Hi Doug
Thanks for responding. in my path. I actually now managed to
run it but it fails at the command (Command not found).
/Users/chdebezenac
flirt.fsl -ref
/Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/refvol.fslregister.nii
-in
/Users/chdebezenac/fmr
That should also be in $FREESURFER_HOME/bin. If not, just copy or
symlink your flirt program to it.
doug
ps. Please remember to post to the FS list and not to me personally. thanks!
On 11/06/2013 05:11 AM, Christophe de Bezenac wrote:
> Thanks for responding Doug,
>
> is in my path. I've act
oops, sorry I just noticed that you did respond to the list!
On 11/06/2013 10:16 AM, Douglas N Greve wrote:
> That should also be in $FREESURFER_HOME/bin. If not, just copy or
> symlink your flirt program to it.
> doug
>
> ps. Please remember to post to the FS list and not to me personally. thanks
So is the problem that the annotation does not look good or is the
problem that you are getting a lot of warnings about unmapped vertices.
Please send the command lines that generate the warnings (and the
terminal output)
doug
On 11/06/2013 10:05 AM, Marcos Martins da Silva wrote:
> Hi, Doug
Hi Doug
Thanks for your answer on my issue "glmfit for paired-diff on 2 groups" in the
mailinglist
Commands:
mris_preproc --target 1_average_30VPs --fsgd responder.txt --hemi lh
--meas thickness --out respnon_lh_thickness.mgh —paired-diff-norm
mri_surf2surf --hemi lh --
Hi Doug,
I have tried the command that you suggested below. Still not working.
System gave the same error message again "segment fault".
Any other ideas?
Best wishes,
Jingjing
*
try running this command
mri_label2vol --label lh.words10_10.label --temp rawavg.mgz --reg
rawreg.dat --fillthresh .5
The FS segmentation is a combined segmentation and registration to an
atlas space. This is probabilistic in that the atlas is built from 40
subjects and uses intensity, location, and neighborhood priors. I think
VBM is using unified segementation which performs intensity
normalization, segmen
It was not in $FREESURFER_HOME/bin so I copied the unix executable from
the fsl/bin and pasted it into $FREESURFER_HOME/bin. It still fails at the
flirt.fsl command?
Thanks,
Christophe
On 6 Nov 2013, at 15:20, Douglas N Greve wrote:
> oops, sorry I just noticed that you did respond to th
Yes, that all looks correct. Though 25mm is a lot of smoothing. I
usually use 10-15mm.
doug
On 11/06/2013 10:34 AM, Vivian R. Steiger wrote:
> Hi Doug
>
> Thanks for your answer on my issue "glmfit for paired-diff on 2 groups" in
> the mailinglist
>
>
> Commands:
>
>
> mris_preproc --t
did you copy it to "flirt.fsl"? Did you rehash afterwards?
On 11/06/2013 10:42 AM, Christophe de Bezenac wrote:
> It was not in $FREESURFER_HOME/bin so I copied the unix executable
> from the fsl/bin and pasted it into $FREESURFER_HOME/bin. It still fails at
> the flirt.fsl command?
>
> Thanks,
OK, try this cmd
mri_vol2vol --mov $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz --targ
aseg.mgz --reg transforms/reg.mni152.1mm.dat --o aseg_mni152.nii.gz
--inv --interp nearest
On 11/05/2013 06:49 PM, Roderick McColl wrote:
> Sure, no problem.
>
> Run from within the folder $SUBJECTS/fsaverage
hi doug
Thanks for checking my code and the hint with the smoothing rate. I appreciate
your time on my issue.
I’ve ran a series of different smoothing rates (from 10-30mm) and 25mm showed
the best results for our data in terms of cluster size but still prominent
effects in summary statistics.
Dear all,
I'm interested in assessing the changes in the volumes of hippocampal
subfields between 2 time points.
Can I use the longitudinal pipeline of Freesurfer and add the
-hippo-subfields flag to the longitudinal runs of the 2 time points?
Thanks!
Adding the .fsl extension to the flirt executable sorted it.
Many thanks,
Christophe
On 6 Nov 2013, at 15:45, Douglas N Greve wrote:
> did you copy it to "flirt.fsl"? Did you rehash afterwards?
>
> On 11/06/2013 10:42 AM, Christophe de Bezenac wrote:
>> It was not in $FREESURFER_HOME/bin so
Dear Joana,
at this point, a "true" longitudinal version of the subfield
segmentation is not available. However, we have noticed that you can get
slightly better (more stable) results by segmenting the subfields in the
longitudinally processed timepoints - rather than the original,
cross-secti
FS experts,
I have two questions, when running mris_preproc and mri_surf2surf should I be
passing these any of the .long directories created with recon-all -long? As I
read through the tutorial I’m missing their significance in the analysis
section of the longitudinal stream. It seems like fsav
Great, thanks!
2013/11/6 Juan Eugenio Iglesias
> Dear Joana,
> at this point, a "true" longitudinal version of the subfield segmentation
> is not available. However, we have noticed that you can get slightly better
> (more stable) results by segmenting the subfields in the longitudinally
> pro
Hi Jon,
passing the --qdec-long flag to mris_preproc will automatically generate the
right names (e.g. the .long. directories) and take the data from there. You can
pass the study_average vie the --target flag. The default is to use fsaverage
which is distributed with FreeSurfer.
So mris_prep
Ups, sorry, missed your mail.
you can get the difference by two ways:
- you simply subtract the thickness maps in each subject by yourself and then
use that for the analysis
- you put 0 and 1 into the longitudinal qdec table for the two time points.
When the time distance is 1, the rate will b
Thanks a ton Martin,
can you possibly clue me into where I could find study_average?
best,
jon
On Nov 6, 2013, at 2:16 PM, Martin Reuter wrote:
> Hi Jon,
>
> passing the --qdec-long flag to mris_preproc will automatically generate the
> right names (e.g. the .long. directories) and take the d
Thank you so much Martin. It is a very simple yet fantastic solution! Keith
On Wed, Nov 6, 2013 at 2:19 PM, Martin Reuter
wrote:
> Ups, sorry, missed your mail.
>
> you can get the difference by two ways:
>
> - you simply subtract the thickness maps in each subject by yourself and
> then use tha
Hi Jon,
that is just a placeholder, indicating that this can be your own average in a
real study. You can simply use 'fsaverage' for it, now.
Best, Martin
On Nov 6, 2013, at 2:22 PM, Jonathan Holt wrote:
> Thanks a ton Martin,
>
> can you possibly clue me into where I could find study_averag
OH,
I see, then how would I generate my own study average, if I wanted to do so?
On Nov 6, 2013, at 2:48 PM, Martin Reuter wrote:
> Hi Jon,
>
> that is just a placeholder, indicating that this can be your own average in a
> real study. You can simply use 'fsaverage' for it, now.
>
> Best, M
Hi Jon,
Usually you would select a specific subject to be the target, sometimes
that subject is in the mid age range, etc. Also sometimes people remove
that subject from the study to not introduce a bias.
In most cases, however, people simply use fsaverage unless they have a
reason to switch
Thank you Martin,
This is more than enough.
Jon
On Nov 6, 2013, at 3:42 PM, Martin Reuter wrote:
> Hi Jon,
>
> Usually you would select a specific subject to be the target, sometimes that
> subject is in the mid age range, etc. Also sometimes people remove that
> subject from the study to no
FS experts,
I’m having a bit of an issue with a single subject. Recon-all -long errors out
after it tells me it cannot open the subjid_to_template.lta file. I’m very
confused, because the file it’s looking for exists in the exact location it’s
looking for but the recon-all.log suggests that the
Dear Freesurfer team
I am still trying to run a glm analysis between 2 surfaces but I am having
weird results so I guess I missed something.
So I sampled a DTI surface 2mm below the WM surface, and another
intracortical surface (T2* actually) at 75% depth from the pial surface.
The question I'd lik
Hi FreeSurfers,
i came across a few subjects in which FreeSurfer 5.3 failed to properly label
most of the hippocampus in one hemisphere. Specifically, it is the left
hippocampus in all of the 5 cases in which this occured. The subjects are
young, healthy, and without any anatomical peculiaritie
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