Re: [HCP-Users] Core Dump ${MSMBINDIR}/msm

[Glasser, Matthew]

You should run the specific command that generates the .rot. file in 
PostFreeSurfer to get that file.  Starting with FreeSurfer for MSMAll is 
definitely not recommended as that will make the problem harder for MSMAll 
(having to try to undo the bad FreeSurfer distortions), and it might be better 
to rerun PostFreeSurfer before using MSMAll.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Tuesday, July 10, 2018 at 10:24 AM
To: "hcp-users@humanconnectome.org" 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] Core Dump ${MSMBINDIR}/msm

Hello,

When I run msm within MSMAll I get a core dump because the --inmesh file could 
not be found: 
${NativeFolder}/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii. I see that 
the file is generated within the PostFreeSurfer pipeline if the MSMSulc 
registration is specified. I've already run minimal preprocessing on this study 
with FS as registration name. While I will ultimately switch all of my 
processing to MSMSulc I would like to keep the preprocessing I have done with 
FS there. What file should I use then for inmesh?

-Tim


Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

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Re: [HCP-Users] FIRST & FAST Data

[Harms, Michael]

Sorry, no.

--
Michael Harms, Ph.D.

---

Associate Professor of Psychiatry

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
On 7/10/18, 3:16 PM, "hcp-users-boun...@humanconnectome.org on behalf of 
Bajada, Claude Julien"  wrote:

Dear all,

Is there any pre computed FIRST & FAST data for the HCP releases?

Regards,
Claude




Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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[HCP-Users] FIRST & FAST Data

[Bajada, Claude Julien]

Dear all,

Is there any pre computed FIRST & FAST data for the HCP releases?

Regards,
Claude




Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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Re: [HCP-Users] Brainstem to cortex baseline r-value

[Timothy Coalson]

There is no threshold for correlation values which says they are
insignificant or "mathematically irrelevant", only statistical tests can
tell you if something is unlikely to be due to chance.  The fact that a
small r-value is statistically significant just means that the r-values if
there was no effect are even closer to zero.  Yes, the *correlations* are
small (which is not a true measure of effect size, it is highly dependent
on SNR), but it is consistent.  Matt was explaining why you should not
expect the correlation values to *ever* be large in any high-resolution
BOLD data.

fMRI BOLD scans do not have much SNR, each voxel's timeseries is dominated
by random noise, this is why you need a lot of timepoints, and use
correlation (or similar things like GLM for task).  However, the MR physics
seems to work out such that when you use large voxel sizes (low
resolutions), you get all of the signal "within" that voxel, while all the
independent noise coming from "within" that voxel all gets averaged
together, and therefore doesn't add up to much.  Thus, if you are used to
large-voxel data (or if you are used to doing a lot of smoothing, which has
similar effects), you may expect per-voxel correlation values that are
rather larger than 0.05.  However, in HCP data, we acquire smaller voxels,
resulting in less signal per voxel, while the noise within the voxel isn't
"averaged" over as much volume, and thus the per-voxel timecourse is more
dominated by random noise.  However, since random noise has expected
covariance of 0 with other noise, this isn't an issue for finding
statistically robust effects as long as you have enough timepoints.

However, correlation is not trying to find the effect size - in particular,
it divides by the *total* standard deviation of the timeseries (which is
basically equal to the standard deviation of the noise, because of how much
noise dominates in BOLD data), while only the signal of interest adds to
the numerator.  Thus, with less signal *per voxel* with high resolution
scans, you get lower correlation values *per voxel*.  This is expected, but
not really meaningful - really, it just means that your signal is divided
up into smaller spatial units, and your noise also (which is exactly what
it means to have higher resolution data).  If you smoothed the data to be
more like low-resolution data, your correlation values would increase,
since the noise standard deviation would decrease (but smoothing like this
is not a good idea since you lose spatial localization - as I said, a low
correlation value doesn't mean that something is due to chance, that is for
statistical tests to decide).

Tim


On Tue, Jul 10, 2018 at 5:54 AM, Amin Dadashi  wrote:

> Thank you Matthew. To be more accurate, my question is about the expected
> r-values indicating an existing connectivity between brainstem ROI to the
> cortical areas. I have not seen many articles reporting the values of the
> significant correlation coefficients and so I am wondering why it is not
> considered to be important.
>
> In my case, I have found significant connectivity from the specific
> brainstem ROIs, but looking at the peak significant r-values, they are not
> exceeding 0.05. From the mathematical point of view, such a small r-value
> means the two compared variables are irrelevant; at the same time, it is
> not possible to ignore that the cortical pattern of these significant
> mathematical irrelevance seem to be meaningful. I believe that I am missing
> a point, where your expert opinion might help me to figure out.
>
> Thanks a lot,
> Amin
>
>
>
> On Mon, Jul 9, 2018 at 10:48 PM, Glasser, Matthew 
> wrote:
>
>> There is more unstructured noise in HCP data because of small voxel size
>> and fast TR.  Basically that means the ratio between the neural signal and
>> the random noise is lower and that leads to lower correlation coefficients.
>>
>>
>> Peace,
>>
>> Matt.
>>
>> From:  on behalf of Amin Dadashi <
>> amin.dada...@uni-tuebingen.de>
>> Date: Monday, July 9, 2018 at 4:14 AM
>> To: hcp-users 
>> Subject: [HCP-Users] Brainstem to cortex baseline r-value
>>
>> Dear HCP users,
>>
>> Recently, I have tried to calculate the zero-order correlation between
>> some brainstem ROIs and the cortical vertices. Looking at the mean
>> subjects' correlation map, the connectivity pattern totally makes sense.
>> Even after doing the statistical testing (using permutation based on
>> maximum t-statistics) the significant correlated clusters are located in
>> the expected areas. However, the magnitude of the correlation coefficients
>> are very small (in the order of 0.05 for the peak vertices in the mean
>> map). I have also done the volume-based voxel-wise analysis for the same
>> brainstem ROIs and I had similar findings there.
>> Is there any explanation for such small r-values even though the
>> significant correlations seem to be meaningful?
>>
>> Thank you all,
>> Amin
>>
>> ___
>> HCP

Re: [HCP-Users] Brainstem to cortex baseline r-value

[Amin Dadashi]

Thank you Matthew. To be more accurate, my question is about the expected
r-values indicating an existing connectivity between brainstem ROI to the
cortical areas. I have not seen many articles reporting the values of the
significant correlation coefficients and so I am wondering why it is not
considered to be important.

In my case, I have found significant connectivity from the specific
brainstem ROIs, but looking at the peak significant r-values, they are not
exceeding 0.05. From the mathematical point of view, such a small r-value
means the two compared variables are irrelevant; at the same time, it is
not possible to ignore that the cortical pattern of these significant
mathematical irrelevance seem to be meaningful. I believe that I am missing
a point, where your expert opinion might help me to figure out.

Thanks a lot,
Amin


On Mon, Jul 9, 2018 at 10:48 PM, Glasser, Matthew 
wrote:

> There is more unstructured noise in HCP data because of small voxel size
> and fast TR.  Basically that means the ratio between the neural signal and
> the random noise is lower and that leads to lower correlation coefficients.
>
>
> Peace,
>
> Matt.
>
> From:  on behalf of Amin Dadashi <
> amin.dada...@uni-tuebingen.de>
> Date: Monday, July 9, 2018 at 4:14 AM
> To: hcp-users 
> Subject: [HCP-Users] Brainstem to cortex baseline r-value
>
> Dear HCP users,
>
> Recently, I have tried to calculate the zero-order correlation between
> some brainstem ROIs and the cortical vertices. Looking at the mean
> subjects' correlation map, the connectivity pattern totally makes sense.
> Even after doing the statistical testing (using permutation based on
> maximum t-statistics) the significant correlated clusters are located in
> the expected areas. However, the magnitude of the correlation coefficients
> are very small (in the order of 0.05 for the peak vertices in the mean
> map). I have also done the volume-based voxel-wise analysis for the same
> brainstem ROIs and I had similar findings there.
> Is there any explanation for such small r-values even though the
> significant correlations seem to be meaningful?
>
> Thank you all,
> Amin
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>

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[HCP-Users] Core Dump ${MSMBINDIR}/msm

[Timothy Hendrickson]

Hello,

When I run msm within MSMAll I get a core dump because the* --inmesh file
could not be found:
${NativeFolder}/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii*. I see
that the file is generated within the PostFreeSurfer pipeline if the
MSMSulc registration is specified. I've already run minimal preprocessing
on this study with FS as registration name. While I will ultimately switch
all of my processing to MSMSulc I would like to keep the preprocessing I
have done with FS there. What file should I use then for inmesh?

-Tim


Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

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