Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

[Dierker, Donna]

Check not only your standard output file, but also your standard error.
Do either indicate whether it is finding matlab/octave?


> On Nov 2, 2018, at 3:02 PM, Jayasekera, Dinal  
> wrote:
>
> Dear Michael and Matt,
>
> I reconfigured R, updated sICA+FIX and FSL but I still continue to get the 
> previous error:
>
> No valid labelling file specified
> Could not find a supported file with prefix 
> "rfMRI_REST1_AP_hp2000.ica/filtered_func_data_clean"
> Could not find a supported file with prefix 
> "rfMRI_REST1_AP_hp2000.ica/filtered_func_data_clean_vn"
>
>
> Do you have any other suggestions?
>
>
> Kind regards,
> Dinal Jayasekera
>
> PhD Candidate | InSITE Fellow
> Ammar Hawasli Lab
> Department of Biomedical Engineering | Washington University in St. Louis
>
> From: Jayasekera, Dinal
> Sent: Thursday, November 1, 2018 8:35:28 PM
> To: Glasser, Matthew; Harms, Michael; hcp-users@humanconnectome.org
> Cc: NEUROSCIENCE tim
> Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
>
> Oh yes definitely not. I also upgraded my R packages.
>
>
> Kind regards,
> Dinal Jayasekera
>
> PhD Candidate | InSITE Fellow
> Ammar Hawasli Lab
> Department of Biomedical Engineering | Washington University in St. Louis
>
> From: Glasser, Matthew
> Sent: Thursday, November 1, 2018 8:33:58 PM
> To: Jayasekera, Dinal; Harms, Michael; hcp-users@humanconnectome.org
> Cc: NEUROSCIENCE tim
> Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
>
> That doesn’t discount Mike’s advice on needing to sort out R packages.
>
> Matt.
>
> From: "Jayasekera, Dinal" 
> Date: Thursday, November 1, 2018 at 8:32 PM
> To: Matt Glasser , "Harms, Michael" , 
> "hcp-users@humanconnectome.org" 
> Cc: Timothy Coalson 
> Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
>
> Matt,
>
> I will update my version of sICA+FIX as well and upgrade to FSL 6.0 and let 
> you know how things change.
>
>
> Kind regards,
> Dinal Jayasekera
>
> PhD Candidate | InSITE Fellow
> Ammar Hawasli Lab
> Department of Biomedical Engineering | Washington University in St. Louis
>
> From: Glasser, Matthew
> Sent: Thursday, November 1, 2018 6:56:26 PM
> To: Harms, Michael; Jayasekera, Dinal; hcp-users@humanconnectome.org
> Cc: NEUROSCIENCE tim
> Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
>
> Hi Dinal,
>
> Also make sure you have the absolutely latest version of sICA+FIX, as there 
> were recent changes and upgrade to FSL 6.0.  Finally, we are testing some 
> updates to hcp_multi_run_fix that you will need to be using for your project, 
> and we can let you know when that is available.  For your project you will be 
> cleaning all of the fMRI runs at the same time with multi-run fix.
>
> Matt.
>
> From:  on behalf of "Harms, Michael" 
> 
> Date: Thursday, November 1, 2018 at 4:18 PM
> To: "Jayasekera, Dinal" , 
> "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
>
>
> Hi,
> Have you configured your R installation correctly, per the FSL FIX Wiki page?
>
> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide
>
> 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 "Jayasekera, 
> Dinal" 
> Date: Thursday, November 1, 2018 at 4:10 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
>
> Dear HCP community,
>
> I am currently running the IcaFixProcessingBatch script on the data 
> processing using the minimal functional pipelines. However, for each of my 
> resting state conditions, I get the following error:
>
> /home/Desktop/Applications/fix1.066/fix: 252: 
> /home/Desktop/Applications/fix1.066/fix: R: not found
> No valid labelling file specified
> Could not find a supported file with prefix 
> "rfMRI_REST1_AP_hp2000.ica/filtered_func_data_clean"
>
> Has anyone had any experience with a similar issue? Is this error indicative 
> of a missing step from before?
>
> Kind regards,
> Dinal Jayasekera
>
> PhD Candidate | InSITE Fellow
> Ammar Hawasli Lab
> Department of Biomedical Engineering | Washington University in St. Louis
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>
>
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Re: [HCP-Users] drawing borders

[Dierker, Donna]

I had an issue with baby brains where the sphere had too small a diameter.

This caused an issue where ID nodes were displaying with a sphere larger than 
the surface.

This is probably not your issue -- sorry.



From: Gaurav Patel  on behalf of Gaurav Patel 

Sent: Tuesday, October 9, 2018 11:50 AM
To: Dierker, Donna
Cc: Gaurav Patel; hcp-users@humanconnectome.org Users
Subject: Re: [HCP-Users] drawing borders

In the borders menu?  Changing that changes the size of the final border, but 
not the border as I draw it

_
 gaurav patel
 gauravpa...@gmail.com<mailto:gauravpa...@gmail.com>
 pateldsclab.net<http://pateldsclab.net>

On Oct 9, 2018, at 12:42 PM, Dierker, Donna 
mailto:do...@wustl.edu>> wrote:


Check the diameter of your sphere, Gaurav.



From: 
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Gaurav Patel mailto:gauravpa...@gmail.com>>
Sent: Tuesday, October 9, 2018 11:37 AM
To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Users
Subject: [HCP-Users] drawing borders

Hi—when I am drawing borders in wb_view 1.31, the diameters of the red spheres 
is huge, making is difficult to see what I am drawing.  This was not the case 
in 1.23.  Is there a way to change that setting?  Finishing the border reduces 
the size of the spheres to the setting in the borders menu, so that setting 
doesn’t make a difference.  Thanks

 gaurav patel
 gauravpa...@gmail.com<mailto:gauravpa...@gmail.com>
 pateldsclab.net<http://pateldsclab.net>


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Re: [HCP-Users] drawing borders

[Dierker, Donna]

Check the diameter of your sphere, Gaurav.



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Gaurav Patel 

Sent: Tuesday, October 9, 2018 11:37 AM
To: hcp-users@humanconnectome.org Users
Subject: [HCP-Users] drawing borders

Hi—when I am drawing borders in wb_view 1.31, the diameters of the red spheres 
is huge, making is difficult to see what I am drawing.  This was not the case 
in 1.23.  Is there a way to change that setting?  Finishing the border reduces 
the size of the spheres to the setting in the borders menu, so that setting 
doesn’t make a difference.  Thanks

 gaurav patel
 gauravpa...@gmail.com
 pateldsclab.net


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Re: [HCP-Users] map names | wb_command

[Dierker, Donna]

See this page:

https://www.humanconnectome.org/software/workbench-command/-all-commands-help

   wb_command -set-map-names
   - the file to set the map names of

  [-name-file] - use a text file to replace all map names
  - text file containing map names, one per line

  [-map] - repeatable - specify a map to set the name of
  - the map index to change the name of
  - the name to set for the map

  Sets the name of one or more maps for metric, shape, label, volume, cifti
  scalar or cifti label files.  If the -name-file option is not specified,
  the -map option must be specified at least once.  The -map option cannot
  be used when -name-file is specified.


> On Nov 15, 2017, at 8:33 AM, Claude Bajada  wrote:
>
> Dear all,
>
> What is the wb_command syntax to label map names?
>
> 
>
> 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
> 
> 
>
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> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>



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Re: [HCP-Users] Cerebellum surface

[Dierker, Donna]

Maybe also have a look at Joern Diedrichsen’s page:

http://www.diedrichsenlab.org/imaging/propatlas.htm



> On Sep 19, 2017, at 9:42 AM, Glasser, Matthew  wrote:
>
> This is built into the CIFTI format for the future, however we do not yet 
> have an algorithm for making individual subject cerebellar surfaces.  I 
> believe a “Colin” individual surface is available somewhere and perhaps David 
> knows the details.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Avital Hahamy 
> 
> Reply-To: "avitalhah...@gmail.com" 
> Date: Tuesday, September 19, 2017 at 2:37 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Cerebellum surface
>
> Dear experts,
>
> I was wondering whether workbench enables projecting cerebellum group data 
> onto an available surface, and if so, where I could find the relevant surface?
>
> Kind regards,
> Avital
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Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

[Dierker, Donna]

Many of the HCP experts are at OHBM, so replies might take longer.

I know from my own experience with HCP output to look here for the Freesurfer 
subject directories:

subject-id/T1w/subject-id/label/*
subject-id/T1w/subject-id/mri/*
subject-id/T1w/subject-id/surf/*
…

Also see page 21 here:

http://humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Appendix_III.pdf

Hopefully there is no problem! :)

But I must point out that there is a difference between the Freesurfer v5.3 
distribution and Freesurfer 5.3-HCP.
The latter uses both T1w & T2w images, which makes a big difference (e.g., for 
myelin maps).
Not sure which you used, but it is an important difference.


> On Jun 26, 2017, at 12:27 PM, Mandelli, Maria Luisa 
>  wrote:
>
> Hi!
> I m running the structural HCP pipeline and I m using Freesurfer v5.3
> It seems that the job finished without errors but I dont see the files in the 
> T1w folder of the subject.
> For example the wmparc_1mm files
> I m not sure where is the problem!
> Thank you
>
>
> Maria Luisa Mandelli, PhD
> Assistant Professional Researcher
>
> University of California, San Francisco
> 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
>
> Language Neurobiology Lab
> http://albalab.ucsf.edu/
> Memory and Aging Center
> http://memory.ucsf.edu/
> UCSF Dyslexia Center
> http://dyslexia.ucsf.edu/
>
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Re: [HCP-Users] Position of vertices in myelin maps and 164k sphere

[Dierker, Donna]

Nicola,

It is possible to generate a grid on a spherical surface like Alex Cohen did in 
this paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705206/

… and then fold those coordinates back up into midthickness configuration.

The 164k_fs_LR vertex-wise correspondence is as good as can be expected, given 
anatomical variability across subjects.
Just having trouble understanding how you are using x,y,z coords with the 
myelin scalars.

Donna


> On Mar 29, 2017, at 12:22 PM, Timothy Coalson  wrote:
>
> If by 2D images you mean pixel-based (like .png), then the spatial 
> relationships can't be preserved very well.  In order to make flatmaps with 
> moderate distortion, we have to add cuts to the cortical surface, which 
> leaves connected parts of cortex separated by many blank pixels.  Our flat 
> surfaces are intended for visualization, and we do not use them for 
> processing.
>
> I would suggest doing as much of the spatial processing as you can with 
> wb_command - we have smoothing, gradient, dilation, and a few other things - 
> if you want it identical across subjects, rather than based on the cortical 
> distances in each subject, you can use a group average surface along with the 
> corresponding vertex area metric files - this is because group average 
> surfaces have much less folding than individual subjects, and as such, 
> geodesic distances along the cortical surfaces are much shorter than they 
> should be.
>
> As your earlier emails implied use of matlab, you should note that you can 
> load the gifti surface files into matlab, which contain vertex neighbor 
> information, by using the gifti toolbox 
> (https://www.artefact.tk/software/matlab/gifti/).  The easiest way to get 
> vertex correspondence to the data in matlab is currently to use wb_command 
> -cifti-separate to convert the surface data to gifti metric (.func.gii) 
> files, and then load them instead.
>
> Tim
>
>
> On Wed, Mar 29, 2017 at 9:24 AM, Nicola Toschi  wrote:
> Hi,
>
> I'd like to arrive at a set of 2D images (e.g. 'unraveled' myelin maps 
> obtained by cutting and stretching out the sphere), with anatomical 
> correspondence across subjects, which can be used as inputs to external 
> proprietary algorithms (e.g. classification), so I'm pretty sure I'll need to 
> step out of the Workbench.
>
> Thanks!
>
> Nicola
>
>
>
> On 03/29/2017 04:18 PM, Glasser, Matthew wrote:
>> What operations beyond smoothing do you need?  There is wb_command 
>> -cifti-smoothing.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Nicola Toschi 
>> Date: Wednesday, March 29, 2017 at 9:09 AM
>> To: Matt Glasser , "hcp-users@humanconnectome.org" 
>> 
>> Subject: Re: [HCP-Users] Position of vertices in myelin maps and 164k sphere
>>
>> Hi Matt,
>>
>> thank you for your quick answer! That makes sense.
>>
>> I would like to do some spatial operations on the sphere that exploit 
>> spatial neighborhood information (e.g. even simple smoothing or filtering on 
>> the 2D surface), and have these operations be consistent across subjects.
>>
>> What would be the best way to go about this do you think? Incorporate the 
>> exact vertex locations for each subject anyway, or ignore them and (somehow) 
>> just use the fact that vertex n has the same neuroanatomical meaning in 
>> every subject?
>>
>> Thanks again,
>>
>> Nicola
>>
>> On 03/29/2017 04:02 PM, Glasser, Matthew wrote:
>>> We don¹t recommend using the ft_ tools with MRI data.  Instead use
>>> ciftiopen/ciftisave/
>>> ciftisavereset:
>>>
>>>
>>> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ
>>>  item 2B
>>>
>>> As for your other question, the vertex indices have neuroanatomical
>>> correspondence across subjects, but that often does not equate to having
>>> the same 3D coordinates (as volumetric registration is not able to align
>>> cortical areas across subjects).
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> On 3/29/17, 8:41 AM,
>>> "hcp-users-bounces@
>>> humanconnectome.org on behalf of
>>> Nicola Toschi"
>>>  >> humanconnectome.org on behalf of
>>> tos...@med.uniroma2.it>
>>>  wrote:
>>>
>>>
 Dear List,

 I am trying to do some postprocessing on myelin and thickness maps (164k
 versions) contained in the MNINonLinear Directory of the Structural
 dataset (e.g. ${subject}.corrThickness_
 MSMAll.164k_fs_LR.dscalar.nii and
 ${subject}.MyelinMap_BC_
 MSMAll.164k_fs_LR.dscalar.nii)
 .

 I thought these data would all be in the same atlas space across
 subjects, hence I was expecting to find the same vertex coordinates for
 all subjects. Instead, when reading the data into matlab (
 'ft_cifti_read' and gifti') every subject seems to have their own
 distinct vertex locations. Also, the spherical gifti surfaces appear to
 be sampled at different coordinates across subjects.

 Can I assume 

Re: [HCP-Users] Questions regarding coordinates infomation of vertex

[Dierker, Donna]

Hi Qinqin,

As Matt said, the file named like *midthickness*.surf.gii contains the 
vertex-to-3D coordinate mapping that you seek.
This could be an individual’s surface, if the cifti data pertains to a 
particular subject, or it could be a mean midthickness (e.g., HCP500) if it is 
group data.

You can read about the GIFTI file format here:

https://www.nitrc.org/projects/gifti/

Also, have a look here and consider whether this command might help:

https://www.humanconnectome.org/documentation/workbench-command/command-all-commands-help.html
-cifti-rois-from-extrema

You might have to manipulate your ROI to narrow it down first.

Donna


> On Mar 20, 2017, at 7:23 AM, Irisqql0922  wrote:
>
>
> Thank you Glasser, but your answer is not what I'm looking for.  I may not 
> express myself clearly.
> Here is the situation: I am trying to analysis CIFTI data using python.  Now 
> I have got a matrix with all threshold vertex value.  Next, I want to use 
> that matrix to generate a mask for my future analysis .  But now, what I got 
> is just a matrix with only vertex values , thus I cannot use this matrix to 
> generate my ROIs and then get their spatial coordinates.
> So I wonder if there is a transformation matrix to transform vertex index to 
> spatial coordinates, and if there is, where can I find it.
>
> Thanks again,
> Qinqin lee
>
> On 03/20/2017 20:03，Glasser, Matthew wrote：
> In individual subjects, you can use the midthickness surface coordinates as 
> the 3D coordinates.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Irisqql0922 
> 
> Date: Monday, March 20, 2017 at 4:19 AM
> To: hcp-users 
> Subject: [HCP-Users] Questions regarding coordinates infomation of vertex
>
> Dear HCP teams,
>
> I am trying to threshold surface data of file *.dscalar.nii , and after that, 
> I don't know how to link data remains in the matrix with its space 
> coordinates. Is there any matrix contains the information linking vertex 
> index in the matrix with its space location? If there is such a matrix, where 
> can I find it?
>
> Regards,
> Qinqin lee
>
>
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>
>
>
>
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Re: [HCP-Users] Making a movie in connectome workbench

[Dierker, Donna]

Jonathan Power’s tools might be worth a look:

http://www.jonathanpower.net/resources.html

… depending on what you are doing.


> On Feb 28, 2017, at 10:31 AM, Harwell, John  wrote:
>
>
> Hello Kristian,
>
> * Load your files into Workbench and select the first map in your GIFTI file.
> * Select File Menu->Animation Control.
> * On the Animation Control Dialog, press the Record button (near the top 
> right of the dialog).
> * In the Workbench window, click the mouse in the map index control (number 
> with up and down arrows) of the row containing your GIFTI file.  Press the up 
> arrow on your keyboard to move to the next map and continue pressing the up 
> arrow to sequence through all of the maps (You can also click the small up 
> arrow next to the map index).
> * Press the Record button on the Animation Control Dialog and a dialog will 
> appear asking for the name of your movie file.  Enter a name for the file (I 
> think the name should end in “.mpg”) and press the Save button to create the 
> movie file.
>
> As far as I know, there is no way to automatically sequence through all maps 
> in a data file.
>
> John Harwell
>
>> On Feb 26, 2017, at 1:52 AM, Kristian M. Eschenburg  wrote:
>>
>> Hi all
>>
>> I have a large matrix of size NxT, with N observations and T time points.  
>> I'm able to convert this matrix into a gifti .func file using Matlab, load 
>> this single file into the Workbench, and view each time point T as a single 
>> map.  However, I want to convert it to a "time series" file and then animate 
>> it in the Connectome Workbench viewer.  How can I go about doing this?
>>
>> I've looked at the "Animation Control" window, but when I try to record 
>> something, no files are created.
>>
>> Could you shed light on this?
>>
>> Thanks!
>>
>>
>> Kristian
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Re: [HCP-Users] map data between FreeSurfer and HCP

[Dierker, Donna]

Hi Leah,

I wonder if you need to apply an affine transform to your white/pial surfaces 
to adjust for the offset between Freesurfer’s origin and your orig.mgz volume’s 
origin.  See this script:

https://github.com/Washington-University/Pipelines/blob/7cc0bf1863cbc8a1a7ab9c6dd48a25de9be9bae7/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh

Search for c_ras.mat.  This applies to surfaces in subject’s volume space.

If you map MNI FCmaps onto MNI surfaces, I’d expect better alignment, but if 
you use a nonlinear method to get FCmaps on MNI, but just apply the 
talairach.xfm to the surfaces (linear/affine), then that alignment won’t be as 
good as if you used the same method for both.

Donna


> On Jan 15, 2017, at 1:40 AM, Leah Moreno  wrote:
>
> Dear experts,
>
> I have individual FCmaps in mni & subject volume space (not using HCP or 
> FreeSurfer) and individual surface data from FreeSurfer. I want to map data 
> from individual volumes to individual surfaces to then average across 
> subjects on the surface and visualize with workbench. But the volume data is 
> not being well mapped to the surface, please see attachment.
>
> I have also tried section B. of document “How do I map data between 
> FreeSurfer and HCP?”, but either with or without resampling the output does 
> not look ok.
>
> Any help, please?
>
> Thank you,
>
> -L
>
> 
>
>
>
>
>
>
>
>
>
>
> ___
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> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
> 



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Re: [HCP-Users] Threshold p value in workbench view

[Dierker, Donna]

See if you can read this link, Xavier:

https://wustl.box.com/s/uuxn06pjlnn6ts7nhak0zww53l33fxzf

People also use metric- or cifti-math to convert to log p or 1-p.  Whatever 
works for you.


> On Dec 27, 2016, at 10:39 AM, Xavier Guell Paradis  wrote:
>
> Dear Sir or Madam,
> When viewing task contrasts in workbench (the file is 
> HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMSulc.dscalar.nii), is 
> there a way to threshold areas of activation for a given p value (e.g. areas 
> that, in the task contrast, have achieved a p<0.001)?
> A previous post in this mailing list asked the same question (the post was 
> called "thresholding the data to p-value"), but the person that replied to 
> the email included a screen capture which is not available in the mail 
> archive. Without that screen capture, I cannot understand how to threshold 
> data using p values.
>
> Thank you very much,
> Xavier.
>
>
> Xavier Guell Paradis, M.D.
> Visiting Scientist
> Massachusetts Institute of Technology
> McGovern Institute for Brain Research
> Office: 46-4033A
> Phone: (617) 324-4355
> Email: xavie...@mit.edu
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Re: [HCP-Users] thresholding the data to p-value

[Dierker, Donna]

TimH - you mean this one?

On Jul 7, 2016, at 10:26 AM, Dierker, Donna 
<do...@wustl.edu<mailto:do...@wustl.edu>> wrote:

You need to adjust your overlay settings; see attached capture.  Make sure 
Threshold Type is set to On.

[cid:B7646768-2537-4828-8045-A6B646996AD8@wustl.edu]


On Dec 5, 2016, at 11:16 AM, Timothy Hendrickson 
<hendr...@umn.edu<mailto:hendr...@umn.edu>> wrote:

Hi Donna,

Could you please re-attach the screen capture that you took for Vasudev? I 
cannot find it...
I also am looking into how to observe significance levels with a threshold of 
p<0.05.

Respectfully,

-Tim

You need to adjust your overlay settings; see attached capture.  Make sure
Threshold Type is set to On.


From:
hcp-users-boun...@humanconnectome.org<http://humanconnectome.org>

<
hcp-users-boun...@humanconnectome.org<http://humanconnectome.org>
> on behalf of Dev vasu
<
vasudevamurthy.devulapa...@gmail.com<http://gmail.com>
>
Sent: Thursday, July 7, 2016 10:03:28 AM
To: Dierker, Donna
Cc: <
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
>
Subject: Re: [HCP-Users] thresholding the data to p-value

Dear madam,

I don't want to write to an ROI volume, i just want to observe activation
levels with a threshold of p<0.05.


Thanks
Vasudev

On 7 July 2016 at 16:31, Dierker, Donna
<
do...@wustl.edu<mailto:do...@wustl.edu
>> wrote:

Hi Vasudev,


I'm pretty sure wb_view can display voxels within a range of values (inside
upper and lower limit), but I think you mean threshold and write a ROI volume.
For that, try:


  wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x ${PstatFile}


Donna


From:

hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org
>

<
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org
>>
 on behalf of Dev vasu
<
vasudevamurthy.devulapa...@gmail.com<mailto:vasudevamurthy.devulapa...@gmail.com
>>
Sent: Wednesday, July 6, 2016 12:04:50 PM
To: Harms, Michael;
<
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org
>>
Subject: [HCP-Users] thresholding the data to p-value



Dear sir,

I would like to threshold my results to a p-value of p<0.05 and i couldn't do
it from workbench GUI, I can only threshold the data to percentage changes.

Please kindly let me know how i can possibly threshold the results to real
p-stats.



Thanks
Vasudev




Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
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Re: [HCP-Users] group comparison

[Dierker, Donna]

Try the -transposedata option.


> On Nov 29, 2016, at 1:49 PM, Harms, Michael  wrote:
>
>
> Sounds like your design.mat file isn’t set up correctly, or you haven’t 
> supplied a necessary flag to PALM.  Read the PALM documentation carefully.  I 
> believe that there are now examples of using PALM with CIFTI data.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> 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: nailin yao 
> Date: Tuesday, November 29, 2016 at 1:41 PM
> To: Michael Harms 
> Cc: "Glasser, Matthew" , "hcp-users@humanconnectome.org" 
> 
> Subject: Re: [HCP-Users] group comparison
>
> Because I need to do group comparison here , and met this error when running 
> palm:
> Error using palm_takeargs (line 2003)
> The number of rows in the design matrix does
> not match the number of observations in the data.
> - Rows in the matrix: 155
> - Observations in the data: 59412
> In file design.mat
>
> How can I fix this?Thank you!
> Best,
> Nailin
>
> 2016-11-29 14:37 GMT-05:00 Harms, Michael :
>>
>> Hi,
>> Why do you think there is something wrong?  59412 is the expected number of 
>> rows in the *MyelinMap.32k_fs_LR.dscalar.nii files.
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave.Tel: 314-747-6173
>> St. Louis, MO  63110Email: mha...@wustl.edu
>>
>> From:  on behalf of nailin yao 
>> 
>> Date: Tuesday, November 29, 2016 at 1:29 PM
>> To: "Glasser, Matthew" 
>>
>> Cc: "hcp-users@humanconnectome.org" 
>> Subject: Re: [HCP-Users] group comparison
>>
>> Hi,
>>
>> I used "wb_shortcuts -cifti-concatenate output.dtseries.nii *.dscalar.nii" 
>> to concatenate my 155 subjects' MyelinMap.32k_fs_LR.dscalar.nii files. 
>> However, it turn out there are 59412 rows in the output file. What's wrong 
>> with my command then? Thank you very much.
>>
>> Best,
>> Nailin
>>
>> 2016-11-29 13:07 GMT-05:00 Glasser, Matthew :
>>> If you are using CIFTI you don't need to mask the data/can use a CIFTI file 
>>> of all ones.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>>
>>> Sent from my Verizon, Samsung Galaxy smartphone
>>>
>>>
>>>  Original message 
>>> From: nailin yao 
>>> Date: 11/29/16 11:33 AM (GMT-06:00)
>>> To: "Glasser, Matthew" 
>>> Cc: NEUROSCIENCE tim , hcp-users@humanconnectome.org
>>> Subject: Re: [HCP-Users] group comparison
>>>
>>> So how do I deal with the two hemispheres when comparing 
>>> ${subj}.MyelinMap.32k_fs_LR.dscalar.nii if the mask is only for one 
>>> hemisphere?
>>>
>>> Thank you!
>>>
>>> Nailin
>>>
>>> 2016-11-28 20:07 GMT-05:00 Glasser, Matthew :
 You can use the atlas ROI file: 
 ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.atlasroi.32k_fs_LR.shape.gii.

 Peace,

 Matt.

 From:  on behalf of nailin yao 
 
 Date: Monday, November 28, 2016 at 3:06 PM
 To: Timothy Coalson 
 Cc: "hcp-users@humanconnectome.org" 
 Subject: Re: [HCP-Users] group comparison

 Thank you Tim! I have now concatenated the myelin maps and going to do the 
 permutation test with Palm. I plan to do a whole brain vertex level 
 comparison, do you know which existing mask should I use to group level 
 analysis? Thanks!

 Best,
 Nailin

 2016-11-22 16:48 GMT-05:00 Timothy Coalson :
> wb_shortcuts comes with the latest release of workbench, v1.2.3 - 
> however, there are a few bugs in the version that was released that way, 
> and a newer version is available here:
>
> https://github.com/Washington-University/wb_shortcuts
>
> If you want just the script itself, use this link:
>
> https://raw.githubusercontent.com/Washington-University/wb_shortcuts/master/wb_shortcuts
>
> I noticed you used "./wb_command", suggesting that you don't have the 
> workbench executables in your $PATH.  They will need to be in your $PATH 
> in order for wb_shortcuts to work.
>
> As a final note, there is also wb_command -metric-merge and wb_shortcuts 
> -metric-concatenate, which do the same thing for .func.gii files, in case 
> you 

Re: [HCP-Users] Glasser nature atlas

[Dierker, Donna]

If you can’t do MSMAll, then consider using just sulc, rather than sulc+curv.

See figure 4, row B, in Emma Robinson’s paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190319/figure/F4/

I have heard David describe curvature as capturing more local folding, sulc 
global folding.
In my experience, curvature varies too much across subjects, while sulc seems a 
more reasonable driver for intersubject registration.

For intrasubject registration across timepoints, however, curvature is your 
friend.


> On Oct 11, 2016, at 6:54 PM, Glasser, Matthew  wrote:
>
> Using folding-based alignment won’t be as good as areal-feature-based 
> alignment, but I wouldn’t worry about the alignment being any worse than any 
> other comparison of two studies driven by folding-based alignment.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Jared P Zimmerman 
> 
> Date: Tuesday, October 11, 2016 at 3:12 PM
> To: Timothy Coalson 
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] Glasser nature atlas
>
> I have a related question to this.  I’d like to use the parcellation on some 
> more traditional volume data (i.e. 3x3x3mm voxels, 3s TR).  I have made fs_LR 
> surfaces from free surfer using the wb_command shortcuts for it, as in here: 
> https://wiki.humanconnectome.org/download/attachments/63078513/Resampling-FreeSurfer-HCP.pdf?version=1=1472225460934=v2
>  but I am missing the registration from subject surface to group average.
>
> Is this registration, or the validity of the parcellation, dependent on 
> MSMAll or would an MSMSulc registration be effective (enough) here?  The 
> paper and parcellation are clearly based on MSMAll and this was essential in 
> generating parcellation, but since I don’t have the requisite rest data to do 
> an MSMAll register, would an MSMSulc registration be sufficient for 
> ultimately translating back to the subject volume?
>
> I read the above discussion about a month ago and didn’t see this covered, 
> but I don’t know if that was addressed in the discussion since.
>
>
> Tanks,
> Jared
>
>
>
>> On Oct 4, 2016, at 5:45 PM, Timothy Coalson  wrote:
>>
>> Making a "nifti version" isn't a simple conversion, as some lengthy 
>> conversations on this list have elaborated on.
>>
>> The good news: if you want a single-subject-specific version, that is 
>> possible, using -cifti-separate and -label-to-volume-mapping, using the 
>> subject's own surfaces.
>>
>> The bad news: if you want it to be a group atlas, the currently popular 
>> volume registration methods aren't good enough at cortical area alignment to 
>> make our parcellation meaningful in a group-average volume space, and thus 
>> we do not recommend making a volumetric version in such a space.  In the 
>> meantime, surface registration avoids several difficulties inherent to 
>> volume registration, and was instrumental in being able to create the 
>> parcellation at all (via alignment of areal features).
>>
>> For more detailed discussion:
>>
>> https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03078.html
>>
>> Tim
>>
>>
>> On Tue, Oct 4, 2016 at 9:47 AM, Elam, Jennifer  wrote:
>>> Hi Peter,
>>> The data for the new parcellation are available in the BALSA database, see 
>>> this thread: 
>>> http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02876.html
>>>
>>> We recommend using the included Connectome Workbench scene file to 
>>> conveniently view the data in the wb_view part of the software platform. 
>>> Get Connectome Workbench here: 
>>> https://www.humanconnectome.org/software/get-connectome-workbench.html
>>>
>>> Many of the files are in the CIFTI data format, which has a lot of 
>>> advantages, but if you need NIFTI versions, you can use wb_command 
>>> (distributed as part of Connectome Workbench) to do the conversion.
>>>
>>> There's lots of help for using wb_command in the HCP-Users mail archive, 
>>> and/or you could post more questions to the list.
>>>
>>> Best,
>>> Jenn
>>>
>>>
>>> Jennifer Elam, Ph.D.
>>> Scientific Outreach, Human Connectome Project
>>> Washington University School of Medicine
>>> Department of Neuroscience, Box 8108
>>> 660 South Euclid Avenue
>>> St. Louis, MO 63110
>>> 314-362-9387
>>> e...@wustl.edu
>>> www.humanconnectome.org
>>>
>>>
>>> From:hcp-users-boun...@humanconnectome.org 
>>>  on behalf of Peter McColgan 
>>> 
>>> Sent: Tuesday, October 4, 2016 9:29:30 AM
>>> To: hcp-users@humanconnectome.org
>>> Subject: [HCP-Users] Glasser nature atlas
>>>
>>>
>>> Dear HCP team,
>>>
>>> Is it possible to download a nifti version of the Glasser atlas featured 
>>> recently in nature?
>>>
>>> Thanks
>>>
>>> bw
>>>
>>> Peter
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> 

Re: [HCP-Users] PALM Errors

[Dierker, Donna]

Did you try using the -transposedata option?


> On Sep 8, 2016, at 4:54 PM, Michael F.W. Dreyfuss  
> wrote:
>
> Hello,
>
> I am trying to run PALM on subject level betas in cifti to get group means 
> and identify clusters of significant activation. I have tried two things so 
> far, and both have resulted in errors.
>
> The first attempt was the following:
>
> palm $COPE_INPUTS -d $LevelThreeFEATDir/design.mat -t 
> $LevelThreeFEATDir/design.con -fdr -T -ise
>
> $COPE_INPUTS is a list of 41 cope files in the format "-i 
> SC01736/TGNGcope1.feat/cope1.dtseries.nii -i 
> SC01879/TGNGcope1.feat/cope1.dtseries.nii  ..."
>
> The .mat file contains 41 under NumPoints and has equal weighting for all 41 
> inputs.
>
> The resulting error is:
> Error using palm_takeargs (line 1989)
> The number of rows in the design matrix does
> not match the number of observations in the data.
> - Rows in the matrix: 41
> - Observations in the data: 91282
>
> Because this seems to be looking at each grayordinate as an observation, I 
> tried adding the option -evperdat
>
> But then I get the error:
> Index exceeds matrix dimensions.
>
> I am not sure why I am getting this error because I have 41 inputs and a 41 
> inputs specified in the .mat file.
>
> Do you have any advice for how I can get this to run to get clusters of mean 
> activation for a given subject level beta?
>
> Also, what recommendations do you have for identifying clusters beyond -T?
>
> Thank you,
> Michael
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users



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Re: [HCP-Users] create cortical thickness maps for multiple subjects in the same template space

[Dierker, Donna]

I don't know of any software that does a better job at that task.

You do need to run your subject through the Freesurfer pipeline, which does a 
lot of stuff.  It segments into gray matter, white matter, CSF, etc.  And yes 
-- it generates a map of cortical thickness (distance between gm/wm and pial).

Spend some time digesting the Freesurfer wiki.  If you want to do what you want 
to do, Freesurfer can help.

But I still agree with Mike:  If your controls and proband subjects were 
scanned on different scanners, you may have a difficult review process ahead of 
you when it comes time to publish your results.  Something to consider sooner 
rather than later.


On Jul 11, 2016, at 10:36 AM, Dev vasu <vasudevamurthy.devulapa...@gmail.com> 
wrote:

> Dear madam,
> 
> Is there any way to measure the distance from Pial surface boundary with 
> GM/WM boundary in freesurfer ?.
> 
> 
> Thanks
> Vasudev
> 
> On 11 July 2016 at 17:25, Dierker, Donna <do...@wustl.edu> wrote:
> Hi Vasudev,
> 
> This question confuses me a bit, I confess, but I would use Freesurfer to 
> generate cortical thickness measurements from T1w volumes:
> 
> https://surfer.nmr.mgh.harvard.edu/fswiki
> 
> Donna
> 
> 
> On Jul 11, 2016, at 5:20 AM, Dev vasu <vasudevamurthy.devulapa...@gmail.com> 
> wrote:
> 
> > Dear Sir,
> >
> >
> > can we used myelin style as a mapping method for Volume to surface mapping 
> > in wb_command to produce cortical thickness files,Unfortunately i only have 
> > T1w images and we have not acquired T2w images, i would like to use T1w 
> > images to generate Cortical thickness , could you please let me know if its 
> > appropriate way generate them using
> > wb_command -volume-to-surface-mapping command and Myelin style mapping 
> > method ?.
> >
> >
> >
> > Thanks
> > Vasudev
> >
> >
> >
> > On 8 July 2016 at 17:03, Harms, Michael <mha...@wustl.edu> wrote:
> >
> > Hi,
> > For statistical inference, I would recommend that you look into the PALM 
> > tool.
> >
> > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM
> >
> >
> > --
> > Michael Harms, Ph.D.
> > ---
> > Conte Center for the Neuroscience of Mental Disorders
> > 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: Dev vasu <vasudevamurthy.devulapa...@gmail.com>
> > Date: Friday, July 8, 2016 at 9:56 AM
> > To: "Harms, Michael" <mha...@wustl.edu>
> > Cc: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>
> > Subject: Re: [HCP-Users] create cortical thickness maps for multiple 
> > subjects in the same template space
> >
> > Dear Sir,
> >
> > Is there any way to quantify the changes in cortical thickness between 
> > healthy controls and non healthy controls ?.
> >
> >
> > Thanks
> > Vasudev
> >
> > On 8 July 2016 at 16:47, Harms, Michael <mha...@wustl.edu> wrote:
> >
> > HI,
> > Cortical thickness maps on the surface mesh are already created for you.  
> > You should analyze/view the thickness on the surface; not try to project 
> > the thickness back onto the volume.
> >
> > cheers,
> > -MH
> >
> > --
> > Michael Harms, Ph.D.
> > ---
> > Conte Center for the Neuroscience of Mental Disorders
> > 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 Dev vasu 
> > <vasudevamurthy.devulapa...@gmail.com>
> > Date: Friday, July 8, 2016 at 9:35 AM
> > To: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>
> > Subject: [HCP-Users] create cortical thickness maps for multiple subjects 
> > in the same template space
> >
> > Dear Sir /madam,
> >
> > I am able to successfully run Structural preprocessing pipeline on a group 
> > of 24 subjects, I would like to know how i can create cortical thickness 
> > maps for all the subjects in MNI152_T1_0.7mm.nii.gz template.
> >
> >
> >
> > Thanks
> > Vasudev
> >
> >
> > ___
> > HCP-Users mailing list
> > HCP-Use

Re: [HCP-Users] thresholding the data to p-value

[Dierker, Donna]

You need to adjust your overlay settings; see attached capture.  Make sure 
Threshold Type is set to On.


From: hcp-users-boun...@humanconnectome.org 
<hcp-users-boun...@humanconnectome.org> on behalf of Dev vasu 
<vasudevamurthy.devulapa...@gmail.com>
Sent: Thursday, July 7, 2016 10:03:28 AM
To: Dierker, Donna
Cc: <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] thresholding the data to p-value

Dear madam,

I don't want to write to an ROI volume, i just want to observe activation 
levels with a threshold of p<0.05.


Thanks
Vasudev

On 7 July 2016 at 16:31, Dierker, Donna 
<do...@wustl.edu<mailto:do...@wustl.edu>> wrote:

Hi Vasudev,


I'm pretty sure wb_view can display voxels within a range of values (inside 
upper and lower limit), but I think you mean threshold and write a ROI volume.  
For that, try:


  wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x ${PstatFile}


Donna


From: 
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Dev vasu 
<vasudevamurthy.devulapa...@gmail.com<mailto:vasudevamurthy.devulapa...@gmail.com>>
Sent: Wednesday, July 6, 2016 12:04:50 PM
To: Harms, Michael; 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] thresholding the data to p-value



Dear sir,

I would like to threshold my results to a p-value of p<0.05 and i couldn't do 
it from workbench GUI, I can only threshold the data to percentage changes.

Please kindly let me know how i can possibly threshold the results to real 
p-stats.



Thanks
Vasudev


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Re: [HCP-Users] thresholding the data to p-value

[Dierker, Donna]

Hi Vasudev,


I'm pretty sure wb_view can display voxels within a range of values (inside 
upper and lower limit), but I think you mean threshold and write a ROI volume.  
For that, try:


  wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x ${PstatFile}


Donna


From: hcp-users-boun...@humanconnectome.org 
 on behalf of Dev vasu 

Sent: Wednesday, July 6, 2016 12:04:50 PM
To: Harms, Michael; 
Subject: [HCP-Users] thresholding the data to p-value



Dear sir,

I would like to threshold my results to a p-value of p<0.05 and i couldn't do 
it from workbench GUI, I can only threshold the data to percentage changes.

Please kindly let me know how i can possibly threshold the results to real 
p-stats.



Thanks
Vasudev


___
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Re: [HCP-Users] Extracting ROI data from HCP resting state data

[Dierker, Donna]

Hi David,

I hope this publication answers your questions about HCP rfMRI preprocessing:

Resting-state fMRI in the Human Connectome Project.
Smith SM1, Beckmann CF, Andersson J, Auerbach EJ, Bijsterbosch J, Douaud G, 
Duff E, Feinberg DA, Griffanti L, Harms MP, Kelly M, Laumann T, Miller KL, 
Moeller S, Petersen S, Power J, Salimi-Khorshidi G, Snyder AZ, Vu AT, Woolrich 
MW, Xu J, Yacoub E, Uğurbil K, Van Essen DC, Glasser MF; WU-Minn HCP Consortium.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720828/

I am only used to seeing what it is in the fix extended packages, so I'm not 
sure all these volumes are in the basic fix packages, but here are NIFTI 
volumes in a sample subject's rfMRI subdirectories:

177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz
177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/mask.nii.gz
177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/melodic_IC.nii.gz
177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/melodic_oIC.nii.gz
177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz
177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz
177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000.ica/filtered_func_data.ica/mask.nii.gz
177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000.ica/filtered_func_data.ica/melodic_IC.nii.gz
177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000.ica/filtered_func_data.ica/melodic_oIC.nii.gz
177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL.nii.gz
177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000_clean.nii.gz
177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000.ica/filtered_func_data.ica/mask.nii.gz
177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000.ica/filtered_func_data.ica/melodic_IC.nii.gz
177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000.ica/filtered_func_data.ica/melodic_oIC.nii.gz
177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR.nii.gz
177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000_clean.nii.gz
177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000.ica/filtered_func_data.ica/mask.nii.gz
177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000.ica/filtered_func_data.ica/melodic_IC.nii.gz
177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000.ica/filtered_func_data.ica/melodic_oIC.nii.gz
177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL.nii.gz

Maybe this page will help explain those:

http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/rfMRIconnectivity/

But keep in mind that for neocortex, you can take advantage of the surface data 
the HCP provides (e.g., fsaverage_32k/*surf.gii, *dscalar.nii and 
*dtseries.nii).  You can get better inter-subject registration/alignment on the 
surface, if that will be a factor in your study.

Donna


On Jun 28, 2016, at 6:30 PM, David Hofmann  wrote:

> Hi all,
> 
> I would like to extract ROI data (only neocortex) 'manually' e.g. using a ROI 
> from Harvard-Oxford atlas from HCP resting state data, but I'm not sure which 
> (nifti) files to use and where to find them. I'm also looking for some 
> information about the preprocessing steps applied to the resting state data 
> that is, if some additional steps (e.g. filtering) have to be carried out 
> before ROI extraction or if this has already been done.
> 
> Any help on this appreciated!
> 
> Thanks
> 
> David
> ___
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> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 


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Re: [HCP-Users] Define the ROI and signal extraction in ROI

[Dierker, Donna]

Vasudev,

I must repeat Mike Harms' advice:  Start separate threads with appropriate 
subject lines, rather than pile disparate topics onto existing threads, or 
combine separate topics into a single thread.  Having a subject line that 
accurately reflects your issue is especially key to getting the attention of 
experts who might be, say, at the OHBM conference, with no shortage of 
distractions.

With 1200 subjects and thousands of large files, it was necessary to keep 
packages to the minimum of what most users would want/need.

For the Juelich atlas, I'd read the references cited here for insight:

http://neuro.debian.net/pkgs/fsl-juelich-histological-atlas.html

Good luck!

Donna


On Jun 29, 2016, at 10:04 AM, Dev vasu <vasudevamurthy.devulapa...@gmail.com> 
wrote:

> Dear madam,
> 
> 
> I have a slight confusion pertaining to HCP data, when i download HCP 
> preprocessed data, i do not see all the files that i would generally obtain 
> after running HCP-minimal preprocessing pipeline. Could you please let me 
> know the reason for this.
> 
> 
> I have verified if registration was done using HOA atlas and it seems fine, 
> could you please let me know how to register the images ( both volume and 
> surface ) to Jue-lich histological (cyto- and myelo-architectonic) atlas.
> 
> 
> Thanks
> Vasudev
> 
> 
> 
> 
> On 29 June 2016 at 16:25, Dierker, Donna <do...@wustl.edu> wrote:
> Vasudev,
> 
> I would expect the volumes (*.nii.gz) and surfaces (*.surf.gii) under the 
> MNINonLinear subdirectory to already be in register with the Harvard-Oxford 
> Atlas (HOA).  The files under this directory were all fnirted to MNI.
> 
> You can test it yourself by overlaying the HOA volume over individual T1's or 
> T2's under the MNINonLinear subdirectory.
> 
> Donna
> 
> 
> On Jun 29, 2016, at 7:19 AM, Dev vasu <vasudevamurthy.devulapa...@gmail.com> 
> wrote:
> 
> > Dear Sir / madam,
> >
> >  After going through some publications i have found that  Subcortical ROIs, 
> > such as the brainstem and thalamus can be extracted
> > from the Harvard–Oxford subcortical structural atlas, For the cortical core 
> > region of the PIVC many publications have used ,Jue-lich histological 
> > (cyto- and myelo-architectonic) atlas.
> >
> >
> > Could you please let me know how could  i possibly do the registration of 
> > multiple images  from HCP data to these common standard space atlases to 
> > perform group connectivity analysis, in FSL you would use 2-stage 
> > registration with FLIRT & FNIRT , is there any alternative with Workbench?.
> >
> >
> >
> > Thanks
> > Vasudev
> >
> > On 28 June 2016 at 22:04, Timothy Coalson <tsc...@mst.edu> wrote:
> > Connectome Workbench doesn't include data (by design, so there are never 
> > hidden inputs to an operation).  Someone else can probably point you to 
> > atlases containing the regions you want.
> >
> > Tim
> >
> >
> > On Tue, Jun 28, 2016 at 9:44 AM, Dev vasu 
> > <vasudevamurthy.devulapa...@gmail.com> wrote:
> > Dear  madam,
> >
> > Is there any way to extract the ROIs from  probabilistic atlases included 
> > within workbench,I would like to define Vestibulospinal tract as seed and 
> > Parieto insular vestibular cortex(PIVC) as target mask with Brain stem, 
> > Medial and laterall vestibular nuclei as way points.
> >
> >
> >   Is there any way i can obtain co-ordinates for these regions ?.
> >
> >
> > Thanks
> > Vasudev
> >
> > On 28 June 2016 at 16:05, Dev vasu <vasudevamurthy.devulapa...@gmail.com> 
> > wrote:
> > Dear madam,
> >
> >
> > I would like to study the distribution of vestibular tracks from thalamus 
> > to vestibular cortex for which by  i would like to  define a ROI mask ( 
> > seed mask) from all voxels in the right thalamus and using vestibular 
> > cortex region as target mask.
> >
> >
> > I would first like to create a volume mask and convert them into cortical 
> > surface masks to perform tractography.this is my main goal. I have 30 
> > subjects ( male ) -from HCP , I have finished with Pre-processing of all 
> > the data  now i would like to perform analysis.
> >
> > If you have any other better way to map vestibular thalamic connectivity , 
> > i would really appreciate your suggestions.
> >
> >
> > Thanks
> > Vasudev
> >
> >
> > On 28 June 2016 at 15:50, Dierker, Donna <do...@wustl.edu> wrote:
> > Hi Vasudev,
> >
> > You'll probably need to be more specific about 

Re: [HCP-Users] Define the ROI and signal extraction in ROI

[Dierker, Donna]

Vasudev,

I would expect the volumes (*.nii.gz) and surfaces (*.surf.gii) under the 
MNINonLinear subdirectory to already be in register with the Harvard-Oxford 
Atlas (HOA).  The files under this directory were all fnirted to MNI.

You can test it yourself by overlaying the HOA volume over individual T1's or 
T2's under the MNINonLinear subdirectory.

Donna


On Jun 29, 2016, at 7:19 AM, Dev vasu <vasudevamurthy.devulapa...@gmail.com> 
wrote:

> Dear Sir / madam,
> 
>  After going through some publications i have found that  Subcortical ROIs, 
> such as the brainstem and thalamus can be extracted
> from the Harvard–Oxford subcortical structural atlas, For the cortical core 
> region of the PIVC many publications have used ,Jue-lich histological (cyto- 
> and myelo-architectonic) atlas.
> 
> 
> Could you please let me know how could  i possibly do the registration of 
> multiple images  from HCP data to these common standard space atlases to 
> perform group connectivity analysis, in FSL you would use 2-stage 
> registration with FLIRT & FNIRT , is there any alternative with Workbench?.
> 
> 
> 
> Thanks
> Vasudev
> 
> On 28 June 2016 at 22:04, Timothy Coalson <tsc...@mst.edu> wrote:
> Connectome Workbench doesn't include data (by design, so there are never 
> hidden inputs to an operation).  Someone else can probably point you to 
> atlases containing the regions you want.
> 
> Tim
> 
> 
> On Tue, Jun 28, 2016 at 9:44 AM, Dev vasu 
> <vasudevamurthy.devulapa...@gmail.com> wrote:
> Dear  madam,
> 
> Is there any way to extract the ROIs from  probabilistic atlases included 
> within workbench,I would like to define Vestibulospinal tract as seed and 
> Parieto insular vestibular cortex(PIVC) as target mask with Brain stem, 
> Medial and laterall vestibular nuclei as way points.
> 
> 
>   Is there any way i can obtain co-ordinates for these regions ?.
> 
> 
> Thanks
> Vasudev
> 
> On 28 June 2016 at 16:05, Dev vasu <vasudevamurthy.devulapa...@gmail.com> 
> wrote:
> Dear madam,
> 
> 
> I would like to study the distribution of vestibular tracks from thalamus to 
> vestibular cortex for which by  i would like to  define a ROI mask ( seed 
> mask) from all voxels in the right thalamus and using vestibular cortex 
> region as target mask.
> 
> 
> I would first like to create a volume mask and convert them into cortical 
> surface masks to perform tractography.this is my main goal. I have 30 
> subjects ( male ) -from HCP , I have finished with Pre-processing of all the 
> data  now i would like to perform analysis.
> 
> If you have any other better way to map vestibular thalamic connectivity , i 
> would really appreciate your suggestions.
> 
> 
> Thanks
> Vasudev
>  
> 
> On 28 June 2016 at 15:50, Dierker, Donna <do...@wustl.edu> wrote:
> Hi Vasudev,
> 
> You'll probably need to be more specific about your goals, as there are many 
> ways to define a ROI.  The most common is to threshold some functional map 
> (dscalar.nii or func.gii/nifti) at something like p=.05, but there are many 
> other ways to do it.
> 
> If you need to draw a ROI manually in workbench, you can load something like 
> a curvature, myelin, or functional map and display it in multiple tabs or 
> windows (e.g., midthickness surface in one view, very inflated in another).  
> You can draw borders on the very inflated map, and see how they look on the 
> midthickness.  Adjust as needed.
> 
> Then wb_command -border-to-rois can fill in the vertices encircled by the 
> borders to create a cortical ROI.
> 
> For drawing volumetric ROIs, there are all sorts of options out there.
> 
> Donna
> 
> 
> On Jun 27, 2016, at 9:45 AM, Dev vasu <vasudevamurthy.devulapa...@gmail.com> 
> wrote:
> 
> > Dear Sir,
> >
> > I would like to know how to define structural and functional ROI in 
> > workbench,should we define the ROI manually ? or is there any alternate 
> > procedure for it, I am aware of process in SPM but not in workbench.
> >
> >
> >
> > Thanks
> > Vasudev
> > ___
> > HCP-Users mailing list
> > HCP-Users@humanconnectome.org
> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >
> 
> 
> 
> ___
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> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 
> 
> 


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Re: [HCP-Users] Location of CIFTI vertices in standard space

[Dierker, Donna]

Tom has a volumetric parcellation in MNI space that he has used for other 
analyses, so he needs to use the same parcellation for comparison with the 
dconn and dscalar fancy graph stuff.

It might be possible to map the parcellation volume to the S900 midthickness 
and use the mapped parcellation for analysis in surface-land.  You can gauge 
the viability of this method by viewing the parcellation volume over its 
corresponding mean T1/T2 with the S900 midthickness contour overlaid.

Freesurfer has mri_surf2vol, and caret5 has an option for projecting from 
surface to volume, but I am not aware of a feature like this in wb_command.


On Jun 8, 2016, at 12:59 AM, "Glasser, Matthew"  wrote:

> Hi Tom,
> 
> We don’t explicitly do anything to correct surface coordinates for shrinkage. 
>  Tim might have an idea if this were possible, but I think it may be an 
> uncorrectable nonlinear geometrical effect of averaging incompatible folding 
> patterns (though it nicely shows where areas and folds are well aligned and 
> folds are consistent across subjects by being much more similar to the 
> average volume in early sensory areas, insula).  It definitely affects pial 
> surfaces more than white matter surfaces.  I’ve attached an example (green 
> whitematter surface, red midthickness surface, blue pial surface).  This is 
> what happens to neuroanatomically aligned corresponding points in the brain 
> (i.e. MSMAll matched surface vertices in individuals) when you average in the 
> volume.  
> 
> Matt.
> 
> From:  on behalf of Thomas Nichols 
> 
> Date: Wednesday, June 8, 2016 at 12:21 AM
> To: Matt Glasser 
> Cc: HCP Users 
> Subject: Re: [HCP-Users] Location of CIFTI vertices in standard space
> 
> Hi Matt,
> 
> Thanks for the clarification.  I'm aware of the merits of the surface 
> approach (no one would put up with all it's headaches otherwise!) but I'd 
> guess I'm not alone in needing "an answer" of the question how to move from 
> surface back to volume space.  I know there are limitations, but "don't do 
> it" can't be the answer.
> 
> So!  What what I'll try now is using the MNI coordinates for the S900 Group 
> Average space from Q1-Q6_R440.{L,R}.midthickness.32k_fs_LR.surf.gii (in the 
> "900 Subjects Group Average Data" package).  
> 
> The only remaining question is whether there is any volume-based correction 
> for the 'shrinkage' you mention... is there some affine transform that should 
> be applied to the coordinates from the *.midthickness.32k_fs_LR.surf.gii?
> 
> -Tom
> 
> On Wed, Jun 8, 2016 at 5:53 AM, Glasser, Matthew  wrote:
>> Hi Tom,
>> 
>> I think Tim’s earlier e-mail is a good explanation.  It is not possible to 
>> maintain the spatial localization standards and quality of the analysis 
>> approach when making a comparison with average/atlas data in volume MNI 
>> space.  In contrast one can go from an individual’s physical volume space to 
>> standard CIFTI space via MSMAll and back again without a loss of quality 
>> aside from interpolation effects.  This difference is due to the information 
>> loss that comes with group averaging misaligned volume data.  Surface mesh 
>> XYZ coordinates suffer the same issues (e.g. topologically incompatible 
>> folding patterns, differences between folds and cortical areas, etc), and as 
>> a result group average surfaces shrink to some degree (a shrinkage that we 
>> can correct for on the surface for some computations using average vertex 
>> areas) and the folding patterns are blurred in many higher cortical regions. 
>>  As I mentioned below, there are group average midthickness surfaces in the 
>> "900 Subjects Group Average Data” package that have average XYZ coordinates 
>> in MNI space for display purposes.  However, I wouldn't recommend mapping 
>> directly between them and MNI space, as this causes well documented problems 
>> to the underlaying neuroanatomy (e.g Glasser and Van Essen 2011, Van Essen 
>> et al 2012).  These are the same problems caused by volume-based 
>> cross-subject averaging of cortical data in any study.  
>> 
>> Matt.
>> 
>> From:  on behalf of Thomas Nichols 
>> 
>> Date: Tuesday, June 7, 2016 at 11:11 PM
>> To: Matt Glasser 
>> Cc: HCP Users 
>> 
>> Subject: Re: [HCP-Users] Location of CIFTI vertices in standard space
>> 
>> Hi Matthew,
>> 
>> We've already done a bunch of comparisons with data in volume MNI space, and 
>> so we need to continue to use the same volume-based labels with the dense 
>> brainordinate connectome.
>> 
>> -Tom
>> 
>> On Tue, Jun 7, 2016 at 11:30 PM, Glasser, Matthew  wrote:
>>> Hi Tom,
>>> 
>>> Couldn’t you just use something already in surface space like the 
>>> FreeSurfer labels?  Which “known anatomical labels” are  you 

Re: [HCP-Users] [SPAM] ERROR: mpr2mni305 failed in FreesurferPipelineBatch.sh

[Dierker, Donna]

Hi Barbara,

It looks like there was a problem with a runtime library Freesurfer needs.  
Have a look at this similar issue:

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40092.html


I'd report your issue to the Freesurfer mailing list:

https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport


Hopefully there is a fix that won't be too painful.


Donna


From: hcp-users-boun...@humanconnectome.org 
 on behalf of Barbara Kreilkamp 

Sent: Tuesday, May 31, 2016 3:36:30 AM
To: hcp-users@humanconnectome.org
Subject: [SPAM] [HCP-Users] ERROR: mpr2mni305 failed in 
FreesurferPipelineBatch.sh


Dear HCP experts,

I am running freesurfer-Darwin-lion-stable-pub-v5.3.0 on MAC 10.10.5.
Could you please help me with this error message? I think it relates to the 
library, this is what it states in talairach_avi.log.
Running recon-all directly worked, but after that I am missing some files that 
are needed in PostFreesurferPipelineBatch.sh

But I am unsure how to solve this issue.

Any help is greatly appreciated,
Thank you very much,
Barbara




#@# Talairach Sat May 28 14:18:53 CEST 2016

/Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/mri

\n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz \n

\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n

ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

Darwin iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 
2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64


recon-all -s REF088c exited with ERRORS at Sat May 28 14:19:12 CEST 2016


For more details, see the log file 
/Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/scripts/recon-all.log

To report a problem, see 
 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting





talaraich_avi.log output


/Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/mri

/Applications/freesurfer/bin/talairach_avi

--i orig_nu.mgz --xfm transforms/talairach.auto.xfm

$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $

Darwin iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 
2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64

Sat May 28 13:27:28 CEST 2016

mri_convert orig_nu.mgz talsrcimg.img

$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $

reading from orig_nu.mgz...

crypt_gkey = FSaWN44YqKOYA

TR=8.21, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to talsrcimg.img...

crypt_gkey = FSaWN44YqKOYA

Analyze Output Matrix

-1.0   0.0   0.0   128.0;

 0.0   0.0   1.0  -146.0;

 0.0  -1.0   0.0   148.0;

 0.0   0.0   0.0   1.0;



INFO: set hdr.hist.orient to -1

mpr2mni305 talsrcimg

Sat May 28 13:27:29 CEST 2016

/Applications/freesurfer/bin/mpr2mni305 talsrcimg

$Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $

target=711-2C_as_mni_average_305


-

analyzeto4dfp talsrcimg -O0 -y

-


$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $

Sat May 28 13:27:30 2016

Writing: talsrcimg.4dfp.hdr

$Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $

Reading: talsrcimg.hdr

header size 348 bytes

hdr.dime.datatype offset=70 value=2

hdr.dime.bitpix offset=72 value=8

hdr.hist.orient offset=252 value=-1

dimensionality 4

dimensions   256   256   256 1

Reading: talsrcimg.img

Writing: talsrcimg.4dfp.img

Writing: talsrcimg.4dfp.ifh

ifh2hdr talsrcimg -r0to255

ori=2


-

gauss_4dfp talsrcimg 1.1

-


dyld: Library not loaded: /usr/local/gfortran/lib/libgcc_s.1.dylib

  Referenced from: /Applications/freesurfer/bin/gauss_4dfp

  Reason: image not found

Trace/BPT trap

ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133

ERROR: mpr2mni305 execution aborted

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