Hi Cathy,
I think the problem is when there are tabs AND spaces. Only spaces
should also work. I can write some code (when I have time) that checks
these things, maybe for the next release.
Best, Martin
On 05/22/2013 02:21 PM, Catherine Bois wrote:
> Hi,
>
> Thank you for your reply. I finally got it working today.thanks for
> your help=)! You say the qdec table should have only spaces; however
> they only seem to work when they are completely tab separated and not
> a single space? If there is accidently a space it will suddenly not
> work. Is there a way that can solve this problem that you can think
> of? It is very time consuming because suddenly it will jsut stop
> working and I need to start from scratch!
>
>
> Quoting Martin Reuter <mreu...@nmr.mgh.harvard.edu> on Wed, 22 May
> 2013 14:08:44 -0400:
>
>> Hi Cathy,
>>
>> it must be something else (I think). The mris_calc command looks
>> weird ("--label " looks like the label is not passed, but a space
>> instead, it then thinks 'mul' is a file).
>>
>> qdecfinal is your qdec table? Make sure it contains only spaces to
>> separate the fields. It should have at least these columns
>> fsid fsid-base time
>>
>> also in your command below, why are there "?" before do-label and time?
>>
>> Unless you want to use the stack (within subject stack of thickness
>> values), I would drop the --do-stack (maybe also drop do-avg or
>> whatever else you don't need).
>>
>> For debugging, I would create a directory, place a single subject
>> there, create a new qdec table with only that subject and try again
>> there. If it still happens , let me know.
>>
>> Best, Martin
>>
>>
>> On 05/20/2013 10:25 AM, Catherine Bois wrote:
>>> Dear Freesurfer experts,
>>>
>>> I am trying to conduct the long_mris_slopes --qdec qdecfinal --meas
>>> thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack
>>> ?do-label ?time time --qcache fsaverage command for my longitudinal
>>> processing. However I keep getting the error message:
>>>
>>> mris_calc -o /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh
>>> --label /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh mul 100
>>>
>>>
>>> mris_calc:
>>> Sorry, but I seem to have encountered an error.
>>> While accessing file 'mul',
>>>
>>> I read online that this was due to a bug encountered in version 5.1,
>>> however I recently upgraded to version 5.3 and the error message
>>> persists. As my Long and base runs have been done in version 5.1
>>> still, I was wondering whether in order to fix this problem the long
>>> and base runs need to be rerun with version 5.3, or whether the error
>>> I am encountering has another solution/ is caused by another problem
>>> entirely?
>>>
>>> Thank you for your help,
>>>
>>> Best Wishes,
>>>
>>> Cathy
>>>
>>
>> --
>> Martin Reuter, Ph.D.
>> Assistant in Neuroscience - Massachusetts General Hospital
>> Instructor in Neurology - Harvard Medical School
>> MGH / HMS / MIT
>>
>> A.A.Martinos Center for Biomedical Imaging
>> 149 Thirteenth Street, Suite 2301
>> Charlestown, MA 02129
>>
>> Phone: +1-617-724-5652
>> Email:
>> mreu...@nmr.mgh.harvard.edu
>> reu...@mit.edu
>> Web : http://reuter.mit.edu
>>
>>
>>
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>
>
>
--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.edu
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