Log file indicates manual talairach alignment may be necessary.
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0079, pval=0. < threshold=0.0050)
Manual Talairach alignment may be necessary
Can anyone provide direction. Alternatively, the error indicates
Hello,
I am running longitudinal stream processing on mprage scans of some subjects
who have been scanned multiple times using the same sequence with 32 NOVA
channels on GE scanner.
For most subjects the base run exited without error, however for few error was
reported in the runs.
The error wa
Hi Sabin,
what was the recon-all command you used for this?
Thanks, Martin
On 02/05/2013 09:51 AM, Sabin Khadka wrote:
Hi all,
I am running longitudinal processing and it keeps on crashing with no
error message whatsoever in middle of one or the other processing
steps. I am not sure if this
Hi Jon
have you visually inspected the results of the tal xform?
Bruce
On Mon, 1 Jul
2013, Jonathan Holt wrote:
Log file indicates manual talairach alignment may be necessary.
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0079,
pval=0. < threshold
I have tried to inspect the tal xfms that were created in the brief time
this string was running
recon-all -all -s -i path_to_tpN_dcm
while viewing orig.mgz in tkmedit. they were talairach.xfm and
talairach.auto.xfm, both were empty and the tkmedit window was empty.
upon further inspection t
Martin,
I did find that info and tried to follow the instructions, but you'll see
based on my last message the talairach files didn't seem to contain
anything?
On Mon, Jul 1, 2013 at 2:29 PM, Jonathan Holt wrote:
> I have tried to inspect the tal xfms that were created in the brief time
> th
Hi Jon,
are you passing your images?
is a placeholder for the id of your subject+time point, for
example it could be jon_01 the "path_to_tpN_dcm" needs to specify the
path to the dicom files, point it to the first file in the MPRAGE series
(or multi echo mprage or what you are using). This is
Hi Jon,
this is not really a longitudinal problem. You can look at this tutorial
on how to check/fix bad talairach:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview
Best, Martin
On 07/01/2013 01:03 PM, Bruce Fischl wrote:
Hi Jon
have you visually inspected the results
Martin,
definitely passing my images and naming time points appropriately. I have been
passing nifti as opposed to dicom and it's entirely possible that may be the
issue?
jon
On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:
> Hi Jon,
>
> are you passing your images?
> is a placeholder for th
No, it's not nifti, that should work.
Can you send me your log file and the command you issued.
Thanks, Martin
On 07/01/2013 03:13 PM, Jonathan Holt wrote:
Martin,
definitely passing my images and naming time points appropriately. I
have been passing nifti as opposed to dicom and it's entire
Here ya go (to list)
On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt wrote:
> Here ya go.
>
>
> On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter > wrote:
>
>> No, it's not nifti, that should work.
>>
>> Can you send me your log file and the command you issued.
>>
>> Thanks, Martin
>>
>>
>> On 07/
and the command
nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii
On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt wrote:
> Here ya go (to list)
>
>
> On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt wrote:
>
>> Here ya go.
>>
>>
>> On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter <
>> m
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