[Freesurfer] Error using chol

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I am running into an issue with fast_selxavg3b.
I am attempting a first level PPI analysis.

The command is
mkanalysis-sess -fsd bold -native -delay -2/2 -notask -TR 2 -polyfit 6
-analysis [xxx] -funcstem [xxx] -runlistfile mooneyppi.list -nuisreg
motion.dat 6 -tpef tpef_dvars.dat -acfbins 5 -acffwhm 0 -mask [xxx] -force
-nuisreg juice.dat 1 -nuisreg fixation.dat 1 -taskreg ppi.dat 4

I get the following error:

GLS Residual Pass
  run 1t= 0.0
Error using chol
Matrix must be positive definite.

Error in fast_selxavg3b (line 942)
Wseg = inv(chol(toeplitz(acfrun))');

Before that, I am getting several warnings of this kind:
> In fast_selxavg3b (line 895)
Warning: Matrix is singular, close to singular or badly scaled. Results may
be
inaccurate.

A few of them, but not run 1, have RCOND = NaN.

This is with versions 7.2 and 5.3.
I found one previous conversation on the mailing list regarding this error
in the context of a resting state analysis, but no conclusion. Any advice
would be appreciated.
Thanks!
Caspar
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[Freesurfer] Cohen's D from selxavg3-sess output

[Caspar M. Schwiedrzik]

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Hi!
I would like to compute Cohen's D for individual subjects.
I was wondering whether I can use the output from selxavg3-sess for this:
ces./rstd
Or does this only work with gamma and rstd after mri_glmfit?

Thank you, Caspar
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Re: [Freesurfer] selxavg3-sess out of memory error

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Doug,
thanks for the advice! I can compute the GLM and contrasts per run.
But selxavg3 does not compute contrasts across the runs with per-run.
Could you give me some advice on how to concatenate the per run contrasts -
can I just append them and add the df degrees of freedom?
Thanks, Caspar


Am Fr., 24. Juni 2022 um 16:36 Uhr schrieb Douglas N. Greve <
dgr...@mgh.harvard.edu>:

> *Caution: External email*
> Sorry, I thought I sent an email responding to this. Try running it with
> -run-wise. This will analyze each run separately. I can't remember whether
> it generates a final combined average (been a long time since I used this
> option), but run it and see what it does.
>
> On 6/23/2022 2:00 PM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
> Hi!
> Any advice on this issue?
> The error message is:
>
> Starting contrasts
> UrInv J=1 -
> Out of memory. Type "help memory" for your options.
>
> Error in fast_glm_pcc (line 39)
> yhatd = Rd*(X*beta);
>
> Error in fast_fratiow (line 136)
>   if(nargout == 6) pccbin =
> fast_glm_pcc(beta(:,indbin),Xbin,C,rvarbin);
>   end
>
> Error in fast_selxavg3b (line 1148)
>  fast_fratiow(betamat,X,rvarmat,C,acfsegmn,acfseg.vol(:));
>
> >> --
> ERROR: fast_selxavg3() failed\n
>
> Thank you,
> Caspar
>
>
> Am Mo., 20. Juni 2022 um 10:17 Uhr schrieb Caspar M. Schwiedrzik <
> cschwie...@rockefeller.edu>:
>
>> Hi!
>> I am running large single subject GLMs with selxavg3-sess and I run into
>> a Matlab "out of memory" error. I was wondering whether you had any advice
>> on how to get around that.
>>
>> I have 40-50 runs per subject, and the analyses are whole brain.
>> The GLM per subject runs through fine, but the error occurs once
>> selxavg3-sess starts computing contrasts.
>> The problem occurs with v5.3 and v7.2.
>>
>> This is a Centos 7 system with 320 GB of memory, and 7 GB of swap memory.
>>
>> Any advice would be appreciated!
>> Caspar
>>
>>
>>
>>
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Re: [Freesurfer] selxavg3-sess out of memory error

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
Any advice on this issue?
The error message is:

Starting contrasts
UrInv J=1 -
Out of memory. Type "help memory" for your options.

Error in fast_glm_pcc (line 39)
yhatd = Rd*(X*beta);

Error in fast_fratiow (line 136)
  if(nargout == 6) pccbin = fast_glm_pcc(beta(:,indbin),Xbin,C,rvarbin);
  end

Error in fast_selxavg3b (line 1148)
 fast_fratiow(betamat,X,rvarmat,C,acfsegmn,acfseg.vol(:));

>> --
ERROR: fast_selxavg3() failed\n

Thank you,
Caspar


Am Mo., 20. Juni 2022 um 10:17 Uhr schrieb Caspar M. Schwiedrzik <
cschwie...@rockefeller.edu>:

> Hi!
> I am running large single subject GLMs with selxavg3-sess and I run into a
> Matlab "out of memory" error. I was wondering whether you had any advice on
> how to get around that.
>
> I have 40-50 runs per subject, and the analyses are whole brain.
> The GLM per subject runs through fine, but the error occurs once
> selxavg3-sess starts computing contrasts.
> The problem occurs with v5.3 and v7.2.
>
> This is a Centos 7 system with 320 GB of memory, and 7 GB of swap memory.
>
> Any advice would be appreciated!
> Caspar
>
>
>
>
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[Freesurfer] selxavg3-sess out of memory error

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I am running large single subject GLMs with selxavg3-sess and I run into a
Matlab "out of memory" error. I was wondering whether you had any advice on
how to get around that.

I have 40-50 runs per subject, and the analyses are whole brain.
The GLM per subject runs through fine, but the error occurs once
selxavg3-sess starts computing contrasts.
The problem occurs with v5.3 and v7.2.

This is a Centos 7 system with 320 GB of memory, and 7 GB of swap memory.

Any advice would be appreciated!
Caspar
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[Freesurfer] PhD student position in the NCC lab at the European Neuroscience Institute Göttingen, Germany

[Caspar M. Schwiedrzik]

 candidates should send their curriculum vitae, a description of
their scientific interests and the names and contact information of two
references who are able to comment on your academic background and who
agreed to be contacted to Caspar M. Schwiedrzik (cschw...@gwdg.de).

The University Medical Center Göttingen is committed to professional
equality. We therefore seek to increase the proportion of under-represented
genders. Applicants with disabilities and equal qualifications will be
given preferential treatment. We look forward to receiving your application
by 14.01.2022: University Medical Center Göttingen European Neuroscience
Institute Göttingen Dr. Caspar Schwiedrzik Group Leader Grisebachstr. 5
37077 Göttingen Tel.: +49 0551/39-61371 E-Mail: cschw...@gwdg.de Web:
http://secure-web.cisco.com/1-7988TeJhnzxuk_F1uUcu7-YL8le_tn5NmaUJxD5RVg9TaUvSn5MZFenDlOkTzahDYwWEAB2Pjq3i_Wj2QJLjQ4051tvp2DFoYsBjP8gdqZfjYHB6fqn8J18iXEu2fPy2MiQak25BpA6shr9BmAQdxqb8UuebAPCrKF6g3XP5MzWrTRAWhpNEmOxXB-81uBDGcnMVABoAnJAf7_phyiyDwxtpyKBxSxWoZCz5AhhzzUXAq3cS4JP1gKbf1vLyvyeUS3pnVBYj837942OpV1qf72ta7LZgXJkaUSnE4ecduVJJfXTm9MYjuxEILRQxgZL/http%3A%2F%2Fwww.eni-g.de%2F
 Contact person: For questions about the position or
project, please contact Caspar M. Schwiedrzik (cschw...@gwdg.de). For
questions about the application procedure, please contact Christiane Becker
(c.bec...@eni-g.de).

Please send your application via e-mail in PDF-format or via mail in copy
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Re: [Freesurfer] mri_ribbon does not return the ribbon

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Doug,
Thank you - we tried this. We do not have aseg and therefore mris_volmask
will not do it.
Caspar

On Mon, May 10, 2021 at 18:09 Douglas N. Greve 
wrote:

> Try
> cd yoursubjectname/mri
> mris_volmask  --label_left_white 2 --label_left_ribbon 3
> --label_right_white 41 --label_right_ribbon 42 --save_ribbon yoursubjectname
>
>
> On 5/3/2021 4:31 PM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
> Hi!
> I am trying to make a ribbon.mgz from a non-human primate surface recon
> that does not have an aseg. Following this prior discussion: *MailScanner
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming
> to be* Re: [Freesurfer] ribbon.mgz Without aseg.mgz (mail-archive.com)
> <https://secure-web.cisco.com/1VdhFmYoi68s4-hWpx9b4PfGpWUxkuRYYnXFCVuOciL9pr9mToywFyr2sqpYsJf65LEgYSj2hae4hAhYDMAB1jrUggSJWAytxF_88Z1j4Vz9TABX6c6YtM2b4eztak0ks45cDnxK237yA-5nOCA_oBbkEEN_wiSdupbhdIRKh06PnTvRTxsbF0Q42T3bPjecEYo88skGdbzWwu1s3FkEShAUCs4te0t0rtAoOpav5uVwzH1KK2aG-Llm18v6otSq2/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1ak2oe-2DadeCSsLNqdcSfpPz47btc0Bg4-5F-2D64m15yi4A3arakBiE7rQ-2De9Ic-2D-2DHcZjzBr8owRBFUicdouc7e2zl78qnX0T7FnwdllHDGAeM-5F4lAB6y3cenwxCzUG3lomlWl7BjXQbs4PesuZet8wvOXyZgrU9ePd4D9fZQEHvmpLBuI3G-5Fa9NjVljMypuSefd0w8HYbmqeeqk3V6FQctpxtYq7VxlSRohysbd2HtGet4ulmKNUGr16-5FyWQ5tGzBFans-5FD-2DRTGtinwVa8sbtjRjqg_https-253A-252F-252Fwww.mail-2Darchive.com-252Ffreesurfer-2540nmr.mgh.harvard.edu-252Fmsg21349.html%26d%3DDwMDaQ%26c%3DJeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg%26r%3DsgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8%26m%3D2KmDkufF0O3Q4E6ttVSwu3wsGnvInZisgxeLGFgrfuU%26s%3D9xoJKKfQdjJpr9qu9W-wNKDJMWGsyXvHbQb5CcWiPTk%26e%3D>
> I tried mri_ribbon:
>
> mri_ribbon ./surf/rh.white ./surf/rh.pial ./mri/orig.mgz
> rh.ribbon.mgz
>
> Attached is the output. It looks like it roughly follows the grey matter,
> but especially the sulci seem to be filled. Unfortunately, there is no help
> for mri_ribbon. Any advice on how to proceed? The above mentioned
> discussion did not lead to a conclusion on how to get a ribbon without
> aseg.
> Thank you! Caspar
>
>
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[Freesurfer] mri_ribbon does not return the ribbon

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I am trying to make a ribbon.mgz from a non-human primate surface recon
that does not have an aseg. Following this prior discussion: Re:
[Freesurfer] ribbon.mgz Without aseg.mgz (mail-archive.com)

I tried mri_ribbon:

mri_ribbon ./surf/rh.white ./surf/rh.pial ./mri/orig.mgz
rh.ribbon.mgz

Attached is the output. It looks like it roughly follows the grey matter,
but especially the sulci seem to be filled. Unfortunately, there is no help
for mri_ribbon. Any advice on how to proceed? The above mentioned
discussion did not lead to a conclusion on how to get a ribbon without
aseg.
Thank you! Caspar
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Re: [Freesurfer] cannot find freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3 {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Doug,
it turns out part of the v5.3 installation had been accidentally deleted.
After restoring the file, it works fine, and I am happy to report the the
GPU versions work (with CUDA 5).
Thanks!
Caspar


Am Do., 17. Dez. 2020 um 15:37 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> The GPU stuff may or may not work. It was hard to maintain because the
> GPUs kept changing so much, and it would not surprise me that the code from
> 5.3 is incompatable with GPUs today. But it looks like the error is that it
> could not find a file. Does that file actually exist?
>
> On 12/12/2020 3:04 PM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
> Hi!
> I am trying to run recon-all in version 5.3 with the -use-gpu flag. I am
> getting a strange error that I would love to get your input on:  cannot
> find freesurfer/average/RB_all_2008-03-26.gca
> Neither the file nor the path exist.
>
> This is the entire input and output:
>
> recon-all -s hum_14600_parallel -i
> /neuro_tools/freesurfer/subjects/hum_14600/mri/011/mp2rage.nii -all -use-gpu
> Testing for CUDA device:
> nvcc: NVIDIA (R) Cuda compiler driver
> Copyright (c) 2005-2012 NVIDIA Corporation
> Built on Fri_Sep_21_17:28:58_PDT_2012
> Cuda compilation tools, release 5.0, V0.2.1221
>
> Driver : 10.0
> Runtime : 5.0
>
> Acquiring CUDA device
> Using default device
> CUDA device: Tesla K40m
>
>
>  === NUMBER OF OPENMP THREADS = 1 ===
> stable5
>
> NVIDIA driver version info:
> NVRM version: NVIDIA UNIX x86_64 Kernel Module  410.79  Thu Nov 15
> 10:41:04 CST 2018
>
> ERROR: cannot find /neuro_tools/freesurfer/average/RB_all_2008-03-26.gca
>
> Is there some documentation on how to set up the environment beyond
> LD_LIBRARY_PATH? Could that be the issue? Everything works fine without the
> -use-gpu flag.
>
> Thank you! Caspar
>
>
> ___
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[Freesurfer] cannot find freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I am trying to run recon-all in version 5.3 with the -use-gpu flag. I am
getting a strange error that I would love to get your input on:  cannot
find freesurfer/average/RB_all_2008-03-26.gca
Neither the file nor the path exist.

This is the entire input and output:

recon-all -s hum_14600_parallel -i
/neuro_tools/freesurfer/subjects/hum_14600/mri/011/mp2rage.nii -all -use-gpu
Testing for CUDA device:
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2012 NVIDIA Corporation
Built on Fri_Sep_21_17:28:58_PDT_2012
Cuda compilation tools, release 5.0, V0.2.1221

Driver : 10.0
Runtime : 5.0

Acquiring CUDA device
Using default device
CUDA device: Tesla K40m


 === NUMBER OF OPENMP THREADS = 1 ===
stable5

NVIDIA driver version info:
NVRM version: NVIDIA UNIX x86_64 Kernel Module  410.79  Thu Nov 15 10:41:04
CST 2018

ERROR: cannot find /neuro_tools/freesurfer/average/RB_all_2008-03-26.gca

Is there some documentation on how to set up the environment beyond
LD_LIBRARY_PATH? Could that be the issue? Everything works fine without the
-use-gpu flag.

Thank you! Caspar
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[Freesurfer] unpacksdcmdir in version 7: issues with cfg files

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
We are encountering some issues with unpacksdcmdir in version 7.1.1. In
particular, it turns out that the handling of cfg files seems to have
changed, which makes things somewhat impractical.
Old (v5.3) cfg files cannot be used anymore, because only dicom series
names that are actually present in the current session are accepted. This
makes it impossible to have one general cfg file for different experiments,
and also to help structure the cfg files with commented lines. I understand
unpacksdcmdir is being phased out, but the flexibility brought about by cfg
files still makes this a very handy tool. Yet, the current version has lost
much of this flexibility. I suggest reverting to the way unpacksdcmdir
handled cfg files in the past.
Thanks, Caspar
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Re: [Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
Thanks, Doug and Bruce, for your input.
It seems to be a problem with the number of iterations (-n). It is
currently hard coded to run 4 times. If I run it only once, grey and white
are in a normal range (but there are still inhomogeneities). If I run it
twice, grey is at 60 and white is at 100. With every following iteration I
loose overall brightness.
Caspar


Am Fr., 18. Sept. 2020 um 17:16 Uhr schrieb Douglas Greve <
dgr...@mgh.harvard.edu>:

> It's been a while since 5.3, but I vaguely remember something like this
> happening because there were one or two super bright voxels in the image.
> If this is the case, then you can find them and clip them.
>
> On 9/18/20 10:32 AM, Fischl, Bruce wrote:
>
> I don’t think adding 100 will work as once it scales everything down that
> far you only have a couple of bits of representation in the conformed ( 1
> byte/voxel) images. Maybe someone else can comment on fixing nu_correct?
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> 
>  *On Behalf Of *Caspar M.
> Schwiedrzik
> *Sent:* Friday, September 18, 2020 5:04 AM
> *To:* Freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark
> output
>
>
>
> *External Email - Use Caution*
>
> Hi!
>
> I am having some issue at the interface between mri_nu_correct.mni and
> mri_normalize, using v5.3.
>
> Specifically, the output when applying mri_nu_correct to a T1 is quite
> dark, with white matter in the range of 15. Contrast is ok. When I apply
> mri_normalize to nu, it does not scale the data to white matter 110. This
> happens with and without a brain mask, and with various other parameter
> choices.
>
> I am tempted to just add 100 to all voxels.
>
> Any advice?
>
> Thank you,
>
> Caspar
>
>
>
> ___
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[Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I am having some issue at the interface between mri_nu_correct.mni and
mri_normalize, using v5.3.
Specifically, the output when applying mri_nu_correct to a T1 is quite
dark, with white matter in the range of 15. Contrast is ok. When I apply
mri_normalize to nu, it does not scale the data to white matter 110. This
happens with and without a brain mask, and with various other parameter
choices.
I am tempted to just add 100 to all voxels.
Any advice?
Thank you,
Caspar
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Re: [Freesurfer] MEMPRAGE vs. MP2RAGE

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Bruce,
In that paper, you reported that MP2RAGE underestimates cortical thickness
relative to MEMPRAGE and also has slightly lower reproducibility.
Since Recon-all does not seem to have built in functionality to deal with
the background noise in MP2RAGE, I am wondering whether you still
recommend MEMPRAGE
over MP2RAGE. I only have regular MPRAGE for comparison at the moment.
Thank you,
Caspar

On Mon, Sep 7, 2020 at 19:56 Fischl, Bruce  wrote:

>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hi Caspar
>
>
>
>
>
> Can you elaborate? What are the issues?
>
>
>
> Bruce
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu>
>
> *On Behalf Of *Caspar M. Schwiedrzik
>
>
> *Sent:* Monday, September 7, 2020 2:27 AM
>
>
> *To:* Freesurfer@nmr.mgh.harvard.edu
>
>
> *Subject:* [Freesurfer] MEMPRAGE vs. MP2RAGE
>
>
>
>
>
> *External Email - Use Caution*
>
>
>
>
>
>
> Hi!
>
>
>
>
>
>
> I was wondering whether the issues with surface reconstruction from
> MP2RAGE data that were reported for Freesurfer v5.1 in Fujimoto et al.,
> 2014 still persist in more recent releases of Freesurfer, and whether there
> is information to what
>
> extent they apply to 3T data?
>
>
>
>
>
>
> Thank you!
>
>
>
>
>
>
> Caspar
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ___
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>
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[Freesurfer] MEMPRAGE vs. MP2RAGE

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I was wondering whether the issues with surface reconstruction from MP2RAGE
data that were reported for Freesurfer v5.1 in Fujimoto et al., 2014 still
persist in more recent releases of Freesurfer, and whether there is
information to what extent they apply to 3T data?
Thank you!
Caspar
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[Freesurfer] The European Neuroscience Institute in Göttingen (ENI-G) Germany announces positions for Group Leaders (m/f/d)

[Caspar M. Schwiedrzik]

External Email - Use Caution

The European Neuroscience Institute in Göttingen (ENI-G) Germany announces
positions for
Group Leaders (m/f/d)

   - Limitation: fixed-term
   - Working period: full-time
   - Tariff: salary according to TV-L
   - Announcement published on 06.07.2020
   - Vacancy from 01.01.2021
   - Application deadline: 31.08.2020

The ENI-G, a joint initiative between the University Medical Center
Göttingen and the Max-Planck-Society, provides an exceptional environment
for excellent young researchers in the neurosciences.

*We seek:*

Applicants with an outstanding record of research in neuroscience. Topics
range from molecular and cellular physiology, neuronal circuit analysis,
imaging (at all scales), to computational and cognitive neuroscience.
Current work at the ENI-G focuses on physiology, sensory processing and
plasticity in multiple species, from invertebrates to humans. Research that
complements these already established topics, including computational
approaches at the ENI-G is also welcome.

*We offer:*

Group leaders a maximal amount of independence while also providing the
support necessary to build up a new research program. ENI-G will provide
office and laboratory space as well as a generous start-up. State of the
art equipment, including dedicated microscopy infrastructure, animal
facilities, a precision workshop, IT and administrative support are
available in house. Unparalleled opportunities for scientific collaboration
and interaction exist within the Göttingen Research Campus, including the
University of Göttingen and its Medical School, three Max Planck Institutes
(Biophysical Chemistry, Experimental Medicine, and Dynamics and Self
Organization), the German Primate Center and the Bernstein Center for
Computational Neuroscience. We will work closely with the recently
established Cluster of Excellence "Multiscale Bioimaging: from Molecular
Machines to Networks of Excitable Cells (https://mbexc.de/en/)" as well as
the newly starting Heart and Brain Center Göttingen.

In addition to the excellent research environment that ENI-G provides, its
independent group leaders can benefit from the resources and funding
opportunities offered by the Collaborative Research Centers (CRC / SFB)
within the Göttingen Neuroscience community. The ENI-G also houses the
distinguished graduate program ‘IMPRS Neurosciences’, facilitating
interactions with excellent students and providing opportunities for
teaching.

You will have an experienced mentor by your side, receive broad
administrative support, professional leadership training, and help with
relocation and establishing a life in Germany, including visa application,
housing, schooling, and day-care. Successful group leaders will have the
opportunity to obtain a permanent position after a two step internal and
external evaluation.

*We look forward to:*

Applications from outstanding researchers who are enthusiastic about
pursuing an independent research program in an environment that supports
cutting edge research. The successful candidate is expected to develop a
vigorous research program with a Ph.D. received within the last five years.
Relevant research training and outstanding research reflected by
high-impact publications are a prerequisite for consideration. The
applicant is expected to acquire competitive third-party funding, and
eligibility for ERC Starting Grant / DFG Emmy Noether level funding (or
comparable) is a requirement. Details about funding opportunities can be
found at http://www.eni-g.de/career/group-leader. Interested candidates
should submit their curriculum vitae and record of publications
highlighting their 3-5 most significant publications, as well as a research
statement (3-5 pages), and a copy of their PhD degree, preferably in one
pdf. Application deadline: 31 August 2020.
Women are especially encouraged to apply. Applicants with disabilities and
equal qualifications will be given preferential treatment.
We look forward to receiving your application by *31.08.2020*:
University Medical Center Göttingen
European Neuroscience Institute Göttingen
Christiane Becker
Administration Manager
Grisebachstr. 5
37077 Göttingen
Tel.: 0551/39-61300
Fax: 0551/39-61399
E-Mail: c.bec...@eni-g.de
Web: http://www.eni-g.de/index.php?id=groupleader

Please send your application only via e-mail as a PDF-file.

Travel and application fees cannot be refunded or transferred.

https://www.umg.eu/karriere/stellenangebote/stellenanzeigen-detail/?jobId=3342
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[Freesurfer] Scientific Project Coordinator for an open science, large-scale collaboration

[Caspar M. Schwiedrzik]

External Email - Use Caution

Dear all,

If you are seeking a challenge, if you are dynamic and enthusiastic about
managing a large consortium of scientists, then do not hesitate to apply
for the *Scientific Project Coordinator  *position in my group at the Max
Planck Institute for Empirical Aesthetics. You will be coordinating this
 project which was
recently features in science, and involves 11 institutions across Europe,
the US and China running an adversarial collaboration project aimed at
understanding the neural foundations of consciousness.

This is a unique opportunity to contribute to the development of an open
science model for large-scale collaborations. We are looking for an
internationally experienced scientist with knowledge of science management,
networking, and international collaboration, and a keen interest in
developing practices and procedures for open science.  This is a full-time
position for 2 years.

More information on the job requirements and the position can be found here

.

For enquiries concerning this job opportunity please contact *Dr. Lucia
Melloni: **lucia.mell...@ae.mpg.de **.*

Please submit your application - preferably online in a single pdf -
including a CV and a cover letter describing your background, experience
and motivation as well as the names of two references, who have previously
agreed to be contacted, *no later than July 31, 2020 *to: *j...@ae.mpg.de*


Looking forward to the applications!

Best wishes,
Lucia Melloni
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Re: [Freesurfer] circular/cyclic color map for polar data in freeview {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
Jumping in on this, since it has come up many times but is without a
solution so far: the issue is that the color code is now mapped onto a
straight color bar, not a circle. At the same time, it is not documented
what color refers to which angle. That makes it very difficult to work with
this kind of color bar. It would be very helpful to reintroduce the circle,
and to explicitly document how angles are mapped to colors.
Thank you!
Caspar

On Thu, May 21, 2020 at 16:41 Douglas N. Greve 
wrote:

> When you say it is "linear" do you mean it does not wrap-around?
>
>
>
> On 5/19/2020 8:47 PM, Devavrat Vartak PhD wrote:
>
> External Email - Use Caution
> Hello freesurfer community,
>
> I am trying to setup a retinotopy pipeline. I have analysed pRF data
> generating polar angle and eccentricity maps which I project onto an
> inflated surface / flattened surface in freeview.
>
> Is there a way to display a circular/cyclic colour map (for the polar
> angle data) in the overlay screen?, the existing 'colour wheel' option
> seems to be linear?
>
>
> Thank you!
>
> Best,
> DV
>
>
>
> ___
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Re: [Freesurfer] Notice on freesurfer list archives

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
We have a ton of links to the pipermail archives in our wiki. They are all
broken now.
It seems that the message indices in pipermail do not correspond to those
in mail-archive.
Is there a way to find the correspondences?
Thanks,
Caspar


Am Do., 10. Okt. 2019 um 18:58 Uhr schrieb Hoopes, Andrew <
ahoo...@mgh.harvard.edu>:

> Hi all,
>
> Our primary archive for all posts to the mailing list can be found at:
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_freesurfer-40nmr.mgh.harvard.edu=DwICAg=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=klyMSd8yMe6P6HuFKFABKLreefUNZ7cY3VVr6api_uw=NfB3_yHnD2ZU2c9i4NBtVd8FkActo33MPMogexdGXNY=
>
> And we've now disabled the public 'pipermail' archives, which include
> anything under:
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer=DwICAg=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=klyMSd8yMe6P6HuFKFABKLreefUNZ7cY3VVr6api_uw=mwSj_GnkKbWBzzKQq5Njg9NIjV9k2dM-gv0hJU386Rc=
>
> If you come across any broken links pointing to the above, please let us
> know.
>
> best
> Andrew
>
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[Freesurfer] Read out N from mri_glmfit outputs?

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
Is there a way to read out the N of a fixed effects analysis performed with
mri_glmfit?
If not, is it safe to assume that it is (number of volumes*number of
runs)-excluded time points, summed across subjects?
Thanks!
Caspar
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Re: [Freesurfer] Confidence interval for Cohen's d from gamma/rstd {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Ok, thanks! I think the gamma CI will do.
Caspar

On Mon, Oct 7, 2019 at 17:11 Greve, Douglas N.,Ph.D. 
wrote:

> You want the 95% CI for Cohen's d itself? I don't know how to do that. If
> you just want it for the contrast (gamma), then I would just use the
> formula for a gaussian with mean gamma and stddev sqrt(gammavar)
>
> On 10/5/2019 10:43 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
>
> Hi!
> I have an OSGM from a fixed effects group analysis with mri_glmfit. I
> would like to calculate the effect size and the 95% confidence intervals. I
> see from various threads on the mailing list that Cohen's d can easily be
> obtained from the outputs of mri_glmfit by dividing gamma by rstd.
>
> I am wondering now how to compute the 95% CIs for Cohen's d from the
> outputs of mri_glmfit?
>
> Thank you very much!
> Caspar
>
>
> ___
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Re: [Freesurfer] Comparing effects between voxels in a FFX GLM {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

exactly

Am Mo., 7. Okt. 2019 um 17:15 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> I'm not sure what you are trying to do. You want to compare the signal in
> one voxel vs another voxel in the same map?
>
> On 10/7/2019 10:32 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
> Hi Doug,
> I would like to test whether an effect that I observed in a given voxel is
> larger than in other voxels (this is fMRI data). The additional
> complication is that I would like to stick as close as possible to the
> original analysis that yielded these effects, which were fixed effects.
> I am wondering whether that is somehow possible using selxavg3 and
> mri_glmfit?
> Thank you! Caspar
>
>
>
> ___
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[Freesurfer] Comparing effects between voxels in a FFX GLM

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Doug,
I would like to test whether an effect that I observed in a given voxel is
larger than in other voxels (this is fMRI data). The additional
complication is that I would like to stick as close as possible to the
original analysis that yielded these effects, which were fixed effects.
I am wondering whether that is somehow possible using selxavg3 and
mri_glmfit?
Thank you! Caspar
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[Freesurfer] Confidence interval for Cohen's d from gamma/rstd

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I have an OSGM from a fixed effects group analysis with mri_glmfit. I would
like to calculate the effect size and the 95% confidence intervals. I see
from various threads on the mailing list that Cohen's d can easily be
obtained from the outputs of mri_glmfit by dividing gamma by rstd.

I am wondering now how to compute the 95% CIs for Cohen's d from the
outputs of mri_glmfit?

Thank you very much!
Caspar
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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed} {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

following up on this: how do we display complex values from a retinotopy
analysis in freeview?
thanks!
caspar


Am Fr., 20. Sept. 2019 um 14:22 Uhr schrieb Caspar M. Schwiedrzik <
cschwie...@rockefeller.edu>:

> Hi Ruopeng and Doug,
> thanks for the hint with the Freeview update. We can now display a linear
> color bar when choosing the color wheel option.
> However, it is not possible to choose "complex", as it was in tksurfer. Is
> Freeview dealing with that internally, or what should we do to display
> results from the retinotopy analyses?
> Thanks,
> Caspar
>
>
> Am Mi., 11. Sept. 2019 um 17:02 Uhr schrieb Ruopeng Wang <
> rpw...@nmr.mgh.harvard.edu>:
>
>> The scalar bar display for overlay in stable 6.0 is broken. If you can
>> install the latest dev build, you should be able to see the scalar bar:
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_UpdateFreeview=DwMDaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=NTyTkpnsfZNs76-kCFUYCRUi1-qPnk8BuVBf7GbjOlA=c6QwReyrmeAAZ1CwyRK8EzyjKrOEC31A_WtQLGYuKbs=>
>>
>> Best,
>> Ruopeng
>> On 9/11/19 9:57 AM, Caspar M. Schwiedrzik wrote:
>>
>> External Email - Use Caution
>> Hi Doug and Ruopeng,
>> thanks a lot for your advice!
>> Is there a way to display a meaningful legend? In tksurfer/rtview, we get
>> a linear legend that does not seem to make much sense and in freeview we
>> typically do not get anything when we choose color wheel and then click on
>> the legend button.
>> Thanks! Caspar
>>
>>
>> Am Di., 10. Sept. 2019 um 17:23 Uhr schrieb Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu>:
>>
>>> When you run rtview, it will run tksurfer. To get to the color wheel,
>>> open View->Configure->Overlay, then select "Color Wheel" under the
>>> "Color Scale" tab.
>>>
>>> On 9/10/19 4:03 AM, Caspar M. Schwiedrzik wrote:
>>> >
>>> > External Email - Use Caution
>>> >
>>> > Hi Doug and Roupeng,
>>> > did you already have the chance to look into the question how to
>>> > display the color wheel with rtview and/or freeview?
>>> > Thank you! Caspar
>>> >
>>> > Am Sa., 7. Sept. 2019 um 13:13 Uhr schrieb Caspar M. Schwiedrzik
>>> > >> > <mailto:cschwie...@mail.rockefeller.edu>>:
>>> >
>>> > External Email - Use Caution
>>> >
>>> > Hi Doug and Ruopeng,
>>> > it would be amazing if you could dig out the information on how to
>>> > display the color wheel.
>>> > Looking forward to what you find!
>>> > Caspar
>>> >
>>> >
>>> > Am Fr., 6. Sept. 2019 um 17:14 Uhr schrieb Greve, Douglas N.,Ph.D.
>>> > mailto:dgr...@mgh.harvard.edu>>:
>>> >
>>> > Hi Caspar, sorry for the delay. I have not used the retinotoy
>>> > stream in a long, long time so I don't know off the top of my
>>> > head. I'll have to look into it. tksurfer (from rtview) does
>>> > have a way to display using the color wheel, but I don't
>>> >     remember how to do it.
>>> >
>>> > Ruopeng, can freeview display using a color wheel?
>>> >
>>> > On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:
>>> >>
>>> >> External Email - Use Caution
>>> >>
>>> >> Hi!
>>> >> I wanted to ask again whether there is a way to display the
>>> >> color wheel in rtview and/or freeview. We are debugging our
>>> >> analyses and it would be immensely helpful to have a legend
>>> >> that specifies the color assignments.
>>> >> Thank you,
>>> >> Caspar
>>> >>
>>> >> On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik
>>> >> >> >> <mailto:cschwie...@rockefeller.edu>> wrote:
>>> >>
>>> >> Hi!
>>> >> I am following up on this thread trying to understand how
>>> >> to make the color wheel visible in rtview, or, if
>>> >> necessar

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed} {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Ruopeng and Doug,
thanks for the hint with the Freeview update. We can now display a linear
color bar when choosing the color wheel option.
However, it is not possible to choose "complex", as it was in tksurfer. Is
Freeview dealing with that internally, or what should we do to display
results from the retinotopy analyses?
Thanks,
Caspar


Am Mi., 11. Sept. 2019 um 17:02 Uhr schrieb Ruopeng Wang <
rpw...@nmr.mgh.harvard.edu>:

> The scalar bar display for overlay in stable 6.0 is broken. If you can
> install the latest dev build, you should be able to see the scalar bar:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_UpdateFreeview=DwMDaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=NTyTkpnsfZNs76-kCFUYCRUi1-qPnk8BuVBf7GbjOlA=c6QwReyrmeAAZ1CwyRK8EzyjKrOEC31A_WtQLGYuKbs=>
>
> Best,
> Ruopeng
> On 9/11/19 9:57 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
> Hi Doug and Ruopeng,
> thanks a lot for your advice!
> Is there a way to display a meaningful legend? In tksurfer/rtview, we get
> a linear legend that does not seem to make much sense and in freeview we
> typically do not get anything when we choose color wheel and then click on
> the legend button.
> Thanks! Caspar
>
>
> Am Di., 10. Sept. 2019 um 17:23 Uhr schrieb Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu>:
>
>> When you run rtview, it will run tksurfer. To get to the color wheel,
>> open View->Configure->Overlay, then select "Color Wheel" under the
>> "Color Scale" tab.
>>
>> On 9/10/19 4:03 AM, Caspar M. Schwiedrzik wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hi Doug and Roupeng,
>> > did you already have the chance to look into the question how to
>> > display the color wheel with rtview and/or freeview?
>> > Thank you! Caspar
>> >
>> > Am Sa., 7. Sept. 2019 um 13:13 Uhr schrieb Caspar M. Schwiedrzik
>> > > > <mailto:cschwie...@mail.rockefeller.edu>>:
>> >
>> > External Email - Use Caution
>> >
>> > Hi Doug and Ruopeng,
>> > it would be amazing if you could dig out the information on how to
>> > display the color wheel.
>> > Looking forward to what you find!
>> > Caspar
>> >
>> >
>> > Am Fr., 6. Sept. 2019 um 17:14 Uhr schrieb Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>>:
>> >
>> > Hi Caspar, sorry for the delay. I have not used the retinotoy
>> > stream in a long, long time so I don't know off the top of my
>> > head. I'll have to look into it. tksurfer (from rtview) does
>> > have a way to display using the color wheel, but I don't
>> > remember how to do it.
>> >
>> > Ruopeng, can freeview display using a color wheel?
>> >
>> > On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:
>> >>
>> >> External Email - Use Caution
>> >>
>> >> Hi!
>> >> I wanted to ask again whether there is a way to display the
>> >> color wheel in rtview and/or freeview. We are debugging our
>> >> analyses and it would be immensely helpful to have a legend
>> >> that specifies the color assignments.
>> >> Thank you,
>> >> Caspar
>> >>
>> >> On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik
>> >> > >> <mailto:cschwie...@rockefeller.edu>> wrote:
>> >>
>> >> Hi!
>> >> I am following up on this thread trying to understand how
>> >> to make the color wheel visible in rtview, or, if
>> >> necessary, in freeview.
>> >> Thank you! Caspar
>> >>
>> >>
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Re: [Freesurfer] timewindow parameter in mkanalysis-sess {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Yes I did. Caspar

On Fri, Sep 13, 2019 at 16:19 Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Did you put -timewindow before -gammafit ?
>
>
> On 9/12/19 6:08 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
> Hi Doug,
> apart from the question whether or not to set the timewindow parameter to
> 80 for MION responses, I noticed that there is a discrepancy between
> analysis.info
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwMGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=4hnvhCVX4pJzRESmdot0FI0cS7sKUWI-cIDKsihmrao=EmEPqCEEylIHfrDEVX7i7KSiT1QrAnz4423QPVyGdJg=>
> and h.dat with regard to this parameter in v5.3.
> If I set timewindow to 80 in mkanalysis-sess, it correctly prints this
> parameter into analysis.info
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwMGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=4hnvhCVX4pJzRESmdot0FI0cS7sKUWI-cIDKsihmrao=EmEPqCEEylIHfrDEVX7i7KSiT1QrAnz4423QPVyGdJg=>.
> However, in h.dat for the same analysis, timewindow is 40.
> I don't know if that is relevant, but it seems weird. Maybe it was already
> addressed in version 6.
>
> Caspar
>
> Am Di., 13. Aug. 2019 um 22:51 Uhr schrieb Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu>:
>
>> That is in response to a 60 sec stimulus. The time window is the time
>> needed to account for a very brief stimulus (ie, the impulse response).
>> fsfast will automatically take into account the duration of the stimulus
>> as listed in the paradigm file.
>>
>> On 8/13/19 2:14 PM, Caspar M. Schwiedrzik wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hi Doug,
>> > Thanks for the advice.
>> > I think the Leite et al. 2002 NeuroImage paper can be interpreted that
>> > way. See Figure 1 and 2.
>> >
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__pop.cerco.ups-2Dtlse.fr_pdf0609_leite-5Ffp-5F02-5F283.pdf=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs=_NKVTMtmRmOeLrYx6styS12TMjsFNuVd2jKFxUKr85Y=
>> >
>> > Caspar
>> >
>> > On Tue, Aug 13, 2019 at 17:12 Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>> >
>> > When you use -gammafit, it automatically sets the time window to
>> > 40. If
>> > you really want it at 80, but -timewindow before -gammafit. Do you
>> > really expect the MION hrf to last 80 sec?
>> >
>> > On 8/13/19 11:06 AM, Caspar M. Schwiedrzik wrote:
>> > >
>> > > External Email - Use Caution
>> > >
>> > > Hi!
>> > > I am having difficulties setting the timewindow parameter in
>> > > mkanalysis-sess in Freesurfer v5.3.
>> > > I am trying to use 80 (data acquired with MION), but the parameter
>> > > does not seem to affect analysis.info
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwMGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=4hnvhCVX4pJzRESmdot0FI0cS7sKUWI-cIDKsihmrao=EmEPqCEEylIHfrDEVX7i7KSiT1QrAnz4423QPVyGdJg=>
>> <
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs=r6h1NqLGmsc3cSyXVgnrkGSvJNA79vDmmSjMUdNwGOA=
>> >
>> > <
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=CYJUPBXH2fLSD5LjpZmYtjXWz_bC8zt7q5gobDE5VLs=Ba7XLDz4JrZXYf4-uKSwAzN0dCldTpp68Yck9EDkQ4s=
>> > >, where it
>> > > is always 40.
>> > > Is it possible to force a different timewindow?
>> > > Below is some info from analysis.info
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwMGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=4hnvhCVX4pJzRESmdot0FI0cS7sKUWI-cIDKsihmrao=EmEPqCEEylIHfrDEVX7i7KSiT1QrAnz4423QPVyGdJg=>
>> <
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs=r6h1NqLGmsc3cSyXVgnrkGSvJNA79vDmmSjMUdNwGOA=
>> >
>> >  

Re: [Freesurfer] timewindow parameter in mkanalysis-sess

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Doug,
apart from the question whether or not to set the timewindow parameter to
80 for MION responses, I noticed that there is a discrepancy between
analysis.info and h.dat with regard to this parameter in v5.3.
If I set timewindow to 80 in mkanalysis-sess, it correctly prints this
parameter into analysis.info. However, in h.dat for the same analysis,
timewindow is 40.
I don't know if that is relevant, but it seems weird. Maybe it was already
addressed in version 6.

Caspar

Am Di., 13. Aug. 2019 um 22:51 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> That is in response to a 60 sec stimulus. The time window is the time
> needed to account for a very brief stimulus (ie, the impulse response).
> fsfast will automatically take into account the duration of the stimulus
> as listed in the paradigm file.
>
> On 8/13/19 2:14 PM, Caspar M. Schwiedrzik wrote:
> >
> > External Email - Use Caution
> >
> > Hi Doug,
> > Thanks for the advice.
> > I think the Leite et al. 2002 NeuroImage paper can be interpreted that
> > way. See Figure 1 and 2.
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__pop.cerco.ups-2Dtlse.fr_pdf0609_leite-5Ffp-5F02-5F283.pdf=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs=_NKVTMtmRmOeLrYx6styS12TMjsFNuVd2jKFxUKr85Y=
> >
> > Caspar
> >
> > On Tue, Aug 13, 2019 at 17:12 Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > When you use -gammafit, it automatically sets the time window to
> > 40. If
> > you really want it at 80, but -timewindow before -gammafit. Do you
> > really expect the MION hrf to last 80 sec?
> >
> > On 8/13/19 11:06 AM, Caspar M. Schwiedrzik wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hi!
> > > I am having difficulties setting the timewindow parameter in
> > > mkanalysis-sess in Freesurfer v5.3.
> > > I am trying to use 80 (data acquired with MION), but the parameter
> > > does not seem to affect analysis.info <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs=r6h1NqLGmsc3cSyXVgnrkGSvJNA79vDmmSjMUdNwGOA=
> >
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=CYJUPBXH2fLSD5LjpZmYtjXWz_bC8zt7q5gobDE5VLs=Ba7XLDz4JrZXYf4-uKSwAzN0dCldTpp68Yck9EDkQ4s=
> > >, where it
> > > is always 40.
> > > Is it possible to force a different timewindow?
> > > Below is some info from analysis.info <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs=r6h1NqLGmsc3cSyXVgnrkGSvJNA79vDmmSjMUdNwGOA=
> >
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=CYJUPBXH2fLSD5LjpZmYtjXWz_bC8zt7q5gobDE5VLs=Ba7XLDz4JrZXYf4-uKSwAzN0dCldTpp68Yck9EDkQ4s=
> > >.
> > > Thanks, Caspar
> > >
> > >
> > > # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> > > # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.5 2013/01/22 21:52:07
> > greve
> > > Exp $
> > > # MKACMD /neuro_tools/freesurfer/fsfast/bin/mkanalysis-sess -fsd
> > bold
> > > -native -timeoffset -2/2 -event-related -paradigm .para
> > > -nconditions 4 -TR 2 -gammafit 0 8 -gammaexp 0.3 *-timewindow 80*
> > > -refeventdur 0.5 -polyfit 2 -hpf 0.0109 -analysis  -funcstem
> > 
> > > -runlistfile .list -nuisreg motion.dat 6 -tpef tpef.dat
> > -acfbins
> > > 14 -acffwhm 0 -mask  -force
> > >
> > >
> > > analysis 
> > > mcstem fmc
> > > funcstem 
> > > fsd bold
> > > runlistfile .list
> > > TR 2
> > > RegDOF 6
> > > PerSession 1
> > > RawSpace volume native
> > > mask 
> > > RawFWHM 0
> > > RawSTC none
> > > UseB0DC 0
> > > ApplySubCortMask 1
> > > inorm 100
> &g

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Doug and Ruopeng,
thanks a lot for your advice!
Is there a way to display a meaningful legend? In tksurfer/rtview, we get a
linear legend that does not seem to make much sense and in freeview we
typically do not get anything when we choose color wheel and then click on
the legend button.
Thanks! Caspar


Am Di., 10. Sept. 2019 um 17:23 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> When you run rtview, it will run tksurfer. To get to the color wheel,
> open View->Configure->Overlay, then select "Color Wheel" under the
> "Color Scale" tab.
>
> On 9/10/19 4:03 AM, Caspar M. Schwiedrzik wrote:
> >
> > External Email - Use Caution
> >
> > Hi Doug and Roupeng,
> > did you already have the chance to look into the question how to
> > display the color wheel with rtview and/or freeview?
> > Thank you! Caspar
> >
> > Am Sa., 7. Sept. 2019 um 13:13 Uhr schrieb Caspar M. Schwiedrzik
> >  > <mailto:cschwie...@mail.rockefeller.edu>>:
> >
> > External Email - Use Caution
> >
> > Hi Doug and Ruopeng,
> > it would be amazing if you could dig out the information on how to
> > display the color wheel.
> > Looking forward to what you find!
> > Caspar
> >
> >
> > Am Fr., 6. Sept. 2019 um 17:14 Uhr schrieb Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>>:
> >
> > Hi Caspar, sorry for the delay. I have not used the retinotoy
> > stream in a long, long time so I don't know off the top of my
> > head. I'll have to look into it. tksurfer (from rtview) does
> > have a way to display using the color wheel, but I don't
> > remember how to do it.
> >
> > Ruopeng, can freeview display using a color wheel?
> >
> > On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Hi!
> >> I wanted to ask again whether there is a way to display the
> >> color wheel in rtview and/or freeview. We are debugging our
> >> analyses and it would be immensely helpful to have a legend
> >> that specifies the color assignments.
> >> Thank you,
> >> Caspar
> >>
> >> On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik
> >>  >> <mailto:cschwie...@rockefeller.edu>> wrote:
> >>
> >> Hi!
> >> I am following up on this thread trying to understand how
> >> to make the color wheel visible in rtview, or, if
> >> necessary, in freeview.
> >> Thank you! Caspar
> >>
> >>
> >> ___
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> >> Freesurfer@nmr.mgh.harvard.edu   Freesurfer@nmr.mgh.harvard.edu>
> >> *MailScanner has detected a possible fraud attempt from
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> >>
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> >
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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Doug and Roupeng,
did you already have the chance to look into the question how to display
the color wheel with rtview and/or freeview?
Thank you! Caspar

Am Sa., 7. Sept. 2019 um 13:13 Uhr schrieb Caspar M. Schwiedrzik <
cschwie...@mail.rockefeller.edu>:

> External Email - Use Caution
>
> Hi Doug and Ruopeng,
> it would be amazing if you could dig out the information on how to display
> the color wheel.
> Looking forward to what you find!
> Caspar
>
>
> Am Fr., 6. Sept. 2019 um 17:14 Uhr schrieb Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu>:
>
>> Hi Caspar, sorry for the delay. I have not used the retinotoy stream in a
>> long, long time so I don't know off the top of my head. I'll have to look
>> into it. tksurfer (from rtview) does have a way to display using the color
>> wheel, but I don't remember how to do it.
>>
>> Ruopeng, can freeview display using a color wheel?
>>
>> On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:
>>
>> External Email - Use Caution
>> Hi!
>> I wanted to ask again whether there is a way to display the color wheel
>> in rtview and/or freeview. We are debugging our analyses and it would be
>> immensely helpful to have a legend that specifies the color assignments.
>> Thank you,
>> Caspar
>>
>> On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik <
>> cschwie...@rockefeller.edu> wrote:
>>
>>> Hi!
>>> I am following up on this thread trying to understand how to make the
>>> color wheel visible in rtview, or, if necessary, in freeview.
>>> Thank you! Caspar
>>>
>>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "urldefense.proofpoint.com" claiming 
>> to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Doug and Ruopeng,
it would be amazing if you could dig out the information on how to display
the color wheel.
Looking forward to what you find!
Caspar


Am Fr., 6. Sept. 2019 um 17:14 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> Hi Caspar, sorry for the delay. I have not used the retinotoy stream in a
> long, long time so I don't know off the top of my head. I'll have to look
> into it. tksurfer (from rtview) does have a way to display using the color
> wheel, but I don't remember how to do it.
>
> Ruopeng, can freeview display using a color wheel?
>
> On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
> Hi!
> I wanted to ask again whether there is a way to display the color wheel in
> rtview and/or freeview. We are debugging our analyses and it would be
> immensely helpful to have a legend that specifies the color assignments.
> Thank you,
> Caspar
>
> On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik <
> cschwie...@rockefeller.edu> wrote:
>
>> Hi!
>> I am following up on this thread trying to understand how to make the
>> color wheel visible in rtview, or, if necessary, in freeview.
>> Thank you! Caspar
>>
>>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>  
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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I wanted to ask again whether there is a way to display the color wheel in
rtview and/or freeview. We are debugging our analyses and it would be
immensely helpful to have a legend that specifies the color assignments.
Thank you,
Caspar

On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik <
cschwie...@rockefeller.edu> wrote:

> Hi!
> I am following up on this thread trying to understand how to make the
> color wheel visible in rtview, or, if necessary, in freeview.
> Thank you! Caspar
>
>
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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I am following up on this thread trying to understand how to make the color
wheel visible in rtview, or, if necessary, in freeview.
Thank you! Caspar
___
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Re: [Freesurfer] mri_surf2surf without sphere.reg {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Thanks Doug, that worked! Caspar

Am Di., 3. Sept. 2019 um 17:03 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> Yes, just specify --surfreg white (or some other surface you do have).
>
> On 9/3/2019 9:51 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
> Hi!
> I am having some issues projecting retinotopic mapping data from a monkey
> analyzed in surface space onto its surface using rtview. The issue seems to
> be that the data need to be converted into paint format through
> mri_surf2surf, and that we do not have a ?h.sphere.reg file because the
> surface is not aligned to a template.
> Is it possible to run mri_surf2surf without reference to ?h.sphere.reg
> somehow? I tried with --s instead of source and target subject, but that
> didn't work.
> Alternatively, can we provide an identity matrix for ?h.sphere.reg,
> perhaps through mris_register?
>
> Any advice would be appreciated.
> Thanks, Caspar
>
> ___
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[Freesurfer] mri_surf2surf without sphere.reg

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I am having some issues projecting retinotopic mapping data from a monkey
analyzed in surface space onto its surface using rtview. The issue seems to
be that the data need to be converted into paint format through
mri_surf2surf, and that we do not have a ?h.sphere.reg file because the
surface is not aligned to a template.
Is it possible to run mri_surf2surf without reference to ?h.sphere.reg
somehow? I tried with --s instead of source and target subject, but that
didn't work.
Alternatively, can we provide an identity matrix for ?h.sphere.reg, perhaps
through mris_register?

Any advice would be appreciated.
Thanks, Caspar
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[Freesurfer] Two questions about flac_desmat.m for retinotopy analysis in fsfast

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Doug,
I have two quick questions about the analysis of polar angle maps:
1. Does the analysis take the HRF (lag etc.) into account?
2. Our stimulation starts at 12 for clockwise and counter clockwise. I
found this older post
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-August/025241.html
specifying changes to flac_desmat.m to account for that. I was wondering
whether to change case {'fourier'} and/or case {'abret'}?

This is using version 5.3.
Thank you!
Caspar
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Re: [Freesurfer] timewindow parameter in mkanalysis-sess

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Doug,
Thanks for the advice.
I think the Leite et al. 2002 NeuroImage paper can be interpreted that way.
See Figure 1 and 2.
http://pop.cerco.ups-tlse.fr/pdf0609/leite_fp_02_283.pdf

Caspar

On Tue, Aug 13, 2019 at 17:12 Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> When you use -gammafit, it automatically sets the time window to 40. If
> you really want it at 80, but -timewindow before -gammafit. Do you
> really expect the MION hrf to last 80 sec?
>
> On 8/13/19 11:06 AM, Caspar M. Schwiedrzik wrote:
> >
> > External Email - Use Caution
> >
> > Hi!
> > I am having difficulties setting the timewindow parameter in
> > mkanalysis-sess in Freesurfer v5.3.
> > I am trying to use 80 (data acquired with MION), but the parameter
> > does not seem to affect analysis.info <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=CYJUPBXH2fLSD5LjpZmYtjXWz_bC8zt7q5gobDE5VLs=Ba7XLDz4JrZXYf4-uKSwAzN0dCldTpp68Yck9EDkQ4s=
> >, where it
> > is always 40.
> > Is it possible to force a different timewindow?
> > Below is some info from analysis.info <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=CYJUPBXH2fLSD5LjpZmYtjXWz_bC8zt7q5gobDE5VLs=Ba7XLDz4JrZXYf4-uKSwAzN0dCldTpp68Yck9EDkQ4s=
> >.
> > Thanks, Caspar
> >
> >
> > # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> > # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.5 2013/01/22 21:52:07 greve
> > Exp $
> > # MKACMD /neuro_tools/freesurfer/fsfast/bin/mkanalysis-sess -fsd bold
> > -native -timeoffset -2/2 -event-related -paradigm .para
> > -nconditions 4 -TR 2 -gammafit 0 8 -gammaexp 0.3 *-timewindow 80*
> > -refeventdur 0.5 -polyfit 2 -hpf 0.0109 -analysis  -funcstem 
> > -runlistfile .list -nuisreg motion.dat 6 -tpef tpef.dat -acfbins
> > 14 -acffwhm 0 -mask  -force
> >
> >
> > analysis 
> > mcstem fmc
> > funcstem 
> > fsd bold
> > runlistfile .list
> > TR 2
> > RegDOF 6
> > PerSession 1
> > RawSpace volume native
> > mask 
> > RawFWHM 0
> > RawSTC none
> > UseB0DC 0
> > ApplySubCortMask 1
> > inorm 100
> > acfbins 14
> > fixacf  1
> > acffwhm 0
> > acfsvd  0
> > designtype event-related
> > tpexclude tpef.dat
> > nskip 0
> > polyfit 2
> > HPFCutoffHz 0.0109
> > HeteroGCor 0
> > nconditions 4
> > parname .para
> > RefEventDur 0.5
> > *timewindow 40.00*
> > prestim 0
> > TER 0.05
> > gamma 0 8 0.3 0
> > stimulusdelay -2/2
> > Condition 1 Condition01
> > Condition 2 Condition02
> > Condition 3 Condition03
> > Condition 4 Condition04
> > nuisreg motion.dat 6
> >
> > ___
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[Freesurfer] timewindow parameter in mkanalysis-sess

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I am having difficulties setting the timewindow parameter in
mkanalysis-sess in Freesurfer v5.3.
I am trying to use 80 (data acquired with MION), but the parameter does not
seem to affect analysis.info, where it is always 40.
Is it possible to force a different timewindow?
Below is some info from analysis.info.
Thanks, Caspar


# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
# MKAVERSION $Id: mkanalysis-sess,v 1.64.2.5 2013/01/22 21:52:07 greve Exp $
# MKACMD /neuro_tools/freesurfer/fsfast/bin/mkanalysis-sess -fsd bold
-native -timeoffset -2/2 -event-related -paradigm .para -nconditions 4
-TR 2 -gammafit 0 8 -gammaexp 0.3 *-timewindow 80* -refeventdur 0.5
-polyfit 2 -hpf 0.0109 -analysis  -funcstem  -runlistfile .list
-nuisreg motion.dat 6 -tpef tpef.dat -acfbins 14 -acffwhm 0 -mask 
-force


analysis 
mcstem fmc
funcstem 
fsd bold
runlistfile .list
TR 2
RegDOF 6
PerSession 1
RawSpace volume native
mask 
RawFWHM 0
RawSTC none
UseB0DC 0
ApplySubCortMask 1
inorm 100
acfbins 14
fixacf  1
acffwhm 0
acfsvd  0
designtype event-related
tpexclude tpef.dat
nskip 0
polyfit 2
HPFCutoffHz 0.0109
HeteroGCor 0
nconditions 4
parname .para
RefEventDur 0.5
*timewindow 40.00*
prestim 0
TER 0.05
gamma 0 8 0.3 0
stimulusdelay -2/2
Condition 1 Condition01
Condition 2 Condition02
Condition 3 Condition03
Condition 4 Condition04
nuisreg motion.dat 6
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Re: [Freesurfer] Deconvolution with FSFAST {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Doug,
I am referring to deconvolution in the SPM sense, where they use (something
like) ridge regression to get an estimate of neuronal activity from the
measured BOLD response.
The idea is to use that neural time series to construct predictors for a
psycho-physiological interaction (PPI) analysis, as in Gitelman et al. 2003
(
https://cfn.upenn.edu/stslab/wiki_links/fmri_club/fxncxn/Gitelman_etal_2003_Neuroimage.pdf,
see page 201).

Thanks! Caspar

Am Mo., 12. Aug. 2019 um 16:02 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> When you say deconvolution, what do you mean exactly? There is an FIR
> model (finite impulse response) that will extract the hemodynamic response
> without any assumptions, ie, the signal average at stimulus onset, the
> signal average at 1TR post onset, the signal average at 2TR post onset, etc.
>
> On 8/9/2019 7:10 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
> Hi!
> I was wondering whether it is possible to do deconvolution of an fMRI time
> series with FSFAST?
> Specifically, I would like to get a deconvolved signal from a region of
> interest to prepare predictors for a PPI analysis.
> Additional considerations: data is from an event-related design, and was
> acquired with MION contrast agent.
> I found some older documentation on selxavg2, but I am not sure whether
> that still applies (I am using version 5.3). Also, I do not need an
> event-related average as output, but a continuous time series.
>
> Thanks for any advice!
> Caspar
>
>
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[Freesurfer] Deconvolution with FSFAST

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I was wondering whether it is possible to do deconvolution of an fMRI time
series with FSFAST?
Specifically, I would like to get a deconvolved signal from a region of
interest to prepare predictors for a PPI analysis.
Additional considerations: data is from an event-related design, and was
acquired with MION contrast agent.
I found some older documentation on selxavg2, but I am not sure whether
that still applies (I am using version 5.3). Also, I do not need an
event-related average as output, but a continuous time series.

Thanks for any advice!
Caspar
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Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
Unfortunately, it turns out that downgrading glibc does not solve this
issue, neither with .14 nor with .15 versions.

Doug, we are calling mri_convert from a csh script, with the following
options:
mri_convert -i inputvolume.mgz \
-o outputvolume.nii.gz \
--out_orientation LPS \
-iis .5 -ijs .5 -iks .5 \
-vs 1.2 1.2 1.2

We then simply get segmentation fault (core dumped).
It seems to work when we run the same command directly in the terminal.
Caspar


Am Do., 16. Mai 2019 um 23:10 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> Can you send the command line and full terminal output?
>
> On 5/16/19 5:17 AM, Caspar M. Schwiedrzik wrote:
> >
> > External Email - Use Caution
> >
> > Hi!
> > We are getting segmentation fault (core dumped) error when trying to
> > run mri_convert on NIFTI files. This is running Freesurfer v5.3 on
> > Centos6, specifically v1.179.2.7 of mri_convert.
> >
> > I suspect that this has to do with libcrypt incompatibilities
> > described for other operating systems , e.g., here:
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_pipermail__freesurfer_2014-2DSeptember_040528.html=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s=hvSTVmJcAZKj26WCCcgZbqDQcLE9GL1yLaGOXIcGBEY=
> >
> > and in the known issues list of v5.3. here
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_PreviousReleaseNotes=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s=PUDfyokNDX6MKj07m6SVKp-n_mHLc-wsBpe1nedrdD8=
> .
> >
> > We have libcrypt version 2.17 installed and do not have access to
> > libcrypt-2.14.1.so <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__libcrypt-2D2.14.1.so=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s=oWqfVu5YGSWScZMw3Ypfdy53osHoNywLPtAffB75oR8=
> >.
> > Is there a way to get libcrypt-2.14.1.so <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__libcrypt-2D2.14.1.so=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s=oWqfVu5YGSWScZMw3Ypfdy53osHoNywLPtAffB75oR8=>
>
> > from you or is there another known workaround (other then updating to
> > Freesurfer 6)?
> >
> > Thank you very much! Caspar
> >
> >
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[Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
We are getting segmentation fault (core dumped) error when trying to run
mri_convert on NIFTI files. This is running Freesurfer v5.3 on Centos6,
specifically v1.179.2.7 of mri_convert.

I suspect that this has to do with libcrypt incompatibilities described for
other operating systems , e.g., here:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528.html
and in the known issues list of v5.3. here
https://surfer.nmr.mgh.harvard.edu/fswiki/PreviousReleaseNotes.

We have libcrypt version 2.17 installed and do not have access to
libcrypt-2.14.1.so.
Is there a way to get libcrypt-2.14.1.so from you or is there another known
workaround (other then updating to Freesurfer 6)?

Thank you very much! Caspar
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Re: [Freesurfer] dimensions swapped with head first-prone acquisition {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Great, thanks a lot, Doug!
Caspar

On Tue, May 7, 2019 at 17:46 Greve, Douglas N.,Ph.D. 
wrote:

> The --in_orientation should work. The RAS coordinates will reflect subject
> space (which is probably what you want) and  not scanner space.
>
> On 5/7/2019 11:27 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
>
> Hi!
> I have data acquired on a Siemens scanner with head first-prone. When I
> convert the dicom files to MGZ, left and right and superior and inferior,
> respectively, are swapped. The anterior-posterior dimension is ok. I am
> wondering what the correct way to correct this is?
>
> Following this entry in the wiki
> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_LeftRightReversal=DwMGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=cI2TpE_SkFvbwqC84Bc86jo4ozmgNkmU13xjkDLys9A=EXeP167X4yKEzh0Lgc89nZnwFDSIYSl94unVCZxVDsQ=>,
> it seems that I can use mri_convert with --in_orientation for that, and the
> images indeed look correct when I do this. I am however wondering whether I
> have to do the conversion to COR and fix the RAS coordinates as well?
> I found a 2007 entry on the mailing list about that
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-October/006250.html
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_2007-2DOctober_006250.html=DwMGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=cI2TpE_SkFvbwqC84Bc86jo4ozmgNkmU13xjkDLys9A=onANhhGknqVlwbUsGqed52ahoM3izfYDJuN30UbXjC8=>,
> but it does not specify how to proceed.
>
> Your advice would be appreciated!
> Thanks, Caspar
>
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[Freesurfer] dimensions swapped with head first-prone acquisition

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I have data acquired on a Siemens scanner with head first-prone. When I
convert the dicom files to MGZ, left and right and superior and inferior,
respectively, are swapped. The anterior-posterior dimension is ok. I am
wondering what the correct way to correct this is?

Following this entry in the wiki
https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal, it seems that
I can use mri_convert with --in_orientation for that, and the images indeed
look correct when I do this. I am however wondering whether I have to do
the conversion to COR and fix the RAS coordinates as well?
I found a 2007 entry on the mailing list about that
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-October/006250.html,
but it does not specify how to proceed.

Your advice would be appreciated!
Thanks, Caspar
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[Freesurfer] Deadline approaching: Deadline approaching: Neuroscience data analyst (f/m) opening at ENI Göttingen, Germany (new opening)

[Caspar M. Schwiedrzik]

External Email - Use Caution

 The European Neuroscience Institute Göttingen (Germany) is seeking a
*Neuroscience data analyst (f/m) *
initially limited until 31.12.2019 with extension options, full-time |
salary according to TV-L

The European Neuroscience Institute is looking to fill the position of a
data analyst (full time). We are looking for a data analyst with interest
and experience in systems neuroscience. Research at the European
Neuroscience Institute ranges from molecular biology to human psychophysics
and involves a range of model organisms (from drosophila to non-human
primates), techniques and approaches (electrophysiology, two-photon
imaging, fMRI, EEG, behavior). The data analyst will work closely with all
of the various research groups at the European Neuroscience Institute,
supporting research efforts, e.g., through modelling and statistical
analyses of high-dimensional data, image processing, and
programming/development of experiments. S/he will have the opportunity to
develop and publish, e.g., analytical tools that arise from this work.

   - The applicant should possess a university degree (minimally M. Sc. or
   equivalent) in a relevant field, e.g., statistics, biostatistics,
   informatics, or similar. Prior experience in the field of systems
   neuroscience is highly desired.
   - The applicant should have experience in a research setting utilizing
   quantitative methods and statistics. The applicant shall demonstrate strong
   analytical skills and knowledge of novel and emerging analysis techniques
   is highly desired. Future/forward thinking in the area of big data
   analytics/informatics and applying them to contribute to the research
   groups’ scientific process is expected.
   - The applicant should be skilled in the analysis of multivariate
   datasets to reveal patterns and build models; conduct exploratory data
   analysis, and communicate with team lead/team members; identify
   improvements for existing data management and recommend requirements for
   new systems.
   - Contribute to replicability by making suggestions for existing data
   management and recommend requirements for new systems and identify
   potential data integrity issues. We are committed to open data/open
   science and appreciate interest and expertise in this area.
   - Utilize programming languages such as Python, Matlab and/or C++.
   - Good command of English is mandatory.

The University Medical Center Göttingen takes flexible account of the
individual design of working hours at the workplace. It is interested in
implementing the wishes of its employees as far as possible. If you are
interested in this job and have specific questions about working hours,
please contact us.

Women are especially encouraged to apply. Applicants with disabilities and
equal qualifications will be given preferential treatment.
We look forward to receiving your application by * November 30th, 2018*

University Medical Center Göttingen
European Neuroscience Institute Göttingen
Dr. Caspar Schwiedrzik
Group Leader
Grisebachstr. 5
37077 Göttingen
Tel.: 0551/39-61371
Fax: 0551/39-61399
E-Mail: c.schwiedr...@eni-g.de <+c.schwiedr...@eni-g.de>
Web: http://www.eni-g.de/

Please send your application only via e-mail as a PDF-file.

also see:
http://www.med.uni-goettingen.de/de/content/service/stellenanzeigen.php?id=2250
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[Freesurfer] Deadline approaching: PhD in visual perceptual learning at the Neural Circuits and Cognition lab @ ENI & German Primate Center Göttingen

[Caspar M. Schwiedrzik]

External Email - Use Caution

The European Neuroscience Institute in Göttingen (ENI-G) Germany, a
partnership between the University Medical Center Göttingen and the
Max-Planck-Society, is seeking a




*Ph.D. student *

About us:



The Neural Circuits and Cognition lab of Caspar Schwiedrzik at the European
Neuroscience Institute (ENI-G) and the German Primate Center
 (DPZ) in Göttingen, Germany is
looking for an outstanding PhD student interested in studying the neural
basis of perceptual learning in vision. The project investigates neural
mechanisms of learning and perception at the level of circuits and single
cells, utilizing functional magnetic resonance imaging (fMRI) in
combination with electrophysiology and behavioral testing in humans and
non-human primates. It is funded by an ERC Starting Grant (Acronym VarPL;
“Specificity or generalization? Neural mechanisms for perceptual learning
with variability”). The PhD student’s project will focus on developing new
perceptual learning paradigms and investigating the neural basis of
perceptual learning in humans using fMRI. In addition, the PhD student will
cooperate with other lab members on parallel electrophysiological and fMRI
experiments as well as comparative research exploring the same questions in
non-human primates.



The lab seeks to understand the cortical basis and computational principles
of perception and experience-dependent plasticity in the macaque and human
brain (see http://www.eni-g.de/groups/neural-circuits-and-cognition). To
this end, we use a multimodal approach including fMRI-guided
electrophysiological recordings in non-human primates and fMRI and ECoG in
humans. The PhD student will play a key role in our research efforts in
this area. The lab is located at the ENI (http://www.eni-g.de) and the DPZ (
http://www.dpz.eu), which are interdisciplinary research centers with
international faculty and students pursuing cutting-edge research in
neuroscience. The PhD student will have access to a new imaging center
 with a dedicated 3T research scanner,
electrophysiology, and behavioral setups.



ENI-G is engaged in experimental molecular and cellular research on the
central and peripheral nervous systems as well as cognitive and systems
neurosciences research. ENI is part of the University Medical Center
Göttingen and associated with the Max Planck Society. The University
Medical Center Göttingen is a tertiary care center. Its 7,400 employees
work in over 65 departments and facilities to provide top-quality patient
care, excellent research and modern teaching facilities. Göttingen provides
a vibrant and stimulating neuroscience community with a strong background
in computational as well as experimental neurosciences. The PhD student
will have the opportunity to join one of the fourteen programs of the
Göttingen Graduate School for Neurosciences, Biophysics, and Molecular
Biosciences (http://www.ggnb.uni-goettingen.de).



Your profile:



The position will be available starting in November 2018 with an initial
appointment for 3 years and a salary according to 50% TVL-13. Candidates
should have a degree (master, diploma or equivalent) in a relevant field
(e.g., neuroscience, psychology, biology), and ideally prior experience in
fMRI, strong quantitative, programming, and experimental skills, and share
a passion for understanding the neural basis of visual perception and its
plasticity. Interested candidates should send their curriculum vitae, a
description of their scientific interest and the names and contact
information of up to two references who are able to comment on your
academic background and who agreed to be contacted to c.schwiedr...@eni-g.de,
preferably before *October 10th, 2018*, but later expressions of interest
will be considered until the position is filled. A good command of English
is a requirement, but fluency in German is not essential.





Please apply by 10.10.2018 to:
Universitätsmedizin Göttingen

European Neuroscience Institute Göttingen

Neural Circuits and Cognition Lab
Dr. Caspar Schwiedrzik
Grisebachstr. 5
37077 Göttingen
Germany
Tel.: +49-(0)551-39-61371
E-Mail: c.schwiedr...@eni-g.de
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[Freesurfer] PhD in visual perceptual learning at the Neural Circuits and Cognition lab @ ENI & German Primate Center Göttingen

[Caspar M. Schwiedrzik]

External Email - Use Caution

The European Neuroscience Institute in Göttingen (ENI-G) Germany, a
partnership between the University Medical Center Göttingen and the
Max-Planck-Society, is seeking a




*Ph.D. student *

About us:



The Neural Circuits and Cognition lab of Caspar Schwiedrzik at the European
Neuroscience Institute (ENI-G) and the German Primate Center
 (DPZ) in Göttingen, Germany is
looking for an outstanding PhD student interested in studying the neural
basis of perceptual learning in vision. The project investigates neural
mechanisms of learning and perception at the level of circuits and single
cells, utilizing functional magnetic resonance imaging (fMRI) in
combination with electrophysiology and behavioral testing in humans and
non-human primates. It is funded by an ERC Starting Grant (Acronym VarPL;
“Specificity or generalization? Neural mechanisms for perceptual learning
with variability”). The PhD student’s project will focus on developing new
perceptual learning paradigms and investigating the neural basis of
perceptual learning in humans using fMRI. In addition, the PhD student will
cooperate with other lab members on parallel electrophysiological and fMRI
experiments as well as comparative research exploring the same questions in
non-human primates.



The lab seeks to understand the cortical basis and computational principles
of perception and experience-dependent plasticity in the macaque and human
brain (see http://www.eni-g.de/groups/neural-circuits-and-cognition). To
this end, we use a multimodal approach including fMRI-guided
electrophysiological recordings in non-human primates and fMRI and ECoG in
humans. The PhD student will play a key role in our research efforts in
this area. The lab is located at the ENI (http://www.eni-g.de) and the DPZ (
http://www.dpz.eu), which are interdisciplinary research centers with
international faculty and students pursuing cutting-edge research in
neuroscience. The PhD student will have access to a new imaging center
 with a dedicated 3T research scanner,
electrophysiology, and behavioral setups.



ENI-G is engaged in experimental molecular and cellular research on the
central and peripheral nervous systems as well as cognitive and systems
neurosciences research. ENI is part of the University Medical Center
Göttingen and associated with the Max Planck Society. The University
Medical Center Göttingen is a tertiary care center. Its 7,400 employees
work in over 65 departments and facilities to provide top-quality patient
care, excellent research and modern teaching facilities. Göttingen provides
a vibrant and stimulating neuroscience community with a strong background
in computational as well as experimental neurosciences. The PhD student
will have the opportunity to join one of the fourteen programs of the
Göttingen Graduate School for Neurosciences, Biophysics, and Molecular
Biosciences (http://www.ggnb.uni-goettingen.de).



Your profile:



The position will be available starting in November 2018 with an initial
appointment for 3 years and a salary according to 50% TVL-13. Candidates
should have a degree (master, diploma or equivalent) in a relevant field
(e.g., neuroscience, psychology, biology), and ideally prior experience in
fMRI, strong quantitative, programming, and experimental skills, and share
a passion for understanding the neural basis of visual perception and its
plasticity. Interested candidates should send their curriculum vitae, a
description of their scientific interest and the names and contact
information of up to two references who are able to comment on your
academic background and who agreed to be contacted to c.schwiedr...@eni-g.de,
preferably before October 10th, 2018, but later expressions of interest
will be considered until the position is filled. A good command of English
is a requirement, but fluency in German is not essential.





Please apply by 10.10.2018 to:
Universitätsmedizin Göttingen

European Neuroscience Institute Göttingen

Neural Circuits and Cognition Lab
Dr. Caspar Schwiedrzik
Grisebachstr. 5
37077 Göttingen
Germany
Tel.: +49-(0)551-39-61371
E-Mail: c.schwiedr...@eni-g.de
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[Freesurfer] memprage processing steps?

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I was wondering whether there is an overview / walkthrough for all the
steps involved when working with MEMPRAGE?
I am thinking dcmunpack, mri-concat / mri_average, flags for recon-all,
mris_make_surfaces, etc.

Any pointers would be appreciated.
Thanks!
Caspar
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Re: [Freesurfer] No keyboard input accepted in freeview and tkmedit

[Caspar M. Schwiedrzik]

Hi!
We are running Freesurfer on a central server and I don't have a second one
at hand with Freesurfer installed to test this, unfortunately.
It seems that Freeview is working fine now, so this may well have been just
a hickup.
However, the problem persists with tkmedit. If you had any leads on how to
fix this, it would be great.
I love the vintage feel of tkmedit and use it quite a bit :)

Thanks, Caspar


2017-06-20 16:28 GMT+02:00 Z K <zkauf...@nmr.mgh.harvard.edu>:

> The tktools like tkmedit and tksurfer are more-or-less deprecated and we
> do sometimes get user reports about not accepting keyboard input.
> However, freeview should work fine as we use Centos 7 platform for our
> testing and have not seen any such issues for that application. Is it
> possible for you to test this issue on another machine in your
> environment and verify it exists and more than one machine?
>
> On 06/19/2017 11:59 AM, Caspar M. Schwiedrzik wrote:
> > Hi!
> > I have a weird issue where tkmedit and freeview both do not accept any
> > keyboard input.
> > This is Freesurfer v5.3 running on Centos 7, connecting via RDP.
> > I saw a couple of posts by other users having this problem, but I could
> > not find any solutions/replies on the mailing list.
> > Does anyone know how to fix this?
> > Thanks, Caspar
> >
> >
> > ___
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> OBQCWQuisLgFD6kkH7a74=cPVoPh6MMnFjgjL9g4KUV33YHRUJhlfrfLhZcuXWcnA=
> >
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>
>
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[Freesurfer] No keyboard input accepted in freeview and tkmedit

[Caspar M. Schwiedrzik]

Hi!
I have a weird issue where tkmedit and freeview both do not accept any
keyboard input.
This is Freesurfer v5.3 running on Centos 7, connecting via RDP.
I saw a couple of posts by other users having this problem, but I could not
find any solutions/replies on the mailing list.
Does anyone know how to fix this?
Thanks, Caspar
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[Freesurfer] separate medial from lateral part in superiorfrontal parcel of Desikan-Killiany atlas

[Caspar M. Schwiedrzik]

Hi!
Is there by any chance a known demarcation line in in the XYZ coordinates
of the Desikan-Killiany atlas that could be used to separate the
superiorfrontal parcel into a medial and a lateral part?

Thanks!
Caspar
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Re: [Freesurfer] Freesurfer on Centos 7?

[Caspar M. Schwiedrzik]

great, thanks!
caspar


2016-12-09 16:45 GMT-05:00 :

>
> To get 5.3 working on machines with perl 5.22 or later I will refer you to
> the following thread:
>
>   https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
> edu/msg50383.html
>
> I cant say for sure how many mni scripts will need to point the the older
> version of perl, its probably subjects dependant. But I would think it
> would be 5 or less.
>
> > Thanks for letting me know!
> > What about v5.3?
> > Do I merely need to replace nu_estimate_np_and_em and sharpen_volume, or
> > is
> > there anything else I would need to get it running?
> > Caspar
> >
> >
> > 2016-12-09 16:27 GMT-05:00 :
> >
> >>
> >> The dev version of freesurfer (and the upcoming v6 release) is
> >> compatible
> >> with Centos7 and also fixes the perl/MNI issue.
> >>
> >>
> >>
> >> > Hi!
> >> > I was wondering whether there is an update from the 2014 thread on
> >> > Freesurfer's compatibility with Centos 7? The old thread is here:
> >> > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
> >> edu/msg38466.html
> >> >
> >> > I have also come across this website mentioning some changes in the
> >> > installation related to Perl and MNI tools:
> >> > http://miconsult.weebly.com/blog/freesurfer-running-on-centos-7
> >> >
> >> > Any insights would be appreciated.
> >> > Thanks, Caspar
> >> > ___
> >> > Freesurfer mailing list
> >> > Freesurfer@nmr.mgh.harvard.edu
> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >> ___
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> >> it
> >> is
> >> addressed. If you believe this e-mail was sent to you in error and the
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> >> contains patient information, please contact the Partners Compliance
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> >> in
> >> error
> >> but does not contain patient information, please contact the sender and
> >> properly
> >> dispose of the e-mail.
> >>
> >>
> >
>
>
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Re: [Freesurfer] Freesurfer on Centos 7?

[Caspar M. Schwiedrzik]

Thanks for letting me know!
What about v5.3?
Do I merely need to replace nu_estimate_np_and_em and sharpen_volume, or is
there anything else I would need to get it running?
Caspar


2016-12-09 16:27 GMT-05:00 :

>
> The dev version of freesurfer (and the upcoming v6 release) is compatible
> with Centos7 and also fixes the perl/MNI issue.
>
>
>
> > Hi!
> > I was wondering whether there is an update from the 2014 thread on
> > Freesurfer's compatibility with Centos 7? The old thread is here:
> > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
> edu/msg38466.html
> >
> > I have also come across this website mentioning some changes in the
> > installation related to Perl and MNI tools:
> > http://miconsult.weebly.com/blog/freesurfer-running-on-centos-7
> >
> > Any insights would be appreciated.
> > Thanks, Caspar
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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[Freesurfer] Freesurfer on Centos 7?

[Caspar M. Schwiedrzik]

Hi!
I was wondering whether there is an update from the 2014 thread on
Freesurfer's compatibility with Centos 7? The old thread is here:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38466.html

I have also come across this website mentioning some changes in the
installation related to Perl and MNI tools:
http://miconsult.weebly.com/blog/freesurfer-running-on-centos-7

Any insights would be appreciated.
Thanks, Caspar
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Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

[Caspar M. Schwiedrzik]

Hi Zeke,
I tried the is new version. Now I am getting:

mri_coreg: /lib64/libuuid.so.1: no version information available (required
by mri_coreg)
mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found
(required by mri_coreg)
mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
(required by mri_coreg)
mri_coreg: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
mri_coreg)

Caspar


2015-11-23 14:20 GMT-05:00 <zkauf...@nmr.mgh.harvard.edu>:

> There were some recent changes in the build that eliminated the necessity
> for that library. Casper, can you try using this most recent version and
> let me know if it works?
>
>
> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_coreg
>
> Thanks,
>
> -Zeke
>
>
> > Zeke, is this a new library that we need for v6?
> > doug
> >
> > On 11/20/2015 09:42 AM, Caspar M. Schwiedrzik wrote:
> >> Hi Doug,
> >> when I try to execute mri_coreg, I get the following error message:
> >>
> >> error while loading shared libraries: libnetcdf.so.6: cannot open
> >> shared object file: no such file or directory
> >>
> >> Caspar
> >>
> >>
> >> 2015-11-19 18:49 GMT-05:00 Douglas Greve <gr...@nmr.mgh.harvard.edu
> >> <mailto:gr...@nmr.mgh.harvard.edu>>:
> >>
> >>
> >> Can you try mri_coreg instead of fsl?
> >>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
> >>
> >>
> >>
> >>
> >> On 11/19/15 5:25 PM, Caspar M. Schwiedrzik wrote:
> >>> Hi!
> >>> I am trying to align a mean EPI volume and a Bruker magnitude map
> >>> from a fieldmap measurement using tkregister2, fsl_rigid_register
> >>> and mri_vol2vol. Unfortunately, it seems that somewhere, most
> >>> likely during fsl_rigid_register, the image orientation get
> >>> scrambled, and the output has the wrong orientation.
> >>>
> >>> Here is what I get from*tkregister2:*
> >>>
> >>> target  volume epi.nii
> >>> movable volume fieldmap0001.nii
> >>> reg file mag_2_mocovol.register.dat
> >>> LoadVol0
> >>> ZeroCRAS   0
> >>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
> >>> Diagnostic Level -1
> >>> INFO: loading target epi.nii
> >>> Setting targ orientation to RIA
> >>> INFO: target does not conform to COR format, so I'm going to
> >>> reslice to COR. This will not affect the final registration.
> >>> Ttarg: 
> >>> -1.000   0.000   0.000 128.000;
> >>>  0.000   0.000   1.000 -128.000;
> >>>  0.000  -1.000   0.000 128.000;
> >>>  0.000   0.000   0.000   1.000;
> >>> INFO: loading movable fieldmap0001.nii
> >>> Setting mov orientation to RIA
> >>> Tmov: 
> >>> -0.547   0.000   0.000   17.500;
> >>>  0.000   0.000   0.547  -17.500;
> >>>  0.000  -0.547   0.000   17.500;
> >>>  0.000   0.000   0.000   1.000;
> >>> mkheaderreg = 1, float2int = 0
> >>> Computing reg from header (and possibly input matrix)
> >>>  Input registration matrix (computed) 
> >>> -1.000   0.000   0.000  -0.587;
> >>>  0.000   1.000   0.000  -2.150;
> >>>  0.000   0.000   1.000  -2.188;
> >>>  0.000   0.000   0.000   1.000;
> >>> ---
> >>>  Input registration matrix 
> >>> -1.000   0.000   0.000  -0.587;
> >>>  0.000   1.000   0.000  -2.150;
> >>>  0.000   0.000   1.000  -2.188;
> >>>  0.000   0.000   0.000   1.000;
> >>> Determinant -1
> >>> subject = rat
> >>> RegMat ---
> >>>  1.000   0.000   0.000  -0.587;
> >>>  0.000   1.000   0.000  -2.150;
> >>>  0.000   0.000   1.000  -2.188;
> >>>  0.000   0.000   0.000   1.000;
> >>> FSLOUTPUTTYPE NIFTI_GZ
> >>> tkreg2FSL: mov det = 0.163555, ref det = 0.154688
> >>> INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det,
> >>>   applying LR flip to registration matrix.
> >>> INFO: FSL2FreeSurfer: Ref volu

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

[Caspar M. Schwiedrzik]

Red Hat Enterprise Linux Server release 5.9 (Tikanga)
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

Caspar


2015-11-23 14:37 GMT-05:00 <zkauf...@nmr.mgh.harvard.edu>:

> What system are you running on? Also, what are the contents of your
> build-stamp.txt file (in your FREESURFER_HOME directory)?
>
> -Zeke
>
>
> > Hi Zeke,
> > I tried the is new version. Now I am getting:
> >
> > mri_coreg: /lib64/libuuid.so.1: no version information available
> (required
> > by mri_coreg)
> > mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found
> > (required by mri_coreg)
> > mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
> > (required by mri_coreg)
> > mri_coreg: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
> > mri_coreg)
> >
> > Caspar
> >
> >
> > 2015-11-23 14:20 GMT-05:00 <zkauf...@nmr.mgh.harvard.edu>:
> >
> >> There were some recent changes in the build that eliminated the
> >> necessity
> >> for that library. Casper, can you try using this most recent version and
> >> let me know if it works?
> >>
> >>
> >>
> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_coreg
> >>
> >> Thanks,
> >>
> >> -Zeke
> >>
> >>
> >> > Zeke, is this a new library that we need for v6?
> >> > doug
> >> >
> >> > On 11/20/2015 09:42 AM, Caspar M. Schwiedrzik wrote:
> >> >> Hi Doug,
> >> >> when I try to execute mri_coreg, I get the following error message:
> >> >>
> >> >> error while loading shared libraries: libnetcdf.so.6: cannot open
> >> >> shared object file: no such file or directory
> >> >>
> >> >> Caspar
> >> >>
> >> >>
> >> >> 2015-11-19 18:49 GMT-05:00 Douglas Greve <gr...@nmr.mgh.harvard.edu
> >> >> <mailto:gr...@nmr.mgh.harvard.edu>>:
> >> >>
> >> >>
> >> >> Can you try mri_coreg instead of fsl?
> >> >>
> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> On 11/19/15 5:25 PM, Caspar M. Schwiedrzik wrote:
> >> >>> Hi!
> >> >>> I am trying to align a mean EPI volume and a Bruker magnitude
> >> map
> >> >>> from a fieldmap measurement using tkregister2,
> >> fsl_rigid_register
> >> >>> and mri_vol2vol. Unfortunately, it seems that somewhere, most
> >> >>> likely during fsl_rigid_register, the image orientation get
> >> >>> scrambled, and the output has the wrong orientation.
> >> >>>
> >> >>> Here is what I get from*tkregister2:*
> >> >>>
> >> >>> target  volume epi.nii
> >> >>> movable volume fieldmap0001.nii
> >> >>> reg file mag_2_mocovol.register.dat
> >> >>> LoadVol0
> >> >>> ZeroCRAS   0
> >> >>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
> >> >>> Diagnostic Level -1
> >> >>> INFO: loading target epi.nii
> >> >>> Setting targ orientation to RIA
> >> >>> INFO: target does not conform to COR format, so I'm going to
> >> >>> reslice to COR. This will not affect the final registration.
> >> >>> Ttarg: 
> >> >>> -1.000   0.000   0.000 128.000;
> >> >>>  0.000   0.000   1.000 -128.000;
> >> >>>  0.000  -1.000   0.000 128.000;
> >> >>>  0.000   0.000   0.000   1.000;
> >> >>> INFO: loading movable fieldmap0001.nii
> >> >>> Setting mov orientation to RIA
> >> >>> Tmov: 
> >> >>> -0.547   0.000   0.000   17.500;
> >> >>>  0.000   0.000   0.547  -17.500;
> >> >>>  0.000  -0.547   0.000   17.500;
> >> >>>  0.000   0.000   0.000   1.000;
> >> >>> mkheaderreg = 1, float2int = 0
> >> >>> Computing reg from header (and possibly input matrix)
> >> >>>  Input registration matrix (computed) 
> >> >

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

[Caspar M. Schwiedrzik]

Hi Zeke,
thanks for providing the link, and sorry for not clarifying which version I
am using earlier.
The centos4 version you provided now does not throw the previous errors.
Thanks again, Caspar


2015-11-23 14:54 GMT-05:00 <zkauf...@nmr.mgh.harvard.edu>:

> Oh, Sorry about that, I was unaware you were using freesurfer v5.1 on an
> older RedHat system.
>
> Freesurfer v5.1 was released quite awhile ago and its entirely possible
> that the newest development version of the freesurfer binaries are not
> compatible with it. But here is a link to our centos4 build which in
> theory has the best shot of working on your system:
>
>
> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos4_x86_64/mri_coreg
>
> Please give it a shot, and sorry for the initial confusion.
>
> -Zeke
>
>
>
>
>
> > Red Hat Enterprise Linux Server release 5.9 (Tikanga)
> > freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
> >
> > Caspar
> >
> >
> > 2015-11-23 14:37 GMT-05:00 <zkauf...@nmr.mgh.harvard.edu>:
> >
> >> What system are you running on? Also, what are the contents of your
> >> build-stamp.txt file (in your FREESURFER_HOME directory)?
> >>
> >> -Zeke
> >>
> >>
> >> > Hi Zeke,
> >> > I tried the is new version. Now I am getting:
> >> >
> >> > mri_coreg: /lib64/libuuid.so.1: no version information available
> >> (required
> >> > by mri_coreg)
> >> > mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
> >> found
> >> > (required by mri_coreg)
> >> > mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
> >> found
> >> > (required by mri_coreg)
> >> > mri_coreg: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
> >> by
> >> > mri_coreg)
> >> >
> >> > Caspar
> >> >
> >> >
> >> > 2015-11-23 14:20 GMT-05:00 <zkauf...@nmr.mgh.harvard.edu>:
> >> >
> >> >> There were some recent changes in the build that eliminated the
> >> >> necessity
> >> >> for that library. Casper, can you try using this most recent version
> >> and
> >> >> let me know if it works?
> >> >>
> >> >>
> >> >>
> >>
> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_coreg
> >> >>
> >> >> Thanks,
> >> >>
> >> >> -Zeke
> >> >>
> >> >>
> >> >> > Zeke, is this a new library that we need for v6?
> >> >> > doug
> >> >> >
> >> >> > On 11/20/2015 09:42 AM, Caspar M. Schwiedrzik wrote:
> >> >> >> Hi Doug,
> >> >> >> when I try to execute mri_coreg, I get the following error
> >> message:
> >> >> >>
> >> >> >> error while loading shared libraries: libnetcdf.so.6: cannot open
> >> >> >> shared object file: no such file or directory
> >> >> >>
> >> >> >> Caspar
> >> >> >>
> >> >> >>
> >> >> >> 2015-11-19 18:49 GMT-05:00 Douglas Greve
> >> <gr...@nmr.mgh.harvard.edu
> >> >> >> <mailto:gr...@nmr.mgh.harvard.edu>>:
> >> >> >>
> >> >> >>
> >> >> >> Can you try mri_coreg instead of fsl?
> >> >> >>
> >> >>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> On 11/19/15 5:25 PM, Caspar M. Schwiedrzik wrote:
> >> >> >>> Hi!
> >> >> >>> I am trying to align a mean EPI volume and a Bruker magnitude
> >> >> map
> >> >> >>> from a fieldmap measurement using tkregister2,
> >> >> fsl_rigid_register
> >> >> >>> and mri_vol2vol. Unfortunately, it seems that somewhere, most
> >> >> >>> likely during fsl_rigid_register, the image orientation get
> >> >> >>> scrambled, and the output has the wrong orientation.
> >> >> >>>
> >> >> >>> Here is what I get from*tkregister2:*
> >> >> >>>
> >

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

[Caspar M. Schwiedrzik]

Hi Doug,
when I try to execute mri_coreg, I get the following error message:

error while loading shared libraries: libnetcdf.so.6: cannot open shared
object file: no such file or directory

Caspar


2015-11-19 18:49 GMT-05:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>:

>
> Can you try mri_coreg instead of fsl?
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>
>
>
> On 11/19/15 5:25 PM, Caspar M. Schwiedrzik wrote:
>
> Hi!
> I am trying to align a mean EPI volume and a Bruker magnitude map from a
> fieldmap measurement using tkregister2, fsl_rigid_register and mri_vol2vol.
> Unfortunately, it seems that somewhere, most likely during
> fsl_rigid_register, the image orientation get scrambled, and the output has
> the wrong orientation.
>
> Here is what I get from* tkregister2:*
>
> target  volume epi.nii
> movable volume fieldmap0001.nii
> reg file   mag_2_mocovol.register.dat
> LoadVol0
> ZeroCRAS   0
> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
> Diagnostic Level -1
> INFO: loading target epi.nii
> Setting targ orientation to RIA
> INFO: target does not conform to COR format, so I'm going to
> reslice to COR. This will not affect the final registration.
> Ttarg: 
> -1.000   0.000   0.000   128.000;
>  0.000   0.000   1.000  -128.000;
>  0.000  -1.000   0.000   128.000;
>  0.000   0.000   0.000   1.000;
> INFO: loading movable fieldmap0001.nii
> Setting mov orientation to RIA
> Tmov: 
> -0.547   0.000   0.000   17.500;
>  0.000   0.000   0.547  -17.500;
>  0.000  -0.547   0.000   17.500;
>  0.000   0.000   0.000   1.000;
> mkheaderreg = 1, float2int = 0
> Computing reg from header (and possibly input matrix)
>  Input registration matrix (computed) 
> -1.000   0.000   0.000  -0.587;
>  0.000   1.000   0.000  -2.150;
>  0.000   0.000   1.000  -2.188;
>  0.000   0.000   0.000   1.000;
> ---
>  Input registration matrix 
> -1.000   0.000   0.000  -0.587;
>  0.000   1.000   0.000  -2.150;
>  0.000   0.000   1.000  -2.188;
>  0.000   0.000   0.000   1.000;
> Determinant -1
> subject = rat
> RegMat ---
>  1.000   0.000   0.000  -0.587;
>  0.000   1.000   0.000  -2.150;
>  0.000   0.000   1.000  -2.188;
>  0.000   0.000   0.000   1.000;
> FSLOUTPUTTYPE NIFTI_GZ
> tkreg2FSL: mov det = 0.163555, ref det = 0.154688
> INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det,
>   applying LR flip to registration matrix.
> INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det,
>   applying LR flip to registration matrix.
>
> here is what I get from fsl_rigid_register:
> $Id: fsl_rigid_register,v 1.31 2011/03/02 20:16:39 nicks Exp $
> Thu Nov 19 17:13:48 EST 2015
> fieldmap0001_reg.nii
> Reference is nifti, not converting
> Input is nifti, not converting
> Output is nifti, not converting
> --
> /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap
> calling eval flirt.fsl -in ./fieldmap0001.hdr -out ./fieldmap0001_reg.hdr
> -bins 256 -cost corratio -searchrx -10 10 -searchry -10 10 -searchrz -10 10
> -interp trilinear -dof 6 -ref ./epi.hdr -init initxfm.fslmat -omat
> ./fieldmap0001_reg.fslmat
> /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap
> mri_copy_params --pulse fieldmap0001_reg.nii fieldmap0001.nii
> fieldmap0001_reg.nii
> only copying pulse parameters
> WARNING: volume sizes are different
> in_vol : 80, 80, 22
>   temp_vol : 64, 64, 64
> WARNING: voxel sizes are different
> in_vol : 0.375, 0.375, 1.1
>   temp_vol : 0.546875, 0.546875, 0.546875
> --
> /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap
> tkregister2_cmdl --targ epi.nii --mov fieldmap0001.nii --reg
> ./fsl_rigid_register.28592/reg.dat --fslreg fieldmap0001_reg.nii.fslmat
> --noedit
> tkregister_tcl
> /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full/tktools/tkregister2.tcl
>  FSL registration matrix 
>  0.987  -0.164   0.002   0.247;
>  0.157   0.943  -0.295  -5.691;
>  0.046   0.291   0.956   7.475;
>  0.000   0.000   0.000   1.000;
> ---
> target  volume epi.nii
> movable volume fieldmap0001.nii
> reg file   ./fsl_rigid_register.28592/reg.dat
> LoadVol0
> ZeroCRAS   0
> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
> Diagnostic Level -1
> INFO: loading target epi.nii
> INFO: target does not conform to COR format, so I'm going to
> reslice to COR. This will not affect the final registration.

[Freesurfer] fsl_rigid_register fails with wrong orientation

[Caspar M. Schwiedrzik]

Hi!
I am trying to align a mean EPI volume and a Bruker magnitude map from a
fieldmap measurement using tkregister2, fsl_rigid_register and mri_vol2vol.
Unfortunately, it seems that somewhere, most likely during
fsl_rigid_register, the image orientation get scrambled, and the output has
the wrong orientation.

Here is what I get from* tkregister2:*

target  volume epi.nii
movable volume fieldmap0001.nii
reg file   mag_2_mocovol.register.dat
LoadVol0
ZeroCRAS   0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target epi.nii
Setting targ orientation to RIA
INFO: target does not conform to COR format, so I'm going to
reslice to COR. This will not affect the final registration.
Ttarg: 
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable fieldmap0001.nii
Setting mov orientation to RIA
Tmov: 
-0.547   0.000   0.000   17.500;
 0.000   0.000   0.547  -17.500;
 0.000  -0.547   0.000   17.500;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
 Input registration matrix (computed) 
-1.000   0.000   0.000  -0.587;
 0.000   1.000   0.000  -2.150;
 0.000   0.000   1.000  -2.188;
 0.000   0.000   0.000   1.000;
---
 Input registration matrix 
-1.000   0.000   0.000  -0.587;
 0.000   1.000   0.000  -2.150;
 0.000   0.000   1.000  -2.188;
 0.000   0.000   0.000   1.000;
Determinant -1
subject = rat
RegMat ---
 1.000   0.000   0.000  -0.587;
 0.000   1.000   0.000  -2.150;
 0.000   0.000   1.000  -2.188;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI_GZ
tkreg2FSL: mov det = 0.163555, ref det = 0.154688
INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det,
  applying LR flip to registration matrix.
INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det,
  applying LR flip to registration matrix.

here is what I get from fsl_rigid_register:
$Id: fsl_rigid_register,v 1.31 2011/03/02 20:16:39 nicks Exp $
Thu Nov 19 17:13:48 EST 2015
fieldmap0001_reg.nii
Reference is nifti, not converting
Input is nifti, not converting
Output is nifti, not converting
--
/Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap
calling eval flirt.fsl -in ./fieldmap0001.hdr -out ./fieldmap0001_reg.hdr
-bins 256 -cost corratio -searchrx -10 10 -searchry -10 10 -searchrz -10 10
-interp trilinear -dof 6 -ref ./epi.hdr -init initxfm.fslmat -omat
./fieldmap0001_reg.fslmat
/Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap
mri_copy_params --pulse fieldmap0001_reg.nii fieldmap0001.nii
fieldmap0001_reg.nii
only copying pulse parameters
WARNING: volume sizes are different
in_vol : 80, 80, 22
  temp_vol : 64, 64, 64
WARNING: voxel sizes are different
in_vol : 0.375, 0.375, 1.1
  temp_vol : 0.546875, 0.546875, 0.546875
--
/Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap
tkregister2_cmdl --targ epi.nii --mov fieldmap0001.nii --reg
./fsl_rigid_register.28592/reg.dat --fslreg fieldmap0001_reg.nii.fslmat
--noedit
tkregister_tcl
/Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full/tktools/tkregister2.tcl
 FSL registration matrix 
 0.987  -0.164   0.002   0.247;
 0.157   0.943  -0.295  -5.691;
 0.046   0.291   0.956   7.475;
 0.000   0.000   0.000   1.000;
---
target  volume epi.nii
movable volume fieldmap0001.nii
reg file   ./fsl_rigid_register.28592/reg.dat
LoadVol0
ZeroCRAS   0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target epi.nii
INFO: target does not conform to COR format, so I'm going to
reslice to COR. This will not affect the final registration.
Ttarg: 
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable fieldmap0001.nii
Tmov: 
-0.547   0.000   0.000   17.500;
 0.000   0.000   0.547  -17.500;
 0.000  -0.547   0.000   17.500;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI
fsl2TkReg: mov det = 0.163555, ref det = 0.154688
INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det,
  applying LR flip to registration matrix.
INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det,
  applying LR flip to registration matrix.
 Input registration matrix (computed) 
-0.987   0.046  -0.157   0.692;
-0.002   0.956   0.295  -19.148;
-0.164  -0.291   0.943  -0.998;
 0.000   0.000   0.000   1.000;
---
 Input registration matrix 
-0.987   0.046  -0.157   0.692;
-0.002   0.956   0.295  -19.148;

Re: [Freesurfer] Repost: problem with mri_label2label - large amount of holes

[Caspar M. Schwiedrzik]

Hi Zeke, we are getting a license file error:

ERROR: Invalid FreeSurfer license key found in license file
/Applications/freesurfer/.license
How should we proceed?
Thanks, Caspar

On Wednesday, August 5, 2015, zkauf...@nmr.mgh.harvard.edu wrote:

 Hello Caspar,

 I did a quick test and it appears the new dev version of mri_label2label
 is still compatible with the version of 5.1 that you have. Please use the
 following link to download it and also please make sure to back up the
 version you already have.


 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/snowleopard-i686/mri_label2label

 -Zeke


  Hi Bruce, Doug, and Zeke,
  just checking back regarding the dev version for mri_label2label.
  Do you have a build that works on  MAC OS 10.9.5 Mavericks?
  So far, we have been using
  freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.
 
  Thank you, Caspar
 
 
  2015-08-03 6:40 GMT-04:00 Caspar M. Schwiedrzik
  cschwie...@rockefeller.edu javascript:;
  :
 
  We are using MAC OS 10.9.5 Mavericks and freesurfer-Darwin-leopard-
  i686-stable-pub-v5.1.0
 
 
  On Thursday, July 30, 2015, Bruce Fischl fis...@nmr.mgh.harvard.edu
 javascript:;
  wrote:
 
  Hi Caspar
 
  the dev version of label2label doesn't have this problem. If you let us
  know your hardware/software environment Zeke can get you a new binary
  that
  should fix this issue
 
  cheers
  Bruce
 
 
  On Thu, 30 Jul 2015, Caspar M. Schwiedrzik wrote:
 
  Hi Bruce and Doug,
  thanks for looking into this and sorry for the delay.
  The command line we are using is:
 
  mri_label2label
 
 --srclabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/y$1/label/lh.v1.predict0p
  8.label --srcsubject y$1
 
 --trglabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/yx$1/label/yx$1_av1_lh_tp
  2.label --trgsubject yx$1 --regmethod surface --hemi lh
 
  We have several anatomies from the same subject, acquired on different
  occasions.
  We defined labels based on results of an fMRI experiment, and tried to
  use
  mri_label2label to map them within subjects from one anatomy to
  another.
  As a
  control, we also wanted to map the Hinds V1 from one anatomy to
  another,
  but this
  is where we ran into these holes.
  We will make an example subject available for debugging later today.
 
  Thanks! Caspar
 
 
 
 
 
  2015-07-24 12:33 GMT-04:00 Douglas Greve gr...@nmr.mgh.harvard.edu
 javascript:;:
what is your command line? What do you mean by one anatomy to
another?
 
On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote:
 
 
-- Forwarded message --
From: Caspar M. Schwiedrzik cschwie...@rockefeller.edu
 javascript:;
Date: Thursday, July 16, 2015
Subject: problem with mri_label2label - large amount of holes
To: Freesurfer@nmr.mgh.harvard.edu javascript:;
freesurfer@nmr.mgh.harvard.edu javascript:;
 
 
Hi!
  We are doing some analyses in which we map custom labels from one
  anatomy to another, within subjects. As a control, we also tried to
  map anatomically defined V1s according to the method by Hinds within
  subject from one anatomy to another. However, as you can see in the
  attachment, there are very many holes in the labels after using
  mri_label2label. This does not happen with smaller labels. Why is
  this happening and is there a solution?
  Thanks, Caspar
 
 
 
 
 
 
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu javascript:;
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
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  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu javascript:;
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
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  it
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  addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] Repost: problem with mri_label2label - large amount of holes

[Caspar M. Schwiedrzik]

Hi Bruce, Doug, and Zeke,
just checking back regarding the dev version for mri_label2label.
Do you have a build that works on  MAC OS 10.9.5 Mavericks?
So far, we have been using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.

Thank you, Caspar


2015-08-03 6:40 GMT-04:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu
:

 We are using MAC OS 10.9.5 Mavericks and freesurfer-Darwin-leopard-
 i686-stable-pub-v5.1.0


 On Thursday, July 30, 2015, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:

 Hi Caspar

 the dev version of label2label doesn't have this problem. If you let us
 know your hardware/software environment Zeke can get you a new binary that
 should fix this issue

 cheers
 Bruce


 On Thu, 30 Jul 2015, Caspar M. Schwiedrzik wrote:

 Hi Bruce and Doug,
 thanks for looking into this and sorry for the delay.
 The command line we are using is:

 mri_label2label
 --srclabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/y$1/label/lh.v1.predict0p
 8.label --srcsubject y$1
 --trglabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/yx$1/label/yx$1_av1_lh_tp
 2.label --trgsubject yx$1 --regmethod surface --hemi lh

 We have several anatomies from the same subject, acquired on different
 occasions.
 We defined labels based on results of an fMRI experiment, and tried to
 use
 mri_label2label to map them within subjects from one anatomy to another.
 As a
 control, we also wanted to map the Hinds V1 from one anatomy to another,
 but this
 is where we ran into these holes.
 We will make an example subject available for debugging later today.

 Thanks! Caspar





 2015-07-24 12:33 GMT-04:00 Douglas Greve gr...@nmr.mgh.harvard.edu:
   what is your command line? What do you mean by one anatomy to
   another?

   On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote:


   -- Forwarded message --
   From: Caspar M. Schwiedrzik cschwie...@rockefeller.edu
   Date: Thursday, July 16, 2015
   Subject: problem with mri_label2label - large amount of holes
   To: Freesurfer@nmr.mgh.harvard.edu
   freesurfer@nmr.mgh.harvard.edu


   Hi!
 We are doing some analyses in which we map custom labels from one
 anatomy to another, within subjects. As a control, we also tried to
 map anatomically defined V1s according to the method by Hinds within
 subject from one anatomy to another. However, as you can see in the
 attachment, there are very many holes in the labels after using
 mri_label2label. This does not happen with smaller labels. Why is
 this happening and is there a solution?
 Thanks, Caspar







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



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 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
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Re: [Freesurfer] Repost: problem with mri_label2label - large amount of holes

[Caspar M. Schwiedrzik]

Hi Zeke,
Thank you, we will give it a try!
Caspar

On Wednesday, August 5, 2015, zkauf...@nmr.mgh.harvard.edu wrote:

 Hello Caspar,

 I did a quick test and it appears the new dev version of mri_label2label
 is still compatible with the version of 5.1 that you have. Please use the
 following link to download it and also please make sure to back up the
 version you already have.


 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/snowleopard-i686/mri_label2label

 -Zeke


  Hi Bruce, Doug, and Zeke,
  just checking back regarding the dev version for mri_label2label.
  Do you have a build that works on  MAC OS 10.9.5 Mavericks?
  So far, we have been using
  freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.
 
  Thank you, Caspar
 
 
  2015-08-03 6:40 GMT-04:00 Caspar M. Schwiedrzik
  cschwie...@rockefeller.edu javascript:;
  :
 
  We are using MAC OS 10.9.5 Mavericks and freesurfer-Darwin-leopard-
  i686-stable-pub-v5.1.0
 
 
  On Thursday, July 30, 2015, Bruce Fischl fis...@nmr.mgh.harvard.edu
 javascript:;
  wrote:
 
  Hi Caspar
 
  the dev version of label2label doesn't have this problem. If you let us
  know your hardware/software environment Zeke can get you a new binary
  that
  should fix this issue
 
  cheers
  Bruce
 
 
  On Thu, 30 Jul 2015, Caspar M. Schwiedrzik wrote:
 
  Hi Bruce and Doug,
  thanks for looking into this and sorry for the delay.
  The command line we are using is:
 
  mri_label2label
 
 --srclabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/y$1/label/lh.v1.predict0p
  8.label --srcsubject y$1
 
 --trglabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/yx$1/label/yx$1_av1_lh_tp
  2.label --trgsubject yx$1 --regmethod surface --hemi lh
 
  We have several anatomies from the same subject, acquired on different
  occasions.
  We defined labels based on results of an fMRI experiment, and tried to
  use
  mri_label2label to map them within subjects from one anatomy to
  another.
  As a
  control, we also wanted to map the Hinds V1 from one anatomy to
  another,
  but this
  is where we ran into these holes.
  We will make an example subject available for debugging later today.
 
  Thanks! Caspar
 
 
 
 
 
  2015-07-24 12:33 GMT-04:00 Douglas Greve gr...@nmr.mgh.harvard.edu
 javascript:;:
what is your command line? What do you mean by one anatomy to
another?
 
On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote:
 
 
-- Forwarded message --
From: Caspar M. Schwiedrzik cschwie...@rockefeller.edu
 javascript:;
Date: Thursday, July 16, 2015
Subject: problem with mri_label2label - large amount of holes
To: Freesurfer@nmr.mgh.harvard.edu javascript:;
freesurfer@nmr.mgh.harvard.edu javascript:;
 
 
Hi!
  We are doing some analyses in which we map custom labels from one
  anatomy to another, within subjects. As a control, we also tried to
  map anatomically defined V1s according to the method by Hinds within
  subject from one anatomy to another. However, as you can see in the
  attachment, there are very many holes in the labels after using
  mri_label2label. This does not happen with smaller labels. Why is
  this happening and is there a solution?
  Thanks, Caspar
 
 
 
 
 
 
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu javascript:;
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
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  Freesurfer@nmr.mgh.harvard.edu javascript:;
  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.
 
 
 
 
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Re: [Freesurfer] Repost: problem with mri_label2label - large amount of holes

[Caspar M. Schwiedrzik]

We are using MAC OS 10.9.5 Mavericks and freesurfer-Darwin-leopard-
i686-stable-pub-v5.1.0

On Thursday, July 30, 2015, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Caspar

 the dev version of label2label doesn't have this problem. If you let us
 know your hardware/software environment Zeke can get you a new binary that
 should fix this issue

 cheers
 Bruce


 On Thu, 30 Jul 2015, Caspar M. Schwiedrzik wrote:

 Hi Bruce and Doug,
 thanks for looking into this and sorry for the delay.
 The command line we are using is:

 mri_label2label
 --srclabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/y$1/label/lh.v1.predict0p
 8.label --srcsubject y$1
 --trglabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/yx$1/label/yx$1_av1_lh_tp
 2.label --trgsubject yx$1 --regmethod surface --hemi lh

 We have several anatomies from the same subject, acquired on different
 occasions.
 We defined labels based on results of an fMRI experiment, and tried to use
 mri_label2label to map them within subjects from one anatomy to another.
 As a
 control, we also wanted to map the Hinds V1 from one anatomy to another,
 but this
 is where we ran into these holes.
 We will make an example subject available for debugging later today.

 Thanks! Caspar





 2015-07-24 12:33 GMT-04:00 Douglas Greve gr...@nmr.mgh.harvard.edu:
   what is your command line? What do you mean by one anatomy to
   another?

   On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote:


   -- Forwarded message --
   From: Caspar M. Schwiedrzik cschwie...@rockefeller.edu
   Date: Thursday, July 16, 2015
   Subject: problem with mri_label2label - large amount of holes
   To: Freesurfer@nmr.mgh.harvard.edu
   freesurfer@nmr.mgh.harvard.edu


   Hi!
 We are doing some analyses in which we map custom labels from one
 anatomy to another, within subjects. As a control, we also tried to
 map anatomically defined V1s according to the method by Hinds within
 subject from one anatomy to another. However, as you can see in the
 attachment, there are very many holes in the labels after using
 mri_label2label. This does not happen with smaller labels. Why is
 this happening and is there a solution?
 Thanks, Caspar







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



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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 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
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Re: [Freesurfer] Repost: problem with mri_label2label - large amount of holes

[Caspar M. Schwiedrzik]

Hi Bruce and Doug,
thanks for looking into this and sorry for the delay.
The command line we are using is:

mri_label2label --srclabel
/Volumes/Macintosh_HD/Applications/freesurfer/subjects/y$1/label/lh.v1.predict0p8.label
--srcsubject y$1 --trglabel
/Volumes/Macintosh_HD/Applications/freesurfer/subjects/yx$1/label/yx$1_av1_lh_tp2.label
--trgsubject yx$1 --regmethod surface --hemi lh

We have several anatomies from the same subject, acquired on different
occasions. We defined labels based on results of an fMRI experiment, and
tried to use mri_label2label to map them within subjects from one anatomy
to another. As a control, we also wanted to map the Hinds V1 from one
anatomy to another, but this is where we ran into these holes.
We will make an example subject available for debugging later today.

Thanks! Caspar





2015-07-24 12:33 GMT-04:00 Douglas Greve gr...@nmr.mgh.harvard.edu:

  what is your command line? What do you mean by one anatomy to another?


 On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote:



 -- Forwarded message --
 From: *Caspar M. Schwiedrzik* cschwie...@rockefeller.edu
 Date: Thursday, July 16, 2015
 Subject: problem with mri_label2label - large amount of holes
 To: Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu


   Hi!
  We are doing some analyses in which we map custom labels from one anatomy
 to another, within subjects. As a control, we also tried to map
 anatomically defined V1s according to the method by Hinds within subject
 from one anatomy to another. However, as you can see in the attachment,
 there are very many holes in the labels after using mri_label2label. This
 does not happen with smaller labels. Why is this happening and is there a
 solution?
  Thanks, Caspar







 ___
 Freesurfer mailing 
 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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 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
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[Freesurfer] Repost: What algorithm does mri_label2label use?

[Caspar M. Schwiedrzik]

Hi!
We are using mri_label2label to map functionally defined ROIs from one
anatomy to another (within subjects), using --regmethod surface. We were
wondering which algorithm mri_label2label uses to map the labels? Is it
using mri_surf2surf, and if so, which mapmethod is it using?
Thanks, Caspar
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Re: [Freesurfer] selxavg3-sess CPU limits

[Caspar M. Schwiedrzik]

thanks! in your experience, is there a big performance deficit when using
-singleCompThread? caspar

2015-05-28 14:57 GMT-04:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:

 This is actually a matlab problem. In the next version I have fixed this
 so that it only uses one cpu. You can't control the number in newer
 verisons of matlab, it is either all or one. You can try editing
 selxavg3-sess to add -singleCompThread to the matlab command line.

 On 05/28/2015 02:24 PM, Caspar M. Schwiedrzik wrote:
  Hi Doug,
  I noticed that selxavg3-sess uses about half of the currently
  available CPUs on our system, depending on how many CPUs are
  available. I think this is when it is calculating the contrasts. Is
  there a way to up- or downregulate the number of CPUs that the script
  is using?
  Thanks, Caspar
 
 
 
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 --
 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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[Freesurfer] ridge regression

[Caspar M. Schwiedrzik]

Hi!
Has anyone tried to use ridge regression on fMRI data (instead of the
regular GLM) and would be willing to give some tips?
Thanks, Caspar
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Re: [Freesurfer] Whitening in FSFAST

[Caspar M. Schwiedrzik]

Thanks, Doug!
The reason I am asking is that this paper is currently making a bit of
commotion:

*Empirically investigating the statistical validty of SPM, FSL and AFNI for
single subject fMRI analysis*
Eklund, Nichols, Andersson, Knutsson
https://dl.dropboxusercontent.com/u/4494604/article.pdf

Not the first one, of course.
Caspar



On Wednesday, May 13, 2015, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:

 wow, I have not thought about that code in years. It uses an AR1 with
 the bias correction described in Worsley's paper. It bins the AR1 value
 into 30 bins to allow for spatial variability and does the whitening in
 each set of voxels in a bin.

 doug

 On 05/12/2015 10:56 PM, Caspar M. Schwiedrzik wrote:
  Hi Doug,
  I wanted to ask what kind of noise model FSFAST employs for whitening.
  Is it the one described in Worsley, neuroimage 2002?
 
  Is there a place on the wiki or elsewhere where I could find a
  description?
  Thanks,
  Caspar
 
 
 
 
 
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu javascript:;
 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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[Freesurfer] Whitening in FSFAST

[Caspar M. Schwiedrzik]

Hi Doug,
I wanted to ask what kind of noise model FSFAST employs for whitening.
Is it the one described in Worsley, neuroimage 2002?

Is there a place on the wiki or elsewhere where I could find a description?
Thanks,
Caspar
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Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

[Caspar M. Schwiedrzik]

Hi Doug,
coming back to this once more. I am thinking that I can bypass
mkcontrast-sess entirely if I provide a contrast matrix that has
ContrastMtx_0 and WCond set to the contrast that I am interested in.
For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first continuous
predictor and against the remaining five continuous predictors.
For that, I would just place a corresponding mat file in a subdirectory in
mystudy.
Is there anything that speaks that and anything else that I need to
consider?
Thanks!
Caspar





2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu
:

 Hi Doug,
 I am a little bit confused about the variance. Shouldn't the relevant
 variance be the variance over the differences, not the mean variance over
 all?
 Of course at the level of ces and cesvar, I do not have access to the
 timepoint by timepoint differences anymore.
 Is there another way to do this?
 Thanks, Caspar


 2014-11-11 13:54 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:

 yes
 On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote:
  Hi Doug,
  just to clarify:
  If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would
  compute
  ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6))
  and
  cesvar=mean(cesvar(taskreg(1,2,3,4,5,6)))
 
  Is that correct?
  Thanks, Caspar
 
 
  2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu
  mailto:b...@cs.wisc.edu:
 
  Sorry, Though we do have freesurfer pipelines we run in Madison, I
  responded to wrong email.
 
  Bill Taylor
  Center for High Throughput Computing
  Computer Sciences
  University of Wisconsin, Madison
 
  On 11/11/2014 12:09 PM, Bill Taylor wrote:
   I'll start the process thursday.
   On 11/11/2014 12:04 PM, Douglas N Greve wrote:
   It will be the same as the DOF of the individual contrasts
  (don't sum them).
  
   On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote:
   ok, I will try that. How do I get the degrees of freedom?
  Thanks! Caspar
  
   2014-11-11 12:04 GMT-05:00 Douglas N Greve
  gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
   mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu:
  
  
 Actually, you can still do each contrast individually.
  Each will
 produce
 ces and cesvar files. Take the difference between the
  ces files
 and the
 average of the cesvar files, then feed the result into
  mri_glmfit FFX
  
 doug
  
  
 On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote:
  Hi Doug,
  I wanted to follow up on this. Would you be able to
  provide a
  workaround for contrasting multiple taskregs against
  each other? Is
  there something I can try in the meantime? Thanks,
 Caspar
 
 
  2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik
  cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu
 mailto:cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu
 mailto:cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu:
 
  Hi Doug,
  thanks for your reply. I would like to feed the
  differences
 into a
  FFX group analysis, so I think I will need to
  resort to your
  workaround. It would be great if you could provide
  that. Thanks!
  Caspar
 
  2014-11-10 13:45 GMT-05:00 Douglas N Greve
  gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu:
 
 
  To get sig maps for  an individual, this is
  problematic
 but I
  could
  probably come up with a work-around. For a group
 analysis, you can
  simply compute each taskreg separately, then
  subtract
 the two
  prior to
  running mri_glmfit.
  doug
 
  On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik
  wrote:
   Hi!
   A quick follow-up:
   I have a taskreg file with 6 continuous
  predictors. I
 would
  like to
   run specific contrasts, e.g., predictor 1 vs.
 mean(predictor
  2:6

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

[Caspar M. Schwiedrzik]

Hi Doug,
so I made contrast matrices and stored them in mystudy, and then ran
selxavg3-sess per subject.
I defined three different contrasts (in three mat files), but selxacg3-sess
only gives me one analysis, it seems to be an F-test.
When I do isxconcat-sess after that, I get six ces files per analysis (I
presume one for each of my predictors), not three (number of contrasts).

Is there a way for me to force selxavg3-sess to actually compute the
contrasts that I want?

Thanks, Caspar





2014-11-13 12:16 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:

 I don't know whether that will work or not. If it runs, you can compare
 the result to computing the contrast manually to see if there is a
 difference. If there is no difference, then it works.

 On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote:
  Hi Doug,
  coming back to this once more. I am thinking that I can bypass
  mkcontrast-sess entirely if I provide a contrast matrix that has
  ContrastMtx_0 and WCond set to the contrast that I am interested in.
  For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first
  continuous predictor and against the remaining five continuous
  predictors.
  For that, I would just place a corresponding mat file in a
  subdirectory in mystudy.
  Is there anything that speaks that and anything else that I need to
  consider?
  Thanks!
  Caspar
 
 
 
 
 
  2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik
  cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu:
 
  Hi Doug,
  I am a little bit confused about the variance. Shouldn't the
  relevant variance be the variance over the differences, not the
  mean variance over all?
  Of course at the level of ces and cesvar, I do not have access to
  the timepoint by timepoint differences anymore.
  Is there another way to do this?
  Thanks, Caspar
 
 
  2014-11-11 13:54 GMT-05:00 Douglas N Greve
  gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu:
 
  yes
  On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote:
   Hi Doug,
   just to clarify:
   If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6),
  I would
   compute
   ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6))
   and
   cesvar=mean(cesvar(taskreg(1,2,3,4,5,6)))
  
   Is that correct?
   Thanks, Caspar
  
  
   2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu
  mailto:b...@cs.wisc.edu
   mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu:
  
   Sorry, Though we do have freesurfer pipelines we run in
  Madison, I
   responded to wrong email.
  
   Bill Taylor
   Center for High Throughput Computing
   Computer Sciences
   University of Wisconsin, Madison
  
   On 11/11/2014 12:09 PM, Bill Taylor wrote:
I'll start the process thursday.
On 11/11/2014 12:04 PM, Douglas N Greve wrote:
It will be the same as the DOF of the individual
  contrasts
   (don't sum them).
   
On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote:
ok, I will try that. How do I get the degrees of
  freedom?
   Thanks! Caspar
   
2014-11-11 12:04 GMT-05:00 Douglas N Greve
   gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
   mailto:gr...@nmr.mgh.harvard.edu mailto:
 gr...@nmr.mgh.harvard.edu:
   
   
  Actually, you can still do each contrast
  individually.
   Each will
  produce
  ces and cesvar files. Take the difference
  between the
   ces files
  and the
  average of the cesvar files, then feed the
  result into
   mri_glmfit FFX
   
  doug
   
   
  On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik
  wrote:
   Hi Doug,
   I wanted to follow up on this. Would you be
  able to
   provide a
   workaround for contrasting multiple taskregs
  against
   each other? Is
   there something I can try in the meantime?
  Thanks, Caspar
  
  
   2014-11-10 13:54 GMT-05:00 Caspar M.
 Schwiedrzik
   cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

[Caspar M. Schwiedrzik]

ok, so the issue is in fast_ldanaflac.m, around line 520:
flac.con(nthcon).ContrastMtx_0=[];
that effectively ignores the contrasts that are set up in mystudy.
caspar

2014-11-13 17:33 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu
:

 Hi Doug,
 so I made contrast matrices and stored them in mystudy, and then ran
 selxavg3-sess per subject.
 I defined three different contrasts (in three mat files), but
 selxacg3-sess only gives me one analysis, it seems to be an F-test.
 When I do isxconcat-sess after that, I get six ces files per analysis (I
 presume one for each of my predictors), not three (number of contrasts).

 Is there a way for me to force selxavg3-sess to actually compute the
 contrasts that I want?

 Thanks, Caspar





 2014-11-13 12:16 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:

 I don't know whether that will work or not. If it runs, you can compare
 the result to computing the contrast manually to see if there is a
 difference. If there is no difference, then it works.

 On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote:
  Hi Doug,
  coming back to this once more. I am thinking that I can bypass
  mkcontrast-sess entirely if I provide a contrast matrix that has
  ContrastMtx_0 and WCond set to the contrast that I am interested in.
  For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first
  continuous predictor and against the remaining five continuous
  predictors.
  For that, I would just place a corresponding mat file in a
  subdirectory in mystudy.
  Is there anything that speaks that and anything else that I need to
  consider?
  Thanks!
  Caspar
 
 
 
 
 
  2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik
  cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu:
 
  Hi Doug,
  I am a little bit confused about the variance. Shouldn't the
  relevant variance be the variance over the differences, not the
  mean variance over all?
  Of course at the level of ces and cesvar, I do not have access to
  the timepoint by timepoint differences anymore.
  Is there another way to do this?
  Thanks, Caspar
 
 
  2014-11-11 13:54 GMT-05:00 Douglas N Greve
  gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu:
 
  yes
  On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote:
   Hi Doug,
   just to clarify:
   If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6),
  I would
   compute
   ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6))
   and
   cesvar=mean(cesvar(taskreg(1,2,3,4,5,6)))
  
   Is that correct?
   Thanks, Caspar
  
  
   2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu
  mailto:b...@cs.wisc.edu
   mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu:
  
   Sorry, Though we do have freesurfer pipelines we run in
  Madison, I
   responded to wrong email.
  
   Bill Taylor
   Center for High Throughput Computing
   Computer Sciences
   University of Wisconsin, Madison
  
   On 11/11/2014 12:09 PM, Bill Taylor wrote:
I'll start the process thursday.
On 11/11/2014 12:04 PM, Douglas N Greve wrote:
It will be the same as the DOF of the individual
  contrasts
   (don't sum them).
   
On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote:
ok, I will try that. How do I get the degrees of
  freedom?
   Thanks! Caspar
   
2014-11-11 12:04 GMT-05:00 Douglas N Greve
   gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
   mailto:gr...@nmr.mgh.harvard.edu mailto:
 gr...@nmr.mgh.harvard.edu:
   
   
  Actually, you can still do each contrast
  individually.
   Each will
  produce
  ces and cesvar files. Take the difference
  between the
   ces files
  and the
  average of the cesvar files, then feed the
  result into
   mri_glmfit FFX
   
  doug
   
   
  On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik
  wrote:
   Hi Doug,
   I wanted to follow up on this. Would you be
  able to
   provide a
   workaround for contrasting multiple taskregs
  against
   each other? Is
   there something I can try in the meantime

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

[Caspar M. Schwiedrzik]

Hi Doug,
I wanted to follow up on this. Would you be able to provide a workaround
for contrasting multiple taskregs against each other? Is there something I
can try in the meantime? Thanks, Caspar


2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu
:

 Hi Doug,
 thanks for your reply. I would like to feed the differences into a FFX
 group analysis, so I think I will need to resort to your workaround. It
 would be great if you could provide that. Thanks! Caspar

 2014-11-10 13:45 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:


 To get sig maps for  an individual, this is problematic but I could
 probably come up with a work-around. For a group analysis, you can
 simply compute each taskreg separately, then subtract the two prior to
 running mri_glmfit.
 doug

 On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote:
  Hi!
  A quick follow-up:
  I have a taskreg file with 6 continuous predictors. I would like to
  run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6).
  From what I gather, selxavg3-sess will run automatic contrasts on
  taskregs, but the automatic contrasts are against baseline. This is
  not what I need at this point.
  mk-contrast-sess does not like what I am putting in because I do not
  have a paradigm file in which condition numbers are specified.
  Is there a way to compute specific contrasts between multiple
  taskregs, and if not, is there a workaround?
  Thank you very much, Caspar
 
 
  2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik
  cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu:
 
  Hi!
  I have several external regressors in my analysis that I configure
  with -taskreg in mkanalysis-sess (something like -notask -taskreg
  nameoffile 6).
  I was wondering how to set up mkcontrast-sess to contrast these
  regerssors given that I do not have a paradigm file for them.
  Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5?
 
  Thanks, Caspar
 
 
 
 
  ___
  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.



___
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] Running a contrast on multiple taskregs in FSFAST

[Caspar M. Schwiedrzik]

ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar

2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:


 Actually, you can still do each contrast individually. Each will produce
 ces and cesvar files. Take the difference between the ces files and the
 average of the cesvar files, then feed the result into mri_glmfit FFX

 doug


 On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote:
  Hi Doug,
  I wanted to follow up on this. Would you be able to provide a
  workaround for contrasting multiple taskregs against each other? Is
  there something I can try in the meantime? Thanks, Caspar
 
 
  2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik
  cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu:
 
  Hi Doug,
  thanks for your reply. I would like to feed the differences into a
  FFX group analysis, so I think I will need to resort to your
  workaround. It would be great if you could provide that. Thanks!
  Caspar
 
  2014-11-10 13:45 GMT-05:00 Douglas N Greve
  gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu:
 
 
  To get sig maps for  an individual, this is problematic but I
  could
  probably come up with a work-around. For a group analysis, you
 can
  simply compute each taskreg separately, then subtract the two
  prior to
  running mri_glmfit.
  doug
 
  On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote:
   Hi!
   A quick follow-up:
   I have a taskreg file with 6 continuous predictors. I would
  like to
   run specific contrasts, e.g., predictor 1 vs. mean(predictor
  2:6).
   From what I gather, selxavg3-sess will run automatic
  contrasts on
   taskregs, but the automatic contrasts are against baseline.
  This is
   not what I need at this point.
   mk-contrast-sess does not like what I am putting in because
  I do not
   have a paradigm file in which condition numbers are specified.
   Is there a way to compute specific contrasts between multiple
   taskregs, and if not, is there a workaround?
   Thank you very much, Caspar
  
  
   2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik
   cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu:
  
   Hi!
   I have several external regressors in my analysis that I
  configure
   with -taskreg in mkanalysis-sess (something like -notask
  -taskreg
   nameoffile 6).
   I was wondering how to set up mkcontrast-sess to
  contrast these
   regerssors given that I do not have a paradigm file for
  them.
   Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5?
  
   Thanks, Caspar
  
  
  
  
   ___
   Freesurfer mailing list
   Freesurfer@nmr.mgh.harvard.edu
  mailto: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 mailto:gr...@nmr.mgh.harvard.edu
  Phone Number: 617-724-2358 tel:617-724-2358
  Fax: 617-726-7422 tel:617-726-7422
 
  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
  http://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
  mailto: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

 --
 Douglas N. Greve, Ph.D

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

[Caspar M. Schwiedrzik]

Hi Doug,
just to clarify:
If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute
ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6))
and
cesvar=mean(cesvar(taskreg(1,2,3,4,5,6)))

Is that correct?
Thanks, Caspar


2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu:

 Sorry, Though we do have freesurfer pipelines we run in Madison, I
 responded to wrong email.

 Bill Taylor
 Center for High Throughput Computing
 Computer Sciences
 University of Wisconsin, Madison

 On 11/11/2014 12:09 PM, Bill Taylor wrote:
  I'll start the process thursday.
  On 11/11/2014 12:04 PM, Douglas N Greve wrote:
  It will be the same as the DOF of the individual contrasts (don't sum
 them).
 
  On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote:
  ok, I will try that. How do I get the degrees of freedom? Thanks!
 Caspar
 
  2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu:
 
 
Actually, you can still do each contrast individually. Each will
produce
ces and cesvar files. Take the difference between the ces files
and the
average of the cesvar files, then feed the result into
 mri_glmfit FFX
 
doug
 
 
On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote:
 Hi Doug,
 I wanted to follow up on this. Would you be able to provide a
 workaround for contrasting multiple taskregs against each
 other? Is
 there something I can try in the meantime? Thanks, Caspar


 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik
 cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu
 
mailto:cschwie...@rockefeller.edu
mailto:cschwie...@rockefeller.edu:

 Hi Doug,
 thanks for your reply. I would like to feed the differences
into a
 FFX group analysis, so I think I will need to resort to
 your
 workaround. It would be great if you could provide that.
 Thanks!
 Caspar

 2014-11-10 13:45 GMT-05:00 Douglas N Greve
 gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu:


 To get sig maps for  an individual, this is problematic
but I
 could
 probably come up with a work-around. For a group
analysis, you can
 simply compute each taskreg separately, then subtract
the two
 prior to
 running mri_glmfit.
 doug

 On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote:
  Hi!
  A quick follow-up:
  I have a taskreg file with 6 continuous predictors. I
would
 like to
  run specific contrasts, e.g., predictor 1 vs.
mean(predictor
 2:6).
  From what I gather, selxavg3-sess will run automatic
 contrasts on
  taskregs, but the automatic contrasts are against
baseline.
 This is
  not what I need at this point.
  mk-contrast-sess does not like what I am putting in
because
 I do not
  have a paradigm file in which condition numbers are
specified.
  Is there a way to compute specific contrasts between
multiple
  taskregs, and if not, is there a workaround?
  Thank you very much, Caspar
 
 
  2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik
  cschwie...@rockefeller.edu
mailto:cschwie...@rockefeller.edu
 mailto:cschwie...@rockefeller.edu
mailto:cschwie...@rockefeller.edu
 mailto:cschwie...@rockefeller.edu
mailto:cschwie...@rockefeller.edu
 mailto:cschwie...@rockefeller.edu mailto:
 cschwie...@rockefeller.edu:
 
  Hi!
  I have several external regressors in my analysis
that I
 configure
  with -taskreg in mkanalysis-sess (something like
-notask
 -taskreg
  nameoffile 6).
  I was wondering how to set up mkcontrast-sess to
 contrast these
  regerssors given that I do not have a paradigm
file for
 them.
  Can I just do something like -a 1 -c 2 -c 3 -c 4
 -c 5?
 
  Thanks, Caspar
 
 
 
 
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  Freesurfer mailing list

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

[Caspar M. Schwiedrzik]

Hi Doug,
I am a little bit confused about the variance. Shouldn't the relevant
variance be the variance over the differences, not the mean variance over
all?
Of course at the level of ces and cesvar, I do not have access to the
timepoint by timepoint differences anymore.
Is there another way to do this?
Thanks, Caspar


2014-11-11 13:54 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:

 yes
 On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote:
  Hi Doug,
  just to clarify:
  If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would
  compute
  ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6))
  and
  cesvar=mean(cesvar(taskreg(1,2,3,4,5,6)))
 
  Is that correct?
  Thanks, Caspar
 
 
  2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu
  mailto:b...@cs.wisc.edu:
 
  Sorry, Though we do have freesurfer pipelines we run in Madison, I
  responded to wrong email.
 
  Bill Taylor
  Center for High Throughput Computing
  Computer Sciences
  University of Wisconsin, Madison
 
  On 11/11/2014 12:09 PM, Bill Taylor wrote:
   I'll start the process thursday.
   On 11/11/2014 12:04 PM, Douglas N Greve wrote:
   It will be the same as the DOF of the individual contrasts
  (don't sum them).
  
   On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote:
   ok, I will try that. How do I get the degrees of freedom?
  Thanks! Caspar
  
   2014-11-11 12:04 GMT-05:00 Douglas N Greve
  gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
   mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu:
  
  
 Actually, you can still do each contrast individually.
  Each will
 produce
 ces and cesvar files. Take the difference between the
  ces files
 and the
 average of the cesvar files, then feed the result into
  mri_glmfit FFX
  
 doug
  
  
 On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote:
  Hi Doug,
  I wanted to follow up on this. Would you be able to
  provide a
  workaround for contrasting multiple taskregs against
  each other? Is
  there something I can try in the meantime? Thanks, Caspar
 
 
  2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik
  cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu
 mailto:cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu
 mailto:cschwie...@rockefeller.edu
  mailto:cschwie...@rockefeller.edu:
 
  Hi Doug,
  thanks for your reply. I would like to feed the
  differences
 into a
  FFX group analysis, so I think I will need to
  resort to your
  workaround. It would be great if you could provide
  that. Thanks!
  Caspar
 
  2014-11-10 13:45 GMT-05:00 Douglas N Greve
  gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu:
 
 
  To get sig maps for  an individual, this is
  problematic
 but I
  could
  probably come up with a work-around. For a group
 analysis, you can
  simply compute each taskreg separately, then
  subtract
 the two
  prior to
  running mri_glmfit.
  doug
 
  On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik
  wrote:
   Hi!
   A quick follow-up:
   I have a taskreg file with 6 continuous
  predictors. I
 would
  like to
   run specific contrasts, e.g., predictor 1 vs.
 mean(predictor
  2:6).
   From what I gather, selxavg3-sess will run
  automatic
  contrasts on
   taskregs, but the automatic contrasts are
  against
 baseline.
  This is
   not what I need at this point.
   mk-contrast-sess does not like what I am
  putting in
 because
  I do not
   have a paradigm file in which condition
  numbers are
 specified.
   Is there a way to compute specific contrasts
  between

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

[Caspar M. Schwiedrzik]

Hi!
A quick follow-up:
I have a taskreg file with 6 continuous predictors. I would like to run
specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6).
From what I gather, selxavg3-sess will run automatic contrasts on taskregs,
but the automatic contrasts are against baseline. This is not what I need
at this point.
mk-contrast-sess does not like what I am putting in because I do not have a
paradigm file in which condition numbers are specified.
Is there a way to compute specific contrasts between multiple taskregs, and
if not, is there a workaround?
Thank you very much, Caspar


2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu
:

 Hi!
 I have several external regressors in my analysis that I configure with
 -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6).
 I was wondering how to set up mkcontrast-sess to contrast these regerssors
 given that I do not have a paradigm file for them.
 Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5?

 Thanks, Caspar


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Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

[Caspar M. Schwiedrzik]

Hi Doug,
thanks for your reply. I would like to feed the differences into a FFX
group analysis, so I think I will need to resort to your workaround. It
would be great if you could provide that. Thanks! Caspar

2014-11-10 13:45 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:


 To get sig maps for  an individual, this is problematic but I could
 probably come up with a work-around. For a group analysis, you can
 simply compute each taskreg separately, then subtract the two prior to
 running mri_glmfit.
 doug

 On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote:
  Hi!
  A quick follow-up:
  I have a taskreg file with 6 continuous predictors. I would like to
  run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6).
  From what I gather, selxavg3-sess will run automatic contrasts on
  taskregs, but the automatic contrasts are against baseline. This is
  not what I need at this point.
  mk-contrast-sess does not like what I am putting in because I do not
  have a paradigm file in which condition numbers are specified.
  Is there a way to compute specific contrasts between multiple
  taskregs, and if not, is there a workaround?
  Thank you very much, Caspar
 
 
  2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik
  cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu:
 
  Hi!
  I have several external regressors in my analysis that I configure
  with -taskreg in mkanalysis-sess (something like -notask -taskreg
  nameoffile 6).
  I was wondering how to set up mkcontrast-sess to contrast these
  regerssors given that I do not have a paradigm file for them.
  Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5?
 
  Thanks, Caspar
 
 
 
 
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 --
 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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 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
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 but does not contain patient information, please contact the sender and
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[Freesurfer] Running a contrast on multiple taskregs in FSFAST

[Caspar M. Schwiedrzik]

Hi!
I have several external regressors in my analysis that I configure with
-taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6).
I was wondering how to set up mkcontrast-sess to contrast these regerssors
given that I do not have a paradigm file for them.
Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5?

Thanks, Caspar
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Quality of surface-based alignment

[Caspar M. Schwiedrzik]

Hi Freesurfers,
I was wondering whether there is a good way to assess post-hoc how well the
alignment between two surfaces was. I wouldn't like to run the alignment
again, but I could, if necessary. I would like to compare this alignment to
a bunch of other alignments to see whether it was worse than the others.
Thanks, Caspar
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Re: [Freesurfer] Quality of surface-based alignment

[Caspar M. Schwiedrzik]

Hi Bruce and Matt,
I should specify that I am working with non-human primate data, so
unfortunately, looking at the parcellations would not work. I am aligning
individuals to a a custom template that I made.
I was wondering whether there is maybe an output file that has something
numerical on how much one surface had to be transformed to be aligned to
the other.
I could alternatively compute the square difference between the two
surfaces, or something like that.
Thanks! Caspar

2014-11-04 11:19 GMT-05:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:

 Hi Caspar

 the easiest way it so look at the parcellations and see if they are
 accurate. Note that we do subject-to-atlas alignment, not
 subject-to-subject (you get the latter by composing two atlas transforms)

 cheers
 Bruce
 On
 Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote:

  Hi Freesurfers,
  I was wondering whether there is a good way to assess post-hoc how well
 the
  alignment between two surfaces was. I wouldn't like to run the alignment
  again, but I could, if necessary. I would like to compare this alignment
 to
  a bunch of other alignments to see whether it was worse than the others.
  Thanks, Caspar
 
 
 
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Re: [Freesurfer] Quality of surface-based alignment

[Caspar M. Schwiedrzik]

Thanks! But there is nothing like a number I could pull from the
registration process, e.g. the distances of the vertices in registration
space? Caspar

2014-11-04 11:51 GMT-05:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:

 oh, I see. I would paint the folding patterns on the sphere.reg and
 toggle back and forth between them to see if they look right.
 Alternatively you could draw some sulci onto one of your datasets (this
 is easy to do in tksurfer) and use mri_label2label to map it to others
 and see if they land in the right place (central sulcus, calcarine,
 sylvian, etc...)
 On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote:

  Hi Bruce and Matt,
  I should specify that I am working with non-human primate data, so
  unfortunately, looking at the parcellations would not work. I am aligning
  individuals to a a custom template that I made.
  I was wondering whether there is maybe an output file that has something
  numerical on how much one surface had to be transformed to be aligned to
 the
  other.
  I could alternatively compute the square difference between the two
  surfaces, or something like that.
  Thanks! Caspar
 
  2014-11-04 11:19 GMT-05:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
 
the easiest way it so look at the parcellations and see if they
are
accurate. Note that we do subject-to-atlas alignment, not
subject-to-subject (you get the latter by composing two atlas
transforms)
 
cheers
Bruce
On
Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote:
 
 Hi Freesurfers,
 I was wondering whether there is a good way to assess post-hoc
how well the
 alignment between two surfaces was. I wouldn't like to run the
alignment
 again, but I could, if necessary. I would like to compare this
alignment to
 a bunch of other alignments to see whether it was worse than
the others.
 Thanks, Caspar



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  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.
 
 
 
 
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[Freesurfer] effect size for conjunction analyses?

[Caspar M. Schwiedrzik]

Hi!
I am doing some conjunction analyses (Nichols et al.) on my fMRI data, and
I was wondering whether anyone can make a recommendation how to display
effect sizes for this kind of analyses?
Would you show the effect size estimate corresponding to the p-value that
is chosen, an average, or anything else?
Thanks, Caspar
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[Freesurfer] read cluster summary into Matlab?

[Caspar M. Schwiedrzik]

Hi!
I was wondering whether there is code available to quickly read cluster
summary files into Matlab?
I need access to the cluster-wise p-values.
Thank you very much!
Caspar
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[Freesurfer] Applications open for the Neurobiology of Cognition GRC/GRS!

[Caspar M. Schwiedrzik]

(sorry for cross-posting)

 [image: Gordon Research Conferences]

Join us at the 2014 *Gordon Conference* and *Seminar* On

*Neurobiology of
Cognition*http://r20.rs6.net/tn.jsp?f=001WmUIQVsC75imVB3bWl9ZZPIlEuZLUMcBQfSHB8NCzlGRCh10gpaIVlyjuedrrMUIt_rVaFgHt4LRQhIU5dMvuzc4eDhC44ltvU1kWI9IsilkBLKjMWUUwgkTLGwEuu3wODhwtkW-uD2vrMe1r-6oNb5UNzGRL-Mqof35Ifmamifw7WMegE7mYHwLBXYQotzxHeSCOGv8oIXy8IBZvuF3Av10oqSWTE-l2iAivF60zP4=c=2XsJEd2Mr-oC81-GO5JVDJCkC3NkdpRhCK6OK-c_H-n92_mytkxcVg==ch=tfGBLHFYneXvyQQ5tKlVnfyRp37dQluMVMbPwI0KQg_4FVfRKnSYDA==

Circuits, Dynamics, Action and Perception

We are meeting *July 20-25, 2014 -*New GRC site: *Sunday River
Resort*http://r20.rs6.net/tn.jsp?f=001WmUIQVsC75imVB3bWl9ZZPIlEuZLUMcBQfSHB8NCzlGRCh10gpaIVl_6AchsEPpMx5XkiwPybkUULJX7zZLf7tTZvC67j05SJJyZgyhZRcLK9US26j18cx7iO3a3LhsfZsNupP4E_9oAYFLit07P0J0MBXY40rv70IP3Sp7V5bljTZ_7YXzymzoEBaEAzPdhc=2XsJEd2Mr-oC81-GO5JVDJCkC3NkdpRhCK6OK-c_H-n92_mytkxcVg==ch=tfGBLHFYneXvyQQ5tKlVnfyRp37dQluMVMbPwI0KQg_4FVfRKnSYDA==
Newry, Maine

Click 
*here*http://r20.rs6.net/tn.jsp?f=001WmUIQVsC75imVB3bWl9ZZPIlEuZLUMcBQfSHB8NCzlGRCh10gpaIVlyjuedrrMUIt_rVaFgHt4LRQhIU5dMvuzc4eDhC44ltvU1kWI9IsilkBLKjMWUUwgkTLGwEuu3wODhwtkW-uD2vrMe1r-6oNb5UNzGRL-Mqof35Ifmamifw7WMegE7mYHwLBXYQotzxHeSCOGv8oIXy8IBZvuF3Av10oqSWTE-l2iAivF60zP4=c=2XsJEd2Mr-oC81-GO5JVDJCkC3NkdpRhCK6OK-c_H-n92_mytkxcVg==ch=tfGBLHFYneXvyQQ5tKlVnfyRp37dQluMVMbPwI0KQg_4FVfRKnSYDA==to
see the
*GRC* program.

There is also an associated *GRS* *July 19-20 *for students and postdocs

Click 
*here*http://r20.rs6.net/tn.jsp?f=001WmUIQVsC75imVB3bWl9ZZPIlEuZLUMcBQfSHB8NCzlGRCh10gpaIVlyjuedrrMUIdbDiLIxtZ-MhvhSdQcDtQOxwkerfM_Fh2sw9n5tMBMpRIv9vn8xHJFD2NwN1vCQQ70Z8NYtpwFMcpIs20q5u4HuPYrU19F8_sopuGW2GkQnh-fKiVlXxYATbV4FETEPUo6-7iscSDdYqo567crFmktYFfLOrT6Rf_0_QIVK0pEM=c=2XsJEd2Mr-oC81-GO5JVDJCkC3NkdpRhCK6OK-c_H-n92_mytkxcVg==ch=tfGBLHFYneXvyQQ5tKlVnfyRp37dQluMVMbPwI0KQg_4FVfRKnSYDA==to
see the
*GRS* website.

*GRS* application  abstract deadline to be considered for oral
presentation- *April
30*

*Please use attached **flyer
http://r20.rs6.net/tn.jsp?f=001WmUIQVsC75imVB3bWl9ZZPIlEuZLUMcBQfSHB8NCzlGRCh10gpaIVlyjuedrrMUI23HSF0qZbVORYXN2fFmHnWNhmWni89PBecScjhRWIJbtmwPYgkCnQV8reGE_URYNjCSE6cC6cqpo115t7vweTq-bvS8-XZ-grZkSn-B0tapMOWakHKUv5iqCzzoxa_qrJH0ylWNY3Ytpsu_9K_noX_ta5wzP_J_SLNGD3Ze6yHhLjxYIYV5i-5WUTyVnIHMMdij8ZsKyrjg=c=2XsJEd2Mr-oC81-GO5JVDJCkC3NkdpRhCK6OK-c_H-n92_mytkxcVg==ch=tfGBLHFYneXvyQQ5tKlVnfyRp37dQluMVMbPwI0KQg_4FVfRKnSYDA==
**to help spread the word! *



The Neurobiology of Cognition is a recently-inaugurated GRC designed to
foster convergence of traditional neuroscience investigations with more
recent developments in systems, cellular and molecular neurobiology, in
engineering and imaging and in computational sciences. Cognition is
construed broadly to embrace empirical findings in a range of species
including humans, and there is a strong focus on integration of findings
and principles across species and levels of analysis.

In the opening Keynote Session, two leading neuroscientists with provide an
experimental and computational perspective on the recent initiative, termed
Brain Research through Advancing Innovative Neurotechnologies (BRAIN). This
initiative, spearheaded by the President and NIH, is aimed at developing
innovative methodologies to study how complex systems of neurons interact
in time and in space during complex behaviors. Along with recent findings
in a few traditional core areas, formal sessions will then explore
several new themes, including: 1) the neuroanatomy and 2) coordination of
cognitive circuits in the brain, 3) motor cognition and brain-computer
interfaces, 4) music and language, and 5) learning and plasticity. The
program juxtaposes human psychophysical, neuroimaging and
electrophysiological studies with parallel investigations in rodents and
non-human primates, and with computational approaches that explicate
empirical findings and construct robust, detailed models to represent the
developing picture and guide future experimentation. The program also
underscores novel experimental and theoretical approaches that promise to
define fundamental principles that guide and integrate the understanding of
cognition at a fundamental level, and to extend these to improved treatment
of brain dysfunction. The format of the meeting promotes intensive
interactions among investigators and trainees from different perspectives
and analytic levels, and in particular, between experimentalists and
theorists. There is a linked Gordon Research Seminar for trainees, most of
whom also attend the GRC.



All that is missing now is your *application* to attend.

Click 

Re: [Freesurfer] Anonymizing Siemens DICOM files

[Caspar M. Schwiedrzik]

Thanks to all that have replied so far!
Bruce, are you referring to this: http://freesurfer.net/fswiki/BIRND-UP ?
Thanks, Caspar



2014-03-20 17:40 GMT-04:00 Harms, Michael mha...@wustl.edu:


  Hi Caspar,
 I can't address your question regarding a specific tool, but wanted to
 mention a note of caution.
 You need to make sure that you scrub any identifying info from Siemen's
 custom DICOM fields (not just the obvious public DICOM fields).
 The challenge of doing that is why the safest thing is to not enter any
 identifying info at the scanner to begin with.

  cheers,
 -MH

   --
 Michael Harms, Ph.D.
  ---
 Conte Center for the Neuroscience of Mental Disorders
 Washington University School of Medicine
 Department of Psychiatry, Box 8134
 660 South Euclid Ave. Tel: 314-747-6173
 St. Louis, MO  63110 Email: mha...@wustl.edu

   From: Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu
 Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
 Date: Thursday, March 20, 2014 4:29 PM
 To: Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
 Cc: Julia Sliwa jsl...@mail.rockefeller.edu
 Subject: [Freesurfer] Anonymizing Siemens DICOM files

   Hi Freesurfer Experts,
 we are looking for a good way to remove subject names and dates of birth
 from Siemens DICOM headers. Is there something implemented in Freesurfer?

 Matlab's Image Processing Toolbox has a function to anonymize DICOM files
 (http://www.mathworks.com/help/images/ref/dicomanon.html), but we later
 run into trouble with unpacksdcmdir when we use that.

  Thanks, Caspar


  --

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dispose of the e-mail.

[Freesurfer] Anonymizing Siemens DICOM files

[Caspar M. Schwiedrzik]

Hi Freesurfer Experts,
we are looking for a good way to remove subject names and dates of birth
from Siemens DICOM headers. Is there something implemented in Freesurfer?

Matlab's Image Processing Toolbox has a function to anonymize DICOM files (
http://www.mathworks.com/help/images/ref/dicomanon.html), but we later run
into trouble with unpacksdcmdir when we use that.

Thanks, Caspar
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] FSFAST surface-based analysis to w-file

[Caspar M. Schwiedrzik]

Hi!
I need to export results from a surface-based analysis in FSFAST (v5.1) to
another program (Caret) that accepts .w files. I was wondering what the
recommended way of doing this is.
It seems that mri_surf2surf will do the trick?
Do I set the source and the target to be the same?
Thanks, Caspar
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dispose of the e-mail.

[Freesurfer] Caret F99 to Freesurfer

[Caspar M. Schwiedrzik]

Hi!
This has popped up on the list several times already, but I was wondering
whether someone has figured out how to bring the F99 surface atlas from
Caret into Freesurfer (not Freesurfer to Caret)?
Thanks, Caspar
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[Freesurfer] Problems converting MNC to NII

[Caspar M. Schwiedrzik]

Hi!
I am having some troubles converting MNC files to NII while preserving the
exact values in the MNC file. I have tried to use mri_convert and mnc2nii,
but in both cases, the values in the file output get changed. The help of
mri_convert mentions that the output for MNC files may not work.
Is there a workaround or a recommended procedure to convert MNC into NII?
Thanks, Caspar
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dispose of the e-mail.

Re: [Freesurfer] Problems converting MNC to NII

[Caspar M. Schwiedrzik]

Hi Bruce,
I have tried the two following commands, and various flags on mri_convert:
mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii
mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii

Yhe output of the latter would be:
mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from paxinos-MNI.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to paxinos-MNI.nii...

for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not
make a difference.

It could be that the problem arises once I call mri_binarize afterwards. I
know that there are values between 1 and 256 in the MNC file, but when I
call mri_binarize with -match on the MNC file or on any of the converted
NIFTI files, it does not find any values lower than 53 or so.

Caspar




2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu

 Hi Caspar

 hmm, I don't know why that would be the case. Can you send the full
 command line and screen output?
 cheers
 Bruce

 On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:

  Hi!
 I am having some troubles converting MNC files to NII while preserving the
 exact values in the MNC file. I have tried to use mri_convert and mnc2nii,
 but in both cases, the values in the file output get changed. The help of
 mri_convert mentions that the output for MNC files may not work.
 Is there a workaround or a recommended procedure to convert MNC into NII?
 Thanks, Caspar








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 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
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dispose of the e-mail.

Re: [Freesurfer] Problems converting MNC to NII

[Caspar M. Schwiedrzik]

Hi Bruce,
mri_diff does not return any differences. However, when I load the MNC file
into Matlab using loadminc (
http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do
retain all the values between 0 and 255. Also, I have something like an
annotation file for the MNC file that lists values between 0 and 255.
The MNC is unsigned byte.
Caspar


2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu

 how do you know that the values were there before? Try running mri_diff on
 the .nii and the .mnc and see if it finds any differences

 Bruce


 On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:

  Hi Bruce,
 I have tried the two following commands, and various flags on mri_convert:
 mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii
 mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii

 Yhe output of the latter would be:
 mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii
 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
 reading from paxinos-MNI.mnc...
 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
 i_ras = (1, 0, 0)
 j_ras = (0, 1, 0)
 k_ras = (0, 0, 1)
 writing to paxinos-MNI.nii...

 for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not
 make a difference.

 It could be that the problem arises once I call mri_binarize afterwards. I
 know that there are values between 1 and 256 in the MNC file, but when I
 call mri_binarize with -match on the MNC file or on any of the converted
 NIFTI files, it does not find any values lower than 53 or so.

 Caspar




 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
   Hi Caspar

   hmm, I don't know why that would be the case. Can you send the
   full command line and screen output?
   cheers
   Bruce
   On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:

 Hi!
 I am having some troubles converting MNC files to
 NII while preserving the
 exact values in the MNC file. I have tried to use
 mri_convert and mnc2nii,
 but in both cases, the values in the file output get
 changed. The help of
 mri_convert mentions that the output for MNC files
 may not work.
 Is there a workaround or a recommended procedure to
 convert MNC into NII?
 Thanks, Caspar








 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
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dispose of the e-mail.

Re: [Freesurfer] Problems converting MNC to NII

[Caspar M. Schwiedrzik]

Hi Bruce,
I am confused, too.
If the conversion is proper, why does mri_binarize not find values below
~53? when I call mri_binarize with -match on the MNC file or on any of the
converted NIFTI files?
Caspar




2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu

 Hi Caspar

 now, I'm confused. So it sounds like mri_convert is doing the conversion
 properly then?

 Bruce
 On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:

  Hi Bruce,
 mri_diff does not return any differences. However, when I load the MNC
 file
 into Matlab using loadminc
 (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I
 do
 retain all the values between 0 and 255. Also, I have something like an
 annotation file for the MNC file that lists values between 0 and 255.
 The MNC is unsigned byte.
 Caspar


 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
   how do you know that the values were there before? Try running
   mri_diff on the .nii and the .mnc and see if it finds any
   differences
   Bruce


   On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:

 Hi Bruce,
 I have tried the two following commands, and various
 flags on mri_convert:
 mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii
 mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii

 Yhe output of the latter would be:
 mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii
 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47
 greve Exp $
 reading from paxinos-MNI.mnc...
 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
 i_ras = (1, 0, 0)
 j_ras = (0, 1, 0)
 k_ras = (0, 0, 1)
 writing to paxinos-MNI.nii...

 for mri_convert, --nochange, -odt float/int/uchar,
 --no_scale 1 all do not
 make a difference.

 It could be that the problem arises once I call
 mri_binarize afterwards. I
 know that there are values between 1 and 256 in the
 MNC file, but when I
 call mri_binarize with -match on the MNC file or on
 any of the converted
 NIFTI files, it does not find any values lower than
 53 or so.

 Caspar




 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
   Hi Caspar

   hmm, I don't know why that would be the case.
 Can you send the
   full command line and screen output?
   cheers
   Bruce
   On Wed, 22 Jan 2014, Caspar M. Schwiedrzik
 wrote:

 Hi!
 I am having some troubles converting MNC
 files to
 NII while preserving the
 exact values in the MNC file. I have
 tried to use
 mri_convert and mnc2nii,
 but in both cases, the values in the
 file output get
 changed. The help of
 mri_convert mentions that the output for
 MNC files
 may not work.
 Is there a workaround or a recommended
 procedure to
 convert MNC into NII?
 Thanks, Caspar








 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.







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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Problems converting MNC to NII

[Caspar M. Schwiedrzik]

mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque
cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii
sysname  Linux
hostname wiener
machine  x86_64
user cschwiedrz

input  paxinos-MNI.nii
frame  0
nErode3d   0
nErode2d   0
output labels/1.nii
Binarizing based on matching values
nMatch 1
 0 1
binval1
binvalnot 0
Found 0 values in range
Counting number of voxels
Found 0 voxels in final mask
mri_binarize done



2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu

 can you send us the full command line and screen output of the
 mri_binarize command?

 On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:

  Hi Bruce,
 I am confused, too.
 If the conversion is proper, why does mri_binarize not find values below
 ~53? when I call mri_binarize with -match on the MNC file or on any of the
 converted NIFTI files?
 Caspar




 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
   Hi Caspar

   now, I'm confused. So it sounds like mri_convert is doing the
   conversion properly then?
   Bruce
   On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:

 Hi Bruce,
 mri_diff does not return any differences. However,
 when I load the MNC file
 into Matlab using loadminc
 (http://www.mathworks.com/matlabcentral/fileexchange/
 32644-loadminc),
 I do
 retain all the values between 0 and 255. Also, I
 have something like an
 annotation file for the MNC file that lists values
 between 0 and 255.
 The MNC is unsigned byte.
 Caspar


 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
   how do you know that the values were there
 before? Try running
   mri_diff on the .nii and the .mnc and see if
 it finds any
   differences
   Bruce


   On Wed, 22 Jan 2014, Caspar M. Schwiedrzik
 wrote:

 Hi Bruce,
 I have tried the two following commands,
 and various
 flags on mri_convert:
 mnc2nii -nii -int paxinos-MNI.mnc
 paxinos-MNI.nii
 mri_convert -i paxinos-MNI.mnc -o
 paxinos-MNI.nii

 Yhe output of the latter would be:
 mri_convert -i paxinos-MNI.mnc -o
 paxinos-MNI.nii
 $Id: mri_convert.c,v 1.179.2.2
 2011/05/16 20:53:47
 greve Exp $
 reading from paxinos-MNI.mnc...
 TR=0.00, TE=0.00, TI=0.00, flip
 angle=0.00
 i_ras = (1, 0, 0)
 j_ras = (0, 1, 0)
 k_ras = (0, 0, 1)
 writing to paxinos-MNI.nii...

 for mri_convert, --nochange, -odt
 float/int/uchar,
 --no_scale 1 all do not
 make a difference.

 It could be that the problem arises once
 I call
 mri_binarize afterwards. I
 know that there are values between 1 and
 256 in the
 MNC file, but when I
 call mri_binarize with -match on the MNC
 file or on
 any of the converted
 NIFTI files, it does not find any values
 lower than
 53 or so.

 Caspar




 2014/1/22 Bruce Fischl
 fis...@nmr.mgh.harvard.edu
   Hi Caspar

   hmm, I don't know why that would
 be the case.
 Can you send the
   full command line and screen
 output?
   cheers
   Bruce
   On Wed, 22 Jan 2014, Caspar M.
 Schwiedrzik
 wrote:

 Hi!
 I am having some troubles
 converting MNC
 files to
 NII while preserving the
 exact values in the MNC
 file. I have
 tried to use
 mri_convert and mnc2nii,
 but in both cases, the
 values in the
 file output get
 changed

Re: [Freesurfer] Problems converting MNC to NII

[Caspar M. Schwiedrzik]

same thing


2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu

 and what if you run it on the mnc?

 On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:

  mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii

 $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
 cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque
 cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii
 sysname  Linux
 hostname wiener
 machine  x86_64
 user cschwiedrz

 input  paxinos-MNI.nii
 frame  0
 nErode3d   0
 nErode2d   0
 output labels/1.nii
 Binarizing based on matching values
 nMatch 1
  0 1
 binval1
 binvalnot 0
 Found 0 values in range
 Counting number of voxels
 Found 0 voxels in final mask
 mri_binarize done



 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
   can you send us the full command line and screen output of the
   mri_binarize command?
   On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:

 Hi Bruce,
 I am confused, too.
 If the conversion is proper, why does mri_binarize
 not find values below
 ~53? when I call mri_binarize with -match on the MNC
 file or on any of the
 converted NIFTI files?
 Caspar




 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
   Hi Caspar

   now, I'm confused. So it sounds like
 mri_convert is doing the
   conversion properly then?
   Bruce
   On Wed, 22 Jan 2014, Caspar M. Schwiedrzik
 wrote:

 Hi Bruce,
 mri_diff does not return any
 differences. However,
 when I load the MNC file
 into Matlab using loadminc

 (http://www.mathworks.com/matlabcentral/fileexchange/
 32644-loadminc),
 I do
 retain all the values between 0 and 255.
 Also, I
 have something like an
 annotation file for the MNC file that
 lists values
 between 0 and 255.
 The MNC is unsigned byte.
 Caspar


 2014/1/22 Bruce Fischl
 fis...@nmr.mgh.harvard.edu
   how do you know that the values
 were there
 before? Try running
   mri_diff on the .nii and the .mnc
 and see if
 it finds any
   differences
   Bruce


   On Wed, 22 Jan 2014, Caspar M.
 Schwiedrzik
 wrote:

 Hi Bruce,
 I have tried the two
 following commands,
 and various
 flags on mri_convert:
 mnc2nii -nii -int
 paxinos-MNI.mnc
 paxinos-MNI.nii
 mri_convert -i
 paxinos-MNI.mnc -o
 paxinos-MNI.nii

 Yhe output of the latter
 would be:
 mri_convert -i
 paxinos-MNI.mnc -o
 paxinos-MNI.nii
 $Id: mri_convert.c,v
 1.179.2.2
 2011/05/16 20:53:47
 greve Exp $
 reading from
 paxinos-MNI.mnc...
 TR=0.00, TE=0.00, TI=0.00,
 flip
 angle=0.00
 i_ras = (1, 0, 0)
 j_ras = (0, 1, 0)
 k_ras = (0, 0, 1)
 writing to
 paxinos-MNI.nii...

 for mri_convert, --nochange,
 -odt
 float/int/uchar,
 --no_scale 1 all do not
 make a difference.

 It could be that the problem
 arises once
 I call
 mri_binarize afterwards. I
 know that there are values
 between 1 and
 256 in the
 MNC file, but when I
 call mri_binarize with
 -match on the MNC
 file or on
 any

Re: [Freesurfer] Problems converting MNC to NII

[Caspar M. Schwiedrzik]

or, since the correct values display if I load the same MNC file with
Matlab, it could be a problem with mri_binarize?


2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu

 then is seems like the problem is with your mnc, not with anything we are
 doing, right?

 On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:

  same thing


 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
   and what if you run it on the mnc?
   On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:

 mri_binarize --i paxinos-MNI.nii --match 1 --o
 labels/1.nii

 $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50
 greve Exp $
 cwd
 /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque
 cmdline mri_binarize --i paxinos-MNI.nii --match 1
 --o labels/1.nii
 sysname  Linux
 hostname wiener
 machine  x86_64
 user cschwiedrz

 input  paxinos-MNI.nii
 frame  0
 nErode3d   0
 nErode2d   0
 output labels/1.nii
 Binarizing based on matching values
 nMatch 1
  0 1
 binval1
 binvalnot 0
 Found 0 values in range
 Counting number of voxels
 Found 0 voxels in final mask
 mri_binarize done



 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
   can you send us the full command line and
 screen output of the
   mri_binarize command?
   On Wed, 22 Jan 2014, Caspar M. Schwiedrzik
 wrote:

 Hi Bruce,
 I am confused, too.
 If the conversion is proper, why does
 mri_binarize
 not find values below
 ~53? when I call mri_binarize with
 -match on the MNC
 file or on any of the
 converted NIFTI files?
 Caspar




 2014/1/22 Bruce Fischl
 fis...@nmr.mgh.harvard.edu
   Hi Caspar

   now, I'm confused. So it sounds
 like
 mri_convert is doing the
   conversion properly then?
   Bruce
   On Wed, 22 Jan 2014, Caspar M.
 Schwiedrzik
 wrote:

 Hi Bruce,
 mri_diff does not return any
 differences. However,
 when I load the MNC file
 into Matlab using loadminc


 (http://www.mathworks.com/matlabcentral/fileexchange/
 32644-loadminc),
 I do
 retain all the values
 between 0 and 255.
 Also, I
 have something like an
 annotation file for the MNC
 file that
 lists values
 between 0 and 255.
 The MNC is unsigned byte.
 Caspar


 2014/1/22 Bruce Fischl
 fis...@nmr.mgh.harvard.edu
   how do you know that
 the values
 were there
 before? Try running
   mri_diff on the .nii
 and the .mnc
 and see if
 it finds any
   differences
   Bruce


   On Wed, 22 Jan 2014,
 Caspar M.
 Schwiedrzik
 wrote:

 Hi Bruce,
 I have tried the
 two
 following commands,
 and various
 flags on
 mri_convert:
 mnc2nii -nii
 -int
 paxinos-MNI.mnc
 paxinos-MNI.nii
 mri_convert -i
 paxinos-MNI.mnc -o
 paxinos-MNI.nii

 Yhe output of
 the latter

Re: [Freesurfer] Problems converting MNC to NII

[Caspar M. Schwiedrzik]

Hi Doug,
when I try to use mri_binarize with -match, certain values, especially ones
smaller than about 50, are not found.
This happens with the original MNC file as well as with NIFTI files that I
converted from the MNC file.
When I load the MNC file in Matlab, all the values that mri_binarize did
not find show up.
The data type of the MNC file is unsigned byte; it is read as 32bit integer
in Matlab.
Caspar



2014/1/22 Douglas N Greve gr...@nmr.mgh.harvard.edu


 Can you describe the potential problem with mri_binarize more fully?


 On 01/22/2014 12:50 PM, Caspar M. Schwiedrzik wrote:
  or, since the correct values display if I load the same MNC file with
  Matlab, it could be a problem with mri_binarize?
 
 
  2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
  mailto:fis...@nmr.mgh.harvard.edu
 
  then is seems like the problem is with your mnc, not with anything
  we are doing, right?
 
  On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
 
  same thing
 
 
  2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
  mailto:fis...@nmr.mgh.harvard.edu
and what if you run it on the mnc?
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
 
  mri_binarize --i paxinos-MNI.nii --match 1 --o
  labels/1.nii
 
  $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50
  greve Exp $
  cwd
 
  /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque
  cmdline mri_binarize --i paxinos-MNI.nii --match 1
  --o labels/1.nii
  sysname  Linux
  hostname wiener
  machine  x86_64
  user cschwiedrz
 
  input  paxinos-MNI.nii
  frame  0
  nErode3d   0
  nErode2d   0
  output labels/1.nii
  Binarizing based on matching values
  nMatch 1
   0 1
  binval1
  binvalnot 0
  Found 0 values in range
  Counting number of voxels
  Found 0 voxels in final mask
  mri_binarize done
 
 
 
  2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
  mailto:fis...@nmr.mgh.harvard.edu
can you send us the full command line and
  screen output of the
mri_binarize command?
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik
  wrote:
 
  Hi Bruce,
  I am confused, too.
  If the conversion is proper, why does
  mri_binarize
  not find values below
  ~53? when I call mri_binarize with
  -match on the MNC
  file or on any of the
  converted NIFTI files?
  Caspar
 
 
 
 
  2014/1/22 Bruce Fischl
  fis...@nmr.mgh.harvard.edu
  mailto:fis...@nmr.mgh.harvard.edu
Hi Caspar
 
now, I'm confused. So it sounds
  like
  mri_convert is doing the
conversion properly then?
Bruce
On Wed, 22 Jan 2014, Caspar M.
  Schwiedrzik
  wrote:
 
  Hi Bruce,
  mri_diff does not return any
  differences. However,
  when I load the MNC file
  into Matlab using loadminc
 
 
 
  (
 http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc),
  I do
  retain all the values
  between 0 and 255.
  Also, I
  have something like an
  annotation file for the MNC
  file that
  lists values
  between 0 and 255.
  The MNC is unsigned byte.
  Caspar

[Freesurfer] Applying two registration matrices

[Caspar M. Schwiedrzik]

Hi Freesurfer Experts,
I was wondering what the best way to apply two registration matrices to the
same data set would be, ideally without re-slicing after the first
registration?
Thanks, Caspar
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Re: [Freesurfer] spatialsmooth-sess with option to set mask file name

[Caspar M. Schwiedrzik]

Hi Doug,
for this analysis, I would like to stay in volume space; the data are
aligned to a primate volume template. I am trying to do a group analysis of
the functional data as a next step (see this previous email:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33295.html).
If I just want to smooth my data in volume space, is there a better option
than spatialsmooth-sess in v5.1?
Caspar




2014/1/10 Douglas N Greve gr...@nmr.mgh.harvard.edu

 If you just want to sample your volume on the surface and smooth it there,
 use mri_vol2surf with --surf-fwhm. Send me your command line when you have
 one and I'll verify it is the right thing.
 doug



 On 01/09/2014 10:21 PM, Caspar M. Schwiedrzik wrote:

 Hi Doug, I found a way to build it in myself. I am using
 spatialsmooth-sess from v5.1. I need to smooth some functional data that I
 have preprocessed through some other program until this point.
 What should I be using instead of spatialsmooth-sess if I only want to
 smooth?
 Thanks, Caspar

 On Thursday, January 9, 2014, Douglas Greve wrote:


 No, sorry. Why are you using such an old version?
 doug





 On 1/9/14 5:26 PM, Caspar M. Schwiedrzik wrote:

 Hi Doug,
 do you have a version of spatialsmooth-sess with the option to
 set mask file name?
 Thanks, Caspar



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[Freesurfer] spatialsmooth-sess with option to set mask file name

[Caspar M. Schwiedrzik]

Hi Doug,
do you have a version of spatialsmooth-sess with the option to set mask
file name?
Thanks, Caspar
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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.