please ignore the previous post -- the calloc errors i was getting were
restricted to only certain files that somehow got corrupted.
cheers,
@rno
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Hi Bruce, I was just wondering if you had any suggestions on how to fix the
corpus callosum labels?
Corinna
On Wed, Aug 14, 2013 at 11:49 AM, Corinna Bauer wrote:
> In general, it mostly looks ok. There are regions which are labelled as
> hypointensities, but should be CSF or gray matter, parti
Hi Pedro, see the release notes for the issue
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
doug
On 08/19/2013 10:06 PM, Pedro Rosa wrote:
> Hi experts,
> I am processing several subjects, and they all ended up with the same error
> at the autorecon2: ribbon.mgz could not be opened. I ran
Hi Anastasia:
Just a quick question. When comparing FA, AD, RD etc between 2 groups, do
we need to use covariates like Intra Cranial volume or AGE?
If the answer is no, should I do an ANOVA or will T tests be sufficient?
thank you,
Alan
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Freesurfer
Definitely age. You don't need to adjust for volume since these are not
volume/area/length measures that you're comparing. You should also check
for any group differences in motion before you proceed and make sure your
groups are matched in terms of motion. If you do separate t-tests for each
Thank you so much.
Alan
On Tue, Aug 20, 2013 at 11:20 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Definitely age. You don't need to adjust for volume since these are not
> volume/area/length measures that you're comparing. You should also check
> for any group differences i
Hi Corinna
if you upload the dataset I'll take a look.
cheers
Bruce
On Tue, 20 Aug 2013, Corinna Bauer wrote:
Hi Bruce, I was just wondering if you had any suggestions on how to fix the
corpus callosum labels?
Corinna
On Wed, Aug 14, 2013 at 11:49 AM, Corinna Bauer wrote:
In genera
Hi Anastasia,
Thank you for your help.
I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the
command "xfmrot" changed the dots back to commas. So, I changed our system
language from de_AUT.UTF-8 to en_US.UTF-8 and reran trac-all. After changing
the system language everything
Hi Anastasia,
Yes, i am running this on ubuntu 12.04.
Sincerely,
Florian
>>> Anastasia Yendiki 20.08.13 17.38 Uhr >>>
Hi Florian - Are you running this on an ubuntu system by any chance?
a.y
On Tue, 20 Aug 2013, Borsodi Florian wrote:
> Hi Anastasia,
>
> Thank you for your help.
> I change
Hi Florian - Are you running this on an ubuntu system by any chance?
a.y
On Tue, 20 Aug 2013, Borsodi Florian wrote:
Hi Anastasia,
Thank you for your help.
I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the command
"xfmrot" changed the dots back to
commas. So, I chang
This is an Ubuntu-related error that has surfaced recently because in
Ubuntu /bin/sh is not a bash shell any more. To get around this, you can
edit the first line of the scripts $FREESURFER_HOME/bin/bedpostx_mgh and
$FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace "/bin/sh" with
"/bin/
Hi Doug,
I ran 'mri_binarize --i aparc+aseg.nii.gz --match 4 --match 5 --match 43
--match 44 --match 31 --match 63 --count countfile.dat'
The following error message was produced:
ERROR: must specify output volume
So I added -o bin.nii.gz to the end of the command and reran it successfully.
The
They should be fine. BTW, you can run
recon-all -s subject -make all
and it will only run the parts that need to be run
doug
On 08/20/2013 12:13 PM, Pedro Rosa wrote:
> Hi,
> I am mainly interested in using the wmparc.mgz files. Are they alright in the
> subjects with this error in autorecon2
Hi list.
I'm looking mailing list to find responce to this question.
"Estimated Total Intra Cranial Vol" obtained by asegstats2table also included
ventricles volume?
I'd like to assess the volumetric changes of a subcortical structures. Do you
advise me to consider "Estimated Total Intra Cranial
I think the best way to diagnose the issue would be to run the subject
using the standard atlas provided with freesurfer. If that runs to
completion that the .gca is almost certainly the source of the problem.
-Zeke
On 08/19/2013 03:07 PM, Mark Plantz wrote:
> Hello all,
>
> While running
Thanks for the responses.
I think I have determined the cause of the error. I thought it would be OK
to run recon-all with a .gca atlas that contained some different ROI's from
the default .gca atlas. I think that this may be throwing off the
subcortical segmentation.
Does anyone know if the gca
I'm trying to run selxavg on a dataset with a rather large number (930) of
timepoints. Selxavg keeps erroring out with an 'out of memory. Type HELP
MEMORY for your options' error.
I see that this problem has been discussed on the mailing list previously,
and the advice was to split the file into
I'm trying to run selxavg on a dataset with a rather large number (930) of
timepoints. Selxavg keeps erroring out with an 'out of memory. Type HELP
MEMORY for your options' error.
I see that this problem has been discussed on the mailing list previously,
and the advice was to split the file into
Mark,
How was the .gca file created? Can you send us this file?
Nick
On Tue, 2013-08-20 at 14:15 -0500, Mark Plantz wrote:
> Thanks for the responses.
>
>
> I think I have determined the cause of the error. I thought it would
> be OK to run recon-all with a .gca atlas that contained some dif
Dear FS experts,I am contacting you to report an error after launching recon
-all for one of my subjects. I am using a macbook pro with snow leopard version
10.6.8.
I would greatly appreciate if you could advise me which step/s should I take to
correct this.Thank you for your attention,P
Dear Doug et al.,
I have 2 groups, 2 genders, and 2 scanners (A and B). (I also have Age
as a covariate). In my FSGD they are listed in this order:
ControlFemaleA
ControlFemaleB
ControlMaleA
ControlMaleB
CaseFemaleA
CaseFemaleB
CaseMaleA
CaseMaleB
I used the following contrast to test for a
Hi,
Sorry for that!
I tried using several targets: all / autorecon1-2-3, and for all I get 'make:
command not found.'
I used recon-all -s subject -make target
Thank you again,
Pedro Rosa
On 20 Aug 2013, at 12:34 PM, Douglas N Greve wrote:
> They should be fine. BTW, you can run
>
> recon-all -
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