Thank you for your answer!
For future reference, info about the machine can be found in the
scripts/recon-all.done.
Diogo
On 25 April 2017 at 22:24, Douglas Greve wrote:
> There is a file called scripts/build-stamp.txt. Also, if you set
> setenv REQUIRE_FS_MATCH 1
>
> It will compare the curre
There is a file called scripts/build-stamp.txt. Also, if you set
setenv REQUIRE_FS_MATCH 1
It will compare the current version with the version in the build stamp
and exit with error if they don't agree
On 4/25/17 5:14 PM, Diogo Duarte wrote:
Hi everyone,
How can I find the freesurfer versi
Hi everyone,
How can I find the freesurfer version used (recon-all) from the resulting
files?
This would be necessary for keeping freesurfer versions consistent.
Thank you,
Diogo
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nm
As it currently stands, freeview can only be called via the terminal
window by typing the 'freeview' at the command line. Creating a Desktop
short cut will not work properly. We hope to support this feature in the
near future.
-Zeke
On 04/25/2017 04:22 PM, 吕元媛 wrote:
> Dear Experts,
>
> I have
Many thanks for the answer!
Best,
Maria
2017-04-25 21:05 GMT+03:00 Douglas Greve :
> -i{ijk}s will change the voxel size of the columns, rows, and slices,
> respectively
>
> -i{ijk}d will change the direction cosines of the cols, rows, slices
>
>
>
> On 4/25/17 11:47 AM, Maria Hakonen wrote:
>
>
The comman was mri_cvs_register --mov MAE_06072013 --mni (because labels in
MNI space were mapping incorrectly to subject space -- see this thread
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52786.html )
The log is attached. I killed the command once I saw the errors.
Thanks!
The missing/extra are due to sub-1mm estimation. They do not exist
independently. If you want to avoid partially volumed voxels, you can
erode the segmentation to remove border voxels
On 4/25/17 2:50 PM, Gamaliz wrote:
For example.
I register another image to the aseg+aparc file and do some
For example.
I register another image to the aseg+aparc file and do some pixel-by-pixel
calculations; reading the regions from the aseg+aparc and matching them on
the registered file (in this case a DTI) ie: every pixel with value 2 in
aseg+aparc belongs to the Left-Cerebral-White-Matter region.
h
Hi Corinna,
Its been awhile since Ive used Ubuntu12.04. Infact its End of Life date
is 3 days away ;)
Can you please send me the command and the log file which gives the
exact error. Thanks.
-Zeke
On 04/25/2017 01:49 PM, Corinna Bauer wrote:
> Hi Zeke,
>
> I am also having this same problem.
more exact than what?
On 4/25/17 2:07 PM, Gamaliz wrote:
Is there any way to generate a file which is more exact? Or perhaps,
is that file already there?
On Tue, Apr 25, 2017 at 2:04 PM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
The aseg.stats is generated with partial vo
Is there any way to generate a file which is more exact? Or perhaps, is
that file already there?
On Tue, Apr 25, 2017 at 2:04 PM, Douglas Greve
wrote:
> The aseg.stats is generated with partial volume estimation
>
> On 4/25/17 12:40 PM, Gamaliz wrote:
>
> I wrote an algorithm which uses the numb
-i{ijk}s will change the voxel size of the columns, rows, and slices,
respectively
-i{ijk}d will change the direction cosines of the cols, rows, slices
On 4/25/17 11:47 AM, Maria Hakonen wrote:
Dear Freesurfer experts,
Could someone please let me know what is the meaning of the arguments
-
The aseg.stats is generated with partial volume estimation
On 4/25/17 12:40 PM, Gamaliz wrote:
I wrote an algorithm which uses the number of pixels per region in the
aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the
number of pixels to match very closely the value of the volum
Hi Zeke,
I am also having this same problem. Even after completing the steps you
listed above. I am running Ubuntu 12.04.
Any suggetions?
Thanks
On Wed, May 28, 2014 at 1:50 PM, Z K wrote:
> You will need to install libboost v1.41 onto your system. You should be
> able to install it using yum
I wrote an algorithm which uses the number of pixels per region in the
aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the number
of pixels to match very closely the value of the volume; as each pixel
represents a 1 mm3 cube.(I did the same for cortical volume and got a
similar resul
Dear Freesurfer experts,
Could someone please let me know what is the meaning of the arguments -iid,
-ijd, -ikd, -iis, -ijs, and -iks of mri_covert?
>From the internet and by typing mri_convert on the command line I only
managed to find the following information:
-iis, --in_i_size
-ijs, --in_j_s
Hi Gustav,
use -all and -mprage for all steps
use -qcache and -hippo..subfields only in the -long step.
Best, Martin
On 04/25/2017 12:51 PM, Gustav Mårtensson wrote:
Hi,
I have a question regarding the longitudinal pipeline.
We are following the workflow summary as outlined in
https://
Hi,
I have a question regarding the longitudinal pipeline.
We are following the workflow summary as outlined in
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, essentially:
1. recon-all -all -s -i path_to_tpN_dcm
2. recon-all -base -tp -tp ... -all
3. recon-all -long -
Hi Martin,
thanks for your reply. From your email I understand that looking at the rate of
change between time points is more useful than spc if I want to look at only 2
time points at a time.
I have a pre training scan, a post training scan (approximately 3 weeks apart
with a training interve
Of course, here it is. Thank you for taking a look at it!
Best,
Joëlle
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Yendiki, Anastasia
Envoyé : mardi 25 avril 2017 10:25
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstr
Hi Joëlle - I can't come up with a config file without knowing the locations of
your files. If you send me the trac-all.log, I can figure out at what step it
fails.
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu]
Hi Anastasia,
I still can't seem to make it run when I don't specify the gradient tables, so
I think I'm probably doing something wrong in the configuration of the dmrirc
file... Would you mind sending me the dmrirc file you would use to run this
subject?
Best,
Joëlle
__
Dear FS experts,
I'm trying to transform some files from fsaverage space to
fsaverage5 space using mri_surf2surf(fs version: 6.0), however, it is weird
that the results turn out to be all zeros on the fsaverage5 surface, the
command line I used if : mri_surf2surf -srcsubject fsaverage -sv
23 matches
Mail list logo
