Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

2019-04-22 Thread Yizhou Ma 
Great that's quick!

On Mon, Apr 22, 2019 at 9:09 PM Glasser, Matthew  wrote:

> A few weeks maybe if you want a pre-release version.
>
> Matt.
>
> From: Yizhou Ma 
> Date: Monday, April 22, 2019 at 9:06 PM
> To: Matt Glasser 
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] Multi-run ICA-FIX with excessive movement
>
> Thank you Matt. This is really helpful. Any idea when the new classifier
> you mentioned in 1. will be available?
>
> On Mon, Apr 22, 2019 at 8:50 PM Glasser, Matthew 
> wrote:
>
>> I guess I haven’t been in the habit of throwing out data like this.
>> Things I would consider would include:
>>
>>1. MR+FIX classification accuracy (if runs were poorly classified,
>>they won’t be denoised well).  I’ll note that we are training an improved
>>MR+FIX classifier using a combination of HCP-YA resting state (single run
>>FIX), HCP-YA task (MR+FIX), and HCP Lifespan (MR+FIX) to address
>>classification issues we have observed with very large numbers of
>>components, subject with very large amounts of motion, and other artifacts
>>that were not a part of the HCP-YA original training data.
>>2. Unusually small numbers of signal components (though note we found
>>a recent subtle bug whereby if melodic does not finish mixture modeling
>>components, FIX will fail to classify signal components correctly).  If
>>there are few signal components this means that either the SNR is very bad
>>or the structured noise has overwhelmed the signal and mixed in too much
>>with the signal, making it hard to separate.
>>3. DVARS Spikes above baseline (not dips below baseline) in the
>>cleaned timeseries suggest residual noise.  I prefer DVARS derived 
>> measures
>>to movement tracer derived measures because they tell you something about
>>what is actually happening to the intensities inside the data, whereas
>>movement tracers may be inaccurate reflections of signal intensity
>>fluctuations for a variety of reasons (see Glasser et al 2018 Neuroimage:
>>https://www.sciencedirect.com/science/article/pii/S1053811918303963 for
>>examples).
>>
>> Others in the HCP used different means to identify some of the noise
>> components I mentioned above that weren’t being classified correctly by
>> regular FIX, and might be able to share their suggestions.
>>
>> Matt.
>>
>> From: Yizhou Ma 
>> Date: Monday, April 22, 2019 at 8:25 PM
>> To: Matt Glasser 
>> Cc: "hcp-users@humanconnectome.org" 
>> Subject: Re: [HCP-Users] Multi-run ICA-FIX with excessive movement
>>
>> Thank you Matt. Do you have some suggestions for the metrics to use to
>> determine scan quality after ICA FIX?
>>
>> Thanks,
>> Cherry
>>
>> On Mon, Apr 22, 2019 at 8:15 PM Glasser, Matthew 
>> wrote:
>>
>>> I would decide after cleaning with MR ICA+FIX if you actually have to
>>> exclude the scans and run with them all.
>>>
>>> Matt.
>>>
>>> From:  on behalf of Yizhou Ma <
>>> maxxx...@umn.edu>
>>> Date: Monday, April 22, 2019 at 3:47 PM
>>> To: "hcp-users@humanconnectome.org" 
>>> Subject: [HCP-Users] Multi-run ICA-FIX with excessive movement
>>>
>>> Dear HCP experts,
>>>
>>> I am writing for a question with multi-run ICA-FIX for my dataset. I
>>> have 4 resting state scans (TR=0.8, length=6.5min each) and 3 task scans
>>> (TR=0.8, length=6min each) that I intend to run multi-run ICA-FIX on. We
>>> used Euclidean norm values to threshold volumes with excessive movement and
>>> decided that scans with more than 20% volumes with excessive movement are
>>> not usable. I wonder with multi-run ICA-FIX, if it would be problematic to
>>> include these scans. In other words, I am trying to decide if I should 1)
>>> run multi-run ICA-FIX on scans with less motion, therefore each subject may
>>> have different number of scans that are included in multi-run ICA-FIX; or
>>> 2) run multi-run ICA-FIX on all scans, and throw out scans with excessive
>>> motion afterward.
>>>
>>> Thank you very much,
>>> Cherry
>>>
>>> ___
>>> 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.
>>>
>>
>> --
>>
>> 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

Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

2019-04-22 Thread Glasser, Matthew 
A few weeks maybe if you want a pre-release version.

Matt.

From: Yizhou Ma mailto:maxxx...@umn.edu>>
Date: Monday, April 22, 2019 at 9:06 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

Thank you Matt. This is really helpful. Any idea when the new classifier you 
mentioned in 1. will be available?

On Mon, Apr 22, 2019 at 8:50 PM Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
I guess I haven’t been in the habit of throwing out data like this.  Things I 
would consider would include:

  1.  MR+FIX classification accuracy (if runs were poorly classified, they 
won’t be denoised well).  I’ll note that we are training an improved MR+FIX 
classifier using a combination of HCP-YA resting state (single run FIX), HCP-YA 
task (MR+FIX), and HCP Lifespan (MR+FIX) to address classification issues we 
have observed with very large numbers of components, subject with very large 
amounts of motion, and other artifacts that were not a part of the HCP-YA 
original training data.
  2.  Unusually small numbers of signal components (though note we found a 
recent subtle bug whereby if melodic does not finish mixture modeling 
components, FIX will fail to classify signal components correctly).  If there 
are few signal components this means that either the SNR is very bad or the 
structured noise has overwhelmed the signal and mixed in too much with the 
signal, making it hard to separate.
  3.  DVARS Spikes above baseline (not dips below baseline) in the cleaned 
timeseries suggest residual noise.  I prefer DVARS derived measures to movement 
tracer derived measures because they tell you something about what is actually 
happening to the intensities inside the data, whereas movement tracers may be 
inaccurate reflections of signal intensity fluctuations for a variety of 
reasons (see Glasser et al 2018 Neuroimage: 
https://www.sciencedirect.com/science/article/pii/S1053811918303963 for 
examples).

Others in the HCP used different means to identify some of the noise components 
I mentioned above that weren’t being classified correctly by regular FIX, and 
might be able to share their suggestions.

Matt.

From: Yizhou Ma mailto:maxxx...@umn.edu>>
Date: Monday, April 22, 2019 at 8:25 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

Thank you Matt. Do you have some suggestions for the metrics to use to 
determine scan quality after ICA FIX?

Thanks,
Cherry

On Mon, Apr 22, 2019 at 8:15 PM Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
I would decide after cleaning with MR ICA+FIX if you actually have to exclude 
the scans and run with them all.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Yizhou Ma mailto:maxxx...@umn.edu>>
Date: Monday, April 22, 2019 at 3:47 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Multi-run ICA-FIX with excessive movement

Dear HCP experts,

I am writing for a question with multi-run ICA-FIX for my dataset. I have 4 
resting state scans (TR=0.8, length=6.5min each) and 3 task scans (TR=0.8, 
length=6min each) that I intend to run multi-run ICA-FIX on. We used Euclidean 
norm values to threshold volumes with excessive movement and decided that scans 
with more than 20% volumes with excessive movement are not usable. I wonder 
with multi-run ICA-FIX, if it would be problematic to include these scans. In 
other words, I am trying to decide if I should 1) run multi-run ICA-FIX on 
scans with less motion, therefore each subject may have different number of 
scans that are included in multi-run ICA-FIX; or 2) run multi-run ICA-FIX on 
all scans, and throw out scans with excessive motion afterward.

Thank you very much,
Cherry

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Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

2019-04-22 Thread Yizhou Ma 
Thank you Matt. This is really helpful. Any idea when the new classifier
you mentioned in 1. will be available?

On Mon, Apr 22, 2019 at 8:50 PM Glasser, Matthew  wrote:

> I guess I haven’t been in the habit of throwing out data like this.
> Things I would consider would include:
>
>1. MR+FIX classification accuracy (if runs were poorly classified,
>they won’t be denoised well).  I’ll note that we are training an improved
>MR+FIX classifier using a combination of HCP-YA resting state (single run
>FIX), HCP-YA task (MR+FIX), and HCP Lifespan (MR+FIX) to address
>classification issues we have observed with very large numbers of
>components, subject with very large amounts of motion, and other artifacts
>that were not a part of the HCP-YA original training data.
>2. Unusually small numbers of signal components (though note we found
>a recent subtle bug whereby if melodic does not finish mixture modeling
>components, FIX will fail to classify signal components correctly).  If
>there are few signal components this means that either the SNR is very bad
>or the structured noise has overwhelmed the signal and mixed in too much
>with the signal, making it hard to separate.
>3. DVARS Spikes above baseline (not dips below baseline) in the
>cleaned timeseries suggest residual noise.  I prefer DVARS derived measures
>to movement tracer derived measures because they tell you something about
>what is actually happening to the intensities inside the data, whereas
>movement tracers may be inaccurate reflections of signal intensity
>fluctuations for a variety of reasons (see Glasser et al 2018 Neuroimage:
>https://www.sciencedirect.com/science/article/pii/S1053811918303963 for
>examples).
>
> Others in the HCP used different means to identify some of the noise
> components I mentioned above that weren’t being classified correctly by
> regular FIX, and might be able to share their suggestions.
>
> Matt.
>
> From: Yizhou Ma 
> Date: Monday, April 22, 2019 at 8:25 PM
> To: Matt Glasser 
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] Multi-run ICA-FIX with excessive movement
>
> Thank you Matt. Do you have some suggestions for the metrics to use to
> determine scan quality after ICA FIX?
>
> Thanks,
> Cherry
>
> On Mon, Apr 22, 2019 at 8:15 PM Glasser, Matthew 
> wrote:
>
>> I would decide after cleaning with MR ICA+FIX if you actually have to
>> exclude the scans and run with them all.
>>
>> Matt.
>>
>> From:  on behalf of Yizhou Ma <
>> maxxx...@umn.edu>
>> Date: Monday, April 22, 2019 at 3:47 PM
>> To: "hcp-users@humanconnectome.org" 
>> Subject: [HCP-Users] Multi-run ICA-FIX with excessive movement
>>
>> Dear HCP experts,
>>
>> I am writing for a question with multi-run ICA-FIX for my dataset. I have
>> 4 resting state scans (TR=0.8, length=6.5min each) and 3 task scans
>> (TR=0.8, length=6min each) that I intend to run multi-run ICA-FIX on. We
>> used Euclidean norm values to threshold volumes with excessive movement and
>> decided that scans with more than 20% volumes with excessive movement are
>> not usable. I wonder with multi-run ICA-FIX, if it would be problematic to
>> include these scans. In other words, I am trying to decide if I should 1)
>> run multi-run ICA-FIX on scans with less motion, therefore each subject may
>> have different number of scans that are included in multi-run ICA-FIX; or
>> 2) run multi-run ICA-FIX on all scans, and throw out scans with excessive
>> motion afterward.
>>
>> Thank you very much,
>> Cherry
>>
>> ___
>> 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.
>>
>
> --
>
> 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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Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

2019-04-22 Thread Glasser, Matthew 
I guess I haven’t been in the habit of throwing out data like this.  Things I 
would consider would include:

  1.  MR+FIX classification accuracy (if runs were poorly classified, they 
won’t be denoised well).  I’ll note that we are training an improved MR+FIX 
classifier using a combination of HCP-YA resting state (single run FIX), HCP-YA 
task (MR+FIX), and HCP Lifespan (MR+FIX) to address classification issues we 
have observed with very large numbers of components, subject with very large 
amounts of motion, and other artifacts that were not a part of the HCP-YA 
original training data.
  2.  Unusually small numbers of signal components (though note we found a 
recent subtle bug whereby if melodic does not finish mixture modeling 
components, FIX will fail to classify signal components correctly).  If there 
are few signal components this means that either the SNR is very bad or the 
structured noise has overwhelmed the signal and mixed in too much with the 
signal, making it hard to separate.
  3.  DVARS Spikes above baseline (not dips below baseline) in the cleaned 
timeseries suggest residual noise.  I prefer DVARS derived measures to movement 
tracer derived measures because they tell you something about what is actually 
happening to the intensities inside the data, whereas movement tracers may be 
inaccurate reflections of signal intensity fluctuations for a variety of 
reasons (see Glasser et al 2018 Neuroimage: 
https://www.sciencedirect.com/science/article/pii/S1053811918303963 for 
examples).

Others in the HCP used different means to identify some of the noise components 
I mentioned above that weren’t being classified correctly by regular FIX, and 
might be able to share their suggestions.

Matt.

From: Yizhou Ma mailto:maxxx...@umn.edu>>
Date: Monday, April 22, 2019 at 8:25 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

Thank you Matt. Do you have some suggestions for the metrics to use to 
determine scan quality after ICA FIX?

Thanks,
Cherry

On Mon, Apr 22, 2019 at 8:15 PM Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
I would decide after cleaning with MR ICA+FIX if you actually have to exclude 
the scans and run with them all.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Yizhou Ma mailto:maxxx...@umn.edu>>
Date: Monday, April 22, 2019 at 3:47 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Multi-run ICA-FIX with excessive movement

Dear HCP experts,

I am writing for a question with multi-run ICA-FIX for my dataset. I have 4 
resting state scans (TR=0.8, length=6.5min each) and 3 task scans (TR=0.8, 
length=6min each) that I intend to run multi-run ICA-FIX on. We used Euclidean 
norm values to threshold volumes with excessive movement and decided that scans 
with more than 20% volumes with excessive movement are not usable. I wonder 
with multi-run ICA-FIX, if it would be problematic to include these scans. In 
other words, I am trying to decide if I should 1) run multi-run ICA-FIX on 
scans with less motion, therefore each subject may have different number of 
scans that are included in multi-run ICA-FIX; or 2) run multi-run ICA-FIX on 
all scans, and throw out scans with excessive motion afterward.

Thank you very much,
Cherry

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Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
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strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
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intended recipient, be advised that any unauthorized use, disclosure, copying 
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strictly prohibited. If you have received this email in error, please 
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Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

2019-04-22 Thread Yizhou Ma 
Thank you Matt. Do you have some suggestions for the metrics to use to
determine scan quality after ICA FIX?

Thanks,
Cherry

On Mon, Apr 22, 2019 at 8:15 PM Glasser, Matthew  wrote:

> I would decide after cleaning with MR ICA+FIX if you actually have to
> exclude the scans and run with them all.
>
> Matt.
>
> From:  on behalf of Yizhou Ma <
> maxxx...@umn.edu>
> Date: Monday, April 22, 2019 at 3:47 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Multi-run ICA-FIX with excessive movement
>
> Dear HCP experts,
>
> I am writing for a question with multi-run ICA-FIX for my dataset. I have
> 4 resting state scans (TR=0.8, length=6.5min each) and 3 task scans
> (TR=0.8, length=6min each) that I intend to run multi-run ICA-FIX on. We
> used Euclidean norm values to threshold volumes with excessive movement and
> decided that scans with more than 20% volumes with excessive movement are
> not usable. I wonder with multi-run ICA-FIX, if it would be problematic to
> include these scans. In other words, I am trying to decide if I should 1)
> run multi-run ICA-FIX on scans with less motion, therefore each subject may
> have different number of scans that are included in multi-run ICA-FIX; or
> 2) run multi-run ICA-FIX on all scans, and throw out scans with excessive
> motion afterward.
>
> Thank you very much,
> Cherry
>
> ___
> 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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Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

2019-04-22 Thread Glasser, Matthew 
I would decide after cleaning with MR ICA+FIX if you actually have to exclude 
the scans and run with them all.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Yizhou Ma mailto:maxxx...@umn.edu>>
Date: Monday, April 22, 2019 at 3:47 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Multi-run ICA-FIX with excessive movement

Dear HCP experts,

I am writing for a question with multi-run ICA-FIX for my dataset. I have 4 
resting state scans (TR=0.8, length=6.5min each) and 3 task scans (TR=0.8, 
length=6min each) that I intend to run multi-run ICA-FIX on. We used Euclidean 
norm values to threshold volumes with excessive movement and decided that scans 
with more than 20% volumes with excessive movement are not usable. I wonder 
with multi-run ICA-FIX, if it would be problematic to include these scans. In 
other words, I am trying to decide if I should 1) run multi-run ICA-FIX on 
scans with less motion, therefore each subject may have different number of 
scans that are included in multi-run ICA-FIX; or 2) run multi-run ICA-FIX on 
all scans, and throw out scans with excessive motion afterward.

Thank you very much,
Cherry

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[HCP-Users] Multi-run ICA-FIX with excessive movement

2019-04-22 Thread Yizhou Ma 
Dear HCP experts,

I am writing for a question with multi-run ICA-FIX for my dataset. I have 4
resting state scans (TR=0.8, length=6.5min each) and 3 task scans (TR=0.8,
length=6min each) that I intend to run multi-run ICA-FIX on. We used
Euclidean norm values to threshold volumes with excessive movement and
decided that scans with more than 20% volumes with excessive movement are
not usable. I wonder with multi-run ICA-FIX, if it would be problematic to
include these scans. In other words, I am trying to decide if I should 1)
run multi-run ICA-FIX on scans with less motion, therefore each subject may
have different number of scans that are included in multi-run ICA-FIX; or
2) run multi-run ICA-FIX on all scans, and throw out scans with excessive
motion afterward.

Thank you very much,
Cherry

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Re: [HCP-Users] unequal length of movement regressors

2019-04-22 Thread Harms, Michael 

We have seen this occur on rare occasions, and don’t have an explanation for it.

Try just running fMRIVolume again.

Cheers,
-MH

--
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

From:  on behalf of Moataz Assem 

Date: Monday, April 22, 2019 at 1:16 PM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] unequal length of movement regressors

Hi,

Is there a reason why movement_regressors.txt might have unequal length of 
columns (i.e. timepoints)?
I have seen this happen (infrequently) in different runs for different subjects 
for some HCP-style data we collected.
Preprocessing was done using v3.27.0

Moataz



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Re: [HCP-Users] Diffusion Preprocessing Failure

2019-04-22 Thread Timothy Coalson 
I haven't used eddy, but since it looks like an output file, my first
thought is permissions - does that folder exist, and can the user you are
running the eddy job as write files to it?  Does a file with that name
exist, and not have write permissions?

Tim


On Mon, Apr 22, 2019 at 11:39 AM Timothy Hendrickson 
wrote:

> Hello,
>
> I am attempting to run the diffusion preprocessing with HCP version 3.27.0
> with the GPU enabled eddy, however I receive an error that
> "eddy_unwarped_Neg" could not be opened, see below:
>
>  START: eddy_postproc
>
> JAC resampling has been used. Eddy Output is now combined.
>
> Image Exception : #22 :: ERROR: Could not open image
> /output_dir/sub-9276/ses-52
> 742/Diffusion/eddy/eddy_unwarped_Neg
>
> I'm looking for an intuition as to what could have happened.
>
> Best,
>
> -Tim
>
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[HCP-Users] unequal length of movement regressors

2019-04-22 Thread Moataz Assem 
Hi,

Is there a reason why movement_regressors.txt might have unequal length of 
columns (i.e. timepoints)?
I have seen this happen (infrequently) in different runs for different subjects 
for some HCP-style data we collected.
Preprocessing was done using v3.27.0

Moataz



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Re: [HCP-Users] wb_command -metric-tfce

2019-04-22 Thread Timothy Coalson 
For the most part, it exists because I was testing a new method for
computing the TFCE transform itself (it is an integral containing cluster
size which other utilities generally approximate by using many different
thresholds).  We do not currently do statistical testing within wb_command.

Tim


On Sun, Apr 21, 2019 at 7:00 AM Reza Rajimehr  wrote:

> Thanks Michael. We will use PALM. But what is the application of
> wb_command -metric-tfce then?
>
>
> On Sun, Apr 21, 2019 at 2:38 AM Harms, Michael  wrote:
>
>>
>>
>> Hi,
>>
>> We suggest you use PALM, since you need to use permutation to determine
>> the distribution of the TFCE metric.
>>
>>
>>
>> Cheers,
>>
>> -MH
>>
>>
>>
>> --
>>
>> 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
>>
>>
>>
>> *From: * on behalf of Reza
>> Rajimehr 
>> *Date: *Saturday, April 20, 2019 at 7:18 PM
>> *To: *hcp-users 
>> *Subject: *[HCP-Users] wb_command -metric-tfce
>>
>>
>>
>> Hi,
>>
>>
>>
>> We have curvature data from two groups of subjects in a common anatomical
>> space (MSMAll). We performed a univariate comparison between the two groups
>> using t-test. We now have a map, which shows vertex-wise curvature
>> difference between the two groups (the curvature difference is shown only
>> for vertices which have a significant difference). The next step is to do
>> cluster-wise correction using TFCE method. It looks like this command can
>> do what we want:
>>
>>
>>
>> https://www.humanconnectome.org/software/workbench-command/-metric-tfce
>>
>>
>>
>> However, we couldn’t find any example command, and its usage is a bit
>> unclear for us. For example, how should we specify the two groups?
>>
>>
>>
>> Any help would be appreciated.
>>
>>
>>
>> Note: Our analysis here is somewhat similar to the analysis in Figure 5B
>> in Van Essen et al. 2012 paper:
>>
>>
>>
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3432236/pdf/bhr291.pdf
>>
>>
>>
>> Best,
>>
>> Reza
>>
>> ___
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>> 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] Diffusion Preprocessing Failure

2019-04-22 Thread Timothy Hendrickson 
Hello,

I am attempting to run the diffusion preprocessing with HCP version 3.27.0
with the GPU enabled eddy, however I receive an error that
"eddy_unwarped_Neg" could not be opened, see below:

 START: eddy_postproc

JAC resampling has been used. Eddy Output is now combined.

Image Exception : #22 :: ERROR: Could not open image
/output_dir/sub-9276/ses-52
742/Diffusion/eddy/eddy_unwarped_Neg

I'm looking for an intuition as to what could have happened.

Best,

-Tim

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Re: [HCP-Users] DeDriftAndResamplePipeline error

2019-04-22 Thread Marta Moreno 
OK, thank you very much.
You guys are doing an awesome work!

Leah.

> On Apr 20, 2019, at 5:18 PM, Harms, Michael  wrote:
> 
>  
> That particular error message can be ignored.  We’ll fix the scripts so that 
> it doesn’t occur in the future.
>  
> Cheers,
> -MH
>  
> -- 
> 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
>  
> From:  on behalf of Marta Moreno 
> 
> Date: Saturday, April 20, 2019 at 12:02 PM
> To: "Glasser, Matthew" 
> Cc: HCP Users 
> Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error
>  
> Thanks for your response!
>  
> Case Syntax on Mac is as follow and same for unix/linux as far as I know: 
>   case word in [ [(] pattern [ | pattern ] ... ) list ;; ] … esac
>  
> Also there are 2 errors in the log file DeDriftAndResamplePipeline.sh.e42974 
> but 3 case...esac statements in DeDriftAndResamplePipeline.sh
>  
> I do not think this is a problem since it does seem to have completed 
> successfully, but do you have any other suggestion?
>  
> Thanks for your help,
> Leah.
>  
>  
> On Apr 19, 2019, at 8:26 AM, Glasser, Matthew  wrote:
>  
> It does seem to have completed successfully.  I wonder if “case” doesn’t work 
> the same on Mac?
>  
> Matt.
>  
> From: Marta Moreno 
> Date: Thursday, April 18, 2019 at 11:19 PM
> To: Timothy Coalson 
> Cc: Matt Glasser , "Harwell, John" , 
> HCP Users 
> Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error
>  
> I think it worked now. The script finished pretty fast without prompting an 
> error on the screen except for the following found In 
> DeDriftAndResamplePipeline.sh.e42974:
>  
>  # Do NOT wrap the following in quotes (o.w. the entire set of commands gets 
> interpreted as a single string)
>  |
> Error: The input character is not valid in MATLAB statements or expressions.
>  
>  # Do NOT wrap the following in quotes (o.w. the entire set of commands gets 
> interpreted as a single string)
>  |
> Error: The input character is not valid in MATLAB statements or expressions.
> 
> 
> 
> 
> I am attaching the log files to make sure the DeDriftAndResamplePipeline.sh 
> script was completed successfully.
> 
> 
> Thanks a lot!
> 
> 
> Leah.
> 
> 
>  
> On Apr 18, 2019, at 2:45 PM, Timothy Coalson  wrote:
>  
> Make sure you have the whole pipelines repo for 4.0.0, do not try to mix and 
> match folders from different versions, and make sure your setup script is 
> pointed to the 4.0.0 version when running things from 4.0.0.  The log_Warn 
> function is defined inside global/scripts, and it should get sourced 
> automatically based on HCPPIPEDIR, so make sure that is set correctly 
> (pointed to the 4.0.0 version).
>  
> Tim
>  
>  
> On Thu, Apr 18, 2019 at 1:39 PM Marta Moreno  wrote:
> Thanks for your response. And sorry to bother again with this issue but I am 
> still getting the following error: ReApplyFixMultiRunPipeline.sh: line 592: 
> log_Warn: command not found
>  
> Please find log files attached.
>  
> Pipelines for MR+FIX, MSMAll and DeDriftAndResample are from version version 
> 4.0.0.
> PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface are from 
> version  3_22 
> Since MR+FIX and MSMAll were run successfully, why it should be a version 
> issue in ReApplyFixMultiRunPipeline.sh?
>  
> I want to be sure this is a version issue because I have already run 
> PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface version  
> 3_22 on a sample of 30 patients pre/post tx.
>  
> Thanks a lot for your help and patience. 
>  
> Leah.
>  
>  
>  
> On Apr 15, 2019, at 9:39 PM, Timothy Coalson  wrote:
>  
> I would also suggest changing your log level to INFO in wb_view, preferences 
> (the wb_command option does not store the logging level change to 
> preferences).  We should probably change the default level, or change the 
> level of that volume coloring message.
>  
> Tim
>  
>  
> On Mon, Apr 15, 2019 at 8:34 PM Timothy Coalson  wrote:
> I have pushed a similar edit to reapply MR fix, please update to the latest 
> master.
>  
> Tim
>  
>  
> On Mon, Apr 15, 2019 at 8:27 PM Timothy Coalson  wrote:
> They weren't instructions, I pushed an edit, and it was a different script.
>  
> Tim
>  
>  
> On Mon, Apr 15, 2019 at 8:08 PM Glasser, Matthew  wrote:
> Here is the error: 
>  
> readlink: illegal option -- f
> usage: readlink [-n] [file ...]
>  
> I believe Tim already gave you instructions for this.  
>  
> Also, the log_Warn line is again concerning as to whether you followed the 
> installation instructions and all version 4.0.0 files here.
>  
> Matt.
>  
> From: Marta Moreno 
> Date: Monday, April 15, 2019 at 8:53 AM
> To: Matt Glasser 
> Cc: HCP Users , Timothy Coalson 
> , "Brown, Tim" 
> Subject: Re: