number of slices generated in the brainmask.mgz
&
is "coronal" is actually horizonatal).
>
> How did you create the nifti files? If you give dicom directly to
> recon-all you will likely not have this problem
>
> cheers
> Bruce
>
>
> On Thu, 11 Dec 2014, Gunjan Gautam wrote:
>
> ​Dear all,
>>
>> I
l never be able to distinguish left from right again
>
> cheers
> Bruce
>
>
> On Tue, 16 Dec 2014, Gunjan Gautam wrote:
>
>
>> Thanks Bruce,
>>
>> I used "medcon" command (Ubuntu) for the stacking of 2D slices in order to
>> convert it in a
give recon-all the dicom file that
> contains a single one of those slices. It doesn't matter which one - we
> will figure out the rest of them from any of them
>
> On Tue, 16 Dec 2014, Gunjan Gautam wrote:
>
>
>> Hi Bruce,
>>
>> I am sorry to say that I d
to start further upstream
>
> cheers
> Bruce
>
>
> On Tue, 16 Dec 2014, Gunjan Gautam wrote:
>
>
>> I don't have dicom for this subject but it can easily be converted to from
>> .nii to .dcm.
>> I try this out and get back to you if I stuck at some poin
o you need to convert it to nifti? Can you process the minc directly?
> See if freeview can display it:
>
> freeview -v file.mnc
>
>
>
> On Tue, 16 Dec 2014, Gunjan Gautam wrote:
>
>
>> Hi Bruce,
>>
>> Originally, data was in MINC format.
>>
>>
thout coming in 2D space.
Any suggestion will be highly appreciate.
On Dec 16, 2014 7:22 AM, "Bruce Fischl" wrote:
> isn't the minc a volume? It certainly supports holding an entire volume in
> a single file
> On Tue, 16 Dec 2014, Gunjan Gautam wrote:
>
>
>>
want to make to
> each slice?
>
> Bruce
> On Tue, 16 Dec 2014, Gunjan Gautam wrote:
>
>
>> Yes Bruce, minc is a volume but I want to perform some experiments and see
>> the aftereffects.
>> This is how I come from 3D to 2D to make changes in each slice and again
eal with this kind of thing internally (and in 3D, not on a slice-by-slice
> basis)
>
> cheers
> Bruce
> On Tue, 16 Dec 2014, Gunjan Gautam wrote:
>
>
>> Sure,
>>
>> My data(3D volume) is having different ranges of noise and nonuniformity
>> so
>>
"
>> wrote:
>> have you tried just giving the original volume to recon-all? We
>> typically deal with this kind of thing internally (and in 3D,
>> not on a slice-by-slice basis)
>>
>> cheers
>> Bruce
>> O
fficulty to process these
volumes through FS.
Thanks,
Gunjan
On Tue, Dec 16, 2014 at 7:59 AM, Gunjan Gautam
wrote:
>
> Thank you Bruce,
>
> I try this out.
> On Dec 16, 2014 7:58 AM, "Bruce Fischl"
> wrote:
>
>> I'm not sure what to tell you then. You
nate systems are extensively documented here:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?
> action=AttachFile&do=get&target=fscoordinates.ppt
>
> cheers
> Bruce
>
> On Wed, 17 Dec 2014, Gunjan Gautam wrote:
>
> Hi Bruce,
>>
>> I c
onvert the minc to .mgz with mri_convert, then load the mgz into matlab
> using either MRIread or load_mgh (which will both return the direction
> cosines), and save them with either MRIwrite or save_mgh, given preserving
> the direction info.
>
> cheers
> Bruce
>
> On
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