Re: [Freesurfer] mris__label__calc intersect error in longitudinal qcache

Hi Bhavani,

when I run mris_label_calc intersect MPS-007_2mod.long.MPS-007\ rh.cortex.label MPS-\ 007\ lh.cortex.label out.label

it goes through and writes the out.label file. I used fs 5.3 for that. Can you please send me the command and input files that fail for you?

About your other questions:

qdec tables should be stored in <SUBJECS_DIR>/qdec

not sure about the other error. can you send the cross qdec table. probably you need a level file for group?

Thanks, Martin

P.S. Please post questions to the FreeSurfer list.

On 10/13/2015 10:56 AM, Selvaraj, Bhavani wrote:

Hi Martin, Thanks for the reply. Yes those files are available at these locations. when I run this command for LH long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR it runs smoothly and gave me these results tksurfer MPS-007 lh pial -overlay /Applications/freesurfer/subjects/MPS-007/surf/lh.long.thickness-avg.fwhm25.mgh tksurfer MPS-005 lh pial -overlay /Applications/freesurfer/subjects/MPS-005/surf/lh.long.thickness-avg.fwhm25.mgh

but for the rh only the patients MPS-007 gave me the error MPS-005 worked fine. How do I fix that? I am attaching you the cortex label file I don't know how to tell if it is corrupted.

Also I have two more question where should I store the QDEC data table Is this where I should make it? Applications/freesurfer/subjects/qdec/ long.qdec.table.dat

also when I try to open the table in Qdec I get the following error: freesurfer% qdec --table ./qdec/cross.qdec.table.dat

Reading /Applications/freesurfer/tktools/tkUtils.tcl

Using /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl

Loading data table ./qdec/cross.qdec.table.dat... Number of columns: 13 fsid column: 1 Number of factors: 12 Number of subjects: 2 ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: Group for subject MPS-007

Thanks Martin for your help! bhavani

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From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Friday, October 09, 2015 8:59 PM To: Selvaraj, Bhavani Subject: Re: [Freesurfer] mris__label__calc intersect error in longitudinal qcache

Hi Bhavani,

Strange, are those files available at those locations? Can you also check permissions. Open the label files to see if they are corrupted. Best MartinOn Oct 9, 2015 11:31 AM, "Selvaraj, Bhavani" Bhavani.Selvaraj@nationwidechildrens.org wrote:

...

Hi,

when I try running longitudinal analysis for 2 subjects I get the following error (this error

only persists for the right hemisphere-- left hemisphere works fine for this subject).

mris_label_calc intersect /Applications/freesurfer/subjects/MPS-007_2mod.long.MPS-007/label/rh.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label

ERROR -11 : mris_label_calc intersect did not work?

I saw a similar question in the archived mail list so I tried running this command by itself and this was the comment

Segmentation fault

I didn’t know how to fix this error? should I run them again??

Qdec table

Fsid fsid-base years

MPS-007_1 MPS-007 3

MPS-007_2mod MPS-007 4

MPS-007_3 MPS-007 4

MPS-005_1 MPS-005 5

MPS-005_2 MPS-005 6

MPS-005_3 MPS-005 6

Thanks,

Bhavani

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