hanks a lot,Anil Roy.
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Hello All,
So I tried using recon-all to get a few parcellations stats from a minc
file it but I'm getting the following error. Please could someone say
how this can be rectified. Thanks. - Anil Roy.
This is the command I'm giving:
# recon-all -force -i /root/Desktop/F100.mnc -subji
- Anil.On 6/23/06, Bruce Fischl <[EMAIL PROTECTED]> wrote:
what steps have you run previously? You don't need to specify -i on laterstages, just the subjid and sd.On Fri, 23 Jun 2006, Anil Roy wrote:> Hello All,>> So I tried using recon-all to get a few parcellations stats from a mi
ny help is greatly appreciated.
Thanks - Anil Roy.On 6/23/06, Bruce Fischl <[EMAIL PROTECTED]> wrote:
well, you specified -autorecon3, which assumes some stuff has been runbefore. If you want to do everything from beginning to end run -all insteadBruceOn Fri, 23 Jun 2006, Anil Roy wrote:>
wrote:> Message: 8> Date: Sun, 25 Jun 2006 17:07:36 -0500
> From: "Anil Roy" <[EMAIL PROTECTED]>> Subject: Re: [Freesurfer] recon-all error
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:> <[EMAIL PROTECTED]
>> Content-Type: text/plain; chars
Hi Everyone,
Is there a way to process the minc files I have and only obtain the
anatomical stats without the entire recon-all process. I have a large
number of brains and it would take a couple of weeks if I was to take
every minc file and run recon-all.
Thanks - Anil.
_
but then you'll need to manually edit thesurfaces, which can be time consuming. Running on more than one computerisn't an option for you?On Wed, 28 Jun 2006, Anil Roy wrote:
> Hi Everyone,>> Is there a way to process the minc files I have and only obtain the> anatomical stats w
ocess killed this one.BrucOn Mon, 17 Jul2006, Anil Roy wrote:> Hello All,>
> I've been running recon-all on a couple of minc brains on Fedora Core 4 and> everything thing runs fine. I started running a few on a Mandrake> Linux 9.2system but each time recon-all exits with erro
Hello All,Does freesurfer generate a file with total brain volume after the recon-all procedure? Where can this be accessed?Thanks,AR.
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Hello all,I get the following error when I feed in a dicom file into recon-all. The dicom file is in a directory with 159 other dcm files. Can you please tell me how to rectify this or what the source of the error is.
[EMAIL PROTECTED] freesurfer]# recon-all -i /root/Cath/ADULT\ 14-0005-0001-0001.d
set InputList = ($InputList "$InputVol"); set DoConvertInput = 1; breakswThe change is the inclusion of double-quotes "" on certain variables.This fix will appear in the next stable release.
NickOn Fri, 2006-10-06 at 16:25 -0500, Anil Roy wrote:> Hello all,>
OTECTED]
[mailto:[EMAIL PROTECTED]] On Behalf Of
Anil Roy
Sent: Monday, October 09, 2006
5:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer]
recon-all error
Thanks a lot. recon-all
runs after applying the fix. However, I seem to have run into a different
error. Here is
Hello everyone,Can someone please point out where freesurfer outputs the total cerebral volume (white + gray).Thanks,Anil.
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Dear Freesurfers,
I am checking out the functionality of using Freesurfer with AFNI and was
wondering if someone could point me in the direction of any good
documentation for this. So far, I can get Freesurfer to register the
functional and hi-res structural but the functional overlay doesn't sho
Hello all,
I have some raw data and I'm not sure of the format. Its definitely not
dicom. I ran recon-all on these files but I get an error saying it can't
read the files. I have posted the output below. I tried to convert the files
to afni format (BRIK + HEAD), and tried recon-all again. It ran
ert it to BRIK and visualize it does it look correct?
On Thu, 8
Feb 2007, Anil Roy wrote:
> Hello all,
>
> I have some raw data and I'm not sure of the format. Its definitely not
> dicom. I ran recon-all on these files but I get an error saying it can't
> read the files. I
I'll install the CentOS build and run the brain again.
Anil.
On 2/8/07, Anil Roy <[EMAIL PROTECTED]> wrote:
Yes. When I convert to BRIK and open with AFNI, the images show up fine in
all three planes.
There is some noise towards the very end but it only shows up after the
sli
m?
On Thu, 8 Feb 2007, Anil Roy wrote:
> Hi All,
>
> I installed the new build and Freesurfer still quits at the same place.
I've
> attached the recon-all.log file to this email. Its still giving an error
at
> the watershed step.
>
> Anil.
>
> On 2/8/07, Anil Roy <
nd pretty vertical so for example the interhemispheric fissure goes
straight up and down in a coronal view
On Thu, 8 Feb 2007, Anil Roy wrote:
I've attached the talairach.xfm to this email. I'm a newbie to MRI analysis
so I don't know what exactly would be a red flag in this file.
7-02-14 at 16:10 -0500, [EMAIL PROTECTED] wrote:
> The following files have been uploaded to the Martinos Center FileDrop
site
> by Anil Roy for you to download:
>
> (1) orig.mgz
>
>
>
> These files will expire in 30 days.
>
> To view or download the
a why it would be so white?
>>>
>>> Nick
>>>
>>>
>>> On Wed, 2007-02-14 at 16:10 -0500, [EMAIL PROTECTED] wrote:
>>>> The following files have been uploaded to the Martinos Center
FileDrop site
>>>> by Anil Roy for you to dow
Also, I ran it on a Red Hat system and I'm still getting the error so I
don't think it is a machine specific problem. Any suggestions.
Thanks.
Anil.
On 2/14/07, Anil Roy <[EMAIL PROTECTED]> wrote:
Here are the details of the acquisitions:
Images acquired on a 3T Signa scanner
atershed is
encountering out-of-memory errors.
Nick
On Wed, 2007-02-14 at 17:20 -0600, Anil Roy wrote:
> Also, I ran it on a Red Hat system and I'm still getting the error so
> I don't think it is a machine specific problem. Any suggestions.
>
> Thanks.
> Anil.
>
> On 2
watershed without any glitches.
Thanks,
Anil.
On 2/15/07, Bruce Fischl <[EMAIL PROTECTED]> wrote:
I think it's because your background values are so high.
On Thu, 15 Feb
2007, Anil Roy wrote:
> Thanks a lot Nick.
>
> I'll try to convert the AFNI skull strip into brai
.
On 2/20/07, Bruce Fischl <[EMAIL PROTECTED] > wrote:
I think it's something afni is doing, but I'm not sure. Did you give us
the data before conversion (either the dicoms or the 001.mgz)
On Tue, 20 Feb 2007,
Anil Roy wrote:
> Hey Freesurfers,
>
> I fed freesurfer the b
Its uploaded
On 2/20/07, Bruce Fischl <[EMAIL PROTECTED]> wrote:
I need the 001.mgz
On Tue, 20 Feb 2007, Anil Roy wrote:
> Bruce, I had uploaded the orig.mgz for Nick. I think you should find the
> link below. I can also upload the 001.mgz for you.
> There are no dicoms beca
I think my last email didn't get through. Bruce, I've uploaded the 001.mgz.
It should arrive in your mailbox. I can upload it again if there was any
problem.
Thanks,
Anil.
On 2/20/07, Anil Roy <[EMAIL PROTECTED]> wrote:
Its uploaded
On 2/20/07, Bruce Fischl <[EMAIL PROTE
I think my last email didn't get through. Bruce, I've uploaded the 001.mgz.
It should arrive in your mailbox. I can upload it again if there was any
problem.
Thanks,
Anil.
On 2/20/07, Anil Roy <[EMAIL PROTECTED]> wrote:
>
> Its uploaded
>
> On 2/20/07, Bruce Fisch
white matter
surface not accurate.
Did you have any suggestions for the background values.
Any ideas.
Thanks,
Anil.
On 2/21/07, Bruce Fischl <[EMAIL PROTECTED]> wrote:
Hi Anil,
I got the email, but I'm out of town and won't get to it until next week
Bruce
On
Wed, 21 Feb 2007,
, I haven't had a chance to
look at it
On Tue, 27 Feb 2007, Anil Roy wrote:
> Hi Bruce,
>
> I've been trying to improve the talairach xfm and try different things
with
> afni, but so far nothing has worked out. The brain still crashes at the
> skull strip. I fed in the afn
[EMAIL PROTECTED] wrote:
>
> The following files have been uploaded to the Martinos Center FileDrop
site
> by Anil Roy for you to download:
>
> (1) 001.mgz
>
>
>
> These files will expire in 30 days.
>
> To view or download these files, go in your web browser
Hi all,
Is Freesurfer going to generate all surfaces properly if I feed in a skull
stripped brain to begin with starting from stage 1. In other words, is there
going to be a problem if the orig.mgz is skull stripped. I checked the
results after autorecon1 and the brainmask.mgz had a decent contra
n't be
accurate.
On Wed, 7 Mar 2007, Anil Roy
wrote:
> Hi all,
>
> Is Freesurfer going to generate all surfaces properly if I feed in a
skull
> stripped brain to begin with starting from stage 1. In other words, is
there
> going to be a problem if the orig.mgz is skull stripped. I c
Hello all,
Is there a method to generate a gray matter mask in Freesurfer that can be
fed into AFNI. Could you please point me to any existing documentation on
the FS wiki that already does this as I was unable to find anything.
Thanks a lot,
Anil.
__
Hi,
When I run tkmedit, I receive the following message. It doesn't seem to
affect the functionality. Could you explain why this message shows up.
Xlib: extension "XFree86-DRI" missing on display ":0.0".
Thanks,
Anil.
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it is here:
>
> http://surfer.nmr.mgh.harvard.edu/pub/dist/X11Update2006.dmg
>
>
>
> Which OS are you using?
>
>
>
> *From:* [EMAIL PROTECTED] [mailto:
> [EMAIL PROTECTED] *On Behalf Of *Anil Roy
> *Sent:* quinta-feira, 4 de outubro de 2007 22:17
> *To:* fr
Hi All,
I got the following error while running recon-all on a set of dicoms. It
seems to be a problem with the intensity correction stage but I can't get it
to work. Any help is appreciated.
Thanks,
Anil.
[EMAIL PROTECTED] freesurfer]# recon-all -i
/mnt/win/MRI_data/MWIN4/O-07-002/anatomical_d
Or all subjects? Is it
> repeatable? Is there another MNI installation somewhere in the path?
>
> Nick
>
>
> On Sun, 2007-11-04 at 15:51 -0600, Anil Roy wrote:
> > Hi All,
> >
> > I got the following error while running recon-all on a set of dicoms.
> > It seems
Hello All,
I wanted to test the Freesurfer installation by running recon-all but I
received an error saying flirt no found. Can someone point me to the cause
of this problem, is it a missing library or some other issue?
I have posted the output from running recon-all on bert below.
Thanks,
Anil
Hello All,
I wanted to convert the brainmask volume to analyze format. I'm not very
familiar with the analyze format and had two questions.
1) The wiki mentions that converting to SPM-Analyze format could involve
converting to multiple or single frames. What exactly are multiple or single
frames?
Hello All,
I want to create a binary mask volume for stg and tried the following
command
# mri_label2vol --label trial_labels/rh.superiortemporal.label --temp
/mnt/win/MRI_data/Trial_Runs/Freesurfer/1195/mri/brainmask.mgz --o
testmask.mgz
The label was created using mri_annotation2label
When I
Hello All,
I used mri_binarize to create stg masks (inclusive of gray and white
matter).
I'm trying to take this a step forward to see if I can extract the actual
brain region encompassed by the mask - in other words, is there a way to cut
out the portion of the brain that the mask encloses. So i
Hi Bruce,
I'm working with Dan on this.
Yes, it does seem to work - sorry for the confusion. I was looking at the
output without zooming in and it seemed to have only one intensity inside
the mask, but on zooming in I could see the variations in intensity.
I did have an additional question - is
Hi Bruce,
I'm working with Dan on this.
Yes, it does seem to work - sorry for the confusion. I was looking at the
output without zooming in and it seemed to have only one intensity inside
the mask, but on zooming in I could see the variations in intensity.
I did have an additional question - is
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