Re: [Freesurfer] Still confused by group analysis..

[Douglas Greve]

On 6/12/13 7:03 AM, Tudor Popescu wrote:


Sorry Doug, wasn't sure whether you'd seen my last reply to this..

On 6 Jun 2013 21:37, "Tudor Popescu" > wrote:


Thanks Doug,



So if I want to use the study-specific "average" subject
surface with mri_surf2surf, rather than the generic
"fsaverage" one, how can this be done given that the
required ls.white file only exists in the latter but not
in the former? Can I just rename (or duplicate) ls.white
into ls.white_avg?

You can copy it or create a symbolic link.

So it is OK to copy the required lh.white file from the generic
average subject "fsaverage" and apply mri_surf2surf upon the
study-specific average subject ("average")? It still seems to me
that "average" should have its own (different) lh.white...


Yes it should. Did make_average_subject not create it?




Shouldn't the input to mri_glmfit be the output of
mri_surf2surf? In the group tutorial, the former is
"lh.gender_age.thickness.10.mgh" while the latter is
"lh.gender_age.thickness.10B.mgh". Or should it just be
the unsmoothed output of mris_preproc?

Yes, I can't remember why I put the "B" there, maybe to keep
people from overwriting  lh.gender_age.thickness.10.mgh during
the tutorial and having to wait the 10min or so for it to get
recreated.

But if all these commands transform the same file (output of
mris_preproc becomes input of mri_surf2surf, which then feeds into
mri_glmfit), then why is it still necessary to keep intact the
original lh.gender_age.thickness.10.mgh, when all you need for the
group analysis is the mri_surf2surf'd version?


Sorry, I'm lost here. What are the names of the files?




Assuming the label files (corresponding to my ROI, and
extracted from the Destrieux atlas) are different for each
subject, and given mri_glmfit is called just once, for all
subjects, which label file (corresponding to what subject)
should I point it to?

You need to create the label in the average subject. There is
a Destrieux atlas there.

Again, by "average subject" do you mean here the generic one
(fsaverage) or the study-specific one (average)? Should the former
be used at any point of a group analysis, if the latter exists?

If you are doing your group analysis on a custom average, then do not 
use fsaverage at any point.

doug



___
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.

Re: [Freesurfer] Still confused by group analysis..

[Tudor Popescu]

Thanks Doug,



 So if I want to use the study-specific average subject surface with
 mri_surf2surf, rather than the generic fsaverage one, how can this be
 done given that the required ls.white file only exists in the latter but
 not in the former? Can I just rename (or duplicate) ls.white into
 ls.white_avg?

  You can copy it or create a symbolic link.

So it is OK to copy the required lh.white file from the generic average
subject fsaverage and apply mri_surf2surf upon the study-specific average
subject (average)? It still seems to me that average should have its
own (different) lh.white...




 Shouldn't the input to mri_glmfit be the output of mri_surf2surf? In the
 group tutorial, the former is lh.gender_age.thickness.10.**mgh while
 the latter is lh.gender_age.thickness.10B.**mgh. Or should it just be
 the unsmoothed output of mris_preproc?

  Yes, I can't remember why I put the B there, maybe to keep people from
 overwriting  lh.gender_age.thickness.10.mgh during the tutorial and having
 to wait the 10min or so for it to get recreated.

But if all these commands transform the same file (output of mris_preproc
becomes input of mri_surf2surf, which then feeds into mri_glmfit), then why
is it still necessary to keep intact the original
lh.gender_age.thickness.10.mgh, when all you need for the group analysis is
the mri_surf2surf'd version?




 Assuming the label files (corresponding to my ROI, and extracted from the
 Destrieux atlas) are different for each subject, and given mri_glmfit is
 called just once, for all subjects, which label file (corresponding to what
 subject) should I point it to?

  You need to create the label in the average subject. There is a
 Destrieux atlas there.

Again, by average subject do you mean here the generic one (fsaverage) or
the study-specific one (average)? Should the former be used at any point of
a group analysis, if the latter exists?
___
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.

Re: [Freesurfer] Still confused by group analysis..

[Tudor Popescu]

 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!
___
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.

Re: [Freesurfer] Still confused by group analysis..

[Douglas N Greve]

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:
 

Re: [Freesurfer] Still confused by group analysis..

[Douglas N Greve]

Sorry, that read gender and age. The contrast takes age into account, it 
is just a problem with the code that generates the sentence.
Have not had a chance to answer the others, I thought I'd try to get one 
wrapped up. It looks like you added a few more questions at the end. 
Unless they are closely related to the previous questions, can you send 
them separately, it is hard to keep track with all the replies to replies.
doug




On 05/23/2013 02:51 PM, Tudor Popescu wrote:
 Thanks Doug, however my question was why does QDEC not also display a 
 contrast to the effect of Does the avg thickness, accounting for 
 *gender and age*, differ between group1 and group2?, instead it only 
 displays Does the avg thickness, accounting for *gender*, differ 
 between group1 and group2?

 Also, I was wondering whether you got a chance to see my other 
 questions from the same email..

 Many thanks!
 Tudor

 On 23 May 2013 17:49, Douglas N Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:

 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 

Re: [Freesurfer] Still confused by group analysis..

[Tudor Popescu]

  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 

Re: [Freesurfer] Still confused by group analysis..

[Douglas N Greve]

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 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?
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!

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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 

Re: [Freesurfer] Still confused by group analysis..

[Tudor Popescu]

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 tud...@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,..?

 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

___
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.

Re: [Freesurfer] Still confused by group analysis..

[Douglas N Greve]

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 tud...@gmail.com 
 mailto:tud...@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

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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.

Re: [Freesurfer] Still confused by group analysis..

[Arman Eshaghi]

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
 gr...@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.
 


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Still confused by group analysis..

[Douglas N Greve]

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
 gr...@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
gr...@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

Re: [Freesurfer] Still confused by group analysis..

[Tudor Popescu]

  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.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)


  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!
___
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.