Re: [Freesurfer] matrix ill-conditioned....

Hi Doug and FreeSurfer Community,

For a cortical thickness analysis, we are interested in the age-x-group interaction. We want to know if the age slope for our pathological group is different than the control group. Do we need to demean age before creating the FSGD file? I was looking at the example: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V#Contrast2group-x-age.mtx

This makes it look like the FSGD does *not* need to be demeaned before examining the interaction. But Doug's email below says, "In general, you should not need to demean. For the interaction, you need to demean before computing the interaction."

Do we need to subtract the mean from each age value in the FSGD file before running mri_glmfit?

Thanks, -Kayle

On Aug 28, 2013, at 11:39 AM, freesurfer-request@nmr.mgh.harvard.edu wrote:

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Today's Topics:

1. Re: Talairach Failure Detection (Bruce Fischl)
2. Re: Recon-all error (Douglas N Greve)
3. pial surface editing (Francesco Siciliano)
4. Re: Talairach Failure Detection (pablo najt)
5. Re: matrix ill-conditioned.... (Douglas N Greve)
6. Re: Talairach Failure Detection (Bruce Fischl)
7. Re: pb reading .annot in matlab/python (Douglas N Greve)
8. Re: Recon-all error (pfotiad@nmr.mgh.harvard.edu)
9. Re: Recon-all error (Douglas N Greve)
10. Re: Recon-all error (pfotiad@nmr.mgh.harvard.edu)
11. Re: Recon-all error (Douglas N Greve)
12. Re: Talairach Failure Detection (pablo najt)
13. Re: Recon-all error (pfotiad@nmr.mgh.harvard.edu)
14. Re: Talairach Failure Detection (pablo najt)
15. Re: pb reading .annot in matlab/python (Alexandre Gramfort)
16. Re: Recon-all error (Douglas N Greve)
17. Re: Talairach Failure Detection (Bruce Fischl)
18. Re: pb reading .annot in matlab/python (Douglas N Greve)
19. Re: pb reading .annot in matlab/python (Alexandre Gramfort)
20. tutorial subject not found (leila nasehy)
21. Otto: update freesurfer to latest version? (Otto Muzik)
22. Re: Freesurfer dependencies (ye tian)
23. apply a label to an overlay in tksurfer (Sarah Madsen)
24. Re: apply a label to an overlay in tksurfer (Douglas Greve)
25. recon-all issue (CSF seg as gray matter) (Alexandre Gramfort)
26. Re: matrix ill-conditioned.... (Jacobs H (NP))
27. Thickness vertex by vertex (Giusy Chinnici)
28. Re: recon-all issue (CSF seg as gray matter) (Bruce Fischl)
29. Re: Thickness vertex by vertex (Bruce Fischl)
30. Re: Thickness vertex by vertex (Avram Holmes)
31. recon-all: 'segmentation fault' (Mark Plantz)
32. Re: matrix ill-conditioned.... (Douglas N Greve)
33. Longitudinal Processing Pipeline (David Tate)
34. Re: Error message of Ubuntu 13.04 and Centos4 & Centos6 (Z K)
35. Re: Thickness vertex by vertex (Giusy Chinnici)

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Message: 1 Date: Tue, 27 Aug 2013 12:08:22 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection To: pablo najt pablonajt@hotmail.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1308271207330.13629@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-15"

Hi Pablo

have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly

cheers Bruce

On Tue, 27 Aug 2013, pablo najt wrote:

...

Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8.?

I would greatly appreciate if you could advise me which step/s should I take to correct this. Thank you for your attention, Pablo

Error:--------------------------------------------------------------------------------------------------------------------------------

#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 /Users/pablonajt/subjects/tr5713/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun ?7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386

recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013

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Message: 2 Date: Tue, 27 Aug 2013 12:11:31 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all error To: freesurfer@nmr.mgh.harvard.edu Message-ID: 521CCFB3.2030909@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed

try this instead

recon-all -all -subjid CAA_022_struc

On 08/27/2013 11:23 AM, pfotiad@nmr.mgh.harvard.edu wrote:

...

Hi FS Commuity,

I am using the stable version 5.3 of FS to recon-all a subject of mine, but the job is aborted and gives the following message:

The command that I ran is: recon-all -all -subjid /cluster/ichresearch/Petechial/MEG/CAA_022_struc

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 INFO: SUBJECTS_DIR is /autofs/cluster/ichresearch/Petechial/MEG Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 Linux eesmith 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Tue Aug 27 11:09:19 EDT 2013 Found 2 runs /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/001.mgz /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... if: Expression Syntax. Exit 1

Also, I tried doing the same recon-all with the stable 5.0 version and it runs fine. Therefore, I was wondering whether you could tell me why is this happening. By the way I have also attached the recon-all.log.

Thank you for your time.

Best, Panos

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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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Message: 3 Date: Tue, 27 Aug 2013 16:13:38 +0000 From: Francesco Siciliano sicilia@nyspi.columbia.edu Subject: [Freesurfer] pial surface editing To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 72EB4D9B5160FC45BCD75ED55E1C8159249D9945@NYSPIDAG01.nyspi.local Content-Type: text/plain; charset="iso-8859-1"

Hello,

I am having a few issues with editing the pial surface in freeview. It appears as though the edits I make to the brainmask are not being taken into account when I re-run recon-all. I work on a MacBook Pro and have been using "shift+click" to delete voxels at a brush value of 1 and then saving the brainmask.mgz back into the mri folder. When making edits to the brainmask I have the brainmask highlighted. Upon clicking save, the mri folder contains both brainmask.mgz and brainmask.mgz~ (The version with a ~ seems to indicate the older version of the file based on modification time).

Additionally, the edits that I make to brain.finalsurfs.manedit.mgz for pial surface that has extended into the cerebellum seems to not be taken into account when I re-run recon-all. I have been making a copy of brain.finalsurfs.mgz, pasting it into the mri folder, and renaming it brain.finalsurfs.manedit.mgz. I then load this volume and make edits to it according to the same specifications as the brainmask.mgz. Shouldn't I be able to see changes made to the pial surface in the brainmask.mgz from edits I make to the brain.finalsurfs.manedit.mgz after running recon-all? Neither the brainmask.mgz nor the brain.finalsurfs.mgz take into account the edits I've made on brain.finalsurfs.manedit.mgz. I'm not sure if I'm deleting voxels incorrectly or saving incorrectly. I've tried to troubleshoot several times and keep encountering similar issues.

The version of FreeSurfer that I am working from is: freesurfer-i686-apple-darwin9.8.0-stable5-20110525 My editing interface looks slightly different from the current version explained on the freesurfer wiki. I do not have an option to select recon-editing. Adding control points, however, has been successful. I have been using the command recon-all -autorecon2 -autorecon3 -s subj001

Any help getting to the bottom of this would be greatly appreciated!

Thanks,

Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155