Hi Cathy,
please cc the freesurfer list when replying, so that other people can profit from or contribute to the discussion.
(Maybe someone else can comment on the transfer of edits in cross processing between versions 5.0.....5.3 ??)
So your cross data is processed with a mix of version 5 and 5.1? or is all processed with 5.1? Within a study you should never mix versions, ie. process some subjects with one versions others with a different version. It is OK to mix some FS versions between the cross and long processing, if it is done for all subjects the same way.
I think you have these options:
1. keep 5.1 cross sectional data (assuming all is 5.1) and run base and long with 5.3. Then start processing base and long (qual check the base and edit if necessary). It should also work if all cross data is in 5.0.
2. reprocess the cross sectionals with 5.3 keeping the edits. Check if edits got transferred correctly, maybe edit more (or remove edits). Then start the base and long (again qual check base and edit if necessary).
Obviously 1. would be less work. If you have mixed versions in your cross data, I'd rather recommend 2.
Best, Martin
On 05/23/2013 05:16 AM, Catherine Bois wrote:
Great,
Thank you very much. I was also hoping to ask for some advice in terms of large dataset handling; I have a dataset of ca 500 scans, with several individuals having only one timepoint. The editing to the -cross runs has been done on version 5 and version 5.1, however we now want to move on to longitudinal processing(I am only completing a "trial" run now). In terms of data management and the laborious task of editing these scans, what to you would be the most time efficient? I would like to, if possible, recon everything again with version 5.3 (as it can handle individuals with only 1 tp) but I would also like to maintain the edits done in version 5 and version 5.1, even thoguh I want to reprocess all the longitudinal runs etc with version 5.3 to maintain consistency. What would be the best plan of action form your point of view/how would you organize this task?
Thank you so much for your help, it would be greatly appreciated.
Best Wishes,
Cathy
Quoting Martin Reuter mreuter@nmr.mgh.harvard.edu on Wed, 22 May 2013 14:33:08 -0400:
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 mreuter@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: mreuter@nmr.mgh.harvard.edu reuter@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: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu