Hi Bruce,
Yes, I would like to reduce the required calculation time, until desired
results are available.
Best regards,
Iven
-Ursprüngliche Nachricht-
Von: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Gesendet: Mittwoch, 20. Juli 2011 15:19
An: Fellhauer, Iven
Cc: freesurfer@nmr.m
Dear All,
I've been trying out the automatic V1 labelling using the Hinds et al.
(NeuroImage, 2008 vol. 39 (4) pp. 1585-99) and, as far as I can tell it seems
to work pretty well on our anatomical scans (In general I'd be interested in
the opinions/experiences of others who've tried it).
I hav
Dear FS and Tracula experts
Because of correction for slice angulation during scanning, I have as many
bvecs files as subjects. Therefore I created a list for the bvecs
set bvecslist = (b101/bvecs b102/bvecs) but tracula reports the following
error:
mv: rename
/Users/juergenhaenggi/Desktop/Trac
Hi Jeff,
I think you'll have to run with -force. In the newer version 5.1, this is
updated so that you don't have to anymore. And you might be right
that deleting the folder is not a good idea since the edits were made in
there. If you made edits in the cross and want to rerun the base, then yo
Hi Jürgen - There is no bvecslist option. Currently there is no support
for multiple bvecs files in one configuration file but it's certainly
something that can be added to the next release. For now you'd have to
change the configuration file accordingly for each subject with a
different bvec
Hi Iven
we don't recommend that as many steps interact. For example, although we
don't do it automatically now, we do have procedures for automatically
correcting the aseg based on the subsequently created surfaces.
cheers
Bruce
On Thu, 21
Jul 2011, Fellhauer, Iven wrote:
Hi Bruce,
Yes,
Hi Krish,
1. What do you mean "just the calcarine itself"? Do you mean the fundus?
mris_divide_parcellation can be used to chop the pericalcarine or V1 labels
up along it's primary eigenaxis, which is a reasonable approximation to
eccentricity.
2. You could draw occipital pole in fsaverage a
Hi Bruce,
thanks for your explanation. I was thinking the the segmentation region is
used to calculate cortical thickness, by the way, is it used for calculate
something? such as the GM volumes? I want to know this to be sure if in some
point I have to fix this.
About the heterotopias, is a good o
Hi Antonella,
for each acquisition you give mri_convert *one* dicom file in that series
and it will figure out the rest. You will then have one volume file per
series. Something like:
mri_convert
Good morning Bruce,
Thank you for your answer and yes, I am posting my question to the list.
F
Hi Carolina,
no, the aseg cortex/wm is not used for thickness or volume (it can be,
but we don't recommend it). The surfaces are. As for the heterotopias, I
don't really know what a good output would be. It depends what you want to
do with them. I guess they should be gray matter, no?
Bruce
Dear list,
Could you please recommend the literature about multiple comparisons
correction, especially about Monte-Carlo simulation.
Thank you,
Tanja.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/li
Check out hayasaka and nichols 2003. pdf below
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/hayasaka.2003.ni.1014.clustersize.pdf
doug
Tetiana Dadakova wrote:
> Dear list,
>
> Could you please recommend the literature about multiple comparisons
> correction, especially about Monte
That paper is great. Lazar also has a nice review of a number of
approaches in her book:
Lazar, N. The statistical analysis of functional MRI data.
On 7/21/11 11:39 AM, Douglas N Greve wrote:
> Check out hayasaka and nichols 2003. pdf below
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fl
Hi all,
I was having consistent errors with two cases during mri_ca_normalize, and
after using an updated version (mri_ca_normalize_centos), one case went
through smoothly. I'm having trouble with the second case, however; it now
repeatedly reports a segmentation fault partway through mri_ca_norma
Hi Tali
can you email me the nu.mgz, the talairach.lta and the brainmask.mgz? I'll
see if I can get it to happen and fix it.
thanks
Bruce
On
Thu, 21 Jul 2011, Tali Swisher wrote:
Hi all,
I was having consistent errors with two cases during mri_ca_normalize, and
after using an updated v
Quick update: this fix worked brilliantly.
Many thanks for the help,
J Richey
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, July 18, 2011 5:20 PM
To: John Richey
Cc: 'Bruce Fischl'; 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer]
I received the follow error while running a set of subjects under
'long_mris_slopes,' and wasn't able to decipher the problem. It appears that
mris_calc is not able to do the division for these files (dividing by 0
perhaps?). Any help appreciated, here's the command and tail end of
output/err
Hi,
I run the trac-all bedp process and it comes up with the following errors:
56 slices processed
56 slices processed
57 slices processed
Queuing post processing stage
58 slices processed
For some reason the bedpostX process DOES NOT appear
to have successfully completed. Please examine your
res
Where is the data?
On Thu, 21 Jul 2011, pho...@nmr.mgh.harvard.edu wrote:
> Hi,
>
> I run the trac-all bedp process and it comes up with the following errors:
>
> 56 slices processed
> 56 slices processed
> 57 slices processed
> Queuing post processing stage
> 58 slices processed
> For some reas
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