Is this significant enough that we should re-run data processed using the
standard recon-all stream in version 5.1?
Thanks,
Peter
On Jun 10, 2011, at 3:28 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
> Message: 2
> Date: Fri, 10 Jun 2011 12:59:34 -0400 (EDT)
> From: Lilla Zollei
> Subject
What do you mean you are doing it with FEAT?
Sudhin A. Shah wrote:
> Hello,
>
> I am a beginner so please bear with me. I want to obtain binary masks
> for every region (Cortical + subcortical). I am using FSL(feat) to do
> this BUT am not sure what the labels would be.
>
> I have looked at Free
Hello,
I am a beginner so please bear with me. I want to obtain binary masks for every
region (Cortical + subcortical). I am using FSL(feat) to do this BUT am not
sure what the labels would be.
I have looked at FreeSurferColorLUT.txt for aparc+aseg-in-highres.mgz BUT do
not know which labels t
Hi FS experts,
We have some legacy code (in a BASH script) that uses mri_cor2label to
convert what it is calling the anterior amygdala to volumetric labels.
However, we get the error that these values (96 and 97) do not exist.
Have the label IDs changed? We are using stable5.1. Our call look
Hi Anastasia
If I have T1 data available in my FS subject directory and I have
Use brain mask extracted from T1 image instead of low-b diffusion image?
# Has no effect if there is no T1 data
# Default: 1 (yes)
#
set usemaskanat = 1
then will the B0 brain mask we spoke of below be used?
Deryk
Hi Carolina,
Sorry My bad. I was inaccurate in my previous message.
-subject should work.
Assuming that the MPRAGE of your subject is under the following directory:
/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
set your SUBJECTS_DIR to
/freesurfer/subjects/buckner_data/tuto
Hi Carolina,
-subject is not recognized by Freesurfer...Use -subjid or -s instead.
setenv SUBJECTS_DIR
recon-all -all -i /MPRAGE.nii.gz -s /hptu_subj001
Priti
> Hello Freesurfer's users,
>
> I'm starting using FS and I have a problem running recon-all
> I create a folder called hptu_subj001 w
Hello Freesurfer's users,
I'm starting using FS and I have a problem running recon-all
I create a folder called hptu_subj001 which contains MPRAGE.nii.gz within
tutorial_subj
First I convert nii.gz to mgz qith the command:
recon-all -i MPRAGE.nii.gz -s hptu_subj001
and then in order to process all
Hi Adam,
the dura correction is really in alpha. We've only run it on a couple of
datasets and haven't tried to integrate it with anything yet. Feel free to
give us an opinion on what works best though :)
Bruce
On Fri, 10 Jun 2011, Martin Reuter wrote:
Hi Adam,
dura correction is not yet
Hi,
We found a bug in the mri_cvs_register script after the
release. Please, download the new version of applyMorph and
mri_cvs_register from one of the below links for Linux Centos4,
Linux Centos4 x86 64 and Mac Leopard respectively:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/l
Hi Adam,
dura correction is not yet incorporated into the longitudinal stream and
I doubt that it will just work out of the box, due to the fact that the
longitudinals are in a different space than the inputs. Of course it
could be done after the cross, but the surfaces there are not important
for
No, that will be fine.
doug
corinna bauer wrote:
> Will I need to re-register the pet to the mri?
>
> On Fri, Jun 10, 2011 at 10:58 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> you'll need to get a new version then. You won't need to reanalyze
> your anatomicals in
Will I need to re-register the pet to the mri?
On Fri, Jun 10, 2011 at 10:58 AM, Douglas N Greve wrote:
> you'll need to get a new version then. You won't need to reanalyze your
> anatomicals in the new version, but you will need it to run these programs.
>
> doug
>
> corinna bauer wrote:
>
>> I
optseq won't be quite what you need because it is going to randomize the
order (so you can't always get a feedback after each response). You can
tell it that there is only one condition, then go back and recode.
You'll probably want to control the min and max fixation, which you can
do with opt
you'll need to get a new version then. You won't need to reanalyze your
anatomicals in the new version, but you will need it to run these programs.
doug
corinna bauer wrote:
> I'm using 4.4.0
>
> On Fri, Jun 10, 2011 at 10:44 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
>
I'm using 4.4.0
On Fri, Jun 10, 2011 at 10:44 AM, Douglas N Greve wrote:
>
> which version are you using? Both should be in both 5.0 and 5.1.
> doug
>
> corinna bauer wrote:
>
>> Hi Doug,
>>
>> I used the mri_compute_volume_fractions and fscalc commands and got this
>> error message:
>>
>> mri_c
Hi Ayaz
this is really hard to say. I would recon them with one and with two and
visually inspect to see which you think are more accurate. Unfortunately we
have no ground truth.
Bruce
On Fri, 10 Jun 2011, Ayaz, Muhammad wrote:
> Dear All,
>
> I have T1 images single scan from Phillips 3T. Im
Hi Corinna,
what version of FS are you using?
Bruce
On Fri, 10 Jun 2011, corinna bauer wrote:
> Hi Doug,
> I used the mri_compute_volume_fractions and fscalc commands and got this
> error message:
>
> mri_compute_volume_fractions: Command not found.
> fscalc: Command not found.
>
> Other FreeSur
Hi Deryk - This variable is only used to average lowb images to create a
mask, so in your case you can set it to 2 and it'll just use the first 2
volumes from your nii file. Sorry for the confusion!
a.y
On Fri, 10 Jun 2011, Deryk S. Beal, Ph.D. wrote:
Dear Tracula Users
Does Tracula assum
which version are you using? Both should be in both 5.0 and 5.1.
doug
corinna bauer wrote:
> Hi Doug,
> I used the mri_compute_volume_fractions and fscalc commands and got
> this error message:
>
> mri_compute_volume_fractions: Command not found.
> fscalc: Command not found.
>
> Other FreeSurfer
Dear All,
I have T1 images single scan from Phillips 3T. Images quality looks good. Since
we use 8 channel should I be collecting 2 data set to average or single data
will be sufficient?
Ayaz
The information contained in this message and any attachments is intended only
for the use of the in
Hi Doug,
I used the mri_compute_volume_fractions and fscalc commands and got this
error message:
mri_compute_volume_fractions: Command not found.
fscalc: Command not found.
Other FreeSurfer commands, such as mri_segstats are working fine in the same
batch script.
Corinna
On Wed, Jun 8, 2011 at
Dear Tracula Users
Does Tracula assume that the number of B0 scans, specified in Step 7.3 of
the config file tutorial (below), are the first X number of volumes in the
4Dnii.gz file or will the Tracula routines know from the bvals file where
the B0 scans are ordered in the file? For example, I hav
Dear Tracula Users
Does Tracula assume that the number of B0 scans, specified in Step 7.3 of
the config file tutorial (below), are the first X number of volumes in the
4Dnii.gz file or will the Tracula routines know from the bvals file where
the B0 scans are ordered in the file? For example, I hav
Hi Yoldanda,
which register do you mean? Talairach? You shouldn't mix versions, but you
could use the correct Talairach from 5.0 and use it to fix the 4.3.1 run.
cheers
Bruce
On Fri, 10 Jun 2011, Yolanda Vives
wrote:
> Dear Freesurfers,
>
> I have a dataset processed with a classical recon-a
Hi Yolanda,
No.
It is better to remove the two subjects. Mixing versions is never a good idea
as results are expected to differ. Same is true for different acquisitions
(parameters, scanners etc). If anything has to be different it needs to be
asserted that it is spread equally among your group
When using MEMPR images (Van der Kouwe et al., 2008) in the longitudinal
processing stream, when should the dura correction (mris_makes_surfaces -dura)
be ran? After the first cross-sectional run of recon-all, after the final
longitudinal run of recon-all, or maybe both?
I have the same questi
Dear Freesurfers,
I have a dataset processed with a classical recon-all of Freesurfer v.4.3.1
and there are two MRIs that were not segmented correctly due to the
register. After several unsuccessful attempts to improve this step using
tkregister2, finally I have successfully processed them with FS
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