Re: [Freesurfer] bbregister problems with PET data

[Adam Martersteck]

Thanks Martin and Doug,

I'll give both robust_register with robent and mri_coreg a try.

RE: Doug
The PET tracer is Avid's amyloid compound -- F18-florbetapir (aka amyvid,
aka AV45).
The asymmetric signal is a result of the population -- individuals with a
non-amnestic language dementia with underlying Alzheimer's pathology. I
realize the focal left lateralized atrophy could play a role in partial
voluming, next step is PVC.

Thanks again,
Adam

On Thu, Mar 31, 2016 at 12:13 PM, Douglas N Greve  wrote:

> btw, what tracer is this? And the asymmetry you are talking about is
> between the hemispheres? Is that typical for this tracer or is this a
> phenomena with this subject (or population)?
>
> On 03/30/2016 03:41 PM, Adam Martersteck wrote:
> > Hi Freesurfer team,
> >
> > I’m encountering a problem using bbregister on PET data:
> >
> > -- When I attempt to register a PET volume to T1-space the asymmetric
> > tracer uptake of the PET throws off proper registration. (Treating the
> > PET as a T1 because of the non-specific white matter uptake > grey
> > matter signal).
> >
> > -- You can really see the bbregister mis-registration in this gif
> > here: https://goo.gl/iM6yrT
> >
> > -- It (expectedly) attempts to find the best match between signal
> > intensities on both the left and right surfaces, but is inherently
> > biased by the asymmetric uptake shifts the entire volume to the right.
> >
> > -- Are there any suggestions for dealing with asymmetric scans like
> > this? Stick with just a simple FLIRT? It doesn't seem to do that great
> > a job for everyone.
> >
> > Cutting left and right hemispheres apart and register separately?
> >
> > Using Martin’s new robust register for multi-modal data? Any
> > suggestions on the parameters of ROBENT?
> >
> > Thanks,
> > Adam
> >
> >
> > ___
> > 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/
>
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>
>
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[Freesurfer] ERROR running mkcontrast

[Joseph Dien]

Hi, I ran into an odd problem which I was able to fix but wanted to let others 
know about.
This is OS X 10.11.4 with Matlab 2016a and FreeSurfer 5.3.

I got the following error when I ran mkcontrast using batch files that 
previously worked fine:

/private/var/folders/wt/vj5q34fs20x50sh_6rcrtkn8gn/T/Cleanup At 
Startup/sh.h4SI0w: No such file or directory.
ERROR running mkcontrast

Looking into the directories in question, I found that while there was no 
directory named 'Cleanup At Startup’ inside the T directory, there was such a 
directory inside ‘vj5q34fs20x50sh_6rcrtkn8gn’.  I’m guessing some version 
update changed the location of this directory.  I went into T and performed the 
following command:

mkdir 'Cleanup At Startup'

after doing so, everything worked again.

Cheers!

Joe



Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com
Cell Phone: 202-297-8117
http://joedien.com

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Re: [Freesurfer] Surface-based PET maps

[Douglas N Greve]

Are those maps corrected for multiple comparisons or uncorrected? If 
corrected, how similar are the uncorrected? When doing a correction, you 
can get clusters that are just above significance in one analysis and 
just below sig in the other making it look like there are huge 
differences. I've looked at a bunch of FDG data comparing spmregister 
and bbregister and not found a big difference. Having said that, I think 
that spmregister in general does a better job on smooth images. I wrote 
my own version (not reliant on matlab or spm) called mri_coreg, which 
you can get from here

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg



On 03/31/2016 02:44 PM, Alshikho, Mohamad J. wrote:
>
> Hi Doug,
>
> In order to run surface based analysis on PET maps, _I used the 
> following steps: _
>
> *_1. Co-registering SUVR to T1_*
>
> bbregister --s name --mov suvr.nii --bold --init-fsl --reg reg.dat --o 
> suvr_T1.mgh
>
> *_2. Concatenate SUVR maps_*
>
> mris_preproc --target fsaverage --hemi lh --iv 
> subject1/suvr/suvr_T1.mgh subject1/suvr/reg.dat  --iv 
> subject2/suvr/suvr_T1.mgh subject2/suvr/reg.dat --iv … --projfrac 0.5 
> --out lh.suvr.mgh
>
> *_3. Smoothing(sm)_*
>
> mri_surf2surf --hemi lh --s fsaverage --fwhm 10 --cortex --sval  
> lh.suvr.mgh --tval lh.suvr.sm10.mgh
>
> *_4.Group analysis (GLM)_*
>
> mri_glmfit--y lh.suvr.sm10.mgh --fsgd fsgd.txt --C X.mtx --surf  
> fsaverage lh --cortex --glmdir lh.suvr
>
> *_5. Correction for multiple comparisons ( Cluster –wise)_*
>
> mri_glmfit-sim --glmdir lh.suvr --cache 1.3 neg --cwp  0.05  --2spaces 
> # Cache 1.3 ( P<0.05)
>
> ·In a second analysis for the same set of data, I replaced the first 
> step ( co registration) by the following command line:
>
> spmregister --s name --mov suvr.nii --reg reg.dat --o suvr_T1.mgh
>
> I got the results as attached ( figure1 using bbregister and figure 2 
> using SPM register)
>
> Kindly,
>
> 1.Where this difference came from? In other words, should I expect 
> such like difference between “bbregister” and “spmregister” ?
>
> 2.For co registration which command do you recommend  “bbregister” or 
> “spmregister” ?
>
> Best,
>
> Mohamad
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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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
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[Freesurfer] Fwd: 5 year Post Doctoral Fellowship in South Korea - Korean Genome and Epidemiology Study

[Douglas N Greve]

FYI

 Original message 
From: "Thomas,Robert" 
Date: 03/30/2016 5:52 AM (GMT+05:30)
To: a...@nmr.mgh.harvard.edu
Cc: Chol Shin 
Subject: 5 year Post Doctoral Fellowship in South Korea - Korean Genome 
and Epidemiology Study

A 5-year Post-Doctoral Fellowship is available in South Korea, at the 
Korean Genome and Epidemiology Study, with the center at Ansan Hospital, 
about 45 minutes outside Seoul. Those with a PhD is the general area of 
neuroimaging are encouraged to apply.  The support is US $ 70,000/ year, 
with direct additional support for accommodation. The program is funded 
by the Korean Government. Agreeing to the full 5 years is necessary, no 
partial support is possible.

The KoGES has been in existence since 2001, and has biannual health 
exams. Rich demographic and cardiovascular information is collected, 
GWAS is available. Brain MRI (structural, DTI), sleep (including 
polysomnography) and detailed cognition evaluations were initiated in 
2008, and is now in the second cycle. The Fellowship will focus on the 
brain-sleep-heart interface, a major role for the Fellow will be 
oversight and aiding the analysis of MRI data, currently obtained at 1.5 
T but to move to 3T during the course of the award. High productivity 
will be expected, and evidence of prior first author publications will 
be desirable. The awardee will also work with investigators from Harvard 
(MGH Martinos Center, Beth Israel Deaconess Medical Center) and Boston 
University-Framingham Heart Study, and can be expected to have 
substantial freedom to pursue cutting edge analysis techniques in the 
neuroimaging and Big Data / “omics” realm.

Decisions will be made by the end of April. Prospective candidates will 
need to travel to Seoul for a meeting with Dr. Chol Shin, the Principal 
Investigator of KoGES, in April; travel costs are covered. Interested 
individuals should send their NIH style biosketch to Chol Shin, M.D. 
chol-s...@hanmail.net   and Robert Thomas, 
M.D. rthom...@bidmc.harvard.edu 




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Re: [Freesurfer] longitudinal pipeline surface error

[Mihaela Stefan]

Wow! I haven't thought about that but it's possible since we had a few
study coordinators along the way. So it could be the case that the study
coordinator didn't know the subject who came at follow-up. Hopefully it
will be just a DICOM mismatch. Will see how it goes.. :)

On Thu, Mar 31, 2016 at 10:38 AM, Martin Reuter  wrote:

> I have seen cases where annonymization messed up ID's and individual time
> points came from a different subject. That could mess things up quite bad.
> (Also if the person sends their sibling or friend, because they don't have
> time to come to the follow up themselves, has also happened - not to me
> though ).
>
> Best, Martin
>
>
> On 03/31/2016 10:21 AM, Mihaela Stefan wrote:
>
> Hi Martin,
>
> We ran this subject twice but we got the same error. The norm is not
> aligned. They almost look like two different brains. I double checked the
> exam numbers to make sure that these three exams belong to the same person.
> They indeed seem to belong to the same person but I will re-run recon cross
> from scratch for MRI3 just to make sure that I started with the right
> DICOMs. I will let you know how it worked.
>
> Thanks!
> Mihaela
>
> On Wed, Mar 30, 2016 at 4:12 PM, Martin Reuter <
> mreu...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Mihaela,
>>
>> does the cross sectional run of that time point, and the base look OK?
>> Also check if this time point is aligned correctly to the base (e.g. open
>> norm.mgz from the long and the base, they should be aligned).  If all this
>> is OK, then I would recommend to re-run this long run again, but make sure
>> you are removing the longitudinal directory first so that it re-runs from
>> scratch. If that does not fix it, we would need to get the data for
>> debugging.
>>
>> Thanks, Martin
>>
>>
>> On 03/30/2016 03:19 PM, Mihaela Stefan wrote:
>>
>> Dear FreeSurfers,
>>
>> We are doing a longitudinal analysis with three time points (MRI1, MRI2,
>> MRI3). All the subjects were processed well except for one. The MRI3.long
>> of that subject has very bad surfaces (see attachment - I am also attaching
>> the log file). The cross, the template and the first two long runs were
>> reconned well, though. We can't figure out why this third run is so bad.
>>
>> As a note, we processed all the cross runs on an Ubuntu machine but we
>> ran the longitudinal pipeline on a computer cluster (both with freesurfer
>> v5.3). We ran the long twice for that subject thinking that the pipeline
>> crashed somehow the first time. However, the results were the same.
>>
>> Any help would be appreciated.
>>
>> Thanks!
>> Mihaela
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> --
>> Martin Reuter, PhD
>> Assistant Professor of Radiology, Harvard Medical School
>> Assistant Professor of Neurology, Harvard Medical School
>> A.A.Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> Research Affiliate, CSAIL, MIT
>> Phone: +1-617-724-5652
>> Web  : http://reuter.mit.edu
>>
>>
>> ___
>> 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 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Research Affiliate, CSAIL, MIT
> Phone: +1-617-724-5652
> Web  : http://reuter.mit.edu
>
>
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>
>
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> is
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> e-mail
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Re: [Freesurfer] bbregister problems with PET data

[Douglas N Greve]

btw, what tracer is this? And the asymmetry you are talking about is 
between the hemispheres? Is that typical for this tracer or is this a 
phenomena with this subject (or population)?

On 03/30/2016 03:41 PM, Adam Martersteck wrote:
> Hi Freesurfer team,
>
> I’m encountering a problem using bbregister on PET data:
>
> -- When I attempt to register a PET volume to T1-space the asymmetric 
> tracer uptake of the PET throws off proper registration. (Treating the 
> PET as a T1 because of the non-specific white matter uptake > grey 
> matter signal).
>
> -- You can really see the bbregister mis-registration in this gif 
> here: https://goo.gl/iM6yrT
>
> -- It (expectedly) attempts to find the best match between signal 
> intensities on both the left and right surfaces, but is inherently 
> biased by the asymmetric uptake shifts the entire volume to the right.
>
> -- Are there any suggestions for dealing with asymmetric scans like 
> this? Stick with just a simple FLIRT? It doesn't seem to do that great 
> a job for everyone.
>
> Cutting left and right hemispheres apart and register separately?
>
> Using Martin’s new robust register for multi-modal data? Any 
> suggestions on the parameters of ROBENT?
>
> Thanks,
> Adam
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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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
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Re: [Freesurfer] DODS vs DOSS for correlation analysis

[Douglas N Greve]

I thought it was disabled in 5.3, thanks for the heads up.

On 03/30/2016 06:32 PM, Cassandra Wannan wrote:
> Hi Doug,
>
> I'm using version 5.3. I had read about the bug but the release notes 
> for 5.3 didn't mention not using DOSS in Qdec, so I thought the issue 
> must have been resolved. If not, I'll let my colleagues know as I 
> believe some of them are still using DOSS in Qdec.
>
> Cheers,
>
> Cassie
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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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
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Re: [Freesurfer] bbregister problems with PET data

[Douglas N Greve]

Try using mri_coreg
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg


On 03/30/2016 04:20 PM, Martin Reuter wrote:
> Hi Adam,
>
> not sure robust_register robent will work on this type of stuff (never 
> tested it). I would recommend to keep the radius small (2,or 3), but 
> switch on --entcorrection.
>
> You can also try robust_register with normalized mutual information 
> (NMI) or simple MI to see how that works.
>
> You will probably be able to tell if a registration is completely off, 
> but if you get something that looks similar to FLIRT it will be hard 
> to judge which one is better.
>
> Good luck, Martin
>
>
> On 03/30/2016 03:41 PM, Adam Martersteck wrote:
>> Hi Freesurfer team,
>>
>> I’m encountering a problem using bbregister on PET data:
>>
>> -- When I attempt to register a PET volume to T1-space the asymmetric 
>> tracer uptake of the PET throws off proper registration. (Treating 
>> the PET as a T1 because of the non-specific white matter uptake > 
>> grey matter signal).
>>
>> -- You can really see the bbregister mis-registration in this gif 
>> here: https://goo.gl/iM6yrT
>>
>> -- It (expectedly) attempts to find the best match between signal 
>> intensities on both the left and right surfaces, but is inherently 
>> biased by the asymmetric uptake shifts the entire volume to the right.
>>
>> -- Are there any suggestions for dealing with asymmetric scans like 
>> this? Stick with just a simple FLIRT? It doesn't seem to do that 
>> great a job for everyone.
>>
>> Cutting left and right hemispheres apart and register separately?
>>
>> Using Martin’s new robust register for multi-modal data? Any 
>> suggestions on the parameters of ROBENT?
>>
>> Thanks,
>> Adam
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- 
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Research Affiliate, CSAIL, MIT
> Phone: +1-617-724-5652
> Web  :http://reuter.mit.edu  
>
>
> ___
> 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
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Re: [Freesurfer] longitudinal pipeline surface error

[Martin Reuter]

I have seen cases where annonymization messed up ID's and individual 
time points came from a different subject. That could mess things up 
quite bad. (Also if the person sends their sibling or friend, because 
they don't have time to come to the follow up themselves, has also 
happened - not to me though ).


Best, Martin

On 03/31/2016 10:21 AM, Mihaela Stefan wrote:

Hi Martin,

We ran this subject twice but we got the same error. The norm is not 
aligned. They almost look like two different brains. I double checked 
the exam numbers to make sure that these three exams belong to the 
same person. They indeed seem to belong to the same person but I will 
re-run recon cross from scratch for MRI3 just to make sure that I 
started with the right DICOMs. I will let you know how it worked.


Thanks!
Mihaela

On Wed, Mar 30, 2016 at 4:12 PM, Martin Reuter 
> wrote:


Hi Mihaela,

does the cross sectional run of that time point, and the base look
OK? Also check if this time point is aligned correctly to the base
(e.g. open norm.mgz from the long and the base, they should be
aligned).  If all this is OK, then I would recommend to re-run
this long run again, but make sure you are removing the
longitudinal directory first so that it re-runs from scratch. If
that does not fix it, we would need to get the data for debugging.

Thanks, Martin


On 03/30/2016 03:19 PM, Mihaela Stefan wrote:

Dear FreeSurfers,

We are doing a longitudinal analysis with three time points
(MRI1, MRI2, MRI3). All the subjects were processed well except
for one. The MRI3.long of that subject has very bad surfaces (see
attachment - I am also attaching the log file). The cross, the
template and the first two long runs were reconned well, though.
We can't figure out why this third run is so bad.

As a note, we processed all the cross runs on an Ubuntu machine
but we ran the longitudinal pipeline on a computer cluster (both
with freesurfer v5.3). We ran the long twice for that subject
thinking that the pipeline crashed somehow the first time.
However, the results were the same.

Any help would be appreciated.

Thanks!
Mihaela


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-- 
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Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone:+1-617-724-5652 
Web  :http://reuter.mit.edu  



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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] Summer School course 'Genetics for Imagers', 8 August - 12 August in Nijmegen, The Netherlands

[Marten.Onnink]

Dear Freesurfer users,

I would like to promote our Radboud Summer School in Nijmegen (The Netherlands) 
which might be interesting for FSL imaging people that would like to expand 
their knowledge in the genetics area. This intensive one-week (8 August - 12 
August 2016) course covers various aspects of genetics analyses of neuroimaging 
data.

More info here: 
http://www.ru.nl/radboudsummerschool/courses/brain-behaviour/vm-more-courses/brain-imaging-genetics-genetics-for-imagers/

Cheers!

Marten
Marten Onnink, Msc
Radboud University Medical Center Nijmegen
Department of Human Genetics (855) | PO Box 9101 | 6500 HB Nijmegen | The 
Netherlands
T +3124 36 10981| Email: 
marten.onn...@radboudumc.nl



Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het 
handelsregister onder nummer 41055629.
The Radboud university medical center is listed in the Commercial Register of 
the Chamber of Commerce under file number 41055629.
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Re: [Freesurfer] longitudinal pipeline surface error

[Mihaela Stefan]

Hi Martin,

We ran this subject twice but we got the same error. The norm is not
aligned. They almost look like two different brains. I double checked the
exam numbers to make sure that these three exams belong to the same person.
They indeed seem to belong to the same person but I will re-run recon cross
from scratch for MRI3 just to make sure that I started with the right
DICOMs. I will let you know how it worked.

Thanks!
Mihaela

On Wed, Mar 30, 2016 at 4:12 PM, Martin Reuter 
wrote:

> Hi Mihaela,
>
> does the cross sectional run of that time point, and the base look OK?
> Also check if this time point is aligned correctly to the base (e.g. open
> norm.mgz from the long and the base, they should be aligned).  If all this
> is OK, then I would recommend to re-run this long run again, but make sure
> you are removing the longitudinal directory first so that it re-runs from
> scratch. If that does not fix it, we would need to get the data for
> debugging.
>
> Thanks, Martin
>
>
> On 03/30/2016 03:19 PM, Mihaela Stefan wrote:
>
> Dear FreeSurfers,
>
> We are doing a longitudinal analysis with three time points (MRI1, MRI2,
> MRI3). All the subjects were processed well except for one. The MRI3.long
> of that subject has very bad surfaces (see attachment - I am also attaching
> the log file). The cross, the template and the first two long runs were
> reconned well, though. We can't figure out why this third run is so bad.
>
> As a note, we processed all the cross runs on an Ubuntu machine but we ran
> the longitudinal pipeline on a computer cluster (both with freesurfer
> v5.3). We ran the long twice for that subject thinking that the pipeline
> crashed somehow the first time. However, the results were the same.
>
> Any help would be appreciated.
>
> Thanks!
> Mihaela
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Research Affiliate, CSAIL, MIT
> Phone: +1-617-724-5652
> Web  : http://reuter.mit.edu
>
>
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> HelpLine at
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] QDEC analysis

[Clara Kühn]

Dear FreeSurfer experts,

I am trying to analyze some single time points of my longitudinal data in QDEC. 
I have 3 groups and created a file for the discrete factor "group" with three 
levels (1,2 and 3). I have done the same for gender (with 2 levels). The 
analysis with gender works just fine but when I try to use group as a factor I 
get an error message that factor 1 must have 2 levels:

SUBJECTS_DIR is '/scr/etsch2/kids/ct'
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
ninputs = 72
Checking inputs
nframestot = 72
Allocing output
Done allocing
nframes = 72
Writing to /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh
gdfReadHeader: reading 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd
INFO: gd2mtx_method is dods
Reading source surface /scr/etsch2/kids/ct/87kids_template/surf/lh.white
ERROR: no contrasts specified.
Error in Analyze: command failed: mri_glmfit --y 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh --fsgd 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd dods --glmdir 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1 --surf 87kids_template lh

In the tutorial it doesn't state that QDEC has to have discrete factors with 2 
levels only.
Am I doing something wrong or is there a work-around for that maybe?

Cheers, Clara
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Re: [Freesurfer] stacked iteration in brainstem segmentation

[Eugenio Iglesias]

Hi again, Claudia.
As a temporary workaround, you can use this flag in your recon-all command:
-itkthreads 1
This will tell the code not to multithread, which will make it slower, but 
should help avoid the problems you have experienced.
Please let us know how that goes!
Cheers,
Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Claudia Testa" 
To: "Freesurfer support list" 
Sent: Thursday, March 31, 2016 11:03:38 AM
Subject: Re: [Freesurfer] stacked iteration in brainstem segmentation

Hi Eugenio,

we run the brainstem segmentation for 7 seven subjects and it succeded for 3 of 
them. Then we did not carry on with the others.
The data are always 3D volumetric FSPGR acquired with the same sequence and 
scanner.
Would you need any other info?

Cheers,
Claudia

Da: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias 
[e.igles...@bcbl.eu]
Inviato: mercoledì 30 marzo 2016 18.56
A: Freesurfer support list
Oggetto: Re: [Freesurfer] stacked iteration in brainstem segmentation

Hi Claudia,
Sorry for the late response.
I am aware of this bug and I'm exploring possible solutions. How often does it 
happen in your data (i.e., how many subjects out of how many)?
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Claudia Testa" 
To: "Freesurfer support list" 
Sent: Friday, March 25, 2016 1:03:42 PM
Subject: [Freesurfer] stacked iteration in brainstem segmentation

Dear all,

I wrote few weeks ago for a problem regarding Freesurfer 6.0 and the 
-brainstem-structures option.
The bug was solved downloading the new available version but I still have some 
problems.
The recon-all -s subject -brainstem-structures
stacks at a certain point (always the same one: "Iteration 2 of 7")  for some 
subjects and for others it succeedes.
In attach there is the log file for one successful segmentation 
(brainstem-structures_ok.log) and one for a failed segmentation 
(brainstem-structures.log).
Can you help me?

Thanks a lot

Claudia

5x1000 AI GIOVANI RICERCATORI
DELL'UNIVERSITÀ DI BOLOGNA
Codice Fiscale: 80007010376

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Re: [Freesurfer] stacked iteration in brainstem segmentation

[Eugenio Iglesias]

In the hippocampal subfield segmentation, this happens once every 100-200 
subjects. Three for seven is pretty bad. I'll take a look as soon as I can.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Claudia Testa" 
To: "Freesurfer support list" 
Sent: Thursday, March 31, 2016 11:03:38 AM
Subject: Re: [Freesurfer] stacked iteration in brainstem segmentation

Hi Eugenio,

we run the brainstem segmentation for 7 seven subjects and it succeded for 3 of 
them. Then we did not carry on with the others.
The data are always 3D volumetric FSPGR acquired with the same sequence and 
scanner.
Would you need any other info?

Cheers,
Claudia

Da: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias 
[e.igles...@bcbl.eu]
Inviato: mercoledì 30 marzo 2016 18.56
A: Freesurfer support list
Oggetto: Re: [Freesurfer] stacked iteration in brainstem segmentation

Hi Claudia,
Sorry for the late response.
I am aware of this bug and I'm exploring possible solutions. How often does it 
happen in your data (i.e., how many subjects out of how many)?
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Claudia Testa" 
To: "Freesurfer support list" 
Sent: Friday, March 25, 2016 1:03:42 PM
Subject: [Freesurfer] stacked iteration in brainstem segmentation

Dear all,

I wrote few weeks ago for a problem regarding Freesurfer 6.0 and the 
-brainstem-structures option.
The bug was solved downloading the new available version but I still have some 
problems.
The recon-all -s subject -brainstem-structures
stacks at a certain point (always the same one: "Iteration 2 of 7")  for some 
subjects and for others it succeedes.
In attach there is the log file for one successful segmentation 
(brainstem-structures_ok.log) and one for a failed segmentation 
(brainstem-structures.log).
Can you help me?

Thanks a lot

Claudia

5x1000 AI GIOVANI RICERCATORI
DELL'UNIVERSITÀ DI BOLOGNA
Codice Fiscale: 80007010376

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Re: [Freesurfer] stacked iteration in brainstem segmentation

[Claudia Testa]

Hi Eugenio,

we run the brainstem segmentation for 7 seven subjects and it succeded for 3 of 
them. Then we did not carry on with the others.
The data are always 3D volumetric FSPGR acquired with the same sequence and 
scanner.
Would you need any other info?

Cheers,
Claudia

Da: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias 
[e.igles...@bcbl.eu]
Inviato: mercoledì 30 marzo 2016 18.56
A: Freesurfer support list
Oggetto: Re: [Freesurfer] stacked iteration in brainstem segmentation

Hi Claudia,
Sorry for the late response.
I am aware of this bug and I'm exploring possible solutions. How often does it 
happen in your data (i.e., how many subjects out of how many)?
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Claudia Testa" 
To: "Freesurfer support list" 
Sent: Friday, March 25, 2016 1:03:42 PM
Subject: [Freesurfer] stacked iteration in brainstem segmentation

Dear all,

I wrote few weeks ago for a problem regarding Freesurfer 6.0 and the 
-brainstem-structures option.
The bug was solved downloading the new available version but I still have some 
problems.
The recon-all -s subject -brainstem-structures
stacks at a certain point (always the same one: "Iteration 2 of 7")  for some 
subjects and for others it succeedes.
In attach there is the log file for one successful segmentation 
(brainstem-structures_ok.log) and one for a failed segmentation 
(brainstem-structures.log).
Can you help me?

Thanks a lot

Claudia

5x1000 AI GIOVANI RICERCATORI
DELL'UNIVERSITÀ DI BOLOGNA
Codice Fiscale: 80007010376

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