>From what I recall, the s3fs mounting doesn't give feedback when it fails,
and the nitrc-ce web interface assumes it succeeds.  Double check for typos
in both your access ID and secret access key (BOTH will have changed, I
believe).  After this, use the command line to issue the mount command, and
then do ls on the mountpoint to ensure the data is there.  Using aws-cli on
my machine, I was able to check that things seem to work on amazon's side
(note, aws-cli DOES give an error message when the credentials are wrong):

$ aws s3 ls s3://hcp-openaccess-temp/
A client error (AccessDenied) occurred when calling the ListObjects
operation: Access Denied
$ aws configure --profile tempbucket
AWS Access Key ID [None]: <redacted>
AWS Secret Access Key [None]: <redacted>
Default region name [None]:
Default output format [None]:
$ aws --profile tempbucket s3 ls s3://hcp-openaccess-temp/
                           PRE HCP/
                           PRE HCP_1200/
                           PRE HCP_900/
                           PRE HCP_Retest/
$

So, you can use this to check that you have the key info correct, before
trying to figure out if other things are going wrong.

Tim


On Tue, Jul 17, 2018 at 8:29 AM, 晴♬小宇 <[email protected]> wrote:

> Hi,
>     Thank you for your reply. I have successfully accessed hcp data on S3
> browser by the new Key Pairs. However, there is still a problem when I try
> to apply the new Key Pairs to my EC2 instance on NITRC-CE.
>     In detail, I updated the AWS access key ID and Secret Access Key to
> the new Key Pairs. And due to the bucket was changed, I used 's3fs mount'
> to mount the temp s3 bucket to /s3/hcp (I clicked 'add mount' with s3
> Bucket as 'hcp-openaccess-temp', with path as '/HCP_1200', and with Mount
> Point as '/s3/hcp' to create a new S3FS Mount. See figure 1 in appendix). I
> got feedback 'Unmounted /s3/hcp. Mounted hcp-openaccess-temp as /s3/hcp',
> and it seemed that everything went well but I couldn't find any mount
> information of the bucket when executed command 'df -h' on the EC2 instance.
>     Do I miss some steps? Or according to your reply, how can I mount
> hcp-openaccess-temp bucket on my EC2 instance without NITRC-CE?
>
>     Many thanks for your help,
>     Best.
>
>     Xiayu Chen
>     Beijing Normal University,
>     2018/07/17
>
>
> ------------------ Original ------------------
> *From: * "hcp-users-request"<[email protected]>;
> *Date: * Thu, Jul 12, 2018 05:57 AM
> *To: * "hcp-users"<[email protected]>;
> *Subject: * HCP-Users Digest, Vol 68, Issue 11
>
> Send HCP-Users mailing list submissions to
> [email protected]
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> or, via email, send a message with subject or body 'help' to
> [email protected]
>
> You can reach the person managing the list at
> [email protected]
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of HCP-Users digest..."
>
>
> Today's Topics:
>
>    1. FreeSurferNHP.sh (Sanchez, Juan (NYSPI))
>    2. Re: A few specific questions about the HCP data | MNI space
>       dedrifting & file structure (Bajada, Claude Julien)
>    3. Re: access to hcp-openaccess-temp (Timothy Coalson)
>    4. Re: A few specific questions about the HCP data | MNI space
>       dedrifting & file structure (Timothy Coalson)
>    5. PreFreeSurferPipeline debugging (Jayasekera, Dinal)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 11 Jul 2018 17:47:32 +0000
> From: "Sanchez, Juan (NYSPI)" <[email protected]>
> Subject: [HCP-Users] FreeSurferNHP.sh
> To: "[email protected]" <[email protected]>
> Message-ID:
> <SN1PR09MB097694BB96A2C3715891A704B75A0@SN1PR09MB0976.
> namprd09.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear HCP community,
>
> We would like to acquire the latest NHP Pipelines for the HCP Pipelines
>
> Thanks so much
>
> Juan Sanchez-Pena
>
> NYSPI
>
> Columbia University
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://lists.humanconnectome.org/pipermail/hcp-users/
> attachments/20180711/f1d644ae/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Wed, 11 Jul 2018 17:50:37 +0000
> From: "Bajada, Claude Julien" <[email protected]>
> Subject: Re: [HCP-Users] A few specific questions about the HCP data |
> MNI space dedrifting & file structure
> To: Timothy Coalson <[email protected]>, "Glasser, Matthew"
> <[email protected]>
> Cc: "[email protected]" <[email protected]>
> Message-ID:
> <99176650acf65a45b95648a7300357f61175f...@mbx2010-e01.ad.fz-juelich.de>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Tim,
>
> I am trying to follow the drifting procedure below. Can I clarify a few
> points?
>
> You state:
> "Once you have this average, you can invert it (like any other warpfield),
> and then concatenate it after the acpc to MNI warp for each subject, giving
> you a new dedrifted (for the chosen population) template space."
>
> >From this I understand that the multiplication and inversion gives us a
> warp field that warps the MNI registered subject to the new "drifted"
> space, correct?
>
> By "concatenate it after the acpc to MNI warp" do you mean multiply the
> acpc2mni warp by the new mni2dedrift? Thus generating an acpc2dedrift?
>
> Second, you state: "By carefully finding the volume of brain masks in acpc
> space and after resampling to this new dedrifted space, you can check for
> this effect"
>
> What exactly am I meant to be checking? I should compare the volume of the
> mask in acpc (native) space and in the drifted space. Should they be
> roughly the same volume? Also you say that I should "carefully find the
> volume" what exactly do you mean by "carefully"
>
> Thanks in advance,
>
> Claude
>
> ________________________________________
> From: Timothy Coalson [[email protected]]
> Sent: 02 July 2018 19:28
> To: Glasser, Matthew
> Cc: Harms, Michael; Bajada, Claude Julien; [email protected]
> Subject: Re: [HCP-Users] A few specific questions about the HCP data | MNI
> space dedrifting & file structure
>
> We previously looked at the MNI drift, and found that it is almost
> entirely an affine, even for the nonlinear template.  We have a suspicion
> that this means that it was originally caused by the early MNI linear
> template, and that the issue was known by the time MNI nonlinear templates
> were released, as it implies that the nonlinear template was dedrifted, but
> then an affine was deliberately added in order to match the previous MNI
> linear template.  However, we have not investigated whether this was the
> case.
>
> Since all of our anatomical size and shape measurements are computed using
> a rigid acpc space (after gradient distortion correction), this drift in
> MNI space is largely unimportant to many steps of analysis of things like
> fMRI.  Be aware that even with proper dedrifting, any non-rigid volume
> registration will hide differences in brain size (and shape if nonlinear)
> across subjects, by design, so non-rigid volume-registered data won't ever
> tell you the whole story of the anatomical features.  If you want to make
> some anatomical measurement (distance, area, volume), then you should
> generally measure it in each individual's own rigid/acpc space, not in any
> kind of template space.
>
> Now, on to the explanation: the registration warpfields from each
> subject's rigid acpc ("T1w") space to MNI nonlinear space provide the
> information needed to compute a dedrifted template that matches the
> population represented by the subjects.  Warpfields are displacement vector
> fields from the output coordinate system to the input coordinate system
> (because of how volume resampling works - the output needs to be a regular
> grid, so you actually need to transform output coordinates backwards to the
> original location).  So, we can take the vector fields for each subjects
> that specify where the MNI-aligned features originally were in acpc space,
> and average those locations for each voxel.  This is simply averaging the
> warpfields that are used to resample volume data from T1w/acpc space to MNI
> space.  Once you have this average, you can invert it (like any other
> warpfield), and then concatenate it after the acpc to MNI warp for each
> subject, giving you a new dedrifted (for the ch
>  osen population) template space.
>
> Note, however, that this requires the acpc alignment to have worked well
> (in the HCP pipelines, it is really a rigid registration to an MNI
> template, not specifically using the ac and pc) - if there are any
> non-matching rotations among the rigidly aligned volumes, they can result
> in causing a shrinkage from the true average brain volume.  By carefully
> finding the volume of brain masks in acpc space and after resampling to
> this new dedrifted space, you can check for this effect (it will never be
> an expansion).  However, the effect may not be isotropic, so actually
> fixing the effect properly requires more thought.  However, if the acpc
> alignments are generally close to being the correct orientation, this
> effect should be small.
>
> Note, in particular, that coordinates in this new space will not match MNI
> coordinates, probably not even at (0, 0, 0), you would need to put any
> coordinates through that same average warpfield in order to go between MNI
> and this new space.  You could also tweak the new space by adding a rigid
> affine to the end, so you could line up (0, 0, 0) with MNI space, or
> similar.
>
> Tim
>
>
> On Mon, Jul 2, 2018 at 10:21 AM, Glasser, Matthew <[email protected]
> <mailto:[email protected]>> wrote:
> Tim Coalson can explain how to dedrift MNI space (which as Mike says is no
> longer true MNI space).
>
> Peace,
>
> Matt.
>
> On 7/2/18, 10:10 AM, "[email protected]<mailto:hcp
> [email protected]> on behalf of
> Harms, Michael" <[email protected]<mailto:hcp
> [email protected]> on behalf of
> [email protected]<mailto:[email protected]>> wrote:
>
> >
> >Hi,
> >Re (1):
> >If you want to work with streamlines in MNI space then you have to accept
> >the "drift" (volume expansion) that is part of MNI space itself.
> >
> >Re (2):
> >Maps may be resampled to surfaces in MNI space.  But all the FreeSurfer
> >structural quantities that we provide in the database/spreadsheet in
> >ConnectomeDB are measured in the subject's real (native) space.
> >
> >Cheers,
> >-MH
> >
> >--
> >Michael Harms, Ph.D.
> >
> >-----------------------------------------------------------
> >
> >Associate Professor of Psychiatry
> >
> >Washington University School of Medicine
> >
> >Department of Psychiatry, Box 8134
> <https://maps.google.com/?q=8134+660+South+Euclid+Ave&entry=gmail&source=g>
> >
> >660 South Euclid Ave
> <https://maps.google.com/?q=8134+660+South+Euclid+Ave&entry=gmail&source=g>.
> Tel: 314-747-6173
> >
> >St. Louis, MO  63110                          Email: [email protected]
> <mailto:[email protected]>
> >On 7/2/18, 7:14 AM, "[email protected]<mailto:hcp
> [email protected]> on behalf of
> >Claude Bajada" <[email protected]<mailto:hcp
> [email protected]> on behalf of
> >[email protected]<mailto:[email protected]>> wrote:
> >
> >Dear experts,
> >
> >I have a few questions:
> >
> >1) I am currently working on a project using tractography and the HCP
> >data. I have used the HCP provided FNIRT based MNI registration in order
> >to register individual streamlines from "native" or diffusion space (as
> >per post HCP minimal processing pipeline) to MNI space. However, in
> >Glasser 2016 supplementary text, it states that the MNI space is drifted
> >relative to the mean brain size of individual brains (greatest along the
> >x and z axes). I've been told that it is possible to "dedrift" these
> >data and I wonder if anyone has experience in doing this and is able to
> >point me in the right direction.
> >
> >2) from what I understand, structural qualities such as cortical
> >thickness etc are measured in the individual's real space. However then,
> >what I do not understand is the file structure of the HCP data. The
> >structural measures such as cortical thickness, curvature and myelin
> >maps etc live in the MNINonLinear/fsaverage_LR32k rather than in the
> >'native space' directory. Can anyone shed light on this?
> >
> >Regards,
> >
> >Claude
> >
> >
> >
> >-----------------------------------------------------------
> ---------------
> >----------------------
> >-----------------------------------------------------------
> ---------------
> >----------------------
> >Forschungszentrum Juelich GmbH
> >52425 Juelich
> >Sitz der Gesellschaft: Juelich
> >Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> >Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> >Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> >Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> >Prof. Dr. Sebastian M. Schmidt
> >-----------------------------------------------------------
> ---------------
> >----------------------
> >-----------------------------------------------------------
> ---------------
> >----------------------
> >
> >
> >_______________________________________________
> >HCP-Users mailing list
> >[email protected]<mailto:[email protected]>
> >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
> >[email protected]<mailto:[email protected]>
> >http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> _______________________________________________
> HCP-Users mailing list
> [email protected]<mailto:[email protected]>
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 11 Jul 2018 13:58:00 -0500
> From: Timothy Coalson <[email protected]>
> Subject: Re: [HCP-Users] access to hcp-openaccess-temp
> To: ???? <[email protected]>
> Cc: hcp-users <[email protected]>
> Message-ID:
> <CAK_=taxsy+tk45a9rx0xkr5j7jvxj4r-r5ehcmznsi-2map...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> The "failed to unmount" error is a flaw in the NITRC-CE web interface code,
> it internally has its own idea of whether it is mounted, and it will refuse
> to try to mount it unless it first successfully unmounts it (annoyingly, s3
> tools didn't return an error code if the mounting didn't work, leading the
> web interface to assume it was mounted even if it failed, putting it into
> this state).  In order to recover from this state, you need to use ssh or
> similar to manually mount the dataset.
>
> Tim
>
>
> On Wed, Jul 11, 2018 at 8:02 AM, ???? <[email protected]>
> wrote:
>
> > Hi,
> >     Because of the migration of HCP data, I have recreated my credentials
> > (access key) for the new, temporary bucket.
> >     Then, I try replacing the old key with the new key on the NITRC-CE.
> > But when I click the "Apply" button, I get a failure message (see the
> > figure below).
> >
> >     Do I miss some important steps? For example, Should I remove the old
> > mount and add a new mount for the temporary bucket?
> >     I have tried remove the old one by clicking the "Remove selected
> > mount(s)" button, but it didn't work.
> >     So can you give me any suggestion to solve the problem? I will
> > appreciate your help.
> >     Thanks!
> > Xiayu Chen
> >
> > _______________________________________________
> > HCP-Users mailing list
> > [email protected]
> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >
> -------------- next part --------------
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> -------------- next part --------------
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>
> ------------------------------
>
> Message: 4
> Date: Wed, 11 Jul 2018 14:38:19 -0500
> From: Timothy Coalson <[email protected]>
> Subject: Re: [HCP-Users] A few specific questions about the HCP data |
> MNI space dedrifting & file structure
> To: "Bajada, Claude Julien" <[email protected]>
> Cc: "[email protected]" <[email protected]>
> Message-ID:
> <CAK_=taxU1wJw5-tuat1GSDsrOMFJ6ZUZ6QHXy+r6MEq4C1+F=a...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Do not multiply any warpfield by anything, that is not a meaningful
> operation.  Concatenation of warpfields is a special operation, use
> convertwarp to do this (this is why it has --warp1 and --warp2 options).
> Be aware that if you have any changes in volume dimension or origin, you
> will have to be very careful about which volume you use as the reference
> space for each step (including inversion), because FSL's spatial transform
> code doesn't use the full nifti header correctly.
>
> Yes, concatenating the group drift removal warp onto each subject's acpc to
> MNI warp will give you the acpc to dedrifted warp for each subject.  You
> can also apply it to any MNI space data to get the version in dedrifted
> space.
>
> The "carefully" in my comment about measuring brain volume is about the
> fact that you are resampling a binary mask, where if you did trilinear
> interpolation (the default in some tools) and then fed it into a tool that
> treats the now-nonbinary volume as if it is supposed to be a binary mask,
> that could result in something similar to a dilation of the original mask.
> Personally, I would probably use trilinear interpolation (not cubic, we
> don't have continuous features to preserve) and then making sure that the
> result was treated as a weighting volume, not a binary mask.  wb_command
> -volume-weighted-stats will use the voxel volume as the weights by default,
> and the input is never specially treated as a binary mask, so it would be a
> good way to calculate the brain volume.
>
> What you would be looking for is, if you take the average of the brain
> volumes across subjects as measured in acpc space, and compared it to the
> average across subjects of those same "masks" after resampling them to the
> dedrifted space, the dedrifted space should have only slightly less average
> volume (~1%?  purely guessing here).  If it is a large change in average
> volume, either the acpc alignments weren't as good as you thought, or
> something else has gone wrong.
>
> Back to your original question: your tractography data is already in
> subject acpc space, yes?  If you want to measure something about the
> tractography data in an anatomically-correct manner, the most obvious thing
> to me is to measure it in each subject's acpc space, and then average or
> look at the distributions of these numbers afterwards.  Of course, if you
> plan on doing patients vs controls or some other condition-related test,
> you may need to control for overall brain size, in which case a dedrifted
> registered space could be a good idea (or maybe you could use the acpc
> space measures with a nuisance regressor based on brain size instead,
> paying attention to the nonlinear relationship between volume, area, and
> length).
>
> Tim
>
>
> On Wed, Jul 11, 2018 at 12:50 PM, Bajada, Claude Julien <
> [email protected]> wrote:
>
> > Hi Tim,
> >
> > I am trying to follow the drifting procedure below. Can I clarify a few
> > points?
> >
> > You state:
> > "Once you have this average, you can invert it (like any other
> warpfield),
> > and then concatenate it after the acpc to MNI warp for each subject,
> giving
> > you a new dedrifted (for the chosen population) template space."
> >
> > From this I understand that the multiplication and inversion gives us a
> > warp field that warps the MNI registered subject to the new "drifted"
> > space, correct?
> >
> > By "concatenate it after the acpc to MNI warp" do you mean multiply the
> > acpc2mni warp by the new mni2dedrift? Thus generating an acpc2dedrift?
> >
> > Second, you state: "By carefully finding the volume of brain masks in
> acpc
> > space and after resampling to this new dedrifted space, you can check for
> > this effect"
> >
> > What exactly am I meant to be checking? I should compare the volume of
> the
> > mask in acpc (native) space and in the drifted space. Should they be
> > roughly the same volume? Also you say that I should "carefully find the
> > volume" what exactly do you mean by "carefully"
> >
> > Thanks in advance,
> >
> > Claude
> >
> > ________________________________________
> > From: Timothy Coalson [[email protected]]
> > Sent: 02 July 2018 19:28
> > To: Glasser, Matthew
> > Cc: Harms, Michael; Bajada, Claude Julien; [email protected]
> > Subject: Re: [HCP-Users] A few specific questions about the HCP data |
> MNI
> > space dedrifting & file structure
> >
> > We previously looked at the MNI drift, and found that it is almost
> > entirely an affine, even for the nonlinear template.  We have a suspicion
> > that this means that it was originally caused by the early MNI linear
> > template, and that the issue was known by the time MNI nonlinear
> templates
> > were released, as it implies that the nonlinear template was dedrifted,
> but
> > then an affine was deliberately added in order to match the previous MNI
> > linear template.  However, we have not investigated whether this was the
> > case.
> >
> > Since all of our anatomical size and shape measurements are computed
> using
> > a rigid acpc space (after gradient distortion correction), this drift in
> > MNI space is largely unimportant to many steps of analysis of things like
> > fMRI.  Be aware that even with proper dedrifting, any non-rigid volume
> > registration will hide differences in brain size (and shape if nonlinear)
> > across subjects, by design, so non-rigid volume-registered data won't
> ever
> > tell you the whole story of the anatomical features.  If you want to make
> > some anatomical measurement (distance, area, volume), then you should
> > generally measure it in each individual's own rigid/acpc space, not in
> any
> > kind of template space.
> >
> > Now, on to the explanation: the registration warpfields from each
> > subject's rigid acpc ("T1w") space to MNI nonlinear space provide the
> > information needed to compute a dedrifted template that matches the
> > population represented by the subjects.  Warpfields are displacement
> vector
> > fields from the output coordinate system to the input coordinate system
> > (because of how volume resampling works - the output needs to be a
> regular
> > grid, so you actually need to transform output coordinates backwards to
> the
> > original location).  So, we can take the vector fields for each subjects
> > that specify where the MNI-aligned features originally were in acpc
> space,
> > and average those locations for each voxel.  This is simply averaging the
> > warpfields that are used to resample volume data from T1w/acpc space to
> MNI
> > space.  Once you have this average, you can invert it (like any other
> > warpfield), and then concatenate it after the acpc to MNI warp for each
> > subject, giving you a new dedrifted (for the chosen population) template
> > space.
> >
> > Note, however, that this requires the acpc alignment to have worked well
> > (in the HCP pipelines, it is really a rigid registration to an MNI
> > template, not specifically using the ac and pc) - if there are any
> > non-matching rotations among the rigidly aligned volumes, they can result
> > in causing a shrinkage from the true average brain volume.  By carefully
> > finding the volume of brain masks in acpc space and after resampling to
> > this new dedrifted space, you can check for this effect (it will never be
> > an expansion).  However, the effect may not be isotropic, so actually
> > fixing the effect properly requires more thought.  However, if the acpc
> > alignments are generally close to being the correct orientation, this
> > effect should be small.
> >
> > Note, in particular, that coordinates in this new space will not match
> MNI
> > coordinates, probably not even at (0, 0, 0), you would need to put any
> > coordinates through that same average warpfield in order to go between
> MNI
> > and this new space.  You could also tweak the new space by adding a rigid
> > affine to the end, so you could line up (0, 0, 0) with MNI space, or
> > similar.
> >
> > Tim
> >
> >
> > On Mon, Jul 2, 2018 at 10:21 AM, Glasser, Matthew <[email protected]
> > <mailto:[email protected]>> wrote:
> > Tim Coalson can explain how to dedrift MNI space (which as Mike says is
> no
> > longer true MNI space).
> >
> > Peace,
> >
> > Matt.
> >
> > On 7/2/18, 10:10 AM, "[email protected]<mailto:hcp
> > [email protected]> on behalf of
> > Harms, Michael" <[email protected]<mailto:hcp
> > [email protected]> on behalf of
> > [email protected]<mailto:[email protected]>> wrote:
> >
> > >
> > >Hi,
> > >Re (1):
> > >If you want to work with streamlines in MNI space then you have to
> accept
> > >the "drift" (volume expansion) that is part of MNI space itself.
> > >
> > >Re (2):
> > >Maps may be resampled to surfaces in MNI space.  But all the FreeSurfer
> > >structural quantities that we provide in the database/spreadsheet in
> > >ConnectomeDB are measured in the subject's real (native) space.
> > >
> > >Cheers,
> > >-MH
> > >
> > >--
> > >Michael Harms, Ph.D.
> > >
> > >-----------------------------------------------------------
> > >
> > >Associate Professor of Psychiatry
> > >
> > >Washington University School of Medicine
> > >
> > >Department of Psychiatry, Box 8134
> <https://maps.google.com/?q=8134+660+South+Euclid+Ave&entry=gmail&source=g>
> > >
> > >660 South Euclid Ave
> <https://maps.google.com/?q=8134+660+South+Euclid+Ave&entry=gmail&source=g>.
> Tel: 314-747-6173
> > >
> > >St. Louis, MO  63110                          Email: [email protected]
> > <mailto:[email protected]>
> > >On 7/2/18, 7:14 AM, "[email protected]<mailto:hcp
> > [email protected]> on behalf of
> > >Claude Bajada" <[email protected]<mailto:hcp
> > [email protected]> on behalf of
> > >[email protected]<mailto:[email protected]>> wrote:
> > >
> > >Dear experts,
> > >
> > >I have a few questions:
> > >
> > >1) I am currently working on a project using tractography and the HCP
> > >data. I have used the HCP provided FNIRT based MNI registration in order
> > >to register individual streamlines from "native" or diffusion space (as
> > >per post HCP minimal processing pipeline) to MNI space. However, in
> > >Glasser 2016 supplementary text, it states that the MNI space is drifted
> > >relative to the mean brain size of individual brains (greatest along the
> > >x and z axes). I've been told that it is possible to "dedrift" these
> > >data and I wonder if anyone has experience in doing this and is able to
> > >point me in the right direction.
> > >
> > >2) from what I understand, structural qualities such as cortical
> > >thickness etc are measured in the individual's real space. However then,
> > >what I do not understand is the file structure of the HCP data. The
> > >structural measures such as cortical thickness, curvature and myelin
> > >maps etc live in the MNINonLinear/fsaverage_LR32k rather than in the
> > >'native space' directory. Can anyone shed light on this?
> > >
> > >Regards,
> > >
> > >Claude
> > >
> > >
> > >
> > >-----------------------------------------------------------
> > ---------------
> > >----------------------
> > >-----------------------------------------------------------
> > ---------------
> > >----------------------
> > >Forschungszentrum Juelich GmbH
> > >52425 Juelich
> > >Sitz der Gesellschaft: Juelich
> > >Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> > >Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> > >Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> > >Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> > >Prof. Dr. Sebastian M. Schmidt
> > >-----------------------------------------------------------
> > ---------------
> > >----------------------
> > >-----------------------------------------------------------
> > ---------------
> > >----------------------
> > >
> > >
> > >_______________________________________________
> > >HCP-Users mailing list
> > >[email protected]<mailto:[email protected]>
> > >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
> > >[email protected]<mailto:[email protected]>
> > >http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >
> >
> > _______________________________________________
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> > [email protected]<mailto:[email protected]>
> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >
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> ------------------------------
>
> Message: 5
> Date: Wed, 11 Jul 2018 21:56:39 +0000
> From: "Jayasekera, Dinal" <[email protected]>
> Subject: [HCP-Users] PreFreeSurferPipeline debugging
> To: "[email protected]" <[email protected]>
> Message-ID:
> <BN6PR02MB2209A9865D8309AD70FFCE4B915A0@BN6PR02MB2209.
> namprd02.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear all,
>
>
> I am a PhD student using the HCP Pipelines on a research project at WUSTL.
> I've been using the pipeline scripts on some of the lab's patient data. I
> have two problems that I haven't been able to solve. For both problems I
> have been calling the pipelines using the following command:
>
>
> "./PreFreeSurferPipelineBatch.sh --runlocal"
>
>
>   1.  The first problem came up when running the PreFreeSurferPipeline
> Batch script. The lab is running the script with a gradient Coeffs file.
> This error appeared when I was running the script
>
> [cid:1679b4c1-0305-4e5a-8729-be629ac738d7]
>
> I previously thought I hadn't correctly installed gradunwarp and I
> reinstalled it but the same problem came up. This IndexError does not
> appear when I don't reference a Coeffs file. Would the index error indicate
> that there's something wrong with the gradient coefficients file we are
> using?
>
> 2.  The second problem came up when I ran the same script without
> including a Gradient Coeffs file.
>
>  I decided to run the PreFreeSurferPipelineBatch script while setting the
> GradientDistortionCoeffs variable to "NONE" and this error appeared.
>
> [cid:30a7ad74-dd73-4d1b-84ac-c7274fbfa6ba]
>
> I was able to isolate this error to somewhere between lines 545 - 570 of
> the PreFreeSurferPipeline script:
>
> [cid:d2315a6d-2163-470a-94e7-6edbd18ea0da]
> Where do you think I'm going wrong?
>
>
> Kind regards,
> Dinal Jayasekera
> PhD Student in Biomedical Engineering
> Washington University in St. Louis
> B.S. in Biomedical Engineering | Minor in Biophysics and Electrical
> Engineering
> The George Washington University
>
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> _______________________________________________
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>
>
> End of HCP-Users Digest, Vol 68, Issue 11
> *****************************************
>
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