Re: [HCP-Users] HCPpipelines Task Analysis Level 2 design error

[Harms, Michael]

Yes, if you have 4 runs in your level 2, then you probably need to start with 
fresh templates derived from a 4 run volume analysis.

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 "Glasser, Matthew" 

Date: Friday, July 27, 2018 at 4:02 PM
To: Mathias Goncalves , "HCP-Users@humanconnectome.org" 

Subject: Re: [HCP-Users] HCPpipelines Task Analysis Level 2 design error

I think this is tricky because the fsf format is somewhat opaque.  What we did 
to make the original FSFs for the HCP was to run the volume analyses in FEAT 
for one subject and then modify the FSFs (minimally) for CIFTI.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Mathias Goncalves mailto:mathi...@mit.edu>>
Date: Friday, July 27, 2018 at 1:33 PM
To: "HCP-Users@humanconnectome.org" 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] HCPpipelines Task Analysis Level 2 design error

Hi all,

I've been using the HCPpipelines scripts for preprocessing / task-analysis, but 
am having trouble with the level2 task analysis. I'm running the current latest 
(v3.27.0), and have modeled my files similar to the FSF 
templates
 on the repo.

I've attached a log of my output, as well as a level 2 design fsf from a 
particular task (made up of 4 runs). Any suggestions would be appreciated, 
thank you.

Cheers,
Mathias

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Re: [HCP-Users] HCPpipelines Task Analysis Level 2 design error

[Glasser, Matthew]

I think this is tricky because the fsf format is somewhat opaque.  What we did 
to make the original FSFs for the HCP was to run the volume analyses in FEAT 
for one subject and then modify the FSFs (minimally) for CIFTI.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Mathias Goncalves mailto:mathi...@mit.edu>>
Date: Friday, July 27, 2018 at 1:33 PM
To: "HCP-Users@humanconnectome.org" 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] HCPpipelines Task Analysis Level 2 design error

Hi all,

I've been using the HCPpipelines scripts for preprocessing / task-analysis, but 
am having trouble with the level2 task analysis. I'm running the current latest 
(v3.27.0), and have modeled my files similar to the FSF 
templates
 on the repo.

I've attached a log of my output, as well as a level 2 design fsf from a 
particular task (made up of 4 runs). Any suggestions would be appreciated, 
thank you.

Cheers,
Mathias

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Re: [HCP-Users] MSMAll

[Glasser, Matthew]

We have not found that is necessary.  sICA+FIX worked on the HCP task data 
using the HCP resting state data training set.

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Friday, July 27, 2018 at 3:15 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

I noticed on the FSL FIX FAQ page the following:

Can I use FIX to clean task fMRI data?

  *   Yes, although you will probably need to create a study-specific training 
dataset

Can you speak to how multi run ICA+FIX gets away without needing a 
study-specific training dataset?

-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)

On Tue, Jul 24, 2018 at 3:28 PM, Timothy Hendrickson 
mailto:hendr...@umn.edu>> wrote:
Sorry for the dumb question, I should have read the code further. Thanks!

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)

On Tue, Jul 24, 2018 at 3:21 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
The MR+FIX pipeline automatically breaks the runs back up at the end.

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Tuesday, July 24, 2018 at 3:17 PM

To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

So once I finish with the multiICAFIX pipeline I wold have to manually separate 
the concatenated cleaned nifti file and then run MSMAll on those scans. Is that 
right?

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)

On Mon, Jul 23, 2018 at 1:31 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
Give it a try, but you may find that you need to split it into two.  Make sure 
you are using the latest released FSL for this.

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Monday, July 23, 2018 at 1:26 PM

To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

I handle processing for several studies, an upward bound for the studies I 
handle would be approximately 3000 frames.

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)

On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
FSL 6.0 hasn’t been released but has some updates to the math library that 
makes melodic much faster.  Also if you make too large of a merged file it will 
crash the old melodic because of some bugs.  How many frames are you wanting to 
do?

Peace,

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Monday, July 23, 2018 at 1:02 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

Thanks Matt.

With the hcp_fix_multi_run script I notice that in the first few lines of code 
there is a line with software requirements which include FIX >= 1.065 and FSL 
6.0 melodic version. I have FIX version = 1.066 and I have FSL 5.0.9 and 
melodic version 3.14. Without the FSL 6.0 release handy to me I am not sure 
what melodic version would be considered equivalent "FSL 6.0". Could you shed 
some light on this for me?

-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)

On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
There is a new Multi-run FIX pipeline currently available in the Git repository 
that you can use.  I would consider it beta a this time.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Thursday, July 19, 2018 at 6:24 PM
To: "hcp-users@humanconnectome.org" 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] MSMAll

Hello,

>From the HCP course material I noticed that that suggested format to use 
>MSMAll is to do so immediately after the Minimal Pre-Processing stream and 
>immediately before subsequent tfMRI and rfMRI processing. As MSMAll 

Re: [HCP-Users] MSMAll

[Timothy Hendrickson]

I noticed on the FSL FIX FAQ page the following:

Can I use FIX to clean task fMRI data?

   - Yes, although you will probably need to create a study-specific
   training dataset


Can you speak to how multi run ICA+FIX gets away without needing a
study-specific training dataset?

-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)

On Tue, Jul 24, 2018 at 3:28 PM, Timothy Hendrickson 
wrote:

> Sorry for the dumb question, I should have read the code further. Thanks!
>
> 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)
>
> On Tue, Jul 24, 2018 at 3:21 PM, Glasser, Matthew 
> wrote:
>
>> The MR+FIX pipeline automatically breaks the runs back up at the end.
>>
>> Matt.
>>
>> From: Timothy Hendrickson 
>> Date: Tuesday, July 24, 2018 at 3:17 PM
>>
>> To: Matt Glasser 
>> Cc: "hcp-users@humanconnectome.org" 
>> Subject: Re: [HCP-Users] MSMAll
>>
>> So once I finish with the multiICAFIX pipeline I wold have to manually
>> separate the concatenated cleaned nifti file and then run MSMAll on those
>> scans. Is that right?
>>
>> 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)
>>
>> On Mon, Jul 23, 2018 at 1:31 PM, Glasser, Matthew 
>> wrote:
>>
>>> Give it a try, but you may find that you need to split it into two.
>>> Make sure you are using the latest released FSL for this.
>>>
>>> Matt.
>>>
>>> From: Timothy Hendrickson 
>>> Date: Monday, July 23, 2018 at 1:26 PM
>>>
>>> To: Matt Glasser 
>>> Cc: "hcp-users@humanconnectome.org" 
>>> Subject: Re: [HCP-Users] MSMAll
>>>
>>> I handle processing for several studies, an upward bound for the studies
>>> I handle would be approximately 3000 frames.
>>>
>>> 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)
>>>
>>> On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew 
>>> wrote:
>>>
 FSL 6.0 hasn’t been released but has some updates to the math library
 that makes melodic much faster.  Also if you make too large of a merged
 file it will crash the old melodic because of some bugs.  How many frames
 are you wanting to do?

 Peace,

 Matt.

 From: Timothy Hendrickson 
 Date: Monday, July 23, 2018 at 1:02 PM
 To: Matt Glasser 
 Cc: "hcp-users@humanconnectome.org" 
 Subject: Re: [HCP-Users] MSMAll

 Thanks Matt.

 With the hcp_fix_multi_run script I notice that in the first few lines
 of code there is a line with software requirements which include FIX >=
 1.065 and FSL 6.0 melodic version. I have FIX version = 1.066 and I have
 FSL 5.0.9 and melodic version 3.14. Without the FSL 6.0 release handy to me
 I am not sure what melodic version would be considered equivalent "FSL
 6.0". Could you shed some light on this for me?

 -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)

 On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew 
 wrote:

> There is a new Multi-run FIX pipeline currently available in the Git
> repository that you can use.  I would consider it beta a this time.
>
> Matt.
>
> From:  on behalf of Timothy
> Hendrickson 
> Date: Thursday, July 19, 2018 at 6:24 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] MSMAll
>
> Hello,
>
> From the HCP course material I noticed that that suggested format to
> use MSMAll is to do so immediately after the Minimal Pre-Processing stream
> and immediately before subsequent tfMRI and rfMRI processing. As MSMAll
> expects the data inputted to be run through ICA-FIX I am curious what I
> should be doing with tfMRI data (i.e. what mods do I have to make to
> hcp_fix, etc). If you could provide me a code snippet/s that would be 
> great!
>
> -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)
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org

Re: [HCP-Users] wb_command error

[Glasser, Matthew]

Hi Mohana,

Is this the latest Connectome Workbench?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Mohana Ramaratnam 
mailto:mohanakann...@gmail.com>>
Date: Friday, July 27, 2018 at 12:44 PM
To: "HCP-Users@humanconnectome.org" 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] wb_command error

Does anyone know why this error would be thrown?

/usr/local/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command -metric-merge /
opt/data/build/TestUmass/20180718_021040/P01_MR1/MNINonLinear/Native/P01_MR1.L.S
trainR_FS.native.shape.gii -metric /opt/data/build/TestUmass/20180718_021040/P01
_MR1/MNINonLinear/Native/P01_MR1.L.Strain_FS.native.shape.gii -column 2

ERROR: column '2' not found in file '/opt/data/build/TestUmass/20180718_021040/P
01_MR1/MNINonLinear/Native/P01_MR1.L.Strain_FS.native.shape.gii'


This error is thrown in the PostFreesurfer step.

HCP-Pipeline version = 3.23.0

Regards,
Mohana

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Re: [HCP-Users] Movie tasks fMRI

[Elam, Jennifer]

Hi Michel,

The Movie stimulus files used for 7T are available on the S1200 Project page in 
ConnectomeDB under "Task 
Resources". See more info on the 7T movie watching experiment on pp.59-61 of 
the S1200 Reference 
Manual.


Best,

Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Michel Thiebaut 

Sent: Friday, July 27, 2018 8:36:02 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Movie tasks fMRI

Dear HCP Experts,

I was wondering whether you would have the kindness to provide me with a link 
to download/watch the movies used for the movie tasks at 7T.

Thank a lot for your time,
Kind regards

michel

Michel Thiebaut de Schotten
Professor, PhD, HDR, CNRS
Sorbonne Universities, UPMC Univ Paris 06
Brain Connectivity and Behaviour Group
Frontlab, Institut du cerveau et la moelle épinière
Hôpital de la Salpêtrière - ICM
47 Bvd de l'Hôpital CS21414
75646 PARIS CEDEX 13

Skype: michel_thiebaut_de_schotten
phone: +33 7 83 50 81 60
http://www.bcblab.com
http://toolkit.bcblab.com


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Re: [HCP-Users] Accessing 7T data in the temporary s3 bucket

[Elam, Jennifer]

Hi John,
Actually, the 7T HCP data is not available on AWS S3 yet due to changes in the 
AWS public access program that have necessitated a switchover to a new HCP AWS 
account and the creation of the temporary hcp-openaccess-temp S3 bucket. Once 
we have the hcp-openaccess S3 bucket back up under our new account, we will 
sync the 7T data and announce that it is available. Moving all the data takes a 
lot of time, so please bear with us!

Thanks,
Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Rodgers-Lee, John 
(NIH/NIMH) [C] 
Sent: Friday, July 27, 2018 1:32:54 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Accessing 7T data in the temporary s3 bucket


Hi I’m having some issues downloading the 7T data from the temporary s3 bucket.



I expect to be able to find 7T data for the following subjects (among others): 
995174, 100610 and 878877. I cannot see any in the bucket though for example 
when I list the results for each subject with:

aws s3 ls  --recursive 
s3://hcp-openaccess-temp/HCP_1200/995174/MNINonLinear/Results



If anyone figures out what I’m doing wrong your help would be greatly 
appreciated.



Regards,



John



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[HCP-Users] Accessing 7T data in the temporary s3 bucket

[Rodgers-Lee, John (NIH/NIMH) [C]]

Hi I’m having some issues downloading the 7T data from the temporary s3 bucket.

I expect to be able to find 7T data for the following subjects (among others): 
995174, 100610 and 878877. I cannot see any in the bucket though for example 
when I list the results for each subject with:
aws s3 ls  --recursive 
s3://hcp-openaccess-temp/HCP_1200/995174/MNINonLinear/Results

If anyone figures out what I’m doing wrong your help would be greatly 
appreciated.

Regards,

John


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[HCP-Users] wb_command error

[Mohana Ramaratnam]

Does anyone know why this error would be thrown?

/usr/local/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command
-metric-merge /
opt/data/build/TestUmass/20180718_021040/P01_MR1/MNINonLinear/Native/P01_MR1.L.S
trainR_FS.native.shape.gii -metric
/opt/data/build/TestUmass/20180718_021040/P01
_MR1/MNINonLinear/Native/P01_MR1.L.Strain_FS.native.shape.gii -column 2

ERROR: column '2' not found in file
'/opt/data/build/TestUmass/20180718_021040/P
01_MR1/MNINonLinear/Native/P01_MR1.L.Strain_FS.native.shape.gii'


This error is thrown in the PostFreesurfer step.

HCP-Pipeline version = 3.23.0

Regards,
Mohana

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Re: [HCP-Users] issues with palm tfce for HCP task func data

[Winkler, Anderson (NIH/NIMH) [E]]

PS: Note that this is about Inf, but you found NaNs. These NaNs are caused by 
the Infs, e.g., Inf-Inf = NaN, which is what happens in line 103 of 
palm_competitive, dd = diff(S(:,c)).


From: "Winkler, Anderson (NIH/NIMH) [E]" 
Date: Friday, July 27, 2018 at 08:29
To: HCP Users 
Subject: Re: [HCP-Users] issues with palm tfce for HCP task func data

Hi Joe,

The problem is this: the input dataset is stored in single precision, not 
double. Internally PALM converts the test statistic (t in this case) to z-stat. 
There are many reasons for doing the transformation: to correct across 
contrasts and design matrices that have different degrees of freedom and to put 
all spatial statistics into a common scale (and here you indeed use TFCE). This 
happens regardless of whether the user chooses the option -zstat or not. If the 
user uses -zstat, the test statistic will be saved as z-stat, otherwise it will 
be saved as the original statistic, but internally it's always z-stat.

This particular input file is stored using single precision, and this is kept 
throughout. That is, PALM doesn't internally convert the inputs to double -- 
what if the user actually wants single precision to, e.g., save memory or allow 
for a large dataset? To further complicate matters in this case, here we are 
testing the mean, and some voxels (4853, precisely) have an average signal 
compared to their variance that is high to the point of going over the limit 
that would allow conversion to a z-stat without overflowing the single 
precision limit.

Take the first voxel with this issue (voxel index 7): it has a test statistic t 
= -21.1164818 (all decimal places included). The df of the numerator is 1 
(t-test) and of the denominator is 216. Then:



>> palm_gtoz(single(-21.1164818), 1, 216)
ans =
   -Inf

But if it were double, we would find the correct result, that is not infinite:



>> palm_gtoz(double(-21.1164818), 1, 216)
ans =
  -15.536373937167403

So, to fix this, convert the input file to double precision and it should work. 
Another option is to edit the file palm_miscread.m, and add a new line right 
after line 304 containing:


X.data = double(X.data);

Hope this solves the issue!

All the best,

Anderson


From: Joseph Orr 
Date: Wednesday, July 25, 2018 at 10:28
To: "Winkler, Anderson (NIH/NIMH) [E]" 
Cc: HCP Users 
Subject: Re: [HCP-Users] issues with palm tfce for HCP task func data

Thanks Anderson - I tried seed set to 1 and 'twist' and both resulted in the 
same error.

Joe

--
Joseph M. Orr, Ph.D.
Assistant Professor
Department of Psychological and Brain Sciences
Texas A Institute for Neuroscience
Texas A University
College Station, TX

On Mon, Jul 23, 2018 at 9:55 PM, Winkler, Anderson (NIH/NIMH) [E] 
mailto:anderson.wink...@nih.gov>> wrote:
Hi Joseph,

I downloaded your files earlier today but couldn’t yet have a look.

It may be that the particular values in the permutation distribution caused the 
tail fitting to fail (simply an unlucky scenario). If that is the case, try 
running again with a different seed (there is an option for that, see among the 
advanced options). The default is 0, so try with a different number (e.g., 1, 
2, ...).

All the best,

Anderson


Sent from mobile. Please excuse brevity.

From: Joseph Orr mailto:joseph@tamu.edu>>
Sent: Monday, July 23, 2018 7:59:26 PM
To: HCP Users
Subject: Re: [HCP-Users] issues with palm tfce for HCP task func data

I inserted a breakpoint in palm_competitive at line 104 right before the error 
(pasted below) occurred. In the first pass. dpv_tstat_fwep, tfce_tstat, and 
tfce_tstat_uncp are saved (now in the folder linked above), but when i 
continue, I get the NaN error. The vector dd is length n-permutation - 1, and 
has a single NaN in row 2499. The workspace at the time of the error is saved 
as post_tfce_uncorrp_workspace.mat in the linked folder.

100% [Design 1/1, Contrast 1/1, Shuffling 2500/2500, Modality 1/1]
Elapsed time with permutations: ~ 4438.79 seconds.
Computing p-values.
Saving p-values (uncorrected, and corrected within modality and within 
contrast).
Saving file: motor_RH_results_L_test_dpv_tstat_uncp
104 if any(isnan(dd)),
Saving file: motor_RH_results_L_test_dpv_tstat_fwep
Saving file: motor_RH_results_L_test_tfce_tstat
Saving file: motor_RH_results_L_test_tfce_tstat_uncp
K>> any(isnan(dd))

ans =

  logical

   1

K>> sum(isnan(dd))

ans =

 1

Error using palm_competitive (line 105)
Data cannot be sorted. Check for NaNs that might be present,
or precision issues that may cause over/underflow.
If you are using "-approx tail", consider adding "-nouncorrected".

Error in palm_datapval (line 67)
[~,cdfG,distp] = palm_competitive(Gvals(:),'descend',true);

Error in palm_saveall (line 303)
Ptosave =

palm_datapval(plm.Gtfce{y}{m}{c},plm.Gtfcemax{y}{m}{c},false);

Error in palm_core (line 2489)
palm_saveall(plm,opts);

Error in palm (line