Re: [HCP-Users] Where to find warp field from standard to original resting state fMRI data

2018-07-24 Thread Glasser, Matthew 
Why do you need that?  The reason for the slice increase is that the image
is rotated into ACPC space and so the slice plane is different.

Peace,

Matt.

On 7/24/18, 4:20 PM, "Sang-Young Kim"  wrote:

>Hi, Matt:
>
>Thanks for your prompt response.
>
>Yes, I can use
>${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to
>warp the data to structural space.
>But the problem is that I want to keep the same number of slice as
>original fMRI data (e.g., N slice=72).
>
>Once I warped rfMRI data to structural space using 2 mm reference volume,
>the number of slice for the output is 91.
>
>Is there a way to solve this issue? Also the warp field for
>standard2rfMRI_REST1_LR.nii.gz is not released, right? The reason is, as
>you mentioned, that there is no need to go to original fMRI space?
>
>Any comments would be appreciated.
>
>Best,
>
>Sang-Young
>
>
>
>> On Jul 24, 2018, at 3:03 PM, Glasser, Matthew 
>>wrote:
>>
>> There is no need to go to original fMRI space in most cases.  If you
>>want
>> data in the native physical space of the subject you can use
>> ${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to
>> warp the data to structural space (and can use a 2mm reference volume in
>> that space if you wish to keep it at the same resolution).
>>
>> Peace,
>>
>> Matt.
>>
>> On 7/24/18, 12:27 PM, "hcp-users-boun...@humanconnectome.org on behalf
>>of
>> Sang-Young Kim" > sykim...@gmail.com> wrote:
>>
>>> Dear HCP experts:
>>>
>>> I have downloaded a HCP data from "S1200 Extensively Processed fMRI
>>> Data".
>>> The downloaded data was just preprocessed for resting state fMRI using
>>> fMRIVolume and fMRISurface pipeline.
>>>
>>> But I cannot find warp field to transform MNI space data to original
>>>fMRI
>>> space, which is normally located in ${Subject}/MNINonLinear/xfms after
>>> fMRIVolume pipeline.
>>>
>>> Could you please let me know where to find it?
>>>
>>> Thanks.
>>>
>>> Sang-Young Kim, Ph.D.
>>>
>>> Postdoctoral Fellow
>>> Department of Radiology
>>> University of Pittsburgh
>>> ___
>>> 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] Where to find warp field from standard to original resting state fMRI data

2018-07-24 Thread Sang-Young Kim 
Hi, Matt:

Thanks for your prompt response. 

Yes, I can use 
${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to warp the 
data to structural space. 
But the problem is that I want to keep the same number of slice as original 
fMRI data (e.g., N slice=72).

Once I warped rfMRI data to structural space using 2 mm reference volume, the 
number of slice for the output is 91. 

Is there a way to solve this issue? Also the warp field for 
standard2rfMRI_REST1_LR.nii.gz is not released, right? The reason is, as you 
mentioned, that there is no need to go to original fMRI space?

Any comments would be appreciated. 

Best, 

Sang-Young
 


> On Jul 24, 2018, at 3:03 PM, Glasser, Matthew  wrote:
> 
> There is no need to go to original fMRI space in most cases.  If you want
> data in the native physical space of the subject you can use
> ${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to
> warp the data to structural space (and can use a 2mm reference volume in
> that space if you wish to keep it at the same resolution).
> 
> Peace,
> 
> Matt.
> 
> On 7/24/18, 12:27 PM, "hcp-users-boun...@humanconnectome.org on behalf of
> Sang-Young Kim"  sykim...@gmail.com> wrote:
> 
>> Dear HCP experts:
>> 
>> I have downloaded a HCP data from "S1200 Extensively Processed fMRI
>> Data".
>> The downloaded data was just preprocessed for resting state fMRI using
>> fMRIVolume and fMRISurface pipeline.
>> 
>> But I cannot find warp field to transform MNI space data to original fMRI
>> space, which is normally located in ${Subject}/MNINonLinear/xfms after
>> fMRIVolume pipeline.
>> 
>> Could you please let me know where to find it?
>> 
>> Thanks.
>> 
>> Sang-Young Kim, Ph.D.
>> 
>> Postdoctoral Fellow
>> Department of Radiology
>> University of Pittsburgh
>> ___
>> 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] MSMAll

2018-07-24 Thread Timothy Hendrickson 
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
 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

Re: [HCP-Users] MSMAll

2018-07-24 Thread Glasser, Matthew 
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 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)

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strictly prohibited. If you have received this email in error, please 
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Re: [HCP-Users] MSMAll

2018-07-24 Thread Timothy Hendrickson 
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
>>> 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.
>>
>
>
> --
>
> 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

Re: [HCP-Users] Where to find warp field from standard to original resting state fMRI data

2018-07-24 Thread Glasser, Matthew 
There is no need to go to original fMRI space in most cases.  If you want
data in the native physical space of the subject you can use
${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to
warp the data to structural space (and can use a 2mm reference volume in
that space if you wish to keep it at the same resolution).

Peace,

Matt.

On 7/24/18, 12:27 PM, "hcp-users-boun...@humanconnectome.org on behalf of
Sang-Young Kim"  wrote:

>Dear HCP experts:
>
>I have downloaded a HCP data from "S1200 Extensively Processed fMRI
>Data".
>The downloaded data was just preprocessed for resting state fMRI using
>fMRIVolume and fMRISurface pipeline.
>
>But I cannot find warp field to transform MNI space data to original fMRI
>space, which is normally located in ${Subject}/MNINonLinear/xfms after
>fMRIVolume pipeline.
>
>Could you please let me know where to find it?
>
>Thanks.
>
>Sang-Young Kim, Ph.D.
>
>Postdoctoral Fellow
>Department of Radiology
>University of Pittsburgh
>___
>HCP-Users mailing list
>HCP-Users@humanconnectome.org
>http://lists.humanconnectome.org/mailman/listinfo/hcp-users



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[HCP-Users] Missing output after running genericfMRISurfaceProcessingPipelineBatch.sh

2018-07-24 Thread Marc Dubin 
Thank you…found them there!

On 24 Jul 2018, at 14:55, Harms, Michael wrote:

> Are you looking in $SUBJID/MNINonLinear/Results/$fMRIName ?
>
>
> --
> 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 7/24/18, 1:53 PM, "hcp-users-boun...@humanconnectome.org on 
> behalf of Marc Dubin"  of mrd9...@med.cornell.edu> wrote:
>
> Hello,
>
> When I run, genericfMRIVolumeProcessingPipelineBatch.sh, everything 
> runs
> smoothly and many output files are generated in the specified subject
> folder.
>
> However, when I run genericfMRISurfaceProcessingPipelineBatch.sh, it
> runs for a few hours, ends gracefully, but then I can’t find any new
> output files that have been generated.
>
> In both cases, I am analyzing the same resting state data and the
> TaskList is identical for both volume and surface scripts (including
> just the resting state AP and PA scans).
>
> Am I looking in the wrong place?
>
> Thanks!
>
> Marc
>
> ___
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> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers=DwIGaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=C9S_n0bF0p6dJ48M-Lgp1b9KBLxvTD5zOml7nDJ1vZU=1D2msivoMI0-HUxjTbCK6b8Lh7NIHMe36M_GIn_od5k=CrN0dtP8p8M0p__JOBJz259CoM_oHGSjh4sNnWV35VE=
>
>
> 
> 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] Missing output after running genericfMRISurfaceProcessingPipelineBatch.sh

2018-07-24 Thread Harms, Michael 

Are you looking in $SUBJID/MNINonLinear/Results/$fMRIName ?


--
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 7/24/18, 1:53 PM, "hcp-users-boun...@humanconnectome.org on behalf of Marc 
Dubin"  wrote:

Hello,

When I run, genericfMRIVolumeProcessingPipelineBatch.sh, everything runs
smoothly and many output files are generated in the specified subject
folder.

However, when I run genericfMRISurfaceProcessingPipelineBatch.sh, it
runs for a few hours, ends gracefully, but then I can’t find any new
output files that have been generated.

In both cases, I am analyzing the same resting state data and the
TaskList is identical for both volume and surface scripts (including
just the resting state AP and PA scans).

Am I looking in the wrong place?

Thanks!

Marc

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[HCP-Users] Missing output after running genericfMRISurfaceProcessingPipelineBatch.sh

2018-07-24 Thread Marc Dubin 
Hello,

When I run, genericfMRIVolumeProcessingPipelineBatch.sh, everything runs 
smoothly and many output files are generated in the specified subject 
folder.

However, when I run genericfMRISurfaceProcessingPipelineBatch.sh, it 
runs for a few hours, ends gracefully, but then I can’t find any new 
output files that have been generated.

In both cases, I am analyzing the same resting state data and the 
TaskList is identical for both volume and surface scripts (including 
just the resting state AP and PA scans).

Am I looking in the wrong place?

Thanks!

Marc

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[HCP-Users] Where to find warp field from standard to original resting state fMRI data

2018-07-24 Thread Sang-Young Kim 
Dear HCP experts:

I have downloaded a HCP data from "S1200 Extensively Processed fMRI Data". 
The downloaded data was just preprocessed for resting state fMRI using 
fMRIVolume and fMRISurface pipeline. 

But I cannot find warp field to transform MNI space data to original fMRI 
space, which is normally located in ${Subject}/MNINonLinear/xfms after 
fMRIVolume pipeline. 

Could you please let me know where to find it? 

Thanks. 

Sang-Young Kim, Ph.D.

Postdoctoral Fellow
Department of Radiology
University of Pittsburgh
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Re: [HCP-Users] HCP pipeline working directory documentation

2018-07-24 Thread Harms, Michael 

Hi,
I took a very quick look to see what direction this is heading.

One initlal thing I noticed -- the files in $SUBJID/T1w are not in MNI152 space.

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, July 24, 2018 at 10:23 AM
To: "Theis, Nicholas" , "hcp-users@humanconnectome.org" 

Subject: Re: [HCP-Users] HCP pipeline working directory documentation

I am not aware of such a document.  I am happy to review it when you are ready 
for accuracy.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Theis, Nicholas" mailto:the...@upmc.edu>>
Date: Tuesday, July 24, 2018 at 9:54 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] HCP pipeline working directory documentation


Dear HCP creators and users-



To better understand the HCP pipelines we have been documenting its output 
files.  We want to identify the specific files produced by each stage of the 
pipeline (PreFreeSurfer, FreeSurfer, etc), and label what MRI preprocessing 
step the files represent (skull stripping, readout distortion correction, etc).



To your knowledge, has anyone already created a similar document?   We are 
hoping to make this list as complete -and helpful - as possible - although it 
is still a work in progress, and some aspects of it reflect our particular 
set-up.  Feel free to view the document in the link below.



https://docs.google.com/spreadsheets/d/16mKW14FvQr_Im57eVvhePeT-yuRl7IiaOfP7eDEfppE/edit?usp=sharing



If this is something the wider community would find useful then we are happy to 
share it by other means, especially as it is completed.  Any suggestions or 
corrections are welcomed.



Best,

Nick Theis
[Image removed by 
sender.]

HCP_filenames_corresponding_processing_step
docs.google.com
HCPstages Pipeline Stage, Location, Output File or Directory, Description, 
Links to References where applicable PreFreeSurfer,/ data2/ MRI/ Maria_K01/ 
HCPproc/${ SUBID}/ T1w, BiasField_acpc_dc, Bias Field( gradual intensity change 
across field of view) is corrected for using equation( 1) of Gl...







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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 
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] HCP pipeline working directory documentation

2018-07-24 Thread Glasser, Matthew 
I am not aware of such a document.  I am happy to review it when you are ready 
for accuracy.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Theis, Nicholas" mailto:the...@upmc.edu>>
Date: Tuesday, July 24, 2018 at 9:54 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] HCP pipeline working directory documentation


Dear HCP creators and users-


To better understand the HCP pipelines we have been documenting its output 
files.  We want to identify the specific files produced by each stage of the 
pipeline (PreFreeSurfer, FreeSurfer, etc), and label what MRI preprocessing 
step the files represent (skull stripping, readout distortion correction, etc).


To your knowledge, has anyone already created a similar document?   We are 
hoping to make this list as complete -and helpful - as possible - although it 
is still a work in progress, and some aspects of it reflect our particular 
set-up.  Feel free to view the document in the link below.


https://docs.google.com/spreadsheets/d/16mKW14FvQr_Im57eVvhePeT-yuRl7IiaOfP7eDEfppE/edit?usp=sharing


If this is something the wider community would find useful then we are happy to 
share it by other means, especially as it is completed.  Any suggestions or 
corrections are welcomed.


Best,

Nick Theis

[https://lh4.googleusercontent.com/mk6bz0L7UGuQU5CdbmrC666N6PLnFmDWn5QAEWsqVqcGe0cYE_DEctaSkwRf9gNjnXWBjg=w1200-h630-p]

HCP_filenames_corresponding_processing_step
docs.google.com
HCPstages Pipeline Stage, Location, Output File or Directory, Description, 
Links to References where applicable PreFreeSurfer,/ data2/ MRI/ Maria_K01/ 
HCPproc/${ SUBID}/ T1w, BiasField_acpc_dc, Bias Field( gradual intensity change 
across field of view) is corrected for using equation( 1) of Gl...






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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.

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[HCP-Users] HCP pipeline working directory documentation

2018-07-24 Thread Theis, Nicholas 
Dear HCP creators and users-


To better understand the HCP pipelines we have been documenting its output 
files.  We want to identify the specific files produced by each stage of the 
pipeline (PreFreeSurfer, FreeSurfer, etc), and label what MRI preprocessing 
step the files represent (skull stripping, readout distortion correction, etc).


To your knowledge, has anyone already created a similar document?   We are 
hoping to make this list as complete -and helpful - as possible - although it 
is still a work in progress, and some aspects of it reflect our particular 
set-up.  Feel free to view the document in the link below.


https://docs.google.com/spreadsheets/d/16mKW14FvQr_Im57eVvhePeT-yuRl7IiaOfP7eDEfppE/edit?usp=sharing


If this is something the wider community would find useful then we are happy to 
share it by other means, especially as it is completed.  Any suggestions or 
corrections are welcomed.


Best,

Nick Theis

[https://lh4.googleusercontent.com/mk6bz0L7UGuQU5CdbmrC666N6PLnFmDWn5QAEWsqVqcGe0cYE_DEctaSkwRf9gNjnXWBjg=w1200-h630-p]

HCP_filenames_corresponding_processing_step
docs.google.com
HCPstages Pipeline Stage, Location, Output File or Directory, Description, 
Links to References where applicable PreFreeSurfer,/ data2/ MRI/ Maria_K01/ 
HCPproc/${ SUBID}/ T1w, BiasField_acpc_dc, Bias Field( gradual intensity change 
across field of view) is corrected for using equation( 1) of Gl...






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