Yongxia

On Wednesday, May 22, 2013, wrote:

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Today's Topics:

1. recon-all error (Yizhou Ma)
2. Re: Still confused by group analysis.. (Tudor Popescu)
3. Re: ERROR in long_mris_slope (Martin Reuter)
4. Re: ERROR in long_mris_slope (Martin Reuter)
5. temporal lobe left out in pial surface - edits on
brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma)
6. Re: temporal lobe left out in pial surface - edits on
brainmask.mgz or brain.finalsurfs.mgz? (Chris Watson)
7. Re: temporal lobe left out in pial surface - edits on
brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma)
8. Re: temporal lobe left out in pial surface - edits on
brainmask.mgz or brain.finalsurfs.mgz? (Bruce Fischl)
9. Re: temporal lobe left out in pial surface - edits on
brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma)
10. Re: temporal lobe left out in pial surface - edits on
brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma)
11. Re: ERROR: recon-all -subcortseg (Akio Yamamoto)

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Message: 1
Date: Wed, 22 May 2013 13:19:35 -0400
From: Yizhou Ma <ym850@nyu.edu>
Subject: [Freesurfer] recon-all error
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAHqJiV6t-fKQRWcfFg8r5O9gJrtZsTe+ZgKU0qVD2J7aoNSVHw@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear FS experts,

I have a recon-all error regarding one of my subjects. The scan suffers
from weakened signals at the lower part of the brain. Skullstrip stripped
most of the cerebellum at first, and we fixed it manually. After running
recon-all for the first time, large portions of the temporal lobes were
left out of the brain. Knowing that this may not be the correct way, we
still tried to fixed that by adding lots of control points. The second run
of recon-all, then, came back with the following error message:"

Loading source data
Reading curvature file
/space/mdeh3/3/halgdev/projects/nyuproj/subjects/sub4422b/surf/rh.thickness
ERROR: number of vertices in
/space/mdeh3/3/halgdev/projects/nyuproj/subjects/sub4422b/surf/rh.thickness
does not match surface (192226,134773)
ERROR: reading curvature file
Linux mmil-compute-1-11.local 2.6.18-308.16.1.el5 #1 SMP Tue Oct 2 22:01:43
EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub4422b exited with ERRORS at Mon May 20
"

Any ideas for why it is, or how we can fix the problem at the temporal
lobes, will be really appreciated.

Thanks,
Cherry
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Message: 2
Date: Wed, 22 May 2013 18:43:33 +0100
From: Tudor Popescu <tudor3@gmail.com>
Subject: Re: [Freesurfer] Still confused by group analysis..
To: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Cc: free surfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAGBir427LRNUP1ff3CEgstVq0B=DTrZJHmKOqKqF0oHbOCLiWQ@mail.gmail.com>
Content-Type: text/plain; charset="windows-1252"

> > 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
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Message: 3
Date: Wed, 22 May 2013 14:08:44 -0400
From: Martin Reuter <mreuter@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ERROR in long_mris_slope
To: Catherine Bois <C.Bois@sms.ed.ac.uk>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID: <519D09AC.7050408@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Cathy,

it must be something else (I think). The mris_calc command looks weird
("--label " looks like the label is not passed, but a space instead, it
then thinks 'mul' is a file).

qdecfinal is your qdec table? Make sure it contains only spaces to
separate the fields. It should have at least these columns
fsid fsid-base time

also in your command below, why are there "?" before do-label and time?

Unless you want to use the stack (within subject stack of thickness
values), I would drop the --do-stack (maybe also drop do-avg or whatever
else you don't need).

For debugging, I would create a directory, place a single subject there,
create a new qdec table with only that subject and try again there. If
it still happens , let me know.

Best, Martin

On 05/20/2013 10:25 AM, Catherine Bois wrote:
> Dear Freesurfer experts,
>
> I am trying to conduct the long_mris_slopes --qdec qdecfinal --meas
> thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack
> ?do-label ?time time --qcache fsaverage command for my longitudinal
> processing. However I keep getting the error message:
>
> mris_calc -o /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh
> --label /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh mul 100
>
>
> mris_calc:
> Sorry, but I seem to have encountered an error.
> While accessing file 'mul',
>
> I read online that this was due to a bug encountered in version 5.1,
> however I recently upgraded to version 5.3 and the error message
> persists. As my Long and base runs have been done in version 5.1
> still, I was wondering whether in order to fix this problem the long
> and base runs need to be rerun with version 5.3, or whether the error
> I am encountering has another solution/ is caused by another problem
> entirely?
>
> Thank you for your help,
>
> Best Wishes,
>
> Cathy
>

--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
mreuter@nmr.mgh.harvard.edu
reuter@mit.edu
Web : http://reuter.mit.edu

------------------------------

Message: 4
Date: Wed, 22 May 2013 14:33:08 -0400
From: Martin Reuter <mreuter@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ERROR in long_mris_slope
To: Catherine Bois <C.Bois@sms.ed.ac.uk>,
"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <519D0F64.2080309@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Cathy,

I think the problem is when there are tabs AND spaces. Only spaces
should also work. I can write some code (when I have time) that checks
these things, maybe for the next release.

Best, Martin

On 05/22/2013 02:21 PM, Catherine Bois wrote:
> Hi,
>
> Thank you for your reply. I finally got it working today.thanks for
> your help=)! You say the qdec table should have only spaces; however
> they only seem to work when they are completely tab separated and not
> a single space? If there is accidently a space it will suddenly not
> work. Is there a way that can solve this problem that you can think
> of? It is very time consuming because suddenly it will jsut stop
> working and I need to start from scratch!
>
>
> Quoting Martin Reuter <mreuter@nmr.mgh.harvard.edu> on Wed, 22 May
> 2013 14:08:44 -0400:
>
>> Hi Cathy,
>>
>> it must be something else (I think). The mris_calc command looks
>> weird ("--label " looks like the label is not passed, but a space