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Today's Topics:
1. Control points and errors (Herting, Megan)
2. Re: 3rd level surface analysis of fMRI data (Douglas N Greve)
3. Re: In Qdec, what does the 'area' mean within 'Measure' menu
in 'Design' tab (Jeff Sadino)
4. Re: problem with tksurfer (Douglas N Greve)
5. Re: In Qdec, what does the 'area' mean within 'Measure' menu
in 'Design' tab (Douglas N Greve)
6. Re: Surface statistics for PET (Douglas N Greve)
7. Re: mri_segstats error (Douglas N Greve)
8. Re: qdec analyses without interaction effect (Douglas N Greve)
9. tracula trac-all error malloc_error_break (Cat Chong)
10. Re: creating labels, new atlas (Bruce Fischl)
11. Re: creating a gca file from .mgz files (Bruce Fischl)
12. Re: Control points and errors (Bruce Fischl)
----------------------------------------------------------------------
Message: 1
Date: Fri, 24 Aug 2012 18:45:54 +0000
From: "Herting, Megan" <mherting@chla.usc.edu>
Subject: [Freesurfer] Control points and errors
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<7C6AFE602753B44C84DC09C4D69F17B6A41058@CHLAEXMBH01.LA.AD.CHLA.ORG>
Content-Type: text/plain; charset="us-ascii"
Hi,
I have been using freesurfer on a large dataset and I am having some trouble.
Sometimes the temporal lobes are not fully covered, so I will go back to add a
few control points based on the recommendations of freesurfer (voxels that are
<110 and not next to a gray matter voxel) and send it through again. This will
often correct the previous error, but then ends up creating new errors in a
different region (frontal lobe, temporal lobe in the other hemisphere) etc. This
has happened on a large fraction of my data (~25%). What is recommended to fix
this? Should I continue to try to add cp to these new regions and send it
through again, and continue to do this until it looks good? Is there another
method?
Thank you!
Megan
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Message: 2
Date: Fri, 24 Aug 2012 18:16:30 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] 3rd level surface analysis of fMRI data
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5037FD3E.6080707@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
Hi Susan, sorry for the delay. If you want to use a random fx model,
then dont include any of the ffx options, so just
/mri_glmfit --y xrun/lh.cope1.mgh --osgm --glmdir xrun/lh.osgm.ffx
--surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label/
doug
On 08/22/2012 07:21 PM, Susan Alice McLaughlin wrote:
> Hi,
>
> I?m a Freesurfer novice, and am confused about how to run a 3rd level
> cross-subject analysis on the surface using as input cross-run .gfeats
> from 10 subjects generated from a 2nd level analysis of fMRI data in FSL.
>
> Following the directions posted at
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat, I
> have sampled the .gfeat copes and varcopes into standard surface
> space, using /mris_preproc/.
>
> I would then go on to perform a 3rd level surface based analysis as
> the instructions suggest, using:
>
> /mri_glmfit --y xrun/lh.cope1.mgh --yffxvar xrun/lh.varcope1.mgh
> --ffxdof 163 --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh
> --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label/
>
> However, I want to use a random effects rather than fixed effects
> analysis. How do I do this? I tried /--yrfxvar/ as opposed to
> /--yffxvar/ but it didn?t work. And if I?m going to display the map
> resulting from this analysi! s, do I need to correct for multiple
> comparisons?
>
> Many thanks in advance,
>
> Susan McLaughlin
> Doctoral Candidate
> SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex)
> Dept. of Speech and Hearing Sciences
> University of Washington
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
------------------------------
Message: 3
Date: Fri, 24 Aug 2012 12:17:43 -1000
From: Jeff Sadino <jsadino.queens@gmail.com>
Subject: Re: [Freesurfer] In Qdec, what does the 'area' mean within
'Measure' menu in 'Design' tab
To: freesurfer@nmr.mgh.harvard.edu
Cc: Shannon Kogachi <skogachi@gmail.com>, dhaglerjr@hotmail.com, Eric
Cunningham <erictcunningham@gmail.com>
Message-ID:
<CAAK1NkeBnCZwSxocRNJxqGtQE=w+KgX3xks43y8WUqBA0E6dPA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hello FreeSurfers,
I am following up on a previous question by another poster:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21700.html
In here, Doug says that the mris_preproc script was patched to help with
mapping the surface area to a common space, but Doug also hints that it
might also help with the volume. I am using FreeSurfer 5.0.0, mris_preproc
release date 10-13-09, Revision 1.53. If I want to do a qdec analysis in
fsaverage space on just the thickness and volume, can I go ahead with files
previously created using my current mris_preproc, or do I need to download
the updated one at
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc?
We also have some people using FreeSurfer 5.1.0, mris_preproc release date
5-17-11, Revision 1.59.2.1. Do they need to update their mris_preproc
script?
Thank you very much,
Jeff Sadino
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Message: 4
Date: Fri, 24 Aug 2012 18:19:40 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] problem with tksurfer
To: Maryam Vaziri Pashkam <mvaziri@fas.harvard.edu>
Cc: freesurfer maillist <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5037FDFC.8090002@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Maryam, it seems very strange that one hemisphere looks ok but other
looks bad. In fact, I'd say that it cannot happen. The differences are
not likely to be due to version. Can you double check that the tksurfer
commands for the lh and rh are the same (except for lh and rh, of course)
doug
On 08/22/2012 09:13 PM, Maryam Vaziri Pashkam wrote:
> Hi Doug,
>
> I am having a problem with tksurfer overlay function. I ran one
> analysis in freesurfer 5.1 on a mac machine and I cannot properly load
> it on the surface. The analysis was performed in the native space.
> When I use tksurfer to load the analysis on the surface using the
> overlay function I dont get an error but the output image just shows
> small dots on the surface instead of patches of activity. It looks
> like the registration is not correct. I checked the registration on
> the volume and it looks fine to me. This only happens with one of my
> subject and only on his left hemisphere. I have attached two tif
> images called lhnative.tif and rhnative.tif that show the results. I
> also ran the analysis on the surface for both left and right
> hemisphere, and it looks fine (lhsurf.tif and rhsurf.tif files attached).
> Any Idea how to solve this problem? My guess is that the error is in
> the registration of anatomical volume to anatomical surface in the
> left hemisphere of this specific subject, but I dont know how to solve
> this issue.
>
> here is the code that I use to load the data on the surface:
>
> tksurfer teal_tiger_kcb lh inflated -curv -overlay
> /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz
> -overlay-reg
> /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat
> -scalebarflag 1
>
> Just a note that the recon-all was performed in freesurfer 4.5 and the
> analysis on freesurfer 5.1. Any chance this might have caused the error?
>
> Thanks,
> Maryam
--
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
------------------------------
Message: 5
Date: Fri, 24 Aug 2012 18:55:21 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] In Qdec, what does the 'area' mean within
'Measure' menu in 'Design' tab
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <50380659.1010202@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
You'll need the new script for both.
doug
On 08/24/2012 06:17 PM, Jeff Sadino wrote:
> Hello FreeSurfers,
>
> I am following up on a previous question by another poster:
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21700.html
>
> In here, Doug says that the mris_preproc script was patched to help
> with mapping the surface area to a common space, but Doug also hints
> that it might also help with the volume. I am using FreeSurfer 5.0.0,
> mris_preproc release date 10-13-09, Revision 1.53. If I want to do a
> qdec analysis in fsaverage space on just the thickness and volume, can
> I go ahead with files previously created using my current
> mris_preproc, or do I need to download the updated one at
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc?
>
> We also have some people using FreeSurfer 5.1.0, mris_preproc release
> date 5-17-11, Revision 1.59.2.1. Do they need to update their
> mris_preproc script?
>
> Thank you very much,
> Jeff Sadino
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
------------------------------
Message: 6
Date: Fri, 24 Aug 2012 18:57:55 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Surface statistics for PET
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <503806F3.50807@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
You can use mri_segstats for this, something like
mri_segstats --annot subject lh aparc --i lh.pet.mgh --sum sum.dat
where lh.pet.mgh is the surface-sampled pet
BTW, unless you need a .w for something, use a .mgh file (the .w is
becoming obsolete).
doug
On 08/23/2012 07:27 PM, Daniel Tarquinio wrote:
> I would like to calculate average PET intensities for specific labels
> (using the aparc.annot label files).
>
> I have coregistered and used mri_vol2surf to assign PET values to the
> FS generated surface, and viewed the results using qsurfer.
>
> The next step is to take the values from the .w files and calculate
> label-specific stats. I've tried mris_anatomical_stats but I don't
> think this is the right command.
>
> Any advice?
>
> Thank you in advance,
> Daniel
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
------------------------------
Message: 7
Date: Fri, 24 Aug 2012 19:01:44 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_segstats error
To: Natalie Han <zhan1@stanford.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID: <503807D8.8030607@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
The ICV will not change because that depends on the talairach transform.
mri_segstats just reads in the transform that is there and computes the
ICV (note that this is an *estimated* ICV, it is not derived by counting
voxels). There have been several bugs with mri_segstats that are
difficult to explain. Most of them have to do with making small
adjustments to the various brain volume measurements (not ICV), and
there was a fix to the partial volume correction too. The new version
will change all of the measurements (except ICV).
doug
On 08/23/2012 08:31 PM, Natalie Han wrote:
> Hi, Doug and all, I wonder if the new version of mri_segstats on the ftp site
> will change both the ICV and the SupraTentorial volume? Nick seems to
> mention ICV will be different, the ReleaseNotes says the
> SupraTentorial Volume will be changed to smaller. Can you explain more
> on the difference of the new version with the original version in
> FS.5.1.0? Is everything on the morphometry stats website still the
> same? http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats. I'm
> interested in several measurements, including the ICV, and the
> SupraTentorial Volume and all the structures volume, just wondering if
> the new version will change all the measurements.
>
> Thanks.
> -Natalie
>
> On Wed, Aug 22, 2012 at 8:57 AM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu> wrote:
>> yes, this is a fix that will be in the next release. The new results are
>> more accurate.
>> doug
>>
>> On 08/22/2012 11:54 AM, Blazey, Tyler wrote:
>>> Hi Doug,
>>>
>>> Thanks for the quickly reply. The new version of mri_segstats works fine. I
noticed after running it though that all the volumes are slightly different than
those reported by previous version. I think it might have something to do with
the partial volume correction, as the results are the same when I do not use the
--pv flag. Is this expected behavior? And if so, is the new version more
accurate?
>>>
>>> Thanks again,
>>>
>>> -Tyler
>>>
>>>
>>>
>>> ________________________________
>>>
>>> The material in this message is private and may contain Protected Healthcare
Information (PHI). If you are not the intended recipient, be advised that any
unauthorized use, disclosure, copying or the taking of any action in reliance on
the contents of this information is strictly prohibited. If you have received
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>> _______________________________________________
>> 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
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
------------------------------
Message: 8
Date: Fri, 24 Aug 2012 19:05:12 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] qdec analyses without interaction effect
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <503808A8.1060506@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Shannon, you can use the DOSS (different offset/same slope) instead
of DODS
doug
On 08/20/2012 03:47 PM, Shannon Kogachi wrote:
> Hi,
> I was wondering if there is a way to run statistical tests, such as
> a 2-way ANCOVA, on QDEC but without the interaction effect. I ran a
> 2-way ANCOVA for thickness measures for a longitudinal study, and no
> interaction effect was found. Therefore, I would like to run the same
> test but without the interaction effect and see if there are other
> group effects. Please let me know if there is a way to do this in QDEC
> or any other statistical programs in FreeSurfer. Thank you!
>
>
> -Shannon
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
------------------------------
Message: 9
Date: Fri, 24 Aug 2012 16:35:15 -0700 (PDT)
From: Cat Chong <cavecreekcutter@yahoo.com>
Subject: [Freesurfer] tracula trac-all error malloc_error_break
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<1345851315.34874.YahooMailNeo@web140801.mail.bf1.yahoo.com>
Content-Type: text/plain; charset="us-ascii"
Hello Experts,
I get the following error when running trac-all:
*** set a breakpoint in malloc_error_break to debug
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 13th slice
I am using the update for trac-all that was recommended, but it still isn't
working.
I would be grateful for any suggestions.
cheers,
cat
below is the trac-all log:
Loading cortex mask from /Applications/freesurfer//trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz
dmri_train(78737) malloc: *** mmap(size=159744) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 13th slice
Cannot allocate memory
Darwin fmris-Mac-Pro-2.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29
15:16:10 PST 2011; root:xnu-1504.9.37~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Fri Aug 24 15:37:39 MST 2012
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Message: 10
Date: Sat, 25 Aug 2012 11:08:02 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] creating labels, new atlas
To: Jeff Thompson <jeff_rthompson@hotmail.com>
Cc: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.00.1208251107400.10596@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
Hi Jeff
yes, that's true, but for a GCA you will need to combine the different
labels into a single .mgz volume to give to mri_ca_train.
cheers
Bruce
On Thu, 23 Aug
2012, Jeff Thompson wrote:
> I found this info on the tksurfer webpage.?
>
> The label file format is interchangable with?TkMedit. You can create a label
> in?TkSurfer, save it, and load it in?TkMedit, or vice versa.
>
>
>
> Jeff Thompson
>
>
>
> ____________________________________________________________________________
> From: jeff_rthompson@hotmail.com
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: creating labels, new atlas
> Date: Thu, 23 Aug 2012 10:48:46 -0300
>
> Hello,
> How can tksurfer be used to create label files for the purpose of making a
> new atlas, if that atlas is needed to create the surface files needed to
> view the brain in tksurfer? Would people use FSL to create the masks, and
> convert them into what is needed for freesurfer or is there another way?
>
> Thank you,
>
> Jeff Thompson
>
>
>
>
------------------------------
Message: 11
Date: Sat, 25 Aug 2012 11:11:46 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] creating a gca file from .mgz files
To: Jeff Thompson <jeff_rthompson@hotmail.com>
Cc: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.00.1208251108200.10596@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
Hi Jeff
it's more complicated than that. You need a .mgz volume for every subject
you want to train on that contains the labels, and an accompanying
intensity volume (we usually use the norm.mgz for this purpose). Then we
extract statistics to create the .gca across these subjects using
mri_ca_train
cheers
Bruce
On Thu, 23
Aug 2012, Jeff Thompson wrote:
> >From the gcaFormat freesurfer wiki page I know that:?The .gca file is
> composed of three volumes, which can be extracted like this:
>
> mri_convert atlas.gca -nth 0 means.mgz
> mri_convert atlas.gca -nth 1 labels.mgz
> mri_convert atlas.gca -nth 2 priors.mgz
>
> where:
>
> *
>
> means --> the mean intensity of the most likely label
>
> *
>
> labels --> indices of the most likely label at each voxel (indices refer
> to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt)
>
> *
>
> priors --> the probability that that label occurs at that voxel
>
>
> Is it possible to go the other way? I want to create the labels.mgz file and
> the others manually, and turn that into the .gca file with mri_convert.
>
> Can this be done?
>
> Thank you,
>
> Jeff Thompson
>
>
>
>
------------------------------
Message: 12
Date: Sat, 25 Aug 2012 11:29:15 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Control points and errors
To: "Herting, Megan" <mherting@chla.usc.edu>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.00.1208251128180.10596@gate.nmr.mgh.harvard.edu>
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Hi Megan
it's hard for us to diagnose without seeing the details. In general
though you have to be careful to make sure that you aren't putting control
points in partial volumed voxels. When you say it creates new errors, can
you give us some details? Is the wm too bright in those regions? What FS
version are you using?
cheers
Bruce
On Fri, 24 Aug 2012, Herting, Megan wrote:
> Hi,
>
> I have been using freesurfer on a large dataset and I am having some
> trouble. Sometimes the temporal lobes are not fully covered, so I will go
> back to add a few control points based on the recommendations of freesurfer
> (voxels that are <110 and not next to a gray matter voxel) and send it
> through again. This will often correct the previous error, but then ends up
> creating new errors in a different region (frontal lobe, temporal lobe in
> the other hemisphere) etc. This has happened on a large fraction of my data
> (~25%). What is recommended to fix this? Should I continue to ?try to add cp
> to these new regions and send it through again, and continue to do this
> until it looks good? Is there another method?
>
> Thank you!?
> Megan?
>
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End of Freesurfer Digest, Vol 102, Issue 27
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