Hello,
Just a couple more questions that would be great if you could answer in
explanation form:
How do people develop finite element models from brain MRI?
How do people learn and implement the software on an example data set?
Abbie
On Tue, Jul 5, 2016 at 9:42 AM, Abbie McNulty wrote:
> Hell
Hi Richard,
Many thanks for your effort and help. The binaries did not work unfortunately
seemingly because of libcuda from 6.5 not being forward compatible with libcuda
from 7.5, as you noted.
-Derek
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesu
Hi Anastasia,
This occurs for me on both stable and dev versions of freview and trac-all -stat
-Derek
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki
[ayend...@nmr.mgh.harvard.edu]
Sent
Hi there - I think I know what it is, but it's a problem that should be
solved if you have the last tracula update. It means that your LANG
environment variable needs to be set to en_US.UTF-8, which the update does
for you.
a.y
On Tue, 5 Jul 2016, Lars M. Rimol wrote:
Hi Anastasia,
I ha
I think it will be easier with mris_apply_reg. You might need to get the
newest version with can handle labels
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg
run it something like
mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right
rh.sphere.lef
has this question been answered?
On 06/17/2016 09:42 AM, curry_sa...@yahoo.com wrote:
> Hi all,
>
> I am trying to extract mean time series BOLD data using FSFAST from
> Cortical ROIs + sub cortical ROIs and cerebellum.
>
> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305
> -fwh
By the way, freesurfer registers all images to the within subject template in the base stream, so they are already registered for you. The command is mri_robust_template.
Best Martin
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Hi,
I still have a problem as well with the subfields segmentation (ubuntu
14.04, with the files .ctf)
Cheers,
Pierre
Hello FreeSurfer Experts,
I’m having issues with the hippocampal subfields segmentation using OS X
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp:
freesu
Hi,
Images from different scanners can look very differently (intensity, scaling, non linearities). Also acquisition parameters can change images and bias results.
This warning exists to make sure users understand that whatever they get out of the analysis could be completely driven by acquisition
You can use the version 6 mri_glmfit which you can get from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit
On 06/16/2016 07:51 AM, Robby De Pauw wrote:
>
> Dear FreeSurfer users
>
> I am not able to extract the Z-values as they are not present in my
> output:
>
> z
Hello Freesurfers,
Where can I find any documentation about how is retinotopic analysis
performed in Freesurfer? Thanks.
Best
--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.str
Have you verified that the Anat-Func registration in FreeSurfer is
correct? You can view it with tkregister-sess.
On 06/16/2016 10:26 AM, Martin Juneja wrote:
> Hi Dr. Greve,
>
> I used following command for this:
>
> mkanalysis-sess -analysis LH_XY.surf.lh
> -surface fsaverage lh -fwhm 5 -not
Try now
On 06/15/2016 06:30 PM, Leila Reddy wrote:
> Hi Doug,
>
> Thanks for your reply.
>
> When I run mni152reg I get an error : ERROR: Flag --lta unrecognized
>
> I'm using v 1.9 of this file.
>
> I found a post that said to download a newer version from here:
> ftp://surfer.nmr.mgh.harvard.edu
My apologies as I misstated some of the data in my first email,
The voxel sizes are relatively similar, (two of the acquisitions are 1mm vs one
with 0.9mm).
Whereas the FOV is different between the scans being 256x256x176 on one
acquisition, 224x256x176 on the second and 240x240x180 on the thir
Hello Freesurfer team,
I have the unfortunate task of performing longitudinal volumetric analysis on
subjects collected on three different scanners with different voxel
numbers/sizes. I didn't find this out until attempting to run the longitudinal
base and receiving this message:
WARNING: Im
Hello Bruce,
I am uploading the data set to filedrop for you to look over. Can you assist us
in determining the optimal method for parcellation of the white and gray
matter. We are particularly interested in determining the volume of the
hippocampus and amygdala. Are there any special parameter
Hello Freesurfers,
I'm re-posting this question. Where can I find any documentation about how
is the retinotopic analysis performed in Freesurfer? Thanks.
Best
--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972
You can also do this now, by simply changing the alpha level of the
colors in the CLUT, (note this only works in the dev version).
hth
d
On Sat, Jul 2, 2016 at 1:46 PM, Douglas Greve wrote:
> Yes, you can. If I remember correctly, you can goto view->configure overlay,
> then find the item to spe
can you answer the question that it asks?
On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
> Hi everyone,
>
> I’m having some issues converting my DICOMs (DWI) into NIFTI using
> mri_convert. I looked for other topics with people having the same
> kind of problem but couldn’t find an answer.
>
> E
The file has not been anonymized.
Thanks,
Ismail
> On Jul 5, 2016, at 11:20 AM, Douglas N Greve
> wrote:
>
> can you answer the question that it asks?
>
> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
>> Hi everyone,
>>
>> I’m having some issues converting my DICOMs (DWI) into NIFTI using
Hi everyone,
I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert.
I looked for other topics with people having the same kind of problem but
couldn’t find an answer.
Each time I run mri_convert on my DICOMs I get the following error :
WARNING: file MR.1.3.12.2.1107.5.2
Hello FreeSurfer Experts,
I’m having issues with the hippocampal subfields segmentation using OS X
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp:
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.
Hi Anastasia,
I have attached the dmri/bvals and dmri/bvec ("bvals"/"bvecs") and the
dmri/dwi_orig.mghdti* files. I don't know if it's a problem but the
generated bvec file has commas instead of full stop (0,832 instead of
0.832). The input file (attached: "bvec_rows") has full stop. Another thing
You get the same error as trac-all because trac-all runs mri_convert. I'd
send the mri_convert error in a new email with mri_convert somewhere in
the title, so that someone else can help you.
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Also when I run mir_convert on the DICOMs I get the same
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