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Hi all,
Just following up on this as I've run into the exact same problem. Is there
a different recon-all.makefile that should be used for FS 6/6.0.1 ?
Thanks!
On Fri, Mar 29, 2019 at 9:28 AM Matthieu VANHOUTTE <
matthieuvanhou...@gmail.com> wrote:
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Hi,
This won't affect the eTIV as that is derived purely from the affine
registration. See Buckner et al. (2004) NeuroImage 23:724-738. for more
details.
-Niels
On Mon, Nov 26, 2018 at 6:46 AM 박경일 wrote:
> External Email - Use Caution
>
> De
ugenio Iglesias
>
> Centre for Medical Image Computing (CMIC)
>
> Department of Medical Physics and Biomedical Engineering
>
> University College London
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of Niels
> Bergsland
> *Re
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Hi Eugenio,
Just wanted to ask quickly if there is plan to implement longitudinal
processing for the brainstem structures and thalamic nuclei modules?
Thanks!
Niels
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Hi Eugenio,
Thank you again for the fantastic thalamic nuclei segmentation tool!
I'm going through and QC'ing a batch of subjects that were processed
through the pipeline. Data was originally processed with freesurfer-6.0.0
and then processed through t
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Niels Bergsland <
> theni...@gmail.com>
> *Sent:* Wednesday, September 12, 2018 1:25:18 PM
> *To:* Freesurfer Mailing List
> *Subject:* [Freesurfe
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Hi Eugenio,
Just a quick question - is there a minimum version of FS that is required
to run the thalamic nuclei segmentation? I am just thinking about some old
datasets that we have that were run with FS 5.1.
Thanks and best wishes,
Niels
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Hi all,
Not sure if this was resolved off-list or not, but I just ran into it
myself and it turned out to be a permissions-related error in that the user
didn't have read access to some of the required files in the Matlab
runtime. Setting them appropria
Your input here is a localizer image:
Protocol t2_haste_localizer_p2
On Mon, Mar 19, 2018 at 12:51 PM, Z Hessam wrote:
>
> hello, i have problem again with a new data set.
> this is the recon-all.log file in attach
>
> thanks a lot
>
>
> On Fri, Feb 9, 2018 at 2:22 PM, Z Hessam wrote
Hi again,
The latest version is 5.0.10 but the issue was definitely fixed in 5.0.9
(possibly one point release earlier, I can't recall). Regardless, I don't
think there were any changes to flirt between 5.0.9 and 5.0.10.
Good luck!
Niels
On Fri, Feb 16, 2018 at 5:40 PM, John Davis wrote:
> Anas
Hi Anastasia and John,
This looks like the glibc issue that was fixed in more recent versions of
FSL. Given that you are running Ubuntu 16.04, if you are using an older
version of FSL, you will get FLIRT matrices saved in hexadecimal format. If
you upgrade your FSL to a more recent version, you sho
Hi - how much memory do you have on your machine?
On Mon, Dec 14, 2015 at 10:54 AM, salvatoreandrea...@libero.it <
salvatoreandrea...@libero.it> wrote:
> Hi Freesurfer experts!
>
> I tried to run recon-all base for a longitudinal analysis on my data. But
> I get the following error:
>
>
>
> *Exce
Hi - that's way too low, unfortunately. You need at least 4GB and more is
preferred.
See: https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements
On Mon, Nov 30, 2015 at 5:19 PM, salvatoreandrea...@libero.it <
salvatoreandrea...@libero.it> wrote:
> I have around 2 Gb of total RAM. Isn't th
Hi - sounds like it's running out of memory and getting killed. How much
RAM do you have?
On Thu, Nov 26, 2015 at 1:21 PM, salvatoreandrea...@libero.it <
salvatoreandrea...@libero.it> wrote:
> Hi!
> - I am using Ubuntu 14.4 (trusty).
>
> - This is my subject directory: /home/salvatore/freesurfer
Hi all,
Sorry for the repost, was just wondering whether someone might have some
input regarding this issue.
Thanks!
Niels
On Thu, Mar 26, 2015 at 12:10 PM, Niels Bergsland
wrote:
> Hi all,
> I have run into an issue that I am having trouble correcting.
>
> http://imgur.com/a/4Kqp
Hi all,
I have run into an issue that I am having trouble correcting.
http://imgur.com/a/4KqpJ
I have checked the aseg to see if it was labeled as ventricle. This does
not seem to be the cause.
Any other suggestions? I am happy to upload the case if that is necessary.
Best regards,
Niels
__
/color_failure.png
I can also upload the dicoms to the drop box if this would help.
Thanks!
Niels Bergsland
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ior between the 32bit and
64bit builds though. I have not personally encountered the message you
are seeing.
Nick
On Thu, 2006-10-12 at 16:40 -0400, Niels Bergsland wrote:
> Hi,
> I am experiencing quite a strange problem. I have a set of DICOMs
> that when I run the following on a 32b
have used the 64 bit install extensively before and never run into
this issue.
Any insight?
Thanks!
Regards,
Niels Bergsland
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which we can't really do
anything about.
doug
Niels Bergsland wrote:
> Hi again,
> From the last time that I asked about this, the project was
> temporarily put on hold, but now it has started up again...
>
> When looking back at the responses from last time, I realized that
ability. What I actually meant though
is if I can manually insert the values using, for example, dcmodify
(part of the DCMTK) and then process the scans with Freesurfer.
Hopefully this is a bit more clear!
Thanks again,
Niels Bergsland
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slice1.dat
slice1.dat will be a binary file of the pixel data from the file
slice1.dcm. You can do this for each slice, then assemble the data into
a real format. Not fun, but possible. Other tools out there might not
require the direction cosines.
doug
Niels Bergsland wrote:
> Hi Doug,
&g
required it in the
first place. ImagePositionPatient (tag 20,32) is considerably more
important as this is one of the ways the slices are sorted and the
direction cosines estabilished. Are these for mosaics?
doug
Niels Bergsland wrote:
> Hi,
> We have some old scans that were originally in ACR-NEMA form
Doug which I found at
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html
, I am afraid not...
Thank you for any help.
Regards,
Niels Bergsland
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