segmentation program with the additional high
resolution scan works!
Thank you for all the help!
Pradeep
On Thu, Oct 4, 2018 at 11:28 AM Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:
> External Email - Use Caution
>
> Thanks!
>
> Did you check whether t
External Email - Use Caution
I have tried this for two subjects and got the same error.
Thanks,
Pradeep
On Thu, Oct 4, 2018 at 11:14 AM Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:
> External Email - Use Caution
>
> Dear Pradeep,
>
> D
-centos6_x86_64-stable-pub-v6.0.1-f53a55a
with matlab run time from 2012b as suggested
I have also tried to use 2014b runtime which exited right away.
Thank you for your help,
Pradeep
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https
link 'lh.white.H': Operation not supported
but cp works
4172_vsl/surf$ cp lh.white.preaparc.H lh.white.H
has any one come across this problem and what is the best way to fix this?
Thanks,
Pradeep
___
Freesurfer mailing list
Freesurfer
abel unsegmented_WM as WM
Thanks,
Pradeep
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you bel
Its in PET native space.
On Wed, Aug 10, 2016 at 2:55 PM Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> which "native" space? the pet native? the anatomical native?
>
> On 08/09/2016 05:46 PM, Pradeep wrote:
> > Hello Doug,
> >
> > The aux/seg.nii
Thanks responding Doug!
I am interested us using centrum semiovale as reference region. Is there a
way I can save the unsegmented white matter [5001& 5002] during the gtmseg
step or what would be its equivalent label in the gtm_pvc results table?
Thanks,
Pradeep
On Thu, Jul 7, 2016 at 11:2
the coregistered image but just transformation.
Is there a way to generate this image or to just input the mri_coreg.lta as
a flag to mri_segstats?
Thanks,
Pradeep
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman
Thank you! I will.
On Mon, Jun 20, 2016, 7:00 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
> Hi Pradeep
>
> Doug is on vacation and is the best one to answer your question. If you
> don't get a response in a week or 10 days can you repost?
>
> thanks
> Br
pipeline?
Do you have any concrete results to examine the effects of the size
variation over the ROIs used for PVC? Should a threshold be set for the
sizes of these ROIs?
How were the white matter hypo-intensities dealt with while generating the
ROI masks?
Thanks,
Pradeep
Hello Doug,
I was wondering if there is a flag in the command to obtain the SUVRs for
the same ROIs with out partial volume correction so that it would be easier
to compare.
Thanks,
Pradeep
On Fri, Jan 29, 2016 at 1:30 PM, Pradeep <tprad...@gmail.com> wrote:
> It worked!
ve on blurry data)
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>
> mri_coreg --s $fs --mov ${pet_ext}_LIA.nii --lta output.lta
>
> Also, why is the top of the head cut off? That makes it much more
> difficult to register.
>
> doug
>
Reading gtmseg.lta
Replacing 18
ERROR: CheckSegTissueType() no entry for seg 192
Failed tissue type check
Thanks,
Pradeep
On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
>
>
> On 01/28/2016 06:50 PM, Pradeep wrote:
> > Hello Doug,
> >
22
ERROR: CheckSegTissueType() no entry for seg 192
Failed tissue type check
Thank you for looking into this,
Pradeep
On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu
> wrote:
> I think I see the problem. When you run gtmseg, you need to add
> --keep
; without the current replace, then it will create a replacement file in
> the aux folder. Get that, remove the 251 entry, and change the 252-255
> entries to point to 251
>
> On 01/29/2016 02:12 PM, Pradeep wrote:
> > Unfortunately, that did not fix the problem.
> >
> >
ROI as a
reference region,
would it be OK take a ratio of the ROI's in gtm.stats.dat table.
Thanks,
Pradeep
On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
>
> If you want to use partial volume correction, then you are better off
> using mri_gtmp
has worked and I just wanted to conform if it the correct way
to use it.
-Pradeep
On Wed, Nov 18, 2015 at 10:41 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu
> wrote:
> For single frame, you can just run
> mri_convert input.nii output.nii --frame F
> where F is the 0-based frame n
on this would be
appreciated. I have successfully ran steps 1 and 2 from the process you
have outlines above.
Thanks,
Pradeep
On Mon, Sep 28, 2015 at 10:03 PM, Jonathan DuBois <
jonathan.m.dub...@gmail.com> wrote:
> Hi Doug,
>
> I uploaded the files you requested. I'm not sure if it m
Hello All,
I ran the freesurfer longitudinal stream for a subject with three time
points and found that the /stats/lh.BA.stats has remained constant across
all time points where as aseg.stats showed variations.
Sorry if this question is too nieve.
Thanks,
Pradeep
with the
same limits)
On Fri, 17 Apr 2015, Martin Reuter wrote:
Hi Pradeep,
is this the result of a single subject? In a single subject lot's of
things
can happen (e.g. motion artefacts can affect a single time point, other
imaging or measurement noise will have effects). Also how far
Hello All,
I have pre-processed a subject that has T1 scans at 3 time points using the
freesurfer cross-sectional and longitudinal methods. The results show a lot
of variability. I have attached the plots. Any advice would be much
appreciated.
Thanks,
Pradeep
On Wed, Apr 15, 2015 at 5:26 PM
Hi Roberto,
I had the same problem, you need to re run the recon process using
recon-all -s subjid -cortribbon.
Hope it helps
Pradeep.
On Fri, Feb 6, 2015 at 6:37 PM, Roberto Medeiros de Souza
roberto.medeiros.so...@gmail.com wrote:
Hi,
I'm knew to FreeSurfer. I am using the stable v5.3
of images:30. Is it
necessary to have more dicom images to have a better brain mri image . If
yes, what should be the optimal number of images
Thanking You
Pradeep Kumar Mahato
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https
Please tell how to use dcmunpack. Any help converting dicom to nii.
On Jan 27, 2015 9:03 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:
Hi Pradeep, I don't think that we can convert that either. Sorry.
doug
On 1/27/15 7:18 AM, pradeep mahato wrote:
Hi experts,
I am trying
the rebuild_gca_atlas file.
Thanks
Pradeep Kumar Mahato
rebuild_gca_atlas.csh
Description: C-Shell script
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail
Hello experts,
How to view 3D image of hippocampus or any region of interest.
Thanking you
Pradeep Kumar Mahato
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information
.
How much time can we save running each hemisphere parallely.
Thanking you
Pradeep Kumar Mahato
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail
Hi Nick,
Can you tell me what would be best processing time to do recon-all process
on one brain mri image using a high end machine ( Servers ) or using GPU
based machine.
We have more than 1000 of brain mri images, processing all these images is
the bottleneck now.
Pradeep
On Tue, Dec 16
Hello everyone,
Have anyone used Broadwell or Haswell process for Brain MRI image
processing.
If used can you please mention the system configuration you are using.
How long does it take to run recon-all process for one brain MRI image.
Thanking you
Pradeep Kumar Mahato
brain atlas in FreeSurfer.
Thanking You
Pradeep Kumar Mahato
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
.
Pls help
On Thu, Dec 11, 2014 at 8:54 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
the ribbon.mgz isn't part of autorecon2 (or autorecon1) I don't think.
What are you trying to run?
On Thu, 11 Dec 2014, pradeep mahato wrote:
Hi Bruce,
After running autorecon1 and autorecon2, I am
There is no documentation or example for mri_extract_label.
What should be the syntax for it. What kernel and xform file should be used.
On Wed, Dec 10, 2014 at 6:50 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Pradeep
you can use mri_extract_label to copy just the hippocampal labels
After the recon-all process I want to access all the voxels in the left
hippocampus ( any subcortical region ) .
Please tell me is there any method to extract this voxel values from an
segmented image.
Thanking you
Pradeep Kumar Mahato
___
Freesurfer
Hello,
As the complete recon process takes huge time for a single image, is it
possible to register the MRI image using a simple atlas. If yes, please
explain how to do it.
My primary goal is to extract hippocampus in a fastest possible way.
Pradeep Kumar Mahato
): could not
open file
Should I include nuintensitycor.
Thanks
Pradeep
On Mon, Dec 8, 2014 at 7:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Pradeep
you could only run recon-all -autorecon2 instead of -all which should
save you some time. 30 hours is pretty long though. What hardware
get the hippocampus segmented and get the
statistical values faster and efficient way.
Thanking You
Pradeep Kumar Mahato
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
1378828612 slices
Cannot allocate memory
end---
Any suggestion on this would be greatly appreciated.
Thanks,
Pradeep
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
locations, this is what happened.
I also tired running the mris_topo_fixer, but it was complaining that
there is no lh.qshere.
Thanks,
Pradeep
$ 5:10pm ilpc11: scanner_differences tksurfer FirstOrderPoly lh
inflated.nofix
surfer: current subjects dir: /ensc/grad1/pkr1/UNSW/scanner_differences
surfer
/freesurfer@nmr.mgh.harvard.edu/msg09492.html
Thanks,
Pradeep
--
Pradeep Kumar Reddy. Raamana
PhD Student - Biomedical Engg.
Medical Image Analysis Lab,
Simon Fraser University,
Burnaby BC - V5A1S6 - Canada.
Work : +1 778 782 5509
What is written without effort is, in general, read without
pleasure
looked at lh.orig.nofix
surface - screenshots attached. I am not sure whether its alright. No
rh surfaces were created.
Please let me know how to correct this problem and proceed further.
Quick response will be greatly appreciated,
Pradeep
=== Tail end of scripts/recon-all.log
Hello Everybody,
This is Pradeep Reddy, just started my PhD in Medical Image Analysis
and hence a newbie to FreeSurfer.
I've passed the auto-recon2 stage in the reconstruction procedure. Now
I am trying to verify WM segmentation produced by the
recon-all/auto-recon2, before I move on to further
41 matches
Mail list logo
