Hi Martin, Thanks martin for your reply. I am also running v5.3 I am trying to run this command the command works fine for LH only when I run RH it fails long_mris_slopes --qdec $SUBJECTS_DIR/qdec/long.qdec.table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR I am sending the 3 label file please let me if this is the right input file you need 1. MPS-007_1.long.MPS-007/label/rh.cortex.label 2. MPS-007/label/rh.long.cortex.label 3. MPS-007/label/rh.long.cortex.label
The same command for the lh worked fine for this particular subject. I was able to solve the qdec error. This one I am unable to. Thanks , Bhavani
This what I get from my terminal window. freesurfer% long_mris_slopes --qdec $SUBJECTS_DIR/qdec/long.qdec.table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR Parsing the qdec table: /Applications/freesurfer/subjects/qdec/long.qdec.table.dat
Working in SUBJECTS_DIR: /Applications/freesurfer/subjects
Working on hemi: rh
Subject-Template: MPS-007
INFO: 3 TPs in MPS-007 , mean age: 3.66666666667
=============================================================================== SUBJECT MPS-007 Intersecting Within-Subject Cortex Label
cp /Applications/freesurfer/subjects/MPS-007_1.long.MPS-007/label/rh.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label
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? [mcradxym9290:~] freesurfer% 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 Segmentation fault [mcradxym9290:~] freesurfer%
________________________________________ From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Tuesday, October 13, 2015 3:24 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Selvaraj, Bhavani Subject: 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.f whm25.mgh tksurfer MPS-005 lh pial -overlay /Applications/freesurfer/subjects/MPS-005/surf/lh.long.thickness-avg.f whm25.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
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
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_c omplianceline&d=BQIGaQ&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=Hs6n9odtXPNNWQ9Dlp9yZKsYEEJqQzj6Z5qx7CPJzQg&s=_Iw44QDPyqCDPAS553jTtLhz8MykhvP44nRqVJmcZTQ&e= . 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.
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : https://urldefense.proofpoint.com/v2/url?u=http-3A__reuter.mit.edu&d=BQI...
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
Hi Bhavani,
so internally the script stops at the label intersect command:
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
The first 2 file names are the inputs, the second file is then overwritten with the output (3rd file name identical to 2nd). Can you run this command alone? It did work for me with the files you had sent before.
Thanks, Martin
On 10/14/2015 01:42 PM, Selvaraj, Bhavani wrote:
Hi Martin, Thanks martin for your reply. I am also running v5.3 I am trying to run this command the command works fine for LH only when I run RH it fails long_mris_slopes --qdec $SUBJECTS_DIR/qdec/long.qdec.table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR I am sending the 3 label file please let me if this is the right input file you need 1. MPS-007_1.long.MPS-007/label/rh.cortex.label 2. MPS-007/label/rh.long.cortex.label 3. MPS-007/label/rh.long.cortex.label
The same command for the lh worked fine for this particular subject. I was able to solve the qdec error. This one I am unable to. Thanks , Bhavani
This what I get from my terminal window. freesurfer% long_mris_slopes --qdec $SUBJECTS_DIR/qdec/long.qdec.table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR Parsing the qdec table: /Applications/freesurfer/subjects/qdec/long.qdec.table.dat
Working in SUBJECTS_DIR: /Applications/freesurfer/subjects
Working on hemi: rh
Subject-Template: MPS-007
INFO: 3 TPs in MPS-007 , mean age: 3.66666666667
=============================================================================== SUBJECT MPS-007 Intersecting Within-Subject Cortex Label
cp /Applications/freesurfer/subjects/MPS-007_1.long.MPS-007/label/rh.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label
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? [mcradxym9290:~] freesurfer% 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 Segmentation fault [mcradxym9290:~] freesurfer%
From: Martin Reuter [mreuter@nmr.mgh.harvard.edu] Sent: Tuesday, October 13, 2015 3:24 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Selvaraj, Bhavani Subject: 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.f whm25.mgh tksurfer MPS-005 lh pial -overlay /Applications/freesurfer/subjects/MPS-005/surf/lh.long.thickness-avg.f whm25.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
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
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_c omplianceline&d=BQIGaQ&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=Hs6n9odtXPNNWQ9Dlp9yZKsYEEJqQzj6Z5qx7CPJzQg&s=_Iw44QDPyqCDPAS553jTtLhz8MykhvP44nRqVJmcZTQ&e= . 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.
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : https://urldefense.proofpoint.com/v2/url?u=http-3A__reuter.mit.edu&d=BQI...
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
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Selvaraj, Bhavani