Hi Franz - As long as you have a good aparc+aseg, the exact version of the
recon should not matter.
a.y
On Wed, 6 Jul 2011, Franz Liem wrote:
> and another question.
> Is it OK to run tracula with recons done with an earlier version (5.0.0)?
>
> Thank you,
> Franz
>
> Am 06.07.2011 um 00:05 schrieb Anastasia Yendiki:
>
>>
>> Hi Franz - Which of the files that you sent us are the original files (the
>> bvalfile and bvecfile from your dmrirc)? I could not find any files that had
>> 33 lines among your attachments so I'm not sure what your input files look
>> like.
>>
>> Thanks,
>> a.y
>>
>> On Tue, 5 Jul 2011, Franz Liem wrote:
>>
>>> Hello again.
>>>
>>> I dug into the code and could locate the problem (I don't have a solution,
>>> though. My coding skills are quite amateurish.) I think the problem somehow
>>> lies in the format of my bvecs file.
>>>
>>> flip4fsl is not able to read it correctly:
>>> -------
>>> if (-e $inbvecs) then
>>> echo "INFO: found $inbvecs, converting to FSL format"
>>> if $fslflipx then
>>> set sign = `echo $inorient | sed "s/[RAS]/+\ /g; s/[LPI]/-\ /g"`
>>> endif
>>> cp /dev/null $outbvecs
>>> foreach j (1 2 3)
>>> foreach k (1 2 3)
>>> if ($order[$k] == $j) then
>>> printf '%s ' `cat $inbvecs | awk -v sgn=$sign[$k]1 -v n=$k '{print
>>> sgn*$n}'` \
>>> >> $outbvecs
>>> printf '\n' >> $outbvecs
>>> endif
>>> end
>>> end
>>> endif
>>> -------
>>>
>>> I tried
>>> awk '{ print $1 }' bvecs (with my original bvecs file)
>>> this printed:
>>> 0
>>>
>>> This has something to do with the file's carriage return. I then produced a
>>> new bvecs file by manually typing values into a new text file. Now awk '{
>>> print $1 }' bvecs delivers one column with 33 lines.
>>>
>>>
>>> Nevertheless, the bvecs output of flip4fsl is weird (full of zeros; 3 x 66;
>>> see attachment).
>>> I don't really get how this printf & awk command works.
>>>
>>> Any comments are very much appreciated.
>>> Franz
>>>
>>>
>>>
>>>
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>
>
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
