I have two sets of identical blocks within each fMRI run, so conditions {1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two blocks.
If I run the analysis treating each with the contrasts set up with this numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following output from /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
... ntptot = 687, nX = 136, DOF = 551 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat XCond = 2926.01 (normalized)
However, if I want to treat the two sets of blocks separately, i.e., {1,2,3,4,5,6,7,8,9,10} so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then fast_selxavg3.m gives:
ntptot = 687, nX = 146, DOF = 541 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat XCond = 4.33238e+08 (normalized) ERROR: design is ill-conditioned
1) why does nX increase by 10 in the 2nd case? 2) why is fast_selxavg3.m unhappy and XCond so large? Can it not handle 10 separate blocks?
The entire log file in the 2nd case is attached.
Hi Ronny, you added 5 new conditions, so it should have increased by at least 5. However, if you are using a derivative with the HRF, then you will have 2 regressors for each condition and it will increase by 10.
I don't know why it does not like the 2nd one. Can you send me the Xtmp.mat file?
doug
On 10/23/2013 12:16 PM, preciado@nmr.mgh.harvard.edu wrote:
I have two sets of identical blocks within each fMRI run, so conditions {1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two blocks.
If I run the analysis treating each with the contrasts set up with this numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following output from /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
... ntptot = 687, nX = 136, DOF = 551 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat XCond = 2926.01 (normalized)
However, if I want to treat the two sets of blocks separately, i.e., {1,2,3,4,5,6,7,8,9,10} so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then fast_selxavg3.m gives:
ntptot = 687, nX = 146, DOF = 541 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat XCond = 4.33238e+08 (normalized) ERROR: design is ill-conditioned
- why does nX increase by 10 in the 2nd case?
- why is fast_selxavg3.m unhappy and XCond so large? Can it not handle 10
separate blocks?
The entire log file in the 2nd case is attached.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Xtmp.mat Attached
Hi Ronny, you added 5 new conditions, so it should have increased by at least 5. However, if you are using a derivative with the HRF, then you will have 2 regressors for each condition and it will increase by 10.
I don't know why it does not like the 2nd one. Can you send me the Xtmp.mat file?
doug
On 10/23/2013 12:16 PM, preciado@nmr.mgh.harvard.edu wrote:
I have two sets of identical blocks within each fMRI run, so conditions {1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two blocks.
If I run the analysis treating each with the contrasts set up with this numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following output from /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
... ntptot = 687, nX = 136, DOF = 551 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat XCond = 2926.01 (normalized)
However, if I want to treat the two sets of blocks separately, i.e., {1,2,3,4,5,6,7,8,9,10} so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then fast_selxavg3.m gives:
ntptot = 687, nX = 146, DOF = 541 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat XCond = 4.33238e+08 (normalized) ERROR: design is ill-conditioned
- why does nX increase by 10 in the 2nd case?
- why is fast_selxavg3.m unhappy and XCond so large? Can it not handle
10 separate blocks?
The entire log file in the 2nd case is attached.
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
I think the problem is that the order of the conditions is always the same combined with an absence of fixation points. I don't think you can do this analysiswith this design.
doug
On 10/24/2013 12:08 PM, preciado@nmr.mgh.harvard.edu wrote:
Xtmp.mat Attached
Hi Ronny, you added 5 new conditions, so it should have increased by at least 5. However, if you are using a derivative with the HRF, then you will have 2 regressors for each condition and it will increase by 10.
I don't know why it does not like the 2nd one. Can you send me the Xtmp.mat file?
doug
On 10/23/2013 12:16 PM, preciado@nmr.mgh.harvard.edu wrote:
I have two sets of identical blocks within each fMRI run, so conditions {1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two blocks.
If I run the analysis treating each with the contrasts set up with this numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following output from /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
... ntptot = 687, nX = 136, DOF = 551 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat XCond = 2926.01 (normalized)
However, if I want to treat the two sets of blocks separately, i.e., {1,2,3,4,5,6,7,8,9,10} so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then fast_selxavg3.m gives:
ntptot = 687, nX = 146, DOF = 541 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat XCond = 4.33238e+08 (normalized) ERROR: design is ill-conditioned
- why does nX increase by 10 in the 2nd case?
- why is fast_selxavg3.m unhappy and XCond so large? Can it not handle
10 separate blocks?
The entire log file in the 2nd case is attached.
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
I had a very similar design before when I ran this analysis with 5 blocks instead of 10. The Xtmp.mat file is attached for comparison.
I think the problem is that the order of the conditions is always the same combined with an absence of fixation points. I don't think you can do this analysiswith this design.
doug
On 10/24/2013 12:08 PM, preciado@nmr.mgh.harvard.edu wrote:
Xtmp.mat Attached
Hi Ronny, you added 5 new conditions, so it should have increased by at least 5. However, if you are using a derivative with the HRF, then you will have 2 regressors for each condition and it will increase by 10.
I don't know why it does not like the 2nd one. Can you send me the Xtmp.mat file?
doug
On 10/23/2013 12:16 PM, preciado@nmr.mgh.harvard.edu wrote:
I have two sets of identical blocks within each fMRI run, so conditions {1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two blocks.
If I run the analysis treating each with the contrasts set up with this numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following output from /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
... ntptot = 687, nX = 136, DOF = 551 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat XCond = 2926.01 (normalized)
However, if I want to treat the two sets of blocks separately, i.e., {1,2,3,4,5,6,7,8,9,10} so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then fast_selxavg3.m gives:
ntptot = 687, nX = 146, DOF = 541 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat XCond = 4.33238e+08 (normalized) ERROR: design is ill-conditioned
- why does nX increase by 10 in the 2nd case?
- why is fast_selxavg3.m unhappy and XCond so large? Can it not
handle 10 separate blocks?
The entire log file in the 2nd case is attached.
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
-- 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/
The 5 condition analysis is not all that well conditioned either. I have an (arbitrary) threshold of 10^6 max for the condition number. The 5-condition design is safely below the threshold, the 10-condition is well above. Unfortunately, this threshold is hardwired. Do you really need to do the 10-condition? The results may not be very good even if you can analyze it.
doug
On 10/24/2013 12:08 PM, preciado@nmr.mgh.harvard.edu wrote:
Xtmp.mat Attached
Hi Ronny, you added 5 new conditions, so it should have increased by at least 5. However, if you are using a derivative with the HRF, then you will have 2 regressors for each condition and it will increase by 10.
I don't know why it does not like the 2nd one. Can you send me the Xtmp.mat file?
doug
On 10/23/2013 12:16 PM, preciado@nmr.mgh.harvard.edu wrote:
I have two sets of identical blocks within each fMRI run, so conditions {1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two blocks.
If I run the analysis treating each with the contrasts set up with this numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following output from /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
... ntptot = 687, nX = 136, DOF = 551 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat XCond = 2926.01 (normalized)
However, if I want to treat the two sets of blocks separately, i.e., {1,2,3,4,5,6,7,8,9,10} so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then fast_selxavg3.m gives:
ntptot = 687, nX = 146, DOF = 541 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat XCond = 4.33238e+08 (normalized) ERROR: design is ill-conditioned
- why does nX increase by 10 in the 2nd case?
- why is fast_selxavg3.m unhappy and XCond so large? Can it not handle
10 separate blocks?
The entire log file in the 2nd case is attached.
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
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
preciado＠nmr.mgh.harvard.edu