date:20190201

Re: [HCP-Users] Some questions about using the HCP structural preprocessing pipeline

2019-02-01 Thread Glasser, Matthew

1.  You can edit the launcher scripts to point to the files however you want to 
name them.
2.  Yes if they are both at least 1mm isotropic resolution.
3.  You can turn on gradient distortion correction if you want and have the 
appropriate coefficients file from your scanner.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C mailto:aaroncr...@outlook.com>>
Date: Friday, February 1, 2019 at 10:07 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Some questions about using the HCP structural 
preprocessing pipeline

Dear HCP experts,

I have some questions about using the HCP structural preprocessing pipeline.

1. To apply this pipeline on non-HCP data, do I have to rename the filenames of 
my data similar to the HCP unprocessed data as follows?

T1w _MPR1/
{Subject_ID}_3T_AFI.nii.gz
{Subject_ID}_3T_BIAS_32CH.nii.gz
{Subject_ID}_3T_BIAS_BC.nii.gz
{Subject_ID}_3T_FieldMap_Magnitude.nii.gz
{Subject_ID}_3T_FieldMap_Phase.nii.gz
{Subject_ID}_3T_T1w _MPR1.nii.gz

T2w _SPC1/
{Subject_ID}_3T_AFI.nii.gz
{Subject_ID}_3T_BIAS_32CH.nii.gz
{Subject_ID}_3T_BIAS_BC.nii.gz
{Subject_ID}_3T_FieldMap_Magnitude.nii.gz
{Subject_ID}_3T_FieldMap_Phase.nii.gz
{Subject_ID}_3T_T2w _SPC1.nii.gz

2. What are the minimum required MRI data to run the HCP structural 
preprocessing pipeline? Are only "{Subject_ID}_3T_T1w _MPR1.nii.gz" and 
"{Subject_ID}_3T_T2w _SPC1.nii.gz" sufficient for the structural analysis?

3. It seems that the two versions of the example data (with or without GDC) for 
the HCP pipeline have the same files in "T1w _MPR1" and "T2w _SPC1" folders?

Thank you.

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[HCP-Users] Some questions about using the HCP structural preprocessing pipeline

2019-02-01 Thread Aaron C

Dear HCP experts,

I have some questions about using the HCP structural preprocessing pipeline.

1. To apply this pipeline on non-HCP data, do I have to rename the filenames of 
my data similar to the HCP unprocessed data as follows?

T1w _MPR1/
{Subject_ID}_3T_AFI.nii.gz
{Subject_ID}_3T_BIAS_32CH.nii.gz
{Subject_ID}_3T_BIAS_BC.nii.gz
{Subject_ID}_3T_FieldMap_Magnitude.nii.gz
{Subject_ID}_3T_FieldMap_Phase.nii.gz
{Subject_ID}_3T_T1w _MPR1.nii.gz

T2w _SPC1/
{Subject_ID}_3T_AFI.nii.gz
{Subject_ID}_3T_BIAS_32CH.nii.gz
{Subject_ID}_3T_BIAS_BC.nii.gz
{Subject_ID}_3T_FieldMap_Magnitude.nii.gz
{Subject_ID}_3T_FieldMap_Phase.nii.gz
{Subject_ID}_3T_T2w _SPC1.nii.gz

2. What are the minimum required MRI data to run the HCP structural 
preprocessing pipeline? Are only "{Subject_ID}_3T_T1w _MPR1.nii.gz" and 
"{Subject_ID}_3T_T2w _SPC1.nii.gz" sufficient for the structural analysis?

3. It seems that the two versions of the example data (with or without GDC) for 
the HCP pipeline have the same files in "T1w _MPR1" and "T2w _SPC1" folders?

Thank you.

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Re: [HCP-Users] Workbench tools installation in Ubuntu 18.04

2019-02-01 Thread erik lee

Thank you very much! I will give that a try.

Best,
Erik

On Fri, Feb 1, 2019 at 8:23 PM Takuya Hayashi 
wrote:

> We've recently encountered similar problem in our Ubuntu 18.04 and solved
> this by the followings:
>
> Download Zlib 1.2.9 from here:
>
> https://sourceforge.net/projects/libpng/files/zlib/1.2.9/zlib-1.2.9.tar.gz/download
>
> tar -xvf ~/Downloads/zlib-1.2.9.tar.gz
> cd zlib-1.2.9
> ./configure;
> make;
> make install;
> cd ${your workbench dir}/libs_linux64
> mv libz.so.1 libz.so.1.back
> ln -sf /usr/local/lib/libz.so.1.2.9 libz.so.1
>
> You may need to use 'sudo' to run some of commands to avoid permission
> issue.
>
> Takuya
>
> 2019年2月2日(土) 10:06 Glasser, Matthew :
>
>> The person to address this is on vacation and will be back next week.
>>
>> Matt.
>>
>> From:  on behalf of erik lee <
>> erik.lee...@gmail.com>
>> Date: Friday, February 1, 2019 at 6:20 PM
>> To: "hcp-users@humanconnectome.org" 
>> Subject: [HCP-Users] Workbench tools installation in Ubuntu 18.04
>>
>> Hi,
>>
>> I am trying to install the Connectome Workbench software on my linux
>> machine (Ubuntu 18.04). When I try to run wb_view or wb_command, I get the
>> following error:
>>
>> /usr/local/workbench/bin_linux64/../exe_linux64/wb_view:
>> /usr/local/workbench/bin_linux64/../libs_linux64/libz.so.1: version
>> `ZLIB_1.2.9' not found (required by
>> /usr/lib/x86_64-linux-gnu/libpng16.so.16)
>> /usr/local/workbench/bin_linux64/../exe_linux64/wb_view:
>> /usr/local/workbench/bin_linux64/../libs_linux64/libz.so.1: version
>> `ZLIB_1.2.3.4' not found (required by
>> /usr/lib/x86_64-linux-gnu/libpng16.so.16)
>>
>> Does anyone know where to find these packages or how to get around this
>> error??
>>
>> Thanks in advance,
>> Erik
>>
>> ___
>> 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.
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>

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Re: [HCP-Users] Workbench tools installation in Ubuntu 18.04

2019-02-01 Thread Takuya Hayashi

We've recently encountered similar problem in our Ubuntu 18.04 and solved
this by the followings:

Download Zlib 1.2.9 from here:
https://sourceforge.net/projects/libpng/files/zlib/1.2.9/zlib-1.2.9.tar.gz/download

tar -xvf ~/Downloads/zlib-1.2.9.tar.gz
cd zlib-1.2.9
./configure;
make;
make install;
cd ${your workbench dir}/libs_linux64
mv libz.so.1 libz.so.1.back
ln -sf /usr/local/lib/libz.so.1.2.9 libz.so.1

You may need to use 'sudo' to run some of commands to avoid permission
issue.

Takuya

2019年2月2日(土) 10:06 Glasser, Matthew :

> The person to address this is on vacation and will be back next week.
>
> Matt.
>
> From:  on behalf of erik lee <
> erik.lee...@gmail.com>
> Date: Friday, February 1, 2019 at 6:20 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Workbench tools installation in Ubuntu 18.04
>
> Hi,
>
> I am trying to install the Connectome Workbench software on my linux
> machine (Ubuntu 18.04). When I try to run wb_view or wb_command, I get the
> following error:
>
> /usr/local/workbench/bin_linux64/../exe_linux64/wb_view:
> /usr/local/workbench/bin_linux64/../libs_linux64/libz.so.1: version
> `ZLIB_1.2.9' not found (required by
> /usr/lib/x86_64-linux-gnu/libpng16.so.16)
> /usr/local/workbench/bin_linux64/../exe_linux64/wb_view:
> /usr/local/workbench/bin_linux64/../libs_linux64/libz.so.1: version
> `ZLIB_1.2.3.4' not found (required by
> /usr/lib/x86_64-linux-gnu/libpng16.so.16)
>
> Does anyone know where to find these packages or how to get around this
> error??
>
> Thanks in advance,
> Erik
>
> ___
> 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.
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] Workbench tools installation in Ubuntu 18.04

2019-02-01 Thread Glasser, Matthew

Thanks Takuya.

Matt.

From: Takuya Hayashi mailto:takuya.haya...@riken.jp>>
Date: Friday, February 1, 2019 at 8:23 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: erik lee mailto:erik.lee...@gmail.com>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Workbench tools installation in Ubuntu 18.04

We've recently encountered similar problem in our Ubuntu 18.04 and solved this 
by the followings:

Download Zlib 1.2.9 from here:
https://sourceforge.net/projects/libpng/files/zlib/1.2.9/zlib-1.2.9.tar.gz/download

tar -xvf ~/Downloads/zlib-1.2.9.tar.gz
cd zlib-1.2.9
./configure;
make;
make install;
cd ${your workbench dir}/libs_linux64
mv libz.so.1 libz.so.1.back
ln -sf /usr/local/lib/libz.so.1.2.9 libz.so.1

You may need to use 'sudo' to run some of commands to avoid permission issue.

Takuya

2019年2月2日(土) 10:06 Glasser, Matthew 
mailto:glass...@wustl.edu>>:
The person to address this is on vacation and will be back next week.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of erik lee mailto:erik.lee...@gmail.com>>
Date: Friday, February 1, 2019 at 6:20 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Workbench tools installation in Ubuntu 18.04

Hi,

I am trying to install the Connectome Workbench software on my linux machine 
(Ubuntu 18.04). When I try to run wb_view or wb_command, I get the following 
error:

/usr/local/workbench/bin_linux64/../exe_linux64/wb_view: 
/usr/local/workbench/bin_linux64/../libs_linux64/libz.so.1: version 
`ZLIB_1.2.9' not found (required by /usr/lib/x86_64-linux-gnu/libpng16.so.16)
/usr/local/workbench/bin_linux64/../exe_linux64/wb_view: 
/usr/local/workbench/bin_linux64/../libs_linux64/libz.so.1: version 
`ZLIB_1.2.3.4' not found (required by /usr/lib/x86_64-linux-gnu/libpng16.so.16)

Does anyone know where to find these packages or how to get around this error??

Thanks in advance,
Erik

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strictly prohibited. If you have received this email in error, please 
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Re: [HCP-Users] Workbench tools installation in Ubuntu 18.04

2019-02-01 Thread Glasser, Matthew

The person to address this is on vacation and will be back next week.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of erik lee mailto:erik.lee...@gmail.com>>
Date: Friday, February 1, 2019 at 6:20 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Workbench tools installation in Ubuntu 18.04

Hi,

I am trying to install the Connectome Workbench software on my linux machine 
(Ubuntu 18.04). When I try to run wb_view or wb_command, I get the following 
error:

/usr/local/workbench/bin_linux64/../exe_linux64/wb_view: 
/usr/local/workbench/bin_linux64/../libs_linux64/libz.so.1: version 
`ZLIB_1.2.9' not found (required by /usr/lib/x86_64-linux-gnu/libpng16.so.16)
/usr/local/workbench/bin_linux64/../exe_linux64/wb_view: 
/usr/local/workbench/bin_linux64/../libs_linux64/libz.so.1: version 
`ZLIB_1.2.3.4' not found (required by /usr/lib/x86_64-linux-gnu/libpng16.so.16)

Does anyone know where to find these packages or how to get around this error??

Thanks in advance,
Erik

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Re: [HCP-Users] Distortion of fMRI image in MNI space after preprocessing

2019-02-01 Thread Glasser, Matthew

Do you have an SBRef image?  Can you use that instead of the MB images for the 
purposes of this comparison (better grey-white contrast)?  We expect gradient 
echo signal dropout which cannot be fixed by any known processing approach.  
This is different from EPI distortion which we can fix.  That said, I am not 
convinced yet of the distortion correction because the grey/white contrast is 
not so good and I only have one slice.  As far as the masking, if you set the 
color range from 0 to 1 you should see what is actually masked out vs dropped 
out due to gradient echo signal dephasing.  Nothing should be masked out inside 
the pial surface.

It would probably be a good idea to give me the details of your fMRI sequence 
and fieldmap distortion correction method.

Also if you want to make a scene in Connectome Workbench, zip up the 
corresponding scene using Connectome Workbench (to include the data), and 
upload it somewhere, I could take a look.  Before you do that though, answer 
the above questions.

Matt.

From: Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Friday, February 1, 2019 at 5:12 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] Distortion of fMRI image in MNI space after 
preprocessing

Please find attached the requested image. Besides the expected signal drop in 
the orbitofrontal region and inferior temporal, it seems I am losing a bit of 
the occipital and middle temporal lobes as well, but the image seems to be 
coregistered. If you wish, I could also send you a dataset for closer 
inspection.
What surprised me of the images is the striking difference between the same 
image in MNI and native space. If you feel that the images are as is to be 
expected, it might be just that the outputs of the HCP pipelines look different 
that those of other processing streams, see for example the attached image 
comparing the warping with the HCP pipeline and the standard FSL flirt/fnirt 
commands (after topup), side to side. For example, some parts of the HCP images 
look much more intense.
I have noticed that some curved lines were present also in the original 
unprocessed image, so that is probably the source of them. When you say 
slice-based intensity fluctuations in physical space, do you mean due to our 
sequence/magnet? What would you recommend to avoid those forming?
Thank you,

Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu | (650) 5615738


From: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Date: Friday, February 1, 2019 at 1:55 PM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Distortion of fMRI image in MNI space after 
preprocessing

How does the data look if you overlay the white and pial surface contours in 
MNI space using Connectome Workbench.

If there are slice-based intensity fluctuations in physical space, those can 
turn into curvy lines after non-linear registration to MNI space.  I don’t see 
anything obviously wrong with your data, but without seeing the surface 
outlines I cannot comment on alignment or distortion.

Matt.

From: Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Friday, February 1, 2019 at 3:50 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] Distortion of fMRI image in MNI space after 
preprocessing

I added an arrow on the T1 where circular bands can be seen in the occipital 
lobe.
Concerning the image in MNI space, it looks to me as if it were distorted 
throughout. The edges of the brain appear quite irregular and overall there 
seem to be quite some significant distortions to me (I added a couple of arrows 
there too, in one case you can see more bands). This is quite different from 
what I am used to see in a preprocessed image in MNI space, unless this is just 
my impression?



Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu | (650) 5615738


From: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Date: Friday, February 1, 2019 at 1:41 PM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Distortion of fMRI image in MNI space after 
preprocessing

Can you put an arrow on what is bothering you?  I’m not sure what you are 
referring to.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Friday, February 1, 2019 at 3:29 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Distortion of fMRI image in MNI space after preprocessing

Dear Experts,

I have preprocessed some resting state data

[HCP-Users] Workbench tools installation in Ubuntu 18.04

2019-02-01 Thread erik lee

Hi,

I am trying to install the Connectome Workbench software on my linux
machine (Ubuntu 18.04). When I try to run wb_view or wb_command, I get the
following error:

/usr/local/workbench/bin_linux64/../exe_linux64/wb_view:
/usr/local/workbench/bin_linux64/../libs_linux64/libz.so.1: version
`ZLIB_1.2.9' not found (required by
/usr/lib/x86_64-linux-gnu/libpng16.so.16)
/usr/local/workbench/bin_linux64/../exe_linux64/wb_view:
/usr/local/workbench/bin_linux64/../libs_linux64/libz.so.1: version
`ZLIB_1.2.3.4' not found (required by
/usr/lib/x86_64-linux-gnu/libpng16.so.16)

Does anyone know where to find these packages or how to get around this
error??

Thanks in advance,
Erik

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Re: [HCP-Users] Distortion of fMRI image in MNI space after preprocessing

2019-02-01 Thread Glasser, Matthew

How does the data look if you overlay the white and pial surface contours in 
MNI space using Connectome Workbench.

If there are slice-based intensity fluctuations in physical space, those can 
turn into curvy lines after non-linear registration to MNI space.  I don’t see 
anything obviously wrong with your data, but without seeing the surface 
outlines I cannot comment on alignment or distortion.

Matt.

From: Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Friday, February 1, 2019 at 3:50 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] Distortion of fMRI image in MNI space after 
preprocessing

I added an arrow on the T1 where circular bands can be seen in the occipital 
lobe.
Concerning the image in MNI space, it looks to me as if it were distorted 
throughout. The edges of the brain appear quite irregular and overall there 
seem to be quite some significant distortions to me (I added a couple of arrows 
there too, in one case you can see more bands). This is quite different from 
what I am used to see in a preprocessed image in MNI space, unless this is just 
my impression?



Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu | (650) 5615738


From: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Date: Friday, February 1, 2019 at 1:41 PM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Distortion of fMRI image in MNI space after 
preprocessing

Can you put an arrow on what is bothering you?  I’m not sure what you are 
referring to.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Friday, February 1, 2019 at 3:29 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Distortion of fMRI image in MNI space after preprocessing

Dear Experts,

I have preprocessed some resting state data with the minimal preprocessing 
pipeline scripts. I have noticed that when the images are warped to MNI space, 
they become significantly distorted. That is to say, images such as for example:

sub01/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP.nii.gz (Figure 1).

I have checked other images, for example:

sub01/rfMRI_REST1_AP/rfMRI_REST1_AP_gdc.nii.gz (Figure 2)

And they appear not to be distorted.
At first I thought this was due to an error of topup, but even after applying 
only topup on my unpreprocessed images, I get results similar to 
sub01/rfMRI_REST1_AP/rfMRI_REST1_AP_gdc.nii.gz (see Figure 3).
This, coupled with the strange cutting of the brain edges that seems to happen 
when warping to MNI space makes me think something is wrong in the registration 
procedure. I went back to check the file:

sub01/MNINonLinear/T1w_restore_brain.nii.gz

And noticed that there is an artifact on the occipital lobe (Figure 4). Would 
this be sufficient to cause such a dramatic effect? Would you have any ideas 
what the cause could be?
Thank you very much.
Yours faithfully,




Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu | (650) 5615738


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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 
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Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into HCP_2mm MNI Surface and Volume space

2019-02-01 Thread Glasser, Matthew

I suggested he use the mapping from FreeSurfer space not HCP space implemented 
in PostFreeSurfer for wmparc.mgz.

Matt.

From: "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Friday, February 1, 2019 at 11:18 AM
To: "Srivastava, Benjamin (NYSPI)" 
mailto:benjamin.srivast...@nyspi.columbia.edu>>,
 Matt Glasser mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into 
HCP_2mm MNI Surface and Volume space

So, I’m assuming you ran it using the outputs from PreFreeSurfer as its inputs? 
 Otherwise, the mapping that Matt suggested you use from PostFreeSurfer won’t 
be appropriate! ☺

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: "Srivastava, Benjamin (NYSPI)" 
mailto:benjamin.srivast...@nyspi.columbia.edu>>
Date: Wednesday, January 30, 2019 at 4:40 PM
To: "Harms, Michael" mailto:mha...@wustl.edu>>, "Glasser, 
Matthew" mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into 
HCP_2mm MNI Surface and Volume space

Hi we just used the isotropic T1w scan

A. Benjamin Srivastava, M.D.
Clinical and Research Fellow
Division on Substance Use Disorders
Department of Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute

From: "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Wednesday, January 30, 2019 at 9:05 AM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>, 
"Srivastava, Benjamin (NYSPI)" 
mailto:benjamin.srivast...@nyspi.columbia.edu>>,
 "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into 
HCP_2mm MNI Surface and Volume space

ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.

Hi,
I’m curious, did you run the hippocampal/amygdala segmentation using only a 
isotropic T1w scan, or did you add in a high in-plane resolution T2w, as is 
often used for best performance of the hp/amyg segmentation routine?

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: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Glasser, Matthew" mailto:glass...@wustl.edu>>
Date: Tuesday, January 29, 2019 at 5:31 PM
To: "Srivastava, Benjamin (NYSPI)" 
mailto:benjamin.srivast...@nyspi.columbia.edu>>,
 "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into 
HCP_2mm MNI Surface and Volume space

As far as the volume space, have a look at the PostFreeSurfer pipeline for how 
wmparc.mgz gets mapped.  The hippocampus is not fully represented on FreeSurfer 
cortical surfaces.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Srivastava, Benjamin (NYSPI)" 
mailto:benjamin.srivast...@nyspi.columbia.edu>>
Date: Tuesday, January 29, 2019 at 1:56 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Transforming Freesurfer .mgz segmented files into HCP_2mm 
MNI Surface and Volume space

Hi,

We have processed data using the 3_22 HCP Pipelines. We have run (successfully) 
the hippocampal amygdala segmentation script with Freesurfer 6 using 
segmentHA_T1.sh. We are now trying to transform the .mgz segmented files into 
the HCP_2mm MNI surface and volume spaces. Does anyone have any experience 
using FreeSurfer2CaretConvertAndRegisterNonlinear.sh to accomplish this?

Thanks!

A. Benjamin Srivastava, M.D.
Clinical and Research Fellow
Division on Substance Use Disorders
Department of Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute

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Re: [HCP-Users] Distortion of fMRI image in MNI space after preprocessing

2019-02-01 Thread Glasser, Matthew

Can you put an arrow on what is bothering you?  I’m not sure what you are 
referring to.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Friday, February 1, 2019 at 3:29 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Distortion of fMRI image in MNI space after preprocessing

Dear Experts,

I have preprocessed some resting state data with the minimal preprocessing 
pipeline scripts. I have noticed that when the images are warped to MNI space, 
they become significantly distorted. That is to say, images such as for example:

sub01/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP.nii.gz (Figure 1).

I have checked other images, for example:

sub01/rfMRI_REST1_AP/rfMRI_REST1_AP_gdc.nii.gz (Figure 2)

And they appear not to be distorted.
At first I thought this was due to an error of topup, but even after applying 
only topup on my unpreprocessed images, I get results similar to 
sub01/rfMRI_REST1_AP/rfMRI_REST1_AP_gdc.nii.gz (see Figure 3).
This, coupled with the strange cutting of the brain edges that seems to happen 
when warping to MNI space makes me think something is wrong in the registration 
procedure. I went back to check the file:

sub01/MNINonLinear/T1w_restore_brain.nii.gz

And noticed that there is an artifact on the occipital lobe (Figure 4). Would 
this be sufficient to cause such a dramatic effect? Would you have any ideas 
what the cause could be?
Thank you very much.
Yours faithfully,

Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu | (650) 5615738

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Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into HCP_2mm MNI Surface and Volume space

2019-02-01 Thread Harms, Michael


So, I’m assuming you ran it using the outputs from PreFreeSurfer as its inputs? 
 Otherwise, the mapping that Matt suggested you use from PostFreeSurfer won’t 
be appropriate! ☺

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: "Srivastava, Benjamin (NYSPI)" 
Date: Wednesday, January 30, 2019 at 4:40 PM
To: "Harms, Michael" , "Glasser, Matthew" 
, "hcp-users@humanconnectome.org" 

Subject: Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into 
HCP_2mm MNI Surface and Volume space

Hi we just used the isotropic T1w scan

A. Benjamin Srivastava, M.D.
Clinical and Research Fellow
Division on Substance Use Disorders
Department of Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute



From: "Harms, Michael" 
Date: Wednesday, January 30, 2019 at 9:05 AM
To: "Glasser, Matthew" , "Srivastava, Benjamin (NYSPI)" 
, "hcp-users@humanconnectome.org" 

Subject: Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into 
HCP_2mm MNI Surface and Volume space


ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


Hi,
I’m curious, did you run the hippocampal/amygdala segmentation using only a 
isotropic T1w scan, or did you add in a high in-plane resolution T2w, as is 
often used for best performance of the hp/amyg segmentation routine?

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: Tuesday, January 29, 2019 at 5:31 PM
To: "Srivastava, Benjamin (NYSPI)" , 
"hcp-users@humanconnectome.org" 
Subject: Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into 
HCP_2mm MNI Surface and Volume space

As far as the volume space, have a look at the PostFreeSurfer pipeline for how 
wmparc.mgz gets mapped.  The hippocampus is not fully represented on FreeSurfer 
cortical surfaces.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Srivastava, Benjamin (NYSPI)" 
mailto:benjamin.srivast...@nyspi.columbia.edu>>
Date: Tuesday, January 29, 2019 at 1:56 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Transforming Freesurfer .mgz segmented files into HCP_2mm 
MNI Surface and Volume space

Hi,

We have processed data using the 3_22 HCP Pipelines. We have run (successfully) 
the hippocampal amygdala segmentation script with Freesurfer 6 using 
segmentHA_T1.sh. We are now trying to transform the .mgz segmented files into 
the HCP_2mm MNI surface and volume spaces. Does anyone have any experience 
using FreeSurfer2CaretConvertAndRegisterNonlinear.sh to accomplish this?

Thanks!

A. Benjamin Srivastava, M.D.
Clinical and Research Fellow
Division on Substance Use Disorders
Department of Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute



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intended recipient, be advised that any unauthorized use, disclosure, copying 
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Re: [HCP-Users] Regress confounds out of CIFTIs

2019-02-01 Thread Steve Smith

Hi - yes IIRC it's only the demeaning that is important - the scaling of the 
regressors makes no difference to the output from the deconfounding.

Normalising SD is a "sane" step in such processing in general, and sometimes is 
of value (depending on what outputs one is interested in wrt the internal 
multiple regression) - but if you just want the residuals (like here) it 
doesn't change things.

Cheers.




> On 1 Feb 2019, at 05:14, Ely, Benjamin  wrote:
> 
> Hi Matt,
> 
> I’ve been using a matlab command similar to the one you gave to 
> regress/remove timeseries values from our data, based on code from the ICAFIX 
> script fix_3_clean.m. Glad to hear that’s what you suggest! Quick question 
> though: before regressing out ICA component timeseries values, the ICAFIX 
> script runs them through the command "functionnormalise()", which both 
> demeans the data and sets the standard deviation equal to 1. It sounds from 
> your email like only the demeaning part of that is necessary, so what is the 
> purpose of normalizing the SD?
> 
> Thank you!
> -Ely
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---
Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  WIN (FMRIB) Oxford

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 610470
st...@fmrib.ox.ac.ukhttp://www.fmrib.ox.ac.uk/~steve 

---

Stop the cultural destruction of Tibet 









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Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into HCP_2mm MNI Surface and Volume space

Re: [HCP-Users] Distortion of fMRI image in MNI space after preprocessing

Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into HCP_2mm MNI Surface and Volume space

Re: [HCP-Users] Regress confounds out of CIFTIs

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