Dear all,
I have run the recon-all process on my subject im01. Now I am checking for
errors and found some. I also found the solution steps.
However, as far as I understand it, every time I make a change, this will be
permanently done. Is there a way to keep the steps I have done so far and to
There isn't a way to have the new or old results automatically saved under
a different name. I would suggest making copies of the files before edits
and after edits but before rerunning if you want to keep track of the
changes. Depending on what you are making edits to, you would likely need
Even though it is not ideal, manual adjustments can be useful. I would
use manual registration in a small number of cases though. If most of your
data requires it, I would try to play with the automatic registration
parameters more.
--Lilla
On Sun, 16 Oct 2011, Joana Braga Pereira wrote:
hmmm, looks like it is almost finished with mri_cc but doesn't complete.
It usually only takes like 2 minutes for this process, so something must
be wrong. Can you send me aseg.auto_noCCseg.mgz and norm.mgz for this
subject? You can probably just email them.
cheers
Bruce
On Mon, 17 Oct
Hi Maria,
you have to make a copy of the subject dir for this.
cheers
Bruce
On Mon, 17 Oct 2011,
Maria Felber wrote:
Dear all,
I have run the recon-all process on my subject im01. Now I am checking for
errors and found some. I also found the solution steps.
However, as far as I
Hi Joana, how big were the changes that you made? Sometimes the
initialization routine won't get it close enough, then bbregister fails.
Can you send the bbregister log file?
doug
Lilla Zollei wrote:
Even though it is not ideal, manual adjustments can be useful. I would
use manual
Hi Emily, I think the parametric modulation should work. In the example,
there is a ShockOffset and ShockSlope as conditions 1 and 2. In your
case, you would have 4 conditions.
1. IndoorsOffset
2. Indoors-OpennessSlope
3. OutdoorsOffset
4. Outdoors-OpennessSlope
You would then create a contrast
Those almost surely failed because of a bad initialization. You can
usually tell this by looking at the first value in the mincost file. For
these, the mincost is something like .9. The mincost will be a value bet
0 and 1.1, with 0 being perfect. Looks at your good subjects to get an
idea of
Dear Freesurfer developer(s),
Is there a way to get Freesurfer run faster on Neurodebian. While the package
produces
some truly out of the world segmentations and labels for the cortical surface,
it seems
to take time.
For eg:
Defect correction and retesellation takes an hour, other steps take
Hi Bruce-
We'll this was insightful: The norm.mgz file was empty and when I looked at the
original input after (after MRI convert) the sagittal view was rotate by 90
degrees. I'm not sure what caused this, as the input is correctly oriented. The
discrepancy between input and conversion to .mgz
what is your input format? Is it analyze?
On Mon, 17 Oct 2011, Irwin,
William wrote:
Hi Bruce-
We'll this was insightful: The norm.mgz file was empty and when I looked at the
original input after (after MRI convert) the sagittal view was rotate by 90
degrees. I'm not sure what caused this,
Hi all - Since a few of you have inquired about a TRACULA reference in the
past, here's one:
http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstract
There's a link on the right where you can download the PDF. Happy reading!
a.y
How are you generating the masks?
doug
Michelle Umali wrote:
Hi Freesurfers,
I've run reg-feat2anat on several subjects in order to generate binary
masks to use in an FSL ppi.
For 3 subjects, this completely failed.
When I looked at the fsl's own registration of fsl feat 2 standard
(via
We've uploaded the file as 30193retry.tar.gz
Jordan Pierce
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is
Okay, I'll take a look.
Allison
On Mon, 17 Oct 2011, Jordan Pierce wrote:
We've uploaded the file as 30193retry.tar.gz
Jordan Pierce
___
___
Freesurfer mailing list
Hi, just wondering if anyone has any advice on the following questions:
I'm using QDEC to analyze cortical thickness differences between groups and
I have a few questions:
1) There are a few variables that I need to control for. First variable is
scanner - I used two different scanners of
Hi Doug,
Thanks for the reply. I'm not sure i understand how to solve it.
Are you suggesting to re-run bbregister using the --init-reg option and the
register.dat files that were previously created for the badly-registered
subjects?
Joana
2011/10/17 Douglas N Greve gr...@nmr.mgh.harvard.edu
No, use the register.dat that you manually created as the input to
bbregister with the --init-reg. You could move your register.dat to
regidster.man.dat and set the output to be register.dat.
doug
Joana Braga Pereira wrote:
Hi Doug,
Thanks for the reply. I'm not sure i understand how to
Hi all,
I am trying to transform some labels from the aparc to masks in MNI space.
Ideally, I would like to do this for each subject in my study individually
(using their own rawavg.mgz and labels), but for now I started out with
fsaverage. I first converted the label file into a nifti:
Dear experts,
I would like to move my aparc+aseg.mgz image back to the native T1 space
(rawavg.mgz).
I tried:
mri_convert -rl rawavg.mgz -rt nearest aparc+aseg.mgz
./subj001_aparc+aseg2raw.nii.gz
However, it there a way that I don't change the value within the original
aparc+aseg.mgz, so that
Hi Monica
I'm not sure what that means, but adding segmentation labels requires
manual labeling and retraining etc
cheers
Bruce
On Mon, 17 Oct 2011, Hsiao-Ying
(Monica) Wey wrote:
Dear experts,
I would like to move my aparc+aseg.mgz image back to the native T1 space
(rawavg.mgz).
I
See http://www.freesurfer.net/fswiki/FsAnat-to-NativeAnat
doug
Hsiao-Ying (Monica) Wey wrote:
Dear experts,
I would like to move my aparc+aseg.mgz image back to the native T1 space
(rawavg.mgz).
I tried:
mri_convert -rl rawavg.mgz -rt nearest aparc+aseg.mgz
Hi Doug,
I am using reg-feat2anat on the feat directory of each run.
reg-feat2anat --feat feadir.feat --subject XX
Then I checked and adjusted the registration with:
reg-feat2anat --feat featdir.feat --manual
Next I checked and adjusted the registration to the standard with:
23 matches
Mail list logo
