Please help me through answering my question. Thank you!
Best,
Dongjun (DJ) Rew, PhD candidate in Marketing
Robert C. Vackar College of Business & Entrepreneurship
The University of Texas Rio Grande Valley
Email: dongjun.re...@utrgv.edu, Phone: 956.665.2590
-----Original Message-----
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Today's Topics:
1. Re: Blank p-value maps after running PALM on CIFTI files
(Gail Rosenbaum)
2. Data (shalo...@gmail.com)
3. vertex ordering with wb_command -cifti-convert -to-nifti (or
-to-text) and gifti (Jo Etzel)
4. Re: vertex ordering with wb_command -cifti-convert -to-nifti
(or -to-text) and gifti (Timothy Coalson)
5. Re: Blank p-value maps after running PALM on CIFTI files
(Harms, Michael)
6. Re: A few specific questions about the HCP data | MNI space
dedrifting & file structure (Claude Bajada)
7. Re: list of significant parcels (Aaron R)
----------------------------------------------------------------------
Message: 1
Date: Mon, 2 Jul 2018 17:41:44 -0400
From: Gail Rosenbaum <gailrosenb...@nyu.edu>
Subject: Re: [HCP-Users] Blank p-value maps after running PALM on
CIFTI files
To: Timothy Coalson <tsc...@mst.edu>
Cc: hcp-users <hcp-users@humanconnectome.org>
Message-ID:
<caakjpk2w0r8d+aohu8zv3uul4bjv+nmfffwu58ydz3jmpng...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Tim,
Thanks for the clarification.
Here are the calls to palm for the separated subcortical and cortical
files:
palm -i data_sub.nii -d ${StudyFolder}Level3/L3Setup.mat -t
${StudyFolder}Level3/L3Setup.con -o mbmfResults${contrast}_vol -T -logp
palm -i data_L.func.gii -d ${StudyFolder}Level3/L3Setup.mat -t
${StudyFolder}Level3/L3Setup.con -o mbmfResults${contrast}_SurfL -T -tfce2D
-s ${StudyFolder}Level3/mbmfGroup_L.midthick.surf.gii
${StudyFolder}Level3/L_area.func.gii -logp
palm -i data_R.func.gii -d ${StudyFolder}Level3/L3Setup.mat -t
${StudyFolder}Level3/L3Setup.con -o mbmfResults${contrast}_SurfR -T -tfce2D
-s ${StudyFolder}Level3/mbmfGroup_R.midthick.surf.gii
${StudyFolder}Level3/R_area.func.gii -logp
For this analysis, I am simply trying to take the mean of the activation to
see if any clusters are significantly greater than baseline. The design
matrix (L3Setup.mat) is a 36x1 matrix (there are 36 subjects in my current
analysis) and the t- L3Setup.con is just a 1. Maybe I set this up
incorrectly?
Thanks,
Gail
On Mon, Jul 2, 2018 at 5:27 PM, Timothy Coalson <tsc...@mst.edu> wrote:
> As you have found, the outputs from PALM contain only 0s, therefore
> using a different wb_command operation to convert them will not help
> with your current issue.
>
> If you can post the PALM call you used, it might help others who know
> PALM figure out what your problem might be.
>
> Tim
>
>
> On Mon, Jul 2, 2018 at 4:12 PM, Gail Rosenbaum <gailrosenb...@nyu.edu>
> wrote:
>
>> Hi Tim,
>>
>> Thank you for your quick reply.
>>
>> I renamed the maps and confirmed that there are no values in the maps
>> (I pasted the output of wb_command -file-information for the left
>> hemisphere output below in case that is useful).
>>
>> Regarding -cifti-create-dense-from-template: I used this command in
>> the first iteration of my analyses and had the same issue. I switched
>> to -cifti-create-dense-scalar to see if it would work (and because
>> this is the suggested command and usage in the "HCP Practical 11: Task
fMRI Analyses"
>> pdf) and again did not have any luck. That being said, I'm new to
>> CIFTI files so I appreciate the usage suggestions, and I will try
>> -cifti-create-dense-scalar and specify ROIs, but I am not sure this
>> will help this issue because using a full template produced the same
issue.
>>
>> Thanks,
>> Gail
>>
>> Output of wb_command -file-information:
>>
>> Name: mbmfResultsAllRPE3_SurfL_dpv_t
>> stat_uncp.func.gii
>> Type: Metric
>> Structure: CortexLeft
>> Data Size: 129.97 Kilobytes
>> Maps to Surface: true
>> Maps to Volume: false
>> Maps with LabelTable: false
>> Maps with Palette: true
>> All Map Palettes Equal: true
>> Map Interval Units: NIFTI_UNITS_UNKNOWN
>> Number of Maps: 1
>>
>> Number of Vertices: 32492
>> Map Minimum Maximum Mean Sample Dev % Positive % Negative
>> Inf/NaN Map Name
>> 1 0.000 0.000 0.000 0.000 0.000 0.000
>> 0 #1
>>
>> On Mon, Jul 2, 2018 at 4:45 PM, Timothy Coalson <tsc...@mst.edu> wrote:
>>
>>> Please name your tstat and p-value outputs ending in .func.gii, not
>>> simply .gii . This will allow you to open them in wb_view directly,
>>> allowing you to do sanity checks with fewer intervening steps.
>>> However, from what you have said, I am fairly certain they are
>>> entirely 0s (you can use wb_command -file-information to check the
>>> range of the maps, and any non-numeric values, once you have named your
outputs ending in .func.gii).
>>> I am not sure how to check whether PALM was called with meaningful
>>> inputs that would be expected to give significant results.
>>>
>>> On a side note, by using -cifti-create-dense-scalar without
>>> specifying ROIs for right and left cortex, you have generated CIFTI
>>> files that include the medial wall, and do not match the 91k
>>> grayordinates of HCP data. I am guessing that your subcortical
>>> labels are in fact the same as the HCP 91k grayordinate subcortical
>>> labels, so I suggest you use -cifti-create-dense-from-template,
>>> which makes it easier to match an existing specification of
grayordinates.
>>>
>>> Tim
>>>
>>>
>>>
>>> On Mon, Jul 2, 2018 at 3:17 PM, Gail Rosenbaum
>>> <gailrosenb...@nyu.edu>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> I am trying to run PALM with TFCE on dense timeseries CIFTI files
>>>> created through an HCP-style protocol, and preprocessed using the
>>>> HCP pipeline (version 3.22). I am running these analyses on an HPC
>>>> using SLURM.
>>>>
>>>> It seems that I successfully ran PALM (there were no warnings or
>>>> errors). When I use -cifti-create-dense-scalar to merge the
>>>> subcortical and cortical output files, my t-statistic maps look
>>>> fine in wb_view. However, when I use the same code to merge the
>>>> fwep and uncp maps and open them in wb_view, they appear to be
>>>> completely empty (and the range of values when I turn on the color
>>>> bar is just 0). I have tried using workbench versions
>>>> 1.2.3 and 1.3.0.
>>>>
>>>> For reference, here is the command that I used to successfully
>>>> merge the t-stat files:
>>>>
>>>> wb_command -cifti-create-dense-scalar
>>>> mbmfGroup${contrast}_results_merged_tfce_tstat.dscalar.nii
>>>> -volume mbmfResults${contrast}_vol_tfce_tstat.nii
>>>> data_sub_label.nii -left-metric
>>>> mbmfResults${contrast}_SurfL_tfce_tstat.gii -right-metric
>>>> mbmfResults${contrast}_SurfR_tfce_tstat.gii
>>>>
>>>> And here is the command I used for the (seemingly) unsuccessful
>>>> p-value
>>>> maps:
>>>>
>>>> wb_command -cifti-create-dense-scalar
>>>> mbmfGroup${contrast}_results_m erged_tfce_tstat_fwep.dscalar.nii
>>>> -volume mbmfResults${contrast}_vol_tfce_tstat_fwep.nii
>>>> data_sub_label.nii -left-metric
>>>> mbmfResults${contrast}_SurfL_tfce_tstat_fwep.gii
>>>> -right-metric mbmfResults${contrast}_SurfR_tfce_tstat_fwep.gii
>>>>
>>>> My first thought was that there were no significant results, but
>>>> since the t-maps seem reasonable and even the uncorrected p-maps
>>>> are empty (presumably if nothing were signifiant, these uncorrected
>>>> p-values would not 0), I think something must have gone wrong.
>>>>
>>>> Any insights into what might be going on would be appreciated!
>>>> Thank you!
>>>>
>>>> Gail Rosenbaum
>>>>
>>>> --
>>>> Gail Rosenbaum, PhD
>>>> Postdoctoral Fellow | Hartley Lab
>>>> New York University
>>>>
>>>> _______________________________________________
>>>> HCP-Users mailing list
>>>> HCP-Users@humanconnectome.org
>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>
>>>
>>>
>>
>>
>> --
>> Gail Rosenbaum, PhD
>> Postdoctoral Fellow | Hartley Lab
>> New York University
>>
>
>
--
Gail Rosenbaum, PhD
Postdoctoral Fellow | Hartley Lab
New York University
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Message: 2
Date: Mon, 02 Jul 2018 16:52:54 -0500
From: "shalo...@gmail.com" <shalo...@gmail.com>
Subject: [HCP-Users] Data
To: hcp-users@humanconnectome.org
Message-ID: <af7p30gu5pv2o58sbc8n7oop.1530567612...@email.lge.com>
Content-Type: text/plain; charset="utf-8"
Dear experts,?
I have a question about MNI coordinates.?I am trying to find/make sets of
MNI coordinates for my consumer research. However it is difficult for me to
dig into the coordinates of all behaviors for each subject from HCP
images.?So is there any way or suggestion for me to get a set of data of the
MNI cooridnates? Or is there any way to obtain the set of the data from the
software, wb_view??It would be greatly appreciated that you can provide me
the set of MNI coordinates data in a certain type of file such as MS excel
or even text file.?Thank you for your help in advance.??
Best,
Dongjun Rew, MS in Stat, MBA, PhD candidate in MarketingRobert C. Vackar
College of Business & EntrepreneurshipThe University of Texas Rio Grande
ValleyEmail: dongjun.rew01@utrgv.eduOffice: 956.665.2590
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Message: 3
Date: Mon, 2 Jul 2018 17:27:33 -0500
From: Jo Etzel <jet...@wustl.edu>
Subject: [HCP-Users] vertex ordering with wb_command -cifti-convert
-to-nifti (or -to-text) and gifti
To: hcp-users@humanconnectome.org
Message-ID: <1f115dbd-5d1e-d5e5-37ea-e31dc27f0...@wustl.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
Is there a way to determine (or specify) the correspondence between the
vertices when a cifti is converted to a "fake nifti" vs. separated to
giftis?
For example, wb_command -cifti-separate Parcels_LR.dtseries.nii COLUMN
-metric CORTEX_LEFT out.func.gii produces a gifti with 32492 vertices, the
first 10 of which have the values 1 2 3 4 5 6 7 0 8 9.
Converting the same cifti via wb_command -cifti-convert -to-nifti
Parcels_LR.dtseries.nii out.nii.gz -smaller-file gives a file of dimension
29706, 2, 1, 1. 29706*2 = 59412, which is also the number of rows in the
text file that is given by wb_command -cifti-convert -to-text
Parcels_LR.dtseries.nii out.txt. The first 10 values of these files is 1 2
3 4 5 6 7 8 9 10, different than the gifti.
My guess is that the -cifti-convert output has fewer vertices than the
-cifti-separate output because the medial wall is omitted. But is there a
fixed ordering to how the 29706 cifti vertices fit into the 32492 gifti
vertices? (Rephrased, is it something like the vertex in row
17,234 of the -cifti-convert -to-text file is always assigned to slot
10,222 of the -cifti-separate gifti file?) If the reassignment is fixed, is
it available somewhere?
thanks,
Jo
--
Joset A. Etzel, Ph.D.
Staff Scientist
Cognitive Control & Psychopathology Lab
Washington University in St. Louis
mvpa.blogspot.com
------------------------------
Message: 4
Date: Mon, 2 Jul 2018 18:21:07 -0500
From: Timothy Coalson <tsc...@mst.edu>
Subject: Re: [HCP-Users] vertex ordering with wb_command
-cifti-convert -to-nifti (or -to-text) and gifti
To: Jo Etzel <jet...@wustl.edu>
Cc: hcp-users <hcp-users@humanconnectome.org>
Message-ID:
<CAK_=tazs6arGCtNJ0g7F5+Fpxa7aZK289_-Vt=gyozbhdrn...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
-cifti-separate and -cifti-convert have very different purposes.
-cifti-separate is there to make usable volume and metric files from the
information in cifti files. -cifti-convert is there only to get data
values into other tools that can't read cifti, without any respect for
spatial information. Thus, -cifti-separate has to add in all the excluded
voxels and vertices to its outputs, while -cifti-convert does not (however,
-cifti-convert -to-nifti does have to work around the 32,767 limit on
nifti-1 dimensions, which makes things interesting).
The current commands and the 91k grayordinates space always have the
vertices in ascending order. The 0 in your example is just a placeholder
for missing data (medial wall), not a change in order. It is possible to
make a cifti file with arbitrary order of vertices within a hemisphere (you
can't interleave across hemispheres or structures in general), but
wb_command doesn't have a way to make such a file from scratch (it will
accept such files, if anyone makes them, but it strikes me as undesirable,
to the point of thinking maybe the specification should have dictated the
order).
The -cifti-export-dense-mapping command will give you the index translation
information for any dense cifti file. We may have released some cifti
files that did not exclude the medial wall, and we have released some that
have only surface data, and no volume data (~59k indices). All standard
91k grayordinate cifti files have the same index mapping (which is the
definition of what makes them standard).
Tim
On Mon, Jul 2, 2018 at 5:27 PM, Jo Etzel <jet...@wustl.edu> wrote:
> Is there a way to determine (or specify) the correspondence between the
> vertices when a cifti is converted to a "fake nifti" vs. separated to
> giftis?
>
> For example, wb_command -cifti-separate Parcels_LR.dtseries.nii COLUMN
> -metric CORTEX_LEFT out.func.gii produces a gifti with 32492 vertices,
> the first 10 of which have the values 1 2 3 4 5 6 7 0 8 9.
>
> Converting the same cifti via wb_command -cifti-convert -to-nifti
> Parcels_LR.dtseries.nii out.nii.gz -smaller-file gives a file of
> dimension 29706, 2, 1, 1. 29706*2 = 59412, which is also the number of
> rows in the text file that is given by wb_command -cifti-convert
> -to-text Parcels_LR.dtseries.nii out.txt. The first 10 values of these
> files is 1 2 3 4 5 6 7 8 9 10, different than the gifti.
>
> My guess is that the -cifti-convert output has fewer vertices than the
> -cifti-separate output because the medial wall is omitted. But is there
> a fixed ordering to how the 29706 cifti vertices fit into the 32492
> gifti vertices? (Rephrased, is it something like the vertex in row
> 17,234 of the -cifti-convert -to-text file is always assigned to slot
> 10,222 of the -cifti-separate gifti file?) If the reassignment is fixed,
> is it available somewhere?
>
> thanks,
> Jo
>
>
>
> --
> Joset A. Etzel, Ph.D.
> Staff Scientist
> Cognitive Control & Psychopathology Lab
> Washington University in St. Louis
> mvpa.blogspot.com
> _______________________________________________
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
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Message: 5
Date: Tue, 3 Jul 2018 02:05:15 +0000
From: "Harms, Michael" <mha...@wustl.edu>
Subject: Re: [HCP-Users] Blank p-value maps after running PALM on
CIFTI files
To: Gail Rosenbaum <gailrosenb...@nyu.edu>, NEUROSCIENCE tim
<tsc...@mst.edu>
Cc: hcp-users <hcp-users@humanconnectome.org>
Message-ID: <2adf1448-f003-461c-b160-0e6ace462...@wustl.edu>
Content-Type: text/plain; charset="utf-8"
Hi,
If you are just testing the mean activation, then you need to use the -ise
option to allow sign flipping. Otherwise, by default, PALM does
permutations, but permutations of your model will always generate the exact
same mean, which explains your results.
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: <hcp-users-boun...@humanconnectome.org> on behalf of Gail Rosenbaum
<gailrosenb...@nyu.edu>
Date: Monday, July 2, 2018 at 4:42 PM
To: NEUROSCIENCE tim <tsc...@mst.edu>
Cc: hcp-users <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Blank p-value maps after running PALM on CIFTI
files
Hi Tim,
Thanks for the clarification.
Here are the calls to palm for the separated subcortical and cortical
files:
palm -i data_sub.nii -d ${StudyFolder}Level3/L3Setup.mat -t
${StudyFolder}Level3/L3Setup.con -o mbmfResults${contrast}_vol -T -logp
palm -i data_L.func.gii -d ${StudyFolder}Level3/L3Setup.mat -t
${StudyFolder}Level3/L3Setup.con -o mbmfResults${contrast}_SurfL -T -tfce2D
-s ${StudyFolder}Level3/mbmfGroup_L.midthick.surf.gii
${StudyFolder}Level3/L_area.func.gii -logp
palm -i data_R.func.gii -d ${StudyFolder}Level3/L3Setup.mat -t
${StudyFolder}Level3/L3Setup.con -o mbmfResults${contrast}_SurfR -T -tfce2D
-s ${StudyFolder}Level3/mbmfGroup_R.midthick.surf.gii
${StudyFolder}Level3/R_area.func.gii -logp
For this analysis, I am simply trying to take the mean of the activation to
see if any clusters are significantly greater than baseline. The design
matrix (L3Setup.mat) is a 36x1 matrix (there are 36 subjects in my current
analysis) and the t- L3Setup.con is just a 1. Maybe I set this up
incorrectly?
Thanks,
Gail
On Mon, Jul 2, 2018 at 5:27 PM, Timothy Coalson
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:
As you have found, the outputs from PALM contain only 0s, therefore using a
different wb_command operation to convert them will not help with your
current issue.
If you can post the PALM call you used, it might help others who know PALM
figure out what your problem might be.
Tim
On Mon, Jul 2, 2018 at 4:12 PM, Gail Rosenbaum
<gailrosenb...@nyu.edu<mailto:gailrosenb...@nyu.edu>> wrote:
Hi Tim,
Thank you for your quick reply.
I renamed the maps and confirmed that there are no values in the maps (I
pasted the output of wb_command -file-information for the left hemisphere
output below in case that is useful).
Regarding -cifti-create-dense-from-template: I used this command in the
first iteration of my analyses and had the same issue. I switched to
-cifti-create-dense-scalar to see if it would work (and because this is the
suggested command and usage in the "HCP Practical 11: Task fMRI Analyses"
pdf) and again did not have any luck. That being said, I'm new to CIFTI
files so I appreciate the usage suggestions, and I will try
-cifti-create-dense-scalar and specify ROIs, but I am not sure this will
help this issue because using a full template produced the same issue.
Thanks,
Gail
Output of wb_command -file-information:
Name: mbmfResultsAllRPE3_SurfL_dpv_tstat_uncp.func.gii
Type: Metric
Structure: CortexLeft
Data Size: 129.97 Kilobytes
Maps to Surface: true
Maps to Volume: false
Maps with LabelTable: false
Maps with Palette: true
All Map Palettes Equal: true
Map Interval Units: NIFTI_UNITS_UNKNOWN
Number of Maps: 1
Number of Vertices: 32492
Map Minimum Maximum Mean Sample Dev % Positive % Negative
Inf/NaN Map Name
1 0.000 0.000 0.000 0.000 0.000 0.000
0 #1
On Mon, Jul 2, 2018 at 4:45 PM, Timothy Coalson
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:
Please name your tstat and p-value outputs ending in .func.gii, not simply
.gii . This will allow you to open them in wb_view directly, allowing you
to do sanity checks with fewer intervening steps. However, from what you
have said, I am fairly certain they are entirely 0s (you can use wb_command
-file-information to check the range of the maps, and any non-numeric
values, once you have named your outputs ending in .func.gii). I am not
sure how to check whether PALM was called with meaningful inputs that would
be expected to give significant results.
On a side note, by using -cifti-create-dense-scalar without specifying ROIs
for right and left cortex, you have generated CIFTI files that include the
medial wall, and do not match the 91k grayordinates of HCP data. I am
guessing that your subcortical labels are in fact the same as the HCP 91k
grayordinate subcortical labels, so I suggest you use
-cifti-create-dense-from-template, which makes it easier to match an
existing specification of grayordinates.
Tim
On Mon, Jul 2, 2018 at 3:17 PM, Gail Rosenbaum
<gailrosenb...@nyu.edu<mailto:gailrosenb...@nyu.edu>> wrote:
Hi,
I am trying to run PALM with TFCE on dense timeseries CIFTI files created
through an HCP-style protocol, and preprocessed using the HCP pipeline
(version 3.22). I am running these analyses on an HPC using SLURM.
It seems that I successfully ran PALM (there were no warnings or errors).
When I use -cifti-create-dense-scalar to merge the subcortical and cortical
output files, my t-statistic maps look fine in wb_view. However, when I use
the same code to merge the fwep and uncp maps and open them in wb_view, they
appear to be completely empty (and the range of values when I turn on the
color bar is just 0). I have tried using workbench versions 1.2.3 and 1.3.0.
For reference, here is the command that I used to successfully merge the
t-stat files:
wb_command -cifti-create-dense-scalar
mbmfGroup${contrast}_results_merged_tfce_tstat.dscalar.nii -volume
mbmfResults${contrast}_vol_tfce_tstat.nii data_sub_label.nii -left-metric
mbmfResults${contrast}_SurfL_tfce_tstat.gii -right-metric
mbmfResults${contrast}_SurfR_tfce_tstat.gii
And here is the command I used for the (seemingly) unsuccessful p-value
maps:
wb_command -cifti-create-dense-scalar
mbmfGroup${contrast}_results_merged_tfce_tstat_fwep.dscalar.nii -volume
mbmfResults${contrast}_vol_tfce_tstat_fwep.nii data_sub_label.nii
-left-metric mbmfResults${contrast}_SurfL_tfce_tstat_fwep.gii -right-metric
mbmfResults${contrast}_SurfR_tfce_tstat_fwep.gii
My first thought was that there were no significant results, but since the
t-maps seem reasonable and even the uncorrected p-maps are empty (presumably
if nothing were signifiant, these uncorrected p-values would not 0), I think
something must have gone wrong.
Any insights into what might be going on would be appreciated! Thank you!
Gail Rosenbaum
--
Gail Rosenbaum, PhD
Postdoctoral Fellow | Hartley Lab
New York University
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
--
Gail Rosenbaum, PhD
Postdoctoral Fellow | Hartley Lab
New York University
--
Gail Rosenbaum, PhD
Postdoctoral Fellow | Hartley Lab
New York University
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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Message: 6
Date: Tue, 3 Jul 2018 09:35:04 +0200
From: Claude Bajada <c.baj...@fz-juelich.de>
Subject: Re: [HCP-Users] A few specific questions about the HCP data |
MNI space dedrifting & file structure
To: Timothy Coalson <tsc...@mst.edu>
Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Message-ID: <e4d64c78-b62a-d87c-75c1-4df60a6bd...@fz-juelich.de>
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Hi Tim,
Thank you very much for your detailed explanation
Regards,
Claude
On it-Tnejn, 02 ta Lul, 2018 07:35 , Timothy Coalson wrote:
On Mon, Jul 2, 2018 at 7:13 AM, Claude Bajada
<c.baj...@fz-juelich.de<mailto:c.baj...@fz-juelich.de>> wrote:
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?
It was perhaps not the best choice to put these measures inside the
MNINonLinear folder, but for compatibility, that is where they will remain
for now. They were computed in "T1w" space ("native volume space", not to
be confused with "native mesh", which is an unrelated distinction).
However, the myelin measure is based on a combination of imaging contrasts,
and is not sensitive to changes in brain size, so it doesn't quite fit in
the same class as curvature and thickness, which are measures of the
cortical coordinates themselves.
Tim
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Message: 7
Date: Tue, 3 Jul 2018 13:03:21 +0200
From: Aaron R <aaro...@gmail.com>
Subject: Re: [HCP-Users] list of significant parcels
To: Timothy Coalson <tsc...@mst.edu>
Cc: hcp-users <hcp-users@humanconnectome.org>
Message-ID:
<CAE1F8+bWcbumj0ha3bjavyGfvOZF+PVZ=nswgjpa0wfg54l...@mail.gmail.com>
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Ah yes, of course. Thank you for the replies.
Aaron
On Thu, Jun 28, 2018 at 9:45 AM, Timothy Coalson <tsc...@mst.edu> wrote:
> You can export the data from the parcellated cifti file with wb_command
> -cifti-convert -to-text, but that doesn't contain the parcel names. The
> -file-information command will tell you the parcel names, in the order
they
> are in the file, giving you the missing piece.
>
> Tim
>
>
> On Thu, Jun 28, 2018, 8:37 AM Aaron R <aaro...@gmail.com> wrote:
>
>> Hi Matt,
>>
>> Thanks for the reply, but unfortunately wb_command -file-information
>> doesn't help. It shows all of the parcels of the original parcellation.
>> Presumably they're all still there, but some now have a zero value after
>> thresholding.
>>
>> Thanks,
>> Aaron
>>
>>
>> On Wed, Jun 27, 2018 at 11:56 PM, Glasser, Matthew <glass...@wustl.edu>
>> wrote:
>>
>>> wb_command -file-information might be able to help with this.
>>>
>>> Matt.
>>>
>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Aaron R <
>>> aaro...@gmail.com>
>>> Date: Wednesday, June 27, 2018 at 8:19 AM
>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: [HCP-Users] list of significant parcels
>>>
>>> Dear HCP users,
>>>
>>> I would like to know which parcels survived thresholding (using
>>> wb_command -cifti-math on ptseries) - just a list of parcel names, e.g.
>>> L_p10p_ROI, L_p47r_ROI, L_TGv_ROI, AMYGDALA_LEFT, etc.
>>>
>>> I've converting to ROI, cifti-reduce, cifti-restrict-dense-map, etc. No
>>> luck. Is there any way to do this, besides clicking on everything in the
>>> GUI?
>>>
>>> Thanks,
>>> Aaron
>>>
>>>
>>>
>>> _______________________________________________
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>
>> _______________________________________________
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
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