subject:"Re\: \[HCP\-Users\] path to bbregister .dat file for REST call"

Re: [HCP-Users] path to bbregister .dat file for REST call

2018-03-27 Thread Timothy Coalson

planes that are aligned with the scanner
> axes. And you are correct - the B0 axis is along +z.
>
> Thanks again for all the suggestions,
> Olivia
>
>
> 
> Olivia Viessmann, PhD
> A.A. Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Harvard Medical School
> Building 75, Third Ave
> <https://maps.google.com/?q=75,+Third+Ave+%0D%0ACharlestown,+MA+02129=gmail=g>
> Charlestown, MA 02129
>
> On 28 Feb 2018, at 09:23, Hodge, Michael <hod...@wustl.edu> wrote:
>
>
> Hi Olivia,
>
> You can use a script similar to this to iterate over all the experiments
> and preprocessing resources and pull down these files for all subjects:
>
> #!/bin/bash
> #
> # ITERATE OVER 3T EXPERIMENTS
> #
> for CSVROW in $(curl -s -k --cookie JSESSIONID=$JSESSIONID https:/
> /db.humanconnectome.org/data/projects/HCP_1200/experiments?
> xsiType=xnat:mrSessionData\=ID,label,URI\=csv | grep
> "_3T"); do
>   LABEL=$(echo $CSVROW | cut -d, -f3)
>   SUBJ=$(echo $LABEL | sed -e "s/_.*$//")
>   URI=$(echo $CSVROW | cut -d, -f4)
>   #
>   # ITERATE OVER PIPELINE RESOURCES FOR EACH EXPERIMENT
>   #
>   for RESOURCEROW in $(curl -s -k --cookie
> JSESSIONID=$JSESSIONID https://db.humanconnectome.org${URI}/
> resources?xsiType=xnat:resourceCatalog\=csv
> <https://db.humanconnectome.org$%7Buri%7D/resources?xsiType=xnat:resourceCatalog%5C=csv>);
> do
>RESOURCE=$(echo ${RESOURCEROW} | cut -d, -f2)
>#
># DOWNLOAD FILES FROM FMRI PREPROC RESOURCES
>#
>if [[ $RESOURCE =~ ^.*fMRI.*_preproc ]]; then
>  SERIES=$(echo "$RESOURCE" | sed
> -e "s/_preproc//")
>  echo $SUBJ $LABEL $URI $RESOURCE
> $SERIES
>DIRECTORY="$SUBJ/MNINonLinear/
> Results/${SERIES}/DistortionCorrectionAndEPIToT1wReg_
> FLIRTBBRAndFreeSurferBBRbased"
>  mkdir -p $DIRECTORY/FieldMap
>  curl -s -k --cookie
> JSESSIONID=$JSESSIONID https://db.humanconnectome.org${URI}/
> resources/${RESOURCE}/files/${SERIES}/DistortionCorrectionAndEPIToT1wReg_
> FLIRTBBRAndFreeSurferBBRbased/fMRI2str.mat
> <https://db.humanconnectome.org$%7Buri%7D/resources/$%7BRESOURCE%7D/files/$%7BSERIES%7D/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/fMRI2str.mat>
>  -o $DIRECTORY/fMRI2str.mat
>  curl -s -k --cookie
> JSESSIONID=$JSESSIONID https://db.humanconnectome.org${URI}/
> resources/${RESOURCE}/files/${SERIES}/DistortionCorrectionAndEPIToT1wReg_
> FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef_dc_jac.nii.gz
> <https://db.humanconnectome.org$%7Buri%7D/resources/$%7BRESOURCE%7D/files/$%7BSERIES%7D/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef_dc_jac.nii.gz>
>  -o $DIRECTORY/FieldMap/SBRef_dc_jac.nii.gz
>fi
>   done
> done
>
> You can set the JSESSIONID with this call:
>
> read -s -p "ENTER PASSWORD: " PW;JSESSIONID=`curl -s -k -u
> YOUR_USERNAME_HERE:$PW https://db.humanconnectome.org/REST/
> JSESSIONID`;export JSESSIONID;echo $JSESSIONID
>
> I hope this helps.  Note, I didn’t include the file Tim mentioned that you
> would already in your download folders.
>
> Regards,
>
> Mike
>
> *From:* hcp-users-boun...@humanconnectome.org [mailto:hcp-users-bounces@
> humanconnectome.org <hcp-users-boun...@humanconnectome.org>] *On Behalf
> Of *Viessmann, Olivia M.
> *Sent:* Tuesday, February 27, 2018 9:48 AM
> *To:* NEUROSCIENCE tim <tsc...@mst.edu>
> *Cc:* hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] path to bbregister .dat file for REST call
>
> Dear Tim,
>
> thanks a lot for the detailed explanation, this is all tremendously
> helpful and is indeed what I am looking for.
> I hope someone on this list knows where the transforms are stored. As soon
> as I know from where to download it I will give it a try and let you know
> if it worked.
>
> Thanks
> Olivia
>
>
>
>
> On 26 Feb 2018, at 18:22, Timothy Coalson <tsc...@mst.edu> wrote:
>
> 0307_3T/RESOURCES/rfMRI_REST1_LR_preproc/rfMR
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient informatio

Re: [HCP-Users] path to bbregister .dat file for REST call

2018-03-27 Thread Viessmann, Olivia M.

   RESOURCE=$(echo ${RESOURCEROW} | cut -d, -f2)
   #
   # DOWNLOAD FILES FROM FMRI PREPROC RESOURCES
   #
   if [[ $RESOURCE =~ ^.*fMRI.*_preproc ]]; then
 SERIES=$(echo "$RESOURCE" | sed -e 
"s/_preproc//")
 echo $SUBJ $LABEL $URI $RESOURCE 
$SERIES
   
DIRECTORY="$SUBJ/MNINonLinear/Results/${SERIES}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased"
 mkdir -p $DIRECTORY/FieldMap
 curl -s -k --cookie 
JSESSIONID=$JSESSIONID 
https://db.humanconnectome.org${URI}/resources/${RESOURCE}/files/${SERIES}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/fMRI2str.mat<https://db.humanconnectome.org${uri}/resources/$%7BRESOURCE%7D/files/$%7BSERIES%7D/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/fMRI2str.mat>
 -o $DIRECTORY/fMRI2str.mat
 curl -s -k --cookie 
JSESSIONID=$JSESSIONID 
https://db.humanconnectome.org${URI}/resources/${RESOURCE}/files/${SERIES}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef_dc_jac.nii.gz<https://db.humanconnectome.org${uri}/resources/$%7BRESOURCE%7D/files/$%7BSERIES%7D/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef_dc_jac.nii.gz>
 -o $DIRECTORY/FieldMap/SBRef_dc_jac.nii.gz
   fi
  done
done

You can set the JSESSIONID with this call:

read -s -p "ENTER PASSWORD: " PW;JSESSIONID=`curl -s -k -u 
YOUR_USERNAME_HERE:$PW 
https://db.humanconnectome.org/REST/JSESSIONID`;export<https://db.humanconnectome.org/REST/JSESSIONID%60;export>
 JSESSIONID;echo $JSESSIONID

I hope this helps.  Note, I didn’t include the file Tim mentioned that you 
would already in your download folders.

Regards,

Mike

From: 
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Viessmann, Olivia 
M.
Sent: Tuesday, February 27, 2018 9:48 AM
To: NEUROSCIENCE tim <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] path to bbregister .dat file for REST call

Dear Tim,

thanks a lot for the detailed explanation, this is all tremendously helpful and 
is indeed what I am looking for.
I hope someone on this list knows where the transforms are stored. As soon as I 
know from where to download it I will give it a try and let you know if it 
worked.

Thanks
Olivia




On 26 Feb 2018, at 18:22, Timothy Coalson 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:

0307_3T/RESOURCES/rfMRI_REST1_LR_preproc/rfMR


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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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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Re: [HCP-Users] path to bbregister .dat file for REST call

2018-02-28 Thread Hodge, Michael


Hi Olivia,

You can use a script similar to this to iterate over all the experiments and 
preprocessing resources and pull down these files for all subjects:

#!/bin/bash
#
# ITERATE OVER 3T EXPERIMENTS
#
for CSVROW in $(curl -s -k --cookie JSESSIONID=$JSESSIONID 
https://db.humanconnectome.org/data/projects/HCP_1200/experiments?xsiType=xnat:mrSessionData\=ID,label,URI\=csv
 | grep "_3T"); do
  LABEL=$(echo $CSVROW | cut -d, -f3)
  SUBJ=$(echo $LABEL | sed -e "s/_.*$//")
  URI=$(echo $CSVROW | cut -d, -f4)
  #
  # ITERATE OVER PIPELINE RESOURCES FOR EACH EXPERIMENT
  #
  for RESOURCEROW in $(curl -s -k --cookie JSESSIONID=$JSESSIONID 
https://db.humanconnectome.org${URI}/resources?xsiType=xnat:resourceCatalog\=csv);
 do
   RESOURCE=$(echo ${RESOURCEROW} | cut -d, -f2)
   #
   # DOWNLOAD FILES FROM FMRI PREPROC RESOURCES
   #
   if [[ $RESOURCE =~ ^.*fMRI.*_preproc ]]; then
 SERIES=$(echo "$RESOURCE" | sed -e 
"s/_preproc//")
 echo $SUBJ $LABEL $URI $RESOURCE 
$SERIES
   
DIRECTORY="$SUBJ/MNINonLinear/Results/${SERIES}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased"
 mkdir -p $DIRECTORY/FieldMap
 curl -s -k --cookie 
JSESSIONID=$JSESSIONID 
https://db.humanconnectome.org${URI}/resources/${RESOURCE}/files/${SERIES}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/fMRI2str.mat
 -o $DIRECTORY/fMRI2str.mat
 curl -s -k --cookie 
JSESSIONID=$JSESSIONID 
https://db.humanconnectome.org${URI}/resources/${RESOURCE}/files/${SERIES}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef_dc_jac.nii.gz
 -o $DIRECTORY/FieldMap/SBRef_dc_jac.nii.gz
   fi
  done
done

You can set the JSESSIONID with this call:

read -s -p "ENTER PASSWORD: " PW;JSESSIONID=`curl -s -k -u 
YOUR_USERNAME_HERE:$PW https://db.humanconnectome.org/REST/JSESSIONID`;export 
JSESSIONID;echo $JSESSIONID

I hope this helps.  Note, I didn't include the file Tim mentioned that you 
would already in your download folders.

Regards,

Mike

From: hcp-users-boun...@humanconnectome.org 
[mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Viessmann, Olivia M.
Sent: Tuesday, February 27, 2018 9:48 AM
To: NEUROSCIENCE tim <tsc...@mst.edu>
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] path to bbregister .dat file for REST call

Dear Tim,

thanks a lot for the detailed explanation, this is all tremendously helpful and 
is indeed what I am looking for.
I hope someone on this list knows where the transforms are stored. As soon as I 
know from where to download it I will give it a try and let you know if it 
worked.

Thanks
Olivia




On 26 Feb 2018, at 18:22, Timothy Coalson 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:

0307_3T/RESOURCES/rfMRI_REST1_LR_preproc/rfMR


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto: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

Re: [HCP-Users] path to bbregister .dat file for REST call

2018-02-27 Thread Viessmann, Olivia M.

Dear Tim,

thanks a lot for the detailed explanation, this is all tremendously helpful and 
is indeed what I am looking for.
I hope someone on this list knows where the transforms are stored. As soon as I 
know from where to download it I will give it a try and let you know if it 
worked.

Thanks
Olivia



On 26 Feb 2018, at 18:22, Timothy Coalson 
> wrote:

0307_3T/RESOURCES/rfMRI_REST1_LR_preproc/rfMR



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

___
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Re: [HCP-Users] path to bbregister .dat file for REST call

2018-02-26 Thread Timothy Coalson

The 6dof transform using the MNI template is only to get the orientation of
the structural images to be more predictable - we actually refer to the
result of this transform as "native volume space", because it is somewhat
more useful for our purposes than the scanner coordinates.  It is based
only on the T1w scan(s), so it doesn't directly tell you about the
orientation during the functional scans.  However, this space is the space
that the surfaces you need are in, so it is relevant in a sense.

What you actually need is the registration between the distortion-corrected
functional scan sbref images, and the T1w "native space" image that the
surfaces align with.  It is in FSL format, which has coordinate system
oddities, and you probably need to invert it (using convert_xfm).  In order
to get wb_command to interpret it properly, you need to have the original
images used for the registration (or at least volume files with equivalent
header info).  Once it is inverted, the "source" image will be the T1w
image in "native space" (rigidly aligned), and the target will be the
oblique sbref volume.  You can use wb_command -convert-affine to turn the
inverted affine into a more intuitive mm-to-mm affine so that you can
sanity check it, and then use that in wb_command -surface-apply-affine
(that command can instead use the -flirt option to directly read a
fsl-format affine, but I don't know if we have tested the case of oblique
volumes in FSL-format matrices, so sanity checking is good).  This mm-to-mm
affine should only have the difference between head orientation in scanner
coordinate space (which doesn't rotate just by angling the slice planes)
and the rigidly aligned "native space", which is what we want.  The best
sanity check is that the result of -surface-apply-affine lines up well with
the SBRef images, using the "oblique" volume display mode in wb_view (the
default orthogonal view doesn't work correctly on oblique volumes) and the
"volume surface outline" feature.

Hopefully, the scanner b0 direction is constant in scanner coordinate space
(something simple like +z, perhaps).  Someone else will have to comment on
whether this is the case, and how to know what that direction is.  This
also doesn't account for per-frame motion, so if you need more accuracy,
more effort will be required.

The files you need exist in the directories accessible through the REST
interface, something like this, but someone more familiar with the REST api
will have to fill in the blanks:

???/100307_3T/RESOURCES/Structural_preproc/T1w/T1w_acpc_dc_restore.nii.gz —
T1w aligned with surfaces, should be identical to the one in the subject's
T1w folder, so you shouldn't need to re-download it.

???/100307_3T/RESOURCES/rfMRI_REST1_LR_preproc/rfMRI_REST1_
LR/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/fMRI2str.mat
— Affine between T1w and SBRef not including distortions

???/100307_3T/RESOURCES/rfMRI_REST1_LR_preproc/rfMRI_REST1_
LR/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferB
BRbased/FieldMap/SBRef_dc_jac.nii.gz — Undistorted fMRI Volume with oblique
sform

Here is a wiki page on using REST, once someone translates these paths into
the needed URLs:

https://wiki.humanconnectome.org/display/PublicData/How+To+A
ccess+Subject+Data+via+REST

Tim

On Mon, Feb 26, 2018 at 4:06 PM, Viessmann, Olivia M. <
oviessm...@mgh.harvard.edu> wrote:

> Hi Matt,
>
> I would like to transform the surfaces from native space to the EPI run,
> i.e. to the head position of the subject during the rs-fMRI acquisition. My
> final aim is to calculate surface orientations to the main B0 field and
> relate them to the rs-fmri data, so I need to rotate the surface to the
> exact head orientation during the EPI acquisition. I already noticed that
> the T1w image is rigidly transformed before the freeSurfer recon-all is run.
> My plan was to use the inverse of the acpc.mat file (that I understand to
> be the 6 DOF transform used to align the subject rigidly to MNI) and the
> inverse of the EPItoT1w.dat to transform the surfaces.
> But you mention the FSLBBR preregistration - what do you think is the
> correct transformation file for me?
>
> Thanks a lot,
> Olivia
>
>
> On 26 Feb 2018, at 16:42, Glasser, Matthew  wrote:
>
> That will contain an incomplete EPI to T1w registration because we
> preregister with FSLBBR.  Why do you need this transform in this format?
>
> Peace,
>
> Matt.
>
> From:  on behalf of "Viessmann,
> Olivia M." 
> Date: Monday, February 26, 2018 at 3:36 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] path to bbregister .dat file for REST call
>
> Hello,
>
> I would like to retrieve the bbregister .dat file from the EPI to T1w
> registration but don't know its exact path.
> From the shell scripts on github  (Pipelines/fMRIVolume.scripts/
>

Re: [HCP-Users] path to bbregister .dat file for REST call

2018-02-26 Thread Viessmann, Olivia M.

Hi Matt,

I would like to transform the surfaces from native space to the EPI run, i.e. 
to the head position of the subject during the rs-fMRI acquisition. My final 
aim is to calculate surface orientations to the main B0 field and relate them 
to the rs-fmri data, so I need to rotate the surface to the exact head 
orientation during the EPI acquisition. I already noticed that the T1w image is 
rigidly transformed before the freeSurfer recon-all is run.
My plan was to use the inverse of the acpc.mat file (that I understand to be 
the 6 DOF transform used to align the subject rigidly to MNI) and the inverse 
of the EPItoT1w.dat to transform the surfaces.
But you mention the FSLBBR preregistration - what do you think is the correct 
transformation file for me?

Thanks a lot,
Olivia

On 26 Feb 2018, at 16:42, Glasser, Matthew 
> wrote:

That will contain an incomplete EPI to T1w registration because we preregister 
with FSLBBR.  Why do you need this transform in this format?

Peace,

Matt.

From: 
>
 on behalf of "Viessmann, Olivia M." 
>
Date: Monday, February 26, 2018 at 3:36 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] path to bbregister .dat file for REST call

Hello,

I would like to retrieve the bbregister .dat file from the EPI to T1w 
registration but don't know its exact path.
>From the shell scripts on github  
>(Pipelines/fMRIVolume.scripts/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh)
I found out that the file I am looking for is named EPItoT1w.dat. However the 
path in the script is ${WD}, so I don't know what to put into my curl call, eg:
curl -u myUserName:myPassWord -O 
https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/200109/experiments/200109_CREST/resources/200109_CREST/files//EPItoT1w.dat

I'd very much appreciate if someone who knows the naming of this path could let 
me know.

Many thanks
Olivia Viessmann

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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Re: [HCP-Users] path to bbregister .dat file for REST call

2018-02-26 Thread Glasser, Matthew

That will contain an incomplete EPI to T1w registration because we preregister 
with FSLBBR.  Why do you need this transform in this format?

Peace,

Matt.

From: 
>
 on behalf of "Viessmann, Olivia M." 
>
Date: Monday, February 26, 2018 at 3:36 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] path to bbregister .dat file for REST call


Hello,


I would like to retrieve the bbregister .dat file from the EPI to T1w 
registration but don't know its exact path.

>From the shell scripts on github  
>(Pipelines/fMRIVolume.scripts/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh)

I found out that the file I am looking for is named EPItoT1w.dat. However the 
path in the script is ${WD}, so I don't know what to put into my curl call, eg:
curl -u myUserName:myPassWord -O 
https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/200109/experiments/200109_CREST/resources/200109_CREST/files//EPItoT1w.dat

I'd very much appreciate if someone who knows the naming of this path could let 
me know.

Many thanks
Olivia Viessmann

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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Re: [HCP-Users] path to bbregister .dat file for REST call

Re: [HCP-Users] path to bbregister .dat file for REST call

Re: [HCP-Users] path to bbregister .dat file for REST call

Re: [HCP-Users] path to bbregister .dat file for REST call

Re: [HCP-Users] path to bbregister .dat file for REST call

Re: [HCP-Users] path to bbregister .dat file for REST call

Re: [HCP-Users] path to bbregister .dat file for REST call

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