Dear Freesurfer experts,
I very much appreciate your help with an additional set of questions. I feel I'm really close to getting this finished :)
1) In a design with group and gender as discrete factors and age as a continuous factor, why is it that QDEC only displays the contrast "Does the avg thickness, accounting for gender, differ between group1 and group2?" and not also "..acounting for gender and age,.."?
2) In QDEC, if I am left with a cluster after setting the FDR rate to 0.1, does that qualify as a "trend towads significance" in the same way as when obtaining a p value <.1 for a behavioural effect?
3) From the group tutorial, I see that mris_preproc has to be called with flag "--cache-in ess.fwhm10thickn.fsaverage". However, after running recon-all (including with the –qcache option) on all my subjects, none of their folders contains a file named ?h.thickness.fwhm10.fsaverage.mgh
4) When comparing two healthy groups, is there anything to gain from using a fsaverage built from the sample (with make_average_subject) as opposed to using the default fsaverage?
5) What is the difference between running make_average_subject and running mris_preproc with --target fsaverage?
6) For my ROI mri_glmfit analysis, I wanted to use the FSGD and contrast files that were automatically created when I did my QDEC whole-brain analysis, since the design will be the same. However, although I identified the FSGD file (qdec.fsgd), I cannot see any plaintext file in the QDEC folder that looks like it contains contrast definitions!
Thanks! Tudor
Not sure whether anyone'd seen my last email (below). Again apologies for the multitude of questions, I hope this is the last batch for this analysis..
On 12 May 2013 16:45, Tudor Popescu tudor3@gmail.com wrote:
Dear Freesurfer experts,
I very much appreciate your help with an additional set of questions. I feel I'm really close to getting this finished :)
- In a design with group and gender as discrete factors and age as a
continuous factor, why is it that QDEC only displays the contrast "Does the avg thickness, accounting for gender, differ between group1 and group2?" and not also "..acounting for gender and age,.."?
- In QDEC, if I am left with a cluster after setting the FDR rate to 0.1,
does that qualify as a "trend towads significance" in the same way as when obtaining a p value <.1 for a behavioural effect?
- From the group tutorial, I see that mris_preproc has to be called with
flag "--cache-in ess.fwhm10thickn.fsaverage". However, after running recon-all (including with the –qcache option) on all my subjects, none of their folders contains a file named ?h.thickness.fwhm10.fsaverage.mgh
- When comparing two healthy groups, is there anything to gain from using
a fsaverage built from the sample (with make_average_subject) as opposed to using the default fsaverage?
- What is the difference between running make_average_subject and running
mris_preproc with --target fsaverage?
- For my ROI mri_glmfit analysis, I wanted to use the FSGD and contrast
files that were automatically created when I did my QDEC whole-brain analysis, since the design will be the same. However, although I identified the FSGD file (qdec.fsgd), I cannot see any plaintext file in the QDEC folder that looks like it contains contrast definitions!
Thanks! Tudor
On 05/14/2013 10:05 AM, Tudor Popescu wrote:
Not sure whether anyone'd seen my last email (below). Again apologies for the multitude of questions, I hope this is the last batch for this analysis..
On 12 May 2013 16:45, Tudor Popescu <tudor3@gmail.com mailto:tudor3@gmail.com> wrote:
Dear Freesurfer experts, I very much appreciate your help with an additional set of questions. I feel I'm really close to getting this finished :) 1) In a design with group and gender as discrete factors and age as a continuous factor, why is it that QDEC only displays the contrast "Does the avg thickness, accounting for gender, differ between group1 and group2?" and not also "..acounting for gender and age,.."?
I thought that it would have. Are you coding age as a nuisance variable? Also, are you coding gender as a continuous variable? That is something you should not do.
2) In QDEC, if I am left with a cluster after setting the FDR rate to 0.1, does that qualify as a "trend towads significance" in the same way as when obtaining a p value <.1 for a behavioural effect?
It is hard to related FDR to traditional FPR. FDR does not give clusters and there is no FDR associated with the cluster you found. It just gives a list of vertices that meet the FDR criteria. You form the clusters with your eyes. The 0.1 means that 10% of the vertices are falsely activated. If those 10% are all in your cluster, then that is a problem.
3) From the group tutorial, I see that mris_preproc has to be called with flag "--cache-in ess.fwhm10thickn.fsaverage". However, after running recon-all (including with the –qcache option) on all my subjects, none of their folders contains a file named ?h.thickness.fwhm10.fsaverage.mgh
Where does it say to use ess.fwhm10thickn.fsaverage?
4) When comparing two healthy groups, is there anything to gain from using a fsaverage built from the sample (with make_average_subject) as opposed to using the default fsaverage?
Probably not. make_average_subject really just gives you a folding pattern to display your results on. If you want to analyze your data on the actual new average subject, you will need to register to that average subject (takes about 2 hours per subject), then specify the new registration with --surfreg.
5) What is the difference between running make_average_subject and running mris_preproc with --target fsaverage?
make average subject makes the average subject. mris_preproc samples the data into a common space defined by the registration surface and concatenates the input subjects into a single stack.
6) For my ROI mri_glmfit analysis, I wanted to use the FSGD and contrast files that were automatically created when I did my QDEC whole-brain analysis, since the design will be the same. However, although I identified the FSGD file (qdec.fsgd), I cannot see any plaintext file in the QDEC folder that looks like it contains contrast definitions!
Look for C.dat in the contrast folders doug
Thanks! Tudor
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug and others,
I'm sorry to hijack this thread. I noticed in FSL list that it has been recommended to demean gender (and probably other categorical variables) in GLM. As far as I understand, this implies treating a categorical variable as a continuous one. However, I can also see that you recommend not treating gender (and other categorical variables) as a continuous variable in Freesurfer. I would much appreciate if someone can help me to address this problem. I'm CC'ing FSL list so others may also help.
All the best, -Arman
On Tue, 2013-05-14 at 12:04 -0400, Douglas N Greve wrote:
On 05/14/2013 10:05 AM, Tudor Popescu wrote:
I thought that it would have. Are you coding age as a nuisance variable? Also, are you coding gender as a continuous variable? That is something you should not do.
-- 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 Arman, I have not followed the FSL thread, but you would only do this if you have a column of ones in your design matrix. Itdoes not imply that gender is being treated as a continous variable. A continuous variable for gender means that male=1 and female=2. This implies that you expect female thickness or slope vs age, etc, to be twice that of males. Probably this does not make sense. doug
On 05/14/2013 12:24 PM, Arman Eshaghi wrote:
Dear Doug and others,
I'm sorry to hijack this thread. I noticed in FSL list that it has been recommended to demean gender (and probably other categorical variables) in GLM. As far as I understand, this implies treating a categorical variable as a continuous one. However, I can also see that you recommend not treating gender (and other categorical variables) as a continuous variable in Freesurfer. I would much appreciate if someone can help me to address this problem. I'm CC'ing FSL list so others may also help.
All the best, -Arman
On Tue, 2013-05-14 at 12:04 -0400, Douglas N Greve wrote:
On 05/14/2013 10:05 AM, Tudor Popescu wrote: I thought that it would have. Are you coding age as a nuisance variable? Also, are you coding gender as a continuous variable? That is something you should not do.
-- 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.
1) In a design with group and gender as discrete factors and age as a continuous factor, why is it that QDEC only displays the contrast "Does the avg thickness, accounting for gender, differ between group1 and group2?" and not also "..acounting for gender and age,.."?I thought that it would have. Are you coding age as a nuisance variable? Also, are you coding gender as a continuous variable? That is something you should not do.
I was not coding age as a nuisance variable but as a continuous variable (co-variate). Gender was a discrete/fixed factor but I'm not sure whether this means 'continuous' in the sense discussed in your exchange with Arman. Anyway, in this configuration, it seems gender and age are not accounted (controlled) for at the same time.
3) From the group tutorial, I see that mris_preproc has to be called with flag "--cache-in ess.fwhm10thickn.fsaverage". However, after running recon-all (including with the –qcache option) on all my subjects, none of their folders contains a file named ?h.thickness.fwhm10.fsaverage.mghWhere does it say to use ess.fwhm10thickn.fsaverage?
Sorry, typo. The flag is actually "--cache-in thickness.fwhm10.fsaverage", I file that I do not have after having run recon-all (including with the --qcache option)
5) What is the difference between running make_average_subject and running mris_preproc with --target fsaverage?make average subject makes the average subject. mris_preproc samples the data into a common space defined by the registration surface and concatenates the input subjects into a single stack.
But should the registration surface used by mris_preproc (i.e. its "--target" flag) come from the 'average' subject or from 'fsaverage'? In other words, which one of these becomes the study-specific template?
6) For my ROI mri_glmfit analysis, I wanted to use the FSGD and contrast files that were automatically created when I did my QDEC whole-brain analysis, since the design will be the same. However, although I identified the FSGD file (qdec.fsgd), I cannot see any plaintext file in the QDEC folder that looks like it contains contrast definitions!Look for C.dat in the contrast folders
I have no C.dat under /contrasts, only files such as lh-Avg-Intercept-thickness.mat. Don't the different clickable "questions" that appear in QDEC's Display screen each correspond to a contrast, with each contrast sitting in its own file? _____ And a couple more..
A) Why does mris_preproc need to be pointed to a .FSGD, when its output should just be a concatenation of registered structurals, and thus independent from the design of any particular analysis?
B) All concatenated volumes from mris_preproc's output files (?h.thickness.mgh) appear blank in freeview, even though the individual structurals all look fine. Also, lh.thickness.mgh and rh.thickness.mgh have, surprisingly, *exactly* the same file size, which is also a bit small (~25MB) to be able to contain 38 registered structurals, which suggests something went wrong...
C) When running mri_surf2surf, I get an error saying that file /surf/lh.white cannot be opened. The 'average' folder produced after I ran make_average_subject does not contain a /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t find a log file from make_average_subject so i don’t know if it gave any errors..
Thanks again Doug!
On 05/14/2013 02:22 PM, Tudor Popescu wrote:
> 1) In a design with group and gender as discrete factors and age > as a continuous factor, why is it that QDEC only displays the > contrast "Does the avg thickness, accounting for gender, differ > between group1 and group2?" and not also "..acounting for gender > and age,.."? > I thought that it would have. Are you coding age as a nuisance variable? Also, are you coding gender as a continuous variable? That is something you should not do.I was not coding age as a nuisance variable but as a continuous variable (co-variate). Gender was a discrete/fixed factor but I'm not sure whether this means 'continuous' in the sense discussed in your exchange with Arman. Anyway, in this configuration, it seems gender and age are not accounted (controlled) for at the same time.
It should be. Can you send your qdec table?
> 3) From the group tutorial, I see that mris_preproc has to be > called with flag "--cache-in ess.fwhm10thickn.fsaverage". However, > after running recon-all (including with the –qcache option) on all > my subjects, none of their folders contains a file named > ?h.thickness.fwhm10.fsaverage.mgh > Where does it say to use ess.fwhm10thickn.fsaverage?Sorry, typo. The flag is actually "--cache-in thickness.fwhm10.fsaverage", I file that I do not have after having run recon-all (including with the --qcache option)
Try running recon-all again with just the --qcache flag.
> 5) What is the difference between running make_average_subject and > running mris_preproc with --target fsaverage? > make average subject makes the average subject. mris_preproc samples the data into a common space defined by the registration surface and concatenates the input subjects into a single stack.But should the registration surface used by mris_preproc (i.e. its "--target" flag) come from the 'average' subject or from 'fsaverage'? In other words, which one of these becomes the study-specific template?
You have to tell mris_preproc both the target and the surface registration to use if you want to use a different average subject.
> 6) For my ROI mri_glmfit analysis, I wanted to use the FSGD and > contrast files that were automatically created when I did my QDEC > whole-brain analysis, since the design will be the same. However, > although I identified the FSGD file (qdec.fsgd), I cannot see any > plaintext file in the QDEC folder that looks like it contains > contrast definitions! > Look for C.dat in the contrast foldersI have no C.dat under /contrasts, only files such as lh-Avg-Intercept-thickness.mat. Don't the different clickable "questions" that appear in QDEC's Display screen each correspond to a contrast, with each contrast sitting in its own file?
Sorry, not the folder called "contrast". There are several other folders eg lh-Avg-Intercept-thickness. The C.dat file is there.
And a couple more..
A) Why does mris_preproc need to be pointed to a .FSGD, when its output should just be a concatenation of registered structurals, and thus independent from the design of any particular analysis?
It needs to know which subjects you want in your concatenation. This must be in the same order as the order in the FSGD. You can spec the list in other ways. See the help.
B) All concatenated volumes from mris_preproc's output files (?h.thickness.mgh) appear blank in freeview, even though the individual structurals all look fine. Also, lh.thickness.mgh and rh.thickness.mgh have, surprisingly, *exactly* the same file size, which is also a bit small (~25MB) to be able to contain 38 registered structurals, which suggests something went wrong...
These are surface overlay files, not volumes. You can't load surfaces as volumes in freeview.
C) When running mri_surf2surf, I get an error saying that file /surf/lh.white cannot be opened. The 'average' folder produced after I ran make_average_subject does not contain a /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t find a log file from make_average_subject so i don’t know if it gave any errors..
It's extremely helpful to have command lines ...
Thanks again Doug!
> 1) In a design with group and gender as discrete factors and age> as a continuous factor, why is it that QDEC only displays the > contrast "Does the avg thickness, accounting for gender, differ > between group1 and group2?" and not also "..acounting for gender > and age,.."? > I thought that it would have. Are you coding age as a nuisance variable? Also, are you coding gender as a continuous variable? That is something you should not do.I was not coding age as a nuisance variable but as a continuous variable (co-variate). Gender was a discrete/fixed factor but I'm not sure whether this means 'continuous' in the sense discussed in your exchange with Arman. Anyway, in this configuration, it seems gender and age are not accounted (controlled) for at the same time.
It should be. Can you send your qdec table?
See attached
> 3) From the group tutorial, I see that mris_preproc has to be > called with flag "--cache-in ess.fwhm10thickn.fsaverage". However, > after running recon-all (including with the –qcache option) on all > my subjects, none of their folders contains a file named > ?h.thickness.fwhm10.fsaverage.mgh > Where does it say to use ess.fwhm10thickn.fsaverage?Sorry, typo. The flag is actually "--cache-in thickness.fwhm10.fsaverage", I file that I do not have after having run recon-all (including with the --qcache option)
Try running recon-all again with just the --qcache flag.
This is what I had done previously; the command was: recon-all -s C${i} -qcache where the ${i} was a counter in a script, to run the command on all my subjects
> 5) What is the difference between running make_average_subject and > running mris_preproc with --target fsaverage? > make average subject makes the average subject. mris_preproc samples the data into a common space defined by the registration surface and concatenates the input subjects into a single stack.But should the registration surface used by mris_preproc (i.e. its "--target" flag) come from the 'average' subject or from 'fsaverage'? In other words, which one of these becomes the study-specific template?
You have to tell mris_preproc both the target and the surface registration to use if you want to use a different average subject.
The command I used is:
mris_preproc --fsgd group_gender__age.fsgd --target average --hemi rh --meas thickness --out rh.thickness.mgh So if I understand correctly, the fact that I didn't indicate a surface registration means that the surface from the "average" subject will be used, rather than the one from "fsaverage"? I still don't understand the difference between those two, and which, if any, can be referred to as the study-specific template.
B) All concatenated volumes from mris_preproc's output files
(?h.thickness.mgh) appear blank in freeview, even though the individual structurals all look fine. Also, lh.thickness.mgh and rh.thickness.mgh have, surprisingly, *exactly* the same file size, which is also a bit small (~25MB) to be able to contain 38 registered structurals, which suggests something went wrong...
These are surface overlay files, not volumes. You can't load surfaces as volumes in freeview.
So assuming I don't visually inspect the surface overlays, can I assume that mris_preproc ran fine if lh.thickness.mgh and rh.thickness.mgh have exactly the same file size?
C) When running mri_surf2surf, I get an error saying that file
/surf/lh.white cannot be opened. The 'average' folder produced after I ran make_average_subject does not contain a /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t find a log file from make_average_subject so i don’t know if it gave any errors..
It's extremely helpful to have command lines ...
Sorry, my commands were: make_average_subject --subjects C01 C02 C03 C04 C05 C06 C07 C08 C09 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 M01 M02 M03 M04 M05 M06 M07 M08 M09 M10 M11 M12 M13 M14 M15 M16 M17 M18 M19 mri_surf2surf --hemi lh --s average --sval lh.thickness.mgh --fwhm 10 --tval lh.thickness.10.mgh _________________________
Could someone please explain how the following descriptions of a contrast are exactly linked: i) a contrast's namesake folder (including keywords 'Avg'/'Diff'/'X' and 'Intercept'/'Cor'; e.g. "lh-Diff-group1-group2-Cor-thickness-behaviouralMeasure"), ii) its phrasing in QDEC ("Does the thickness-age correlation differ between group1 and group2?"), iii) the assignment of values to each column of the design matrix, in the C.dat contrast vector (e.g. [0, 0, 1, -1])
_________________________ (this is actually a bug report) After setting a different FDR threshold and pressing the "Set Using FDR" button, more often than not the results image doesn’t change accordingly. I noticed that the button only has an effect after moving around the QDEC window and/or waiting a minute or so
when I run qdec using your table and my data, I get a full complement of contrasts, see attached. doug
On 05/22/2013 01:43 PM, Tudor Popescu wrote:
> 1) In a design with group and gender as discrete factors and age > as a continuous factor, why is it that QDEC only displays the > contrast "Does the avg thickness, accounting for gender, differ > between group1 and group2?" and not also "..acounting for gender > and age,.."? > I thought that it would have. Are you coding age as a nuisance variable? Also, are you coding gender as a continuous variable? That is something you should not do. I was not coding age as a nuisance variable but as a continuous variable (co-variate). Gender was a discrete/fixed factor but I'm not sure whether this means 'continuous' in the sense discussed in your exchange with Arman. Anyway, in this configuration, it seems gender and age are not accounted (controlled) for at the same time. It should be. Can you send your qdec table?See attached
> 3) From the group tutorial, I see that mris_preproc has to be > called with flag "--cache-in ess.fwhm10thickn.fsaverage". However, > after running recon-all (including with the –qcache option) on all > my subjects, none of their folders contains a file named > ?h.thickness.fwhm10.fsaverage.mgh > Where does it say to use ess.fwhm10thickn.fsaverage? Sorry, typo. The flag is actually "--cache-in thickness.fwhm10.fsaverage", I file that I do not have after having run recon-all (including with the --qcache option) Try running recon-all again with just the --qcache flag.This is what I had done previously; the command was: recon-all -s C${i} -qcache where the ${i} was a counter in a script, to run the command on all my subjects
> 5) What is the difference between running make_average_subject and > running mris_preproc with --target fsaverage? > make average subject makes the average subject. mris_preproc samples the data into a common space defined by the registration surface and concatenates the input subjects into a single stack. But should the registration surface used by mris_preproc (i.e. its "--target" flag) come from the 'average' subject or from 'fsaverage'? In other words, which one of these becomes the study-specific template? You have to tell mris_preproc both the target and the surface registration to use if you want to use a different average subject.The command I used is:
mris_preproc --fsgd group_gender__age.fsgd --target average --hemi rh --meas thickness --out rh.thickness.mgh
So if I understand correctly, the fact that I didn't indicate a surface registration means that the surface from the "average" subject will be used, rather than the one from "fsaverage"? I still don't understand the difference between those two, and which, if any, can be referred to as the study-specific template.
B) All concatenated volumes from mris_preproc's output files (?h.thickness.mgh) appear blank in freeview, even though the individual structurals all look fine. Also, lh.thickness.mgh and rh.thickness.mgh have, surprisingly, *exactly* the same file size, which is also a bit small (~25MB) to be able to contain 38 registered structurals, which suggests something went wrong... These are surface overlay files, not volumes. You can't load surfaces as volumes in freeview.So assuming I don't visually inspect the surface overlays, can I assume that mris_preproc ran fine if lh.thickness.mgh and rh.thickness.mgh have exactly the same file size?
C) When running mri_surf2surf, I get an error saying that file /surf/lh.white cannot be opened. The 'average' folder produced after I ran make_average_subject does not contain a /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t find a log file from make_average_subject so i don’t know if it gave any errors.. It's extremely helpful to have command lines ...Sorry, my commands were: make_average_subject --subjects C01 C02 C03 C04 C05 C06 C07 C08 C09 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 M01 M02 M03 M04 M05 M06 M07 M08 M09 M10 M11 M12 M13 M14 M15 M16 M17 M18 M19 mri_surf2surf --hemi lh --s average --sval lh.thickness.mgh --fwhm 10 --tval lh.thickness.10.mgh _________________________
Could someone please explain how the following descriptions of a contrast are exactly linked: i) a contrast's namesake folder (including keywords 'Avg'/'Diff'/'X' and 'Intercept'/'Cor'; e.g. "lh-Diff-group1-group2-Cor-thickness-behaviouralMeasure"), ii) its phrasing in QDEC ("Does the thickness-age correlation differ between group1 and group2?"), iii) the assignment of values to each column of the design matrix, in the C.dat contrast vector (e.g. [0, 0, 1, -1])
(this is actually a bug report) After setting a different FDR threshold and pressing the "Set Using FDR" button, more often than not the results image doesn’t change accordingly. I noticed that the button only has an effect after moving around the QDEC window and/or waiting a minute or so
On 05/22/2013 01:43 PM, Tudor Popescu wrote:
> 1) In a design with group and gender as discrete factors and age > as a continuous factor, why is it that QDEC only displays the > contrast "Does the avg thickness, accounting for gender, differ > between group1 and group2?" and not also "..acounting for gender > and age,.."? > I thought that it would have. Are you coding age as a nuisance variable? Also, are you coding gender as a continuous variable? That is something you should not do. I was not coding age as a nuisance variable but as a continuous variable (co-variate). Gender was a discrete/fixed factor but I'm not sure whether this means 'continuous' in the sense discussed in your exchange with Arman. Anyway, in this configuration, it seems gender and age are not accounted (controlled) for at the same time. It should be. Can you send your qdec table?See attached
> 3) From the group tutorial, I see that mris_preproc has to be > called with flag "--cache-in ess.fwhm10thickn.fsaverage". However, > after running recon-all (including with the –qcache option) on all > my subjects, none of their folders contains a file named > ?h.thickness.fwhm10.fsaverage.mgh > Where does it say to use ess.fwhm10thickn.fsaverage? Sorry, typo. The flag is actually "--cache-in thickness.fwhm10.fsaverage", I file that I do not have after having run recon-all (including with the --qcache option) Try running recon-all again with just the --qcache flag.This is what I had done previously; the command was: recon-all -s C${i} -qcache where the ${i} was a counter in a script, to run the command on all my subjects
what files did it create? Please submit this as a separate question, too hard to follow with all this other stuff.
> 5) What is the difference between running make_average_subject and > running mris_preproc with --target fsaverage? > make average subject makes the average subject. mris_preproc samples the data into a common space defined by the registration surface and concatenates the input subjects into a single stack. But should the registration surface used by mris_preproc (i.e. its "--target" flag) come from the 'average' subject or from 'fsaverage'? In other words, which one of these becomes the study-specific template? You have to tell mris_preproc both the target and the surface registration to use if you want to use a different average subject.The command I used is:
mris_preproc --fsgd group_gender__age.fsgd --target average --hemi rh --meas thickness --out rh.thickness.mgh
So if I understand correctly, the fact that I didn't indicate a surface registration means that the surface from the "average" subject will be used, rather than the one from "fsaverage"? I still don't understand the difference between those two, and which, if any, can be referred to as the study-specific template.
If you want to use a different subject, you need to spec the surface registration for that subject and that subject as a target. If you only spec --target and the target is an average you have created with make_average_subject, then it is effectly the same as just using fsaverage because the registration to fsaverage is used.
B) All concatenated volumes from mris_preproc's output files (?h.thickness.mgh) appear blank in freeview, even though the individual structurals all look fine. Also, lh.thickness.mgh and rh.thickness.mgh have, surprisingly, *exactly* the same file size, which is also a bit small (~25MB) to be able to contain 38 registered structurals, which suggests something went wrong... These are surface overlay files, not volumes. You can't load surfaces as volumes in freeview.So assuming I don't visually inspect the surface overlays, can I assume that mris_preproc ran fine if lh.thickness.mgh and rh.thickness.mgh have exactly the same file size?
yes
C) When running mri_surf2surf, I get an error saying that file /surf/lh.white cannot be opened. The 'average' folder produced after I ran make_average_subject does not contain a /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t find a log file from make_average_subject so i don’t know if it gave any errors.. It's extremely helpful to have command lines ...Sorry, my commands were: make_average_subject --subjects C01 C02 C03 C04 C05 C06 C07 C08 C09 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 M01 M02 M03 M04 M05 M06 M07 M08 M09 M10 M11 M12 M13 M14 M15 M16 M17 M18 M19 mri_surf2surf --hemi lh --s average --sval lh.thickness.mgh --fwhm 10 --tval lh.thickness.10.mgh
It might be a version problem. You can create a symbolic link from lh.white_avg to lh.white
Could someone please explain how the following descriptions of a contrast are exactly linked: i) a contrast's namesake folder (including keywords 'Avg'/'Diff'/'X' and 'Intercept'/'Cor'; e.g. "lh-Diff-group1-group2-Cor-thickness-behaviouralMeasure"), ii) its phrasing in QDEC ("Does the thickness-age correlation differ between group1 and group2?"), iii) the assignment of values to each column of the design matrix, in the C.dat contrast vector (e.g. [0, 0, 1, -1])
(this is actually a bug report) After setting a different FDR threshold and pressing the "Set Using FDR" button, more often than not the results image doesn’t change accordingly. I noticed that the button only has an effect after moving around the QDEC window and/or waiting a minute or so
C) When running mri_surf2surf, I get an error saying that file/surf/lh.white cannot be opened. The 'average' folder produced after I ran make_average_subject does not contain a /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t find a log file from make_average_subject so i don’t know if it gave any errors.. It's extremely helpful to have command lines ...Sorry, my commands were: make_average_subject --subjects C01 C02 C03 C04 C05 C06 C07 C08 C09 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 M01 M02 M03 M04 M05 M06 M07 M08 M09 M10 M11 M12 M13 M14 M15 M16 M17 M18 M19 mri_surf2surf --hemi lh --s average --sval lh.thickness.mgh --fwhm 10 --tval lh.thickness.10.mgh
It might be a version problem. You can create a symbolic link from lh.white_avg to lh.white
Under fsaverage/surf there is both an lh.white and an lh.white_avg file, while under average/surf there's only lh.white_avg. I repeated the mri_surf2surf command above with "--s fsaverage" instead of "--s average" (since I understand in this case it's the same thing), and then it ran to completion.
Also, it's not clear from the wiki what flag should an ROI's label/mask be specified into mri_surf2surf with, prior to a ROI analysis. The --cortex flag seems to always be required anyway, and --sval seems to be design-related ("--sval lh.gender_age.thickness.00.mgh" in the group tutorial)! Should the same flag then also be used to specify the ROI in mri_glmfit, the command that follows mri_surf2surf?
Thanks!
On 06/05/2013 11:49 AM, Tudor Popescu wrote:
C) When running mri_surf2surf, I get an error saying that file /surf/lh.white cannot be opened. The 'average' folder produced after I ran make_average_subject does not contain a /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t find a log file from make_average_subject so i don’t know if it gave any errors.. It's extremely helpful to have command lines ... Sorry, my commands were: make_average_subject --subjects C01 C02 C03 C04 C05 C06 C07 C08 C09 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 M01 M02 M03 M04 M05 M06 M07 M08 M09 M10 M11 M12 M13 M14 M15 M16 M17 M18 M19 mri_surf2surf --hemi lh --s average --sval lh.thickness.mgh --fwhm 10 --tval lh.thickness.10.mgh It might be a version problem. You can create a symbolic link from lh.white_avg to lh.whiteUnder fsaverage/surf there is both an lh.white and an lh.white_avg file, while under average/surf there's only lh.white_avg. I repeated the mri_surf2surf command above with "--s fsaverage" instead of "--s average" (since I understand in this case it's the same thing), and then it ran to completion.
It should be close but probably not exact.
Also, it's not clear from the wiki what flag should an ROI's label/mask be specified into mri_surf2surf with, prior to a ROI analysis. The --cortex flag seems to always be required anyway, and --sval seems to be design-related ("--sval lh.gender_age.thickness.00.mgh" in the group tutorial)! Should the same flag then also be used to specify the ROI in mri_glmfit, the command that follows mri_surf2surf?
Look at the mri_surf2surf --help doug
Thanks!
freesurfer@nmr.mgh.harvard.edu
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Arman Eshaghi -
Douglas N Greve -
Tudor Popescu