Thank you for the reply Douglas,
Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi editor, one line for each level. Same as factor 2.
Max
On dijous 14 gener 2016 22:20 CET, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
how many levels does factor 1 have? How did you make the factor file?> On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote:
Hi there experts,
I'm runing qdec to analyze my subject data. I am able to import the qdec.table.dat, but the problem comes in the Design step. I select 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 'LeftAmygdala' as the continuous variable. I don't select any nuisance factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but gives me the following error:
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 137 Checking inputs nframestot = 137 Allocing output Done allocing nframes = 137 Writing to /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh gdfReadHeader: reading /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 LeftAmygdala 1502.65 189.974 Class Means of each Continuous Variable 1 diagnosisBPD 1497.7548 2 diagnosisCCP 1540.8923 3 diagnosisNPC 1488.5490 INFO: gd2mtx_method is dods Reading source surface /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis --surf fsaverage lh
Any recommendations? Any help is much appreciated :)
Best,
Max
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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.
As the error message says, you can only have two levels. With 3 levels, you must use the "command line" stream, ie, mris_preproc, mri_surf2surf, mri_glmfit, and mri_glmfit-sim. There are tutorials on the wiki.
On 01/20/2016 08:53 AM, BAUTISTA-PERPINYA Maximilià wrote:
Thank you for the reply Douglas,
Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi editor, one line for each level. Same as factor 2.
Max
On dijous 14 gener 2016 22:20 CET, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
how many levels does factor 1 have? How did you make the factor file?> On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote:
Hi there experts,
I'm runing qdec to analyze my subject data. I am able to import the qdec.table.dat, but the problem comes in the Design step. I select 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 'LeftAmygdala' as the continuous variable. I don't select any nuisance factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but gives me the following error:
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 137 Checking inputs nframestot = 137 Allocing output Done allocing nframes = 137 Writing to /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh gdfReadHeader: reading /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 LeftAmygdala 1502.65 189.974 Class Means of each Continuous Variable 1 diagnosisBPD 1497.7548 2 diagnosisCCP 1540.8923 3 diagnosisNPC 1488.5490 INFO: gd2mtx_method is dods Reading source surface /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis --surf fsaverage lh
Any recommendations? Any help is much appreciated :)
Best,
Max
_______________________________________________> > Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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.
Hi Douglas,
Thank you for the response. I didn't know I couldn't do it without the command line. I will try it and think like this should work.
Best,
Max
On 21/01/2016, at 18:57, Douglas N Greve wrote:
As the error message says, you can only have two levels. With 3 levels, you must use the "command line" stream, ie, mris_preproc, mri_surf2surf, mri_glmfit, and mri_glmfit-sim. There are tutorials on the wiki.
On 01/20/2016 08:53 AM, BAUTISTA-PERPINYA Maximilià wrote:
Thank you for the reply Douglas,
Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi editor, one line for each level. Same as factor 2.
Max
On dijous 14 gener 2016 22:20 CET, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
how many levels does factor 1 have? How did you make the factor file?> On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote:
Hi there experts,
I'm runing qdec to analyze my subject data. I am able to import the qdec.table.dat, but the problem comes in the Design step. I select 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 'LeftAmygdala' as the continuous variable. I don't select any nuisance factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but gives me the following error:
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 137 Checking inputs nframestot = 137 Allocing output Done allocing nframes = 137 Writing to /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh gdfReadHeader: reading /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 LeftAmygdala 1502.65 189.974 Class Means of each Continuous Variable 1 diagnosisBPD 1497.7548 2 diagnosisCCP 1540.8923 3 diagnosisNPC 1488.5490 INFO: gd2mtx_method is dods Reading source surface /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis --surf fsaverage lh
Any recommendations? Any help is much appreciated :)
Best,
Max
_______________________________________________> > Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________> Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
···························································· Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg
(+49) 015759302368 maximila.bautista-perpinya@etu.unistra.fr maxbauper@gmail.com
freesurfer@nmr.mgh.harvard.edu
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BAUTISTA-PERPINYA Maximilià -
Douglas N Greve -
Maximilià Bautista-Perpinyà