[HCP-Users] table for parcellation

[Marta Moreno]

Dear experts,

After running:
 
1.  PreFreeSurfer
2.  FreeSurfer
3.  PostFreeSurfer
4.  fMRIVolume
5.  fMRISurface
6.  ICA+FIX (MR+FIX)
7.  MSMAll (Do MSM Surface Registration)
8.  dedrift and resample pipeline

2 questions:

(i) I used wb_command -cifti-parcellate and wb_command -cifti-correlation to 
create a parcellation.pconn.nii file per each subject. I have uploaded all 
files into matlab and now would like to create a table that includes all 
subjects’ correlation value from parcel 264 to all 360 parcels, and include the 
variable names for all 360 parcels. How can I do this?

(ii) Is the file “RS_fMRI_MR_Atlas_MSMAll_Test_hp0_clean.dtseries.nii” the 
final step after (8) to use for wb_command -cifti-parcellate and wb_command 
-cifti-correlation

Thanks,

L.




___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] DeDriftAndResamplePipelineBatch.sh

[Marta Moreno]

OK. Thanks!

Leah.


> On May 27, 2019, at 12:59 PM, Glasser, Matthew  wrote:
> 
> Yes. 
>  
> Matt.
>  
> From:  on behalf of Marta Moreno 
> 
> Date: Monday, May 27, 2019 at 11:15 AM
> To: HCP Users 
> Subject: [HCP-Users] DeDriftAndResamplePipelineBatch.sh
>  
> Dear Experts,
>  
> If I run MR ICAFIX regressing motion parameters as part of the cleaning, do I 
> need to set DeDriftAndResamplePipelineBatch.sh as MotionRegression=TRUE?
>  
> Thanks,
>  
> Leah.
>  
>  
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 
>  
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] DeDriftAndResamplePipelineBatch.sh

[Marta Moreno]

Dear Experts,

If I run MR ICAFIX regressing motion parameters as part of the cleaning, do I 
need to set DeDriftAndResamplePipelineBatch.sh as MotionRegression=TRUE?

Thanks,

Leah.



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] DeDriftAndResamplePipeline error

[Marta Moreno]

OK, thank you very much.
You guys are doing an awesome work!

Leah.

> On Apr 20, 2019, at 5:18 PM, Harms, Michael  wrote:
> 
>  
> That particular error message can be ignored.  We’ll fix the scripts so that 
> it doesn’t occur in the future.
>  
> 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 Marta Moreno 
> 
> Date: Saturday, April 20, 2019 at 12:02 PM
> To: "Glasser, Matthew" 
> Cc: HCP Users 
> Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error
>  
> Thanks for your response!
>  
> Case Syntax on Mac is as follow and same for unix/linux as far as I know: 
>   case word in [ [(] pattern [ | pattern ] ... ) list ;; ] … esac
>  
> Also there are 2 errors in the log file DeDriftAndResamplePipeline.sh.e42974 
> but 3 case...esac statements in DeDriftAndResamplePipeline.sh
>  
> I do not think this is a problem since it does seem to have completed 
> successfully, but do you have any other suggestion?
>  
> Thanks for your help,
> Leah.
>  
>  
> On Apr 19, 2019, at 8:26 AM, Glasser, Matthew  wrote:
>  
> It does seem to have completed successfully.  I wonder if “case” doesn’t work 
> the same on Mac?
>  
> Matt.
>  
> From: Marta Moreno 
> Date: Thursday, April 18, 2019 at 11:19 PM
> To: Timothy Coalson 
> Cc: Matt Glasser , "Harwell, John" , 
> HCP Users 
> Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error
>  
> I think it worked now. The script finished pretty fast without prompting an 
> error on the screen except for the following found In 
> DeDriftAndResamplePipeline.sh.e42974:
>  
>  # Do NOT wrap the following in quotes (o.w. the entire set of commands gets 
> interpreted as a single string)
>  |
> Error: The input character is not valid in MATLAB statements or expressions.
>  
>  # Do NOT wrap the following in quotes (o.w. the entire set of commands gets 
> interpreted as a single string)
>  |
> Error: The input character is not valid in MATLAB statements or expressions.
> 
> 
> 
> 
> I am attaching the log files to make sure the DeDriftAndResamplePipeline.sh 
> script was completed successfully.
> 
> 
> Thanks a lot!
> 
> 
> Leah.
> 
> 
>  
> On Apr 18, 2019, at 2:45 PM, Timothy Coalson  wrote:
>  
> Make sure you have the whole pipelines repo for 4.0.0, do not try to mix and 
> match folders from different versions, and make sure your setup script is 
> pointed to the 4.0.0 version when running things from 4.0.0.  The log_Warn 
> function is defined inside global/scripts, and it should get sourced 
> automatically based on HCPPIPEDIR, so make sure that is set correctly 
> (pointed to the 4.0.0 version).
>  
> Tim
>  
>  
> On Thu, Apr 18, 2019 at 1:39 PM Marta Moreno  wrote:
> Thanks for your response. And sorry to bother again with this issue but I am 
> still getting the following error: ReApplyFixMultiRunPipeline.sh: line 592: 
> log_Warn: command not found
>  
> Please find log files attached.
>  
> Pipelines for MR+FIX, MSMAll and DeDriftAndResample are from version version 
> 4.0.0.
> PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface are from 
> version  3_22 
> Since MR+FIX and MSMAll were run successfully, why it should be a version 
> issue in ReApplyFixMultiRunPipeline.sh?
>  
> I want to be sure this is a version issue because I have already run 
> PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface version  
> 3_22 on a sample of 30 patients pre/post tx.
>  
> Thanks a lot for your help and patience. 
>  
> Leah.
>  
>  
>  
> On Apr 15, 2019, at 9:39 PM, Timothy Coalson  wrote:
>  
> I would also suggest changing your log level to INFO in wb_view, preferences 
> (the wb_command option does not store the logging level change to 
> preferences).  We should probably change the default level, or change the 
> level of that volume coloring message.
>  
> Tim
>  
>  
> On Mon, Apr 15, 2019 at 8:34 PM Timothy Coalson  wrote:
> I have pushed a similar edit to reapply MR fix, please update to the latest 
> master.
>  
> Tim
>  
>  
> On Mon, Apr 15, 2019 at 8:27 PM Timothy Coalson  wrote:
> They weren't instructions, I pushed an edit, and it was a different script.
>  
> Tim
>  
>  
> On Mon, Apr 15, 2019 at 8:08 PM Glasser, Matthew  wrote:
> Here is the error: 

Re: [HCP-Users] DeDriftAndResamplePipeline error

[Marta Moreno]

Thanks for your response!

Case Syntax on Mac is as follow and same for unix/linux as far as I know: 
  case word in [ [(] pattern [ | pattern ] ... ) list ;; ] … esac

Also there are 2 errors in the log file DeDriftAndResamplePipeline.sh.e42974 
but 3 case...esac statements in DeDriftAndResamplePipeline.sh

I do not think this is a problem since it does seem to have completed 
successfully, but do you have any other suggestion?

Thanks for your help,
Leah.


> On Apr 19, 2019, at 8:26 AM, Glasser, Matthew  wrote:
> 
> It does seem to have completed successfully.  I wonder if “case” doesn’t work 
> the same on Mac?
> 
> Matt.
> 
> From: Marta Moreno  <mailto:mmorenoort...@icloud.com>>
> Date: Thursday, April 18, 2019 at 11:19 PM
> To: Timothy Coalson mailto:tsc...@mst.edu>>
> Cc: Matt Glasser mailto:glass...@wustl.edu>>, "Harwell, 
> John" mailto:jharw...@wustl.edu>>, HCP Users 
> mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error
> 
> I think it worked now. The script finished pretty fast without prompting an 
> error on the screen except for the following found In 
> DeDriftAndResamplePipeline.sh.e42974:
> 
>  # Do NOT wrap the following in quotes (o.w. the entire set of commands gets 
> interpreted as a single string)
>  |
> Error: The input character is not valid in MATLAB statements or expressions.
>  
>  # Do NOT wrap the following in quotes (o.w. the entire set of commands gets 
> interpreted as a single string)
>  |
> Error: The input character is not valid in MATLAB statements or expressions.
> 
> 
> I am attaching the log files to make sure the DeDriftAndResamplePipeline.sh 
> script was completed successfully.
> 
> Thanks a lot!
> 
> Leah.
> 
> 
>> On Apr 18, 2019, at 2:45 PM, Timothy Coalson > <mailto:tsc...@mst.edu>> wrote:
>> 
>> Make sure you have the whole pipelines repo for 4.0.0, do not try to mix and 
>> match folders from different versions, and make sure your setup script is 
>> pointed to the 4.0.0 version when running things from 4.0.0.  The log_Warn 
>> function is defined inside global/scripts, and it should get sourced 
>> automatically based on HCPPIPEDIR, so make sure that is set correctly 
>> (pointed to the 4.0.0 version).
>> 
>> Tim
>> 
>> 
>> On Thu, Apr 18, 2019 at 1:39 PM Marta Moreno > <mailto:mmorenoort...@icloud.com>> wrote:
>>> Thanks for your response. And sorry to bother again with this issue but I 
>>> am still getting the following error: ReApplyFixMultiRunPipeline.sh: line 
>>> 592: log_Warn: command not found
>>> 
>>> Please find log files attached.
>>> 
>>> Pipelines for MR+FIX, MSMAll and DeDriftAndResample are from version 
>>> version 4.0.0.
>>> PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface are from 
>>> version  3_22 
>>> Since MR+FIX and MSMAll were run successfully, why it should be a version 
>>> issue in ReApplyFixMultiRunPipeline.sh?
>>> 
>>> I want to be sure this is a version issue because I have already run 
>>> PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface version  
>>> 3_22 on a sample of 30 patients pre/post tx.
>>> 
>>> Thanks a lot for your help and patience. 
>>> 
>>> Leah.
>>> 
>>> 
>>> 
>>>> On Apr 15, 2019, at 9:39 PM, Timothy Coalson >>> <mailto:tsc...@mst.edu>> wrote:
>>>> 
>>>> I would also suggest changing your log level to INFO in wb_view, 
>>>> preferences (the wb_command option does not store the logging level change 
>>>> to preferences).  We should probably change the default level, or change 
>>>> the level of that volume coloring message.
>>>> 
>>>> Tim
>>>> 
>>>> 
>>>> On Mon, Apr 15, 2019 at 8:34 PM Timothy Coalson >>> <mailto:tsc...@mst.edu>> wrote:
>>>>> I have pushed a similar edit to reapply MR fix, please update to the 
>>>>> latest master.
>>>>> 
>>>>> Tim
>>>>> 
>>>>> 
>>>>> On Mon, Apr 15, 2019 at 8:27 PM Timothy Coalson >>>> <mailto:tsc...@mst.edu>> wrote:
>>>>>> They weren't instructions, I pushed an edit, and it was a different 
>>>>>> script.
>>>>>> 
>>>>>> Tim
>>>>>> 
>>>>>> 
>>>>>> On Mon, Apr 15, 2019 at 8:08 PM Glasser, Matthew >>>>

Re: [HCP-Users] DeDriftAndResamplePipeline error

[Marta Moreno]

I think it worked now. The script finished pretty fast without prompting an error on the screen except for the following found In DeDriftAndResamplePipeline.sh.e42974: # Do NOT wrap the following in quotes (o.w. the entire set of commands gets interpreted as a single string) |Error: The input character is not valid in MATLAB statements or expressions.  # Do NOT wrap the following in quotes (o.w. the entire set of commands gets interpreted as a single string) |Error: The input character is not valid in MATLAB statements or expressions.I am attaching the log files to make sure the DeDriftAndResamplePipeline.sh script was completed successfully.Thanks a lot!Leah.___HCP-Users mailing listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users


DeDriftAndResamplePipeline.sh.e42974
Description: Binary data


DeDriftAndResamplePipeline.sh.o42974
Description: Binary data


On Apr 18, 2019, at 2:45 PM, Timothy Coalson <tsc...@mst.edu> wrote:Make sure you have the whole pipelines repo for 4.0.0, do not try to mix and match folders from different versions, and make sure your setup script is pointed to the 4.0.0 version when running things from 4.0.0.  The log_Warn function is defined inside global/scripts, and it should get sourced automatically based on HCPPIPEDIR, so make sure that is set correctly (pointed to the 4.0.0 version).TimOn Thu, Apr 18, 2019 at 1:39 PM Marta Moreno <mmorenoort...@icloud.com> wrote:Thanks for your response. And sorry to bother again with this issue but I am still getting the following error: ReApplyFixMultiRunPipeline.sh: line 592: log_Warn: command not foundPlease find log files attached.Pipelines for MR+FIX, MSMAll and DeDriftAndResample are from version version 4.0.0.PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface are from version  3_22 Since MR+FIX and MSMAll were run successfully, why it should be a version issue in ReApplyFixMultiRunPipeline.sh?I want to be sure this is a version issue because I have already run PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface version  3_22 on a sample of 30 patients pre/post tx.Thanks a lot for your help and patience. Leah.On Apr 15, 2019, at 9:39 PM, Timothy Coalson <tsc...@mst.edu> wrote:I would also suggest changing your log level to INFO in wb_view, preferences (the wb_command option does not store the logging level change to preferences).  We should probably change the default level, or change the level of that volume coloring message.TimOn Mon, Apr 15, 2019 at 8:34 PM Timothy Coalson <tsc...@mst.edu> wrote:I have pushed a similar edit to reapply MR fix, please update to the latest master.TimOn Mon, Apr 15, 2019 at 8:27 PM Timothy Coalson <tsc...@mst.edu> wrote:They weren't instructions, I pushed an edit, and it was a different script.TimOn Mon, Apr 15, 2019 at 8:08 PM Glasser, Matthew <glass...@wustl.edu> wrote:




Here is the error: 



readlink: illegal option -- f
usage: readlink [-n] [file ...]



I believe Tim already gave you instructions for this.  


Also, the log_Warn line is again concerning as to whether you followed the installation instructions and all version 4.0.0 files here.


Matt.




From: Marta Moreno <mmorenoort...@icloud.com>
Date: Monday, April 15, 2019 at 8:53 AM
To: Matt Glasser <glass...@wustl.edu>
Cc: HCP Users <hcp-users@humanconnectome.org>, Timothy Coalson <tsc...@mst.edu>, "Brown, Tim" <tbbr...@wustl.edu>
Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error





I had to re-run DeDriftAndResamplePipeline twice because it was searching for settings.sh in the wrong place, and now I am getting the following error message:


ReApplyFixMultiRunPipeline.sh: line 586: log_Warn: command not found




I am attaching log files.




Does the folder containing fix1.067 need to include all the ICAFIX files? 




Thanks a lot!




Leah.





















On Apr 15, 2019, at 12:19 AM, Marta Moreno <mmorenoort...@icloud.com> wrote:



It seams to be working now. Thanks a lot!


Leah.



On Apr 15, 2019, at 12:04 AM, Glasser, Matthew <glass...@wustl.edu> wrote:




If you ran MR+FIX, you need to set these appropriately




MRFixConcatName="NONE"

MRFixNames="NONE"



And not set 


fixNames="RS_fMRI_1 RS_fMRI_2" #Space delimited list or NONE


https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/DeDriftAndResamplePipelineBatch.sh 
Also it looks like line 124 needs an “s” on the end of the flag name to read --multirun-fix-concat-names=${MRFixConcatName} 


Matt.




From: Marta Moreno <mmorenoort...@icloud.com>
Date: Sunday, April 14, 2019 at 10:56 PM
To: Matt Glasser <glass...@wustl.edu>
Cc: HCP Users <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error





Thanks a lot for your response.


I am r

Re: [HCP-Users] DeDriftAndResamplePipeline error

[Marta Moreno]

Thanks for your response. And sorry to bother again with this issue but I am still getting the following error: ReApplyFixMultiRunPipeline.sh: line 592: log_Warn: command not foundPlease find log files attached.Pipelines for MR+FIX, MSMAll and DeDriftAndResample are from version version 4.0.0.PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface are from version  3_22 Since MR+FIX and MSMAll were run successfully, why it should be a version issue in ReApplyFixMultiRunPipeline.sh?I want to be sure this is a version issue because I have already run PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface version  3_22 on a sample of 30 patients pre/post tx.Thanks a lot for your help and patience. Leah.___HCP-Users mailing listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users


DeDriftAndResamplePipeline.sh.e21153
Description: Binary data


DeDriftAndResamplePipeline.sh.o21153
Description: Binary data
On Apr 15, 2019, at 9:39 PM, Timothy Coalson <tsc...@mst.edu> wrote:I would also suggest changing your log level to INFO in wb_view, preferences (the wb_command option does not store the logging level change to preferences).  We should probably change the default level, or change the level of that volume coloring message.TimOn Mon, Apr 15, 2019 at 8:34 PM Timothy Coalson <tsc...@mst.edu> wrote:I have pushed a similar edit to reapply MR fix, please update to the latest master.TimOn Mon, Apr 15, 2019 at 8:27 PM Timothy Coalson <tsc...@mst.edu> wrote:They weren't instructions, I pushed an edit, and it was a different script.TimOn Mon, Apr 15, 2019 at 8:08 PM Glasser, Matthew <glass...@wustl.edu> wrote:




Here is the error: 



readlink: illegal option -- f
usage: readlink [-n] [file ...]



I believe Tim already gave you instructions for this.  


Also, the log_Warn line is again concerning as to whether you followed the installation instructions and all version 4.0.0 files here.


Matt.




From: Marta Moreno <mmorenoort...@icloud.com>
Date: Monday, April 15, 2019 at 8:53 AM
To: Matt Glasser <glass...@wustl.edu>
Cc: HCP Users <hcp-users@humanconnectome.org>, Timothy Coalson <tsc...@mst.edu>, "Brown, Tim" <tbbr...@wustl.edu>
Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error





I had to re-run DeDriftAndResamplePipeline twice because it was searching for settings.sh in the wrong place, and now I am getting the following error message:


ReApplyFixMultiRunPipeline.sh: line 586: log_Warn: command not found




I am attaching log files.




Does the folder containing fix1.067 need to include all the ICAFIX files? 




Thanks a lot!




Leah.





















On Apr 15, 2019, at 12:19 AM, Marta Moreno <mmorenoort...@icloud.com> wrote:



It seams to be working now. Thanks a lot!


Leah.



On Apr 15, 2019, at 12:04 AM, Glasser, Matthew <glass...@wustl.edu> wrote:




If you ran MR+FIX, you need to set these appropriately




MRFixConcatName="NONE"

MRFixNames="NONE"



And not set 


fixNames="RS_fMRI_1 RS_fMRI_2" #Space delimited list or NONE


https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/DeDriftAndResamplePipelineBatch.sh 
Also it looks like line 124 needs an “s” on the end of the flag name to read --multirun-fix-concat-names=${MRFixConcatName} 


Matt.




From: Marta Moreno <mmorenoort...@icloud.com>
Date: Sunday, April 14, 2019 at 10:56 PM
To: Matt Glasser <glass...@wustl.edu>
Cc: HCP Users <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error





Thanks a lot for your response.


I am running v.4.0.0 now. And I have set up the script as follow:





HighResMesh="164"

LowResMesh="32"

RegName="MSMAll_InitalReg_2_d40_WRN"

DeDriftRegFiles="${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.L.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii@${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.R.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii"

ConcatRegName="MSMAll_Test"

Maps="sulc curvature corrThickness thickness"

MyelinMaps="MyelinMap SmoothedMyelinMap" #No _BC, this will be reapplied

MRFixConcatName="NONE"

MRFixNames="NONE"

#fixNames="rfMRI_REST1_LR rfMRI_REST1_RL rfMRI_REST2_LR rfMRI_REST2_RL" #Space delimited list or NONE

fixNames="RS_fMRI_1 RS_fMRI_2" #Space delimited list or NONE

#dontFixNames="tfMRI_WM_LR tfMRI_WM_RL tfMRI_GAMBLING_LR tfMRI_GAMBLING_RL tfMRI_MOTOR_LR tfMRI_MOTOR_RL tfMRI_LANGUAGE_LR tfMRI_LANGUAGE_RL tfMRI_SOCIAL_LR tfMRI_SOCIAL_RL tfMRI_RELATIONAL_LR
 tfMRI_RELATIONAL_RL tfMRI_EMOTION_LR tfMRI_EMOTION_RL" #Space delimited list or NONE

dontFixNames="NONE"

SmoothingFWHM="2" #Should equal previous grayordinates smoothing (bec

Re: [HCP-Users] DeDriftAndResamplePipeline error

[Marta Moreno]

I had to re-run DeDriftAndResamplePipeline twice because it was searching for settings.sh in the wrong place, and now I am getting the following error message:ReApplyFixMultiRunPipeline.sh: line 586: log_Warn: command not foundI am attaching log files.Does the folder containing fix1.067 need to include all the ICAFIX files? Thanks a lot!Leah.___HCP-Users mailing listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users


DeDriftAndResamplePipeline.sh.e40867
Description: Binary data


DeDriftAndResamplePipeline.sh.o40867
Description: Binary data

On Apr 15, 2019, at 12:19 AM, Marta Moreno <mmorenoort...@icloud.com> wrote:It seams to be working now. Thanks a lot!Leah.
On Apr 15, 2019, at 12:04 AM, Glasser, Matthew <glass...@wustl.edu> wrote:




If you ran MR+FIX, you need to set these appropriately




MRFixConcatName="NONE"

MRFixNames="NONE"



And not set 


fixNames="RS_fMRI_1 RS_fMRI_2" #Space delimited list or NONE


https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/DeDriftAndResamplePipelineBatch.sh 
Also it looks like line 124 needs an “s” on the end of the flag name to read --multirun-fix-concat-names=${MRFixConcatName} 


Matt.




From: Marta Moreno <mmorenoort...@icloud.com>
Date: Sunday, April 14, 2019 at 10:56 PM
To: Matt Glasser <glass...@wustl.edu>
Cc: HCP Users <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error





Thanks a lot for your response.


I am running v.4.0.0 now. And I have set up the script as follow:





HighResMesh="164"

LowResMesh="32"

RegName="MSMAll_InitalReg_2_d40_WRN"

DeDriftRegFiles="${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.L.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii@${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.R.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii"

ConcatRegName="MSMAll_Test"

Maps="sulc curvature corrThickness thickness"

MyelinMaps="MyelinMap SmoothedMyelinMap" #No _BC, this will be reapplied

MRFixConcatName="NONE"

MRFixNames="NONE"

#fixNames="rfMRI_REST1_LR rfMRI_REST1_RL rfMRI_REST2_LR rfMRI_REST2_RL" #Space delimited list or NONE

fixNames="RS_fMRI_1 RS_fMRI_2" #Space delimited list or NONE

#dontFixNames="tfMRI_WM_LR tfMRI_WM_RL tfMRI_GAMBLING_LR tfMRI_GAMBLING_RL tfMRI_MOTOR_LR tfMRI_MOTOR_RL tfMRI_LANGUAGE_LR tfMRI_LANGUAGE_RL tfMRI_SOCIAL_LR tfMRI_SOCIAL_RL tfMRI_RELATIONAL_LR
 tfMRI_RELATIONAL_RL tfMRI_EMOTION_LR tfMRI_EMOTION_RL" #Space delimited list or NONE

dontFixNames="NONE"

SmoothingFWHM="2" #Should equal previous grayordinates smoothing (because we are resampling from unsmoothed native mesh timeseries)

HighPass="0"

MotionRegression=TRUE

MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab, Mode=2 octave

#MatlabMode="0" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab, Mode=2 octave




But the script does not run and it is aborted with the following message:

DeDriftAndResamplePipeline.sh - ABORTING: unrecognized option: --multirun-fix-concat-name=NONE


I am attaching the log files.


Leah.







































On Apr 14, 2019, at 11:10 PM, Glasser, Matthew <glass...@wustl.edu> wrote:




In this case you do run it with the individual fMRI names and that doesn’t look like the version 4.0.0 example script...


Matt.




From: <hcp-users-boun...@humanconnectome.org> on behalf of Marta Moreno <mmorenoort...@icloud.com>
Date: Sunday, April 14, 2019 at 10:06 PM
To: HCP Users <hcp-users@humanconnectome.org>
Subject: [HCP-Users] DeDriftAndResamplePipeline error





Dear Experts,


I have run DeDriftAndResamplePipelineBatch.sh from from ${StudyFolder}/${Subject}/scripts after running MSMAII and getting the following error:





While running:

/Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command -metric-resample /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR.L.native.func.gii
 /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Native/NTTMS_s002_170812.L.sphere.MSMAll_Test.native.surf.gii /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/fsaverage_LR32k/NTTMS_s002_170812.L.sphere.32k_fs_LR.surf.gii
 ADAP_BARY_AREA /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_MSMAll_Test.L.atlasroi.32k_fs_LR.func.gii -area-surfs /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/T1w/Native/NTTMS_s002_170812.L.midthickness.native.surf.gii
 /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/T1w/fsaverage_LR32k/NTTMS_s002_170812.L.midthickness_MSMAll_Test.32k_fs_LR.surf.gii -current-roi /Volumes/data/data3/NTTMS/NTTMS

Re: [HCP-Users] DeDriftAndResamplePipeline error

[Marta Moreno]

It seams to be working now. Thanks a lot!

Leah.

> On Apr 15, 2019, at 12:04 AM, Glasser, Matthew  wrote:
> 
> If you ran MR+FIX, you need to set these appropriately
> 
> MRFixConcatName="NONE"
> MRFixNames="NONE"
> 
> And not set 
> 
> fixNames="RS_fMRI_1 RS_fMRI_2" #Space delimited list or NONE
> 
> https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/DeDriftAndResamplePipelineBatch.sh
>  
> <https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/DeDriftAndResamplePipelineBatch.sh>
>  
> Also it looks like line 124 needs an “s” on the end of the flag name to read 
> --multirun-fix-concat-names=${MRFixConcatName} 
> 
> Matt.
> 
> From: Marta Moreno  <mailto:mmorenoort...@icloud.com>>
> Date: Sunday, April 14, 2019 at 10:56 PM
> To: Matt Glasser mailto:glass...@wustl.edu>>
> Cc: HCP Users  <mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error
> 
> Thanks a lot for your response.
> 
> I am running v.4.0.0 now. And I have set up the script as follow:
> 
> HighResMesh="164"
> LowResMesh="32"
> RegName="MSMAll_InitalReg_2_d40_WRN"
> DeDriftRegFiles="${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.L.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii@${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.R.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii"
> ConcatRegName="MSMAll_Test"
> Maps="sulc curvature corrThickness thickness"
> MyelinMaps="MyelinMap SmoothedMyelinMap" #No _BC, this will be reapplied
> MRFixConcatName="NONE"
> MRFixNames="NONE"
> #fixNames="rfMRI_REST1_LR rfMRI_REST1_RL rfMRI_REST2_LR rfMRI_REST2_RL" 
> #Space delimited list or NONE
> fixNames="RS_fMRI_1 RS_fMRI_2" #Space delimited list or NONE
> #dontFixNames="tfMRI_WM_LR tfMRI_WM_RL tfMRI_GAMBLING_LR tfMRI_GAMBLING_RL 
> tfMRI_MOTOR_LR tfMRI_MOTOR_RL tfMRI_LANGUAGE_LR tfMRI_LANGUAGE_RL 
> tfMRI_SOCIAL_LR tfMRI_SOCIAL_RL tfMRI_RELATIONAL_LR tfMRI_RELATIONAL_RL 
> tfMRI_EMOTION_LR tfMRI_EMOTION_RL" #Space delimited list or NONE
> dontFixNames="NONE"
> SmoothingFWHM="2" #Should equal previous grayordinates smoothing (because we 
> are resampling from unsmoothed native mesh timeseries)
> HighPass="0"
> MotionRegression=TRUE
> MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab, Mode=2 
> octave
> #MatlabMode="0" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab, Mode=2 
> octave
> 
> But the script does not run and it is aborted with the following message:
> DeDriftAndResamplePipeline.sh - ABORTING: unrecognized option: 
> --multirun-fix-concat-name=NONE
> 
> I am attaching the log files.
> 
> Leah.
> 
> 
>> On Apr 14, 2019, at 11:10 PM, Glasser, Matthew > <mailto:glass...@wustl.edu>> wrote:
>> 
>> In this case you do run it with the individual fMRI names and that doesn’t 
>> look like the version 4.0.0 example script...
>> 
>> Matt.
>> 
>> From: > <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
>> mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, April 14, 2019 at 10:06 PM
>> To: HCP Users > <mailto:hcp-users@humanconnectome.org>>
>> Subject: [HCP-Users] DeDriftAndResamplePipeline error
>> 
>> Dear Experts,
>> 
>> I have run DeDriftAndResamplePipelineBatch.sh from from 
>> ${StudyFolder}/${Subject}/scripts after running MSMAII and getting the 
>> following error:
>> 
>> While running:
>> /Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command
>>  -metric-resample 
>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR.L.native.func.gii
>>  
>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Native/NTTMS_s002_170812.L.sphere.MSMAll_Test.native.surf.gii
>>  
>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/fsaverage_LR32k/NTTMS_s002_170812.L.sphere.32k_fs_LR.surf.gii
>>  ADAP_BARY_AREA 
>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_MSMAll_Test.L.atlasroi.32k_fs_LR.func.gii
>>  -area-surfs 
>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/T1w/Native/NTTMS_s002_170812.L.midthickness.native.surf.gii
>>  
>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/T1w/fsaverage_LR32k/NTTMS_s002_170812.L.midthickness_MSMAll_Test.32k_fs_LR.surf.gii
>>  -current-roi 
>

Re: [HCP-Users] DeDriftAndResamplePipeline error

[Marta Moreno]

Thanks a lot for your response.I am running v.4.0.0 now. And I have set up the script as follow:HighResMesh="164"LowResMesh="32"RegName="MSMAll_InitalReg_2_d40_WRN"DeDriftRegFiles="${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.L.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii@${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.R.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii"ConcatRegName="MSMAll_Test"Maps="sulc curvature corrThickness thickness"MyelinMaps="MyelinMap SmoothedMyelinMap" #No _BC, this will be reappliedMRFixConcatName="NONE"MRFixNames="NONE"#fixNames="rfMRI_REST1_LR rfMRI_REST1_RL rfMRI_REST2_LR rfMRI_REST2_RL" #Space delimited list or NONEfixNames="RS_fMRI_1 RS_fMRI_2" #Space delimited list or NONE#dontFixNames="tfMRI_WM_LR tfMRI_WM_RL tfMRI_GAMBLING_LR tfMRI_GAMBLING_RL tfMRI_MOTOR_LR tfMRI_MOTOR_RL tfMRI_LANGUAGE_LR tfMRI_LANGUAGE_RL tfMRI_SOCIAL_LR tfMRI_SOCIAL_RL tfMRI_RELATIONAL_LR tfMRI_RELATIONAL_RL tfMRI_EMOTION_LR tfMRI_EMOTION_RL" #Space delimited list or NONEdontFixNames="NONE"SmoothingFWHM="2" #Should equal previous grayordinates smoothing (because we are resampling from unsmoothed native mesh timeseries)HighPass="0"MotionRegression=TRUEMatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab, Mode=2 octave#MatlabMode="0" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab, Mode=2 octaveBut the script does not run and it is aborted with the following message:DeDriftAndResamplePipeline.sh - ABORTING: unrecognized option: --multirun-fix-concat-name=NONEI am attaching the log files.Leah.___HCP-Users mailing listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users


DeDriftAndResamplePipeline.sh.e20908
Description: Binary data


DeDriftAndResamplePipeline.sh.o20908
Description: Binary data

On Apr 14, 2019, at 11:10 PM, Glasser, Matthew <glass...@wustl.edu> wrote:




In this case you do run it with the individual fMRI names and that doesn’t look like the version 4.0.0 example script...


Matt.




From: <hcp-users-boun...@humanconnectome.org> on behalf of Marta Moreno <mmorenoort...@icloud.com>
Date: Sunday, April 14, 2019 at 10:06 PM
To: HCP Users <hcp-users@humanconnectome.org>
Subject: [HCP-Users] DeDriftAndResamplePipeline error





Dear Experts,


I have run DeDriftAndResamplePipelineBatch.sh from from ${StudyFolder}/${Subject}/scripts after running MSMAII and getting the following error:





While running:

/Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command -metric-resample /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR.L.native.func.gii
 /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Native/NTTMS_s002_170812.L.sphere.MSMAll_Test.native.surf.gii /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/fsaverage_LR32k/NTTMS_s002_170812.L.sphere.32k_fs_LR.surf.gii
 ADAP_BARY_AREA /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_MSMAll_Test.L.atlasroi.32k_fs_LR.func.gii -area-surfs /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/T1w/Native/NTTMS_s002_170812.L.midthickness.native.surf.gii
 /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/T1w/fsaverage_LR32k/NTTMS_s002_170812.L.midthickness_MSMAll_Test.32k_fs_LR.surf.gii -current-roi /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Native/NTTMS_s002_170812.L.roi.native.shape.gii




ERROR: NAME OF FILE: RS_fMRI_MR.L.native.func.gii

PATH TO FILE: /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR




File does not exist.





I set up the script DeDriftAndResamplePipelineBatch.sh as follow (rfMRINames=“RS_fMRI_MR”, the concatenated name from MR+FIX):





HighResMesh="164"
LowResMesh="32"
RegName="MSMAll_InitalReg_2_d40_WRN"
DeDriftRegFiles="${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.L.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii@${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.R.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii"
ConcatRegName="MSMAll_Test"
Maps="sulc curvature corrThickness thickness"
MyelinMaps="MyelinMap SmoothedMyelinMap" #No _BC, this will be reapplied
rfMRINames="RS_fMRI_MR" #Space delimited list or NONE
tfMRINames="NONE"
SmoothingFWHM="2" #Should equal previous grayordiantes smoothing (because we are resampling from unsmoothed native mesh timeseries
HighPass="0"
MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab


I am attaching the log files.


Thanks a lot!


Leah.




___
HCP-Users mailing list
HCP-Users@humanc

[HCP-Users] DeDriftAndResamplePipeline error

[Marta Moreno]

Dear Experts,I have run DeDriftAndResamplePipelineBatch.sh from from ${StudyFolder}/${Subject}/scripts after running MSMAII and getting the following error:While running:/Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command -metric-resample /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR.L.native.func.gii /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Native/NTTMS_s002_170812.L.sphere.MSMAll_Test.native.surf.gii /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/fsaverage_LR32k/NTTMS_s002_170812.L.sphere.32k_fs_LR.surf.gii ADAP_BARY_AREA /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_MSMAll_Test.L.atlasroi.32k_fs_LR.func.gii -area-surfs /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/T1w/Native/NTTMS_s002_170812.L.midthickness.native.surf.gii /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/T1w/fsaverage_LR32k/NTTMS_s002_170812.L.midthickness_MSMAll_Test.32k_fs_LR.surf.gii -current-roi /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Native/NTTMS_s002_170812.L.roi.native.shape.giiERROR: NAME OF FILE: RS_fMRI_MR.L.native.func.giiPATH TO FILE: /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MRFile does not exist.I set up the script DeDriftAndResamplePipelineBatch.sh as follow (rfMRINames=“RS_fMRI_MR”, the concatenated name from MR+FIX):HighResMesh="164"LowResMesh="32"RegName="MSMAll_InitalReg_2_d40_WRN"DeDriftRegFiles="${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.L.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii@${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.R.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii"ConcatRegName="MSMAll_Test"Maps="sulc curvature corrThickness thickness"MyelinMaps="MyelinMap SmoothedMyelinMap" #No _BC, this will be reappliedrfMRINames="RS_fMRI_MR" #Space delimited list or NONEtfMRINames="NONE"SmoothingFWHM="2" #Should equal previous grayordiantes smoothing (because we are resampling from unsmoothed native mesh timeseriesHighPass="0"MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted MatlabI am attaching the log files.Thanks a lot!Leah.___HCP-Users mailing listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users


DeDriftAndResamplePipeline.sh.e17336
Description: Binary data


DeDriftAndResamplePipeline.sh.o17336
Description: Binary data

Re: [HCP-Users] MSMAllPipeline error

[Marta Moreno]

It worked! Thanks a lot!

Two questions regarding MR+FIX and MSMAII:
(i) what is the final file you use for functional connectivity, 
RS_fMRI_MR_Atlas_hp0_clean.dtseries.nii? What is 
RS_fMRI_MR_Atlas_hp0_clean_vn.dtseries.nii used for?
(ii) Which files do you use after MSMAII? Is there a documentation I can read 
to understand what MSMAII does and how to use its outputs?

Thanks again.

Leah.


> On Apr 14, 2019, at 2:17 PM, Glasser, Matthew  wrote:
> 
> You can work around this by adding 
> https://github.com/Washington-University/HCPpipelines/tree/master/global/matlab
>  
> <https://github.com/Washington-University/HCPpipelines/tree/master/global/matlab>
>  to your matlab path.
> 
> Matt.
> 
> From: Matt Glasser mailto:glass...@wustl.edu>>
> Date: Sunday, April 14, 2019 at 1:16 PM
> To: Marta Moreno mailto:mmorenoort...@icloud.com>>
> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users 
> mailto:hcp-users@humanconnectome.org>>, 
> Timothy Coalson mailto:tsc...@mst.edu>>, "Brown, Tim" 
> mailto:tbbr...@wustl.edu>>
> Subject: Re: [HCP-Users] MSMAllPipeline error
> 
> It looks like only the first matlab call has the matlab global variable, 
> which needs to be propagated to all the calls: 
> 
> https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/MSMAll.sh
>  
> <https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/MSMAll.sh>
> 
> Line 751
> Line 754
> Line 756
> 
> Are correct, but 
> 
> Lines 847-854, Lines 1256-1275, Lines 1346-1356 are not.  
> 
> We wil need to release a bugfix for this and a few other things.
> 
> Matt.
> 
> From: Marta Moreno  <mailto:mmorenoort...@icloud.com>>
> Date: Sunday, April 14, 2019 at 12:00 PM
> To: Matt Glasser mailto:glass...@wustl.edu>>
> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users 
> mailto:hcp-users@humanconnectome.org>>, 
> Timothy Coalson mailto:tsc...@mst.edu>>, "Brown, Tim" 
> mailto:tbbr...@wustl.edu>>
> Subject: Re: [HCP-Users] MSMAllPipeline error
> 
> Thanks for your help!
> 
> I am attaching log files below.
> 
> Leah.
> 
> 
> 
> 
>> On Apr 14, 2019, at 12:37 PM, Glasser, Matthew > <mailto:glass...@wustl.edu>> wrote:
>> 
>> It might be a better idea to attach whole log files to the e-mail in case 
>> you haven?™t selected the right bits.
>> 
>> Matt.
>> 
>> From: Marta Moreno > <mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, April 14, 2019 at 11:33 AM
>> To: Matt Glasser mailto:glass...@wustl.edu>>
>> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users 
>> mailto:hcp-users@humanconnectome.org>>, 
>> Timothy Coalson mailto:tsc...@mst.edu>>, "Brown, Tim" 
>> mailto:tbbr...@wustl.edu>>
>> Subject: Re: [HCP-Users] MSMAllPipeline error
>> 
>> Sorry to bother again. The script ended with an error in MSMregression. The 
>> file 
>> ".individual_Topography_MSMAll_InitalReg_1_d40_WRN.32k_fs_LR.dscalar.nii? 
>> is missing. I am pasting the error message below:
>> 
>> (??
>> Error in MSMregression (line 124)
>> NODEts=demean((pinv(demean(GM.*DesignWeights)) *
>> (demean(BO.cdata).*DenseWeights))');
>> 
>> Config: Volume coloring is disabled.
>> 
>> While running:
>> /Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command
>>  -cifti-resample 
>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/fsaverage_LR32k/NTTMS_s002_170812.individual_Topography_MSMAll_InitalReg_1_d40_WRN.32k_fs_LR.dscalar.nii
>>  COLUMN 
>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/fsaverage_LR32k/NTTMS_s002_170812.individual_Topography_MSMAll_InitalReg_1_d40_WRN.32k_fs_LR.dscalar.nii
>>  COLUMN ADAP_BARY_AREA ENCLOSING_VOXEL 
>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/fsaverage_LR32k/NTTMS_s002_170812.individual_Topography_MSMAll_InitalReg_1_d40_WRN.32k_fs_LR.dscalar.nii
>>  -surface-postdilate 40 -left-spheres 
>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/fsaverage_LR32k/NTTMS_s002_170812.L.sphere.MSMAll_InitalReg_1_d40_WRN.32k_fs_LR.surf.gii
>>  
>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/fsaverage_LR32k/NTTMS_s002_170812.L.sphere.32k_fs_LR.surf.gii
>>  -left-area-surfs 
>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/fsaverage_LR32k/NTTMS_s002_170812.L.midthickness.32k_fs_LR.surf.g

Re: [HCP-Users] MSMAllPipeline error

[Marta Moreno]

ench/bin_macosx64//wb_command','WRN','/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Native/MSMAll_InitalReg_2_d40_WRN/Params.txt','NO',0,'NO','NO');
Sun Apr 14 11:35:35 EDT 2019 - MSMAll.sh - Resample the individual maps so they 
are in the correct space

Thanks a lot!,

Leah.

> On Apr 14, 2019, at 11:13 AM, Marta Moreno  wrote:
> 
> Now it seams to be working! Thanks a lot!
> 
> Leah.
> 
>> On Apr 14, 2019, at 10:58 AM, Glasser, Matthew > <mailto:glass...@wustl.edu>> wrote:
>> 
>> Well we don’t support old versions of the HCP Pipelines so you should in 
>> fact upgrade to the current version: from here: 
>> 
>> https://github.com/Washington-University/HCPpipelines/releases 
>> <https://github.com/Washington-University/HCPpipelines/releases> 
>> 
>> This file is where you had the error:
>> 
>> https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/MSMAll.sh
>>  
>> <https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/MSMAll.sh>
>> 
>> Matt.
>> 
>> From: Marta Moreno > <mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, April 14, 2019 at 9:49 AM
>> To: Matt Glasser mailto:glass...@wustl.edu>>
>> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users 
>> mailto:hcp-users@humanconnectome.org>>, 
>> Timothy Coalson mailto:tsc...@mst.edu>>, "Brown, Tim" 
>> mailto:tbbr...@wustl.edu>>
>> Subject: Re: [HCP-Users] MSMAllPipeline error
>> 
>> Thanks for your response, and sorry to bother with this issue.
>> 
>> I went back to previous MSMAII version not to mix different versions but the 
>> problem persists. 
>> I have checked --verbose but the only line that includes it with mkdir (or 
>> cp) is in line 473 of SingleSubjectConcat.sh. 
>> I also checked MSMAllPipeline.sh.
>> 
>> Any other suggestion?
>> 
>> Leah.
>> 
>>> On Apr 14, 2019, at 10:16 AM, Glasser, Matthew >> <mailto:glass...@wustl.edu>> wrote:
>>> 
>>> You can delete the --verbose from all the cp lines.  All these flags appear 
>>> not to be compatible with mac os x built in utilities.
>>> 
>>> You certainly should actually download the entire pipelines 4.0.0 release 
>>> and follow the instructions there.  Running code from multiple versions is 
>>> likely to create problems, though the issues with mac that you have 
>>> encountered thus far are likely still there.
>>> 
>>> Matt.
>>> 
>>> From: Marta Moreno >> <mailto:mmorenoort...@icloud.com>>
>>> Date: Sunday, April 14, 2019 at 2:17 AM
>>> To: Matt Glasser mailto:glass...@wustl.edu>>
>>> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP 
>>> Users >> <mailto:hcp-users@humanconnectome.org>>, Timothy Coalson >> <mailto:tsc...@mst.edu>>
>>> Subject: Re: [HCP-Users] MSMAllPipeline error
>>> 
>>> I downloaded the last version of MSMAll to see if is a version problem. The 
>>> script now gives me the following error:
>>> Sun Apr 14 03:11:18 EDT 2019 - MSMAllPipeline.sh - HCPPIPEDIR: 
>>> /usr/local/bin/HCP/Connectome_Project_3_22/Pipelines
>>> Sun Apr 14 03:11:18 EDT 2019 - MSMAllPipeline.sh - ABORTING: MSMCONFIGDIR 
>>> environment variable must be set
>>> 
>>> How should i configure the environment variable: MSMCONFIGDIR?
>>> 
>>> Thanks!
>>> 
>>> Leah.
>>> 
>>>> On Apr 14, 2019, at 2:54 AM, Marta Moreno >>> <mailto:mmorenoort...@icloud.com>> wrote:
>>>> 
>>>> Thanks for your response!
>>>> 
>>>> Sorry to bother you but still I am getting an error. Now it says:
>>>> cp: illegal option -- -
>>>> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file
>>>>cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file … 
>>>> target_directory
>>>> 
>>>> In cat MSMAllPipeline.sh.o31773, says:
>>>> (…)
>>>> un Apr 14 02:52:14 EDT 2019 - MSMAll.sh - RSNTargetFile: 
>>>> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/melodic_oIC.dscalar.nii
>>>> Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - File: 
>>>> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_RES

Re: [HCP-Users] MSMAllPipeline error

[Marta Moreno]

Now it seams to be working! Thanks a lot!

Leah.

> On Apr 14, 2019, at 10:58 AM, Glasser, Matthew  wrote:
> 
> Well we don’t support old versions of the HCP Pipelines so you should in fact 
> upgrade to the current version: from here: 
> 
> https://github.com/Washington-University/HCPpipelines/releases 
> <https://github.com/Washington-University/HCPpipelines/releases> 
> 
> This file is where you had the error:
> 
> https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/MSMAll.sh
>  
> <https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/MSMAll.sh>
> 
> Matt.
> 
> From: Marta Moreno  <mailto:mmorenoort...@icloud.com>>
> Date: Sunday, April 14, 2019 at 9:49 AM
> To: Matt Glasser mailto:glass...@wustl.edu>>
> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users 
> mailto:hcp-users@humanconnectome.org>>, 
> Timothy Coalson mailto:tsc...@mst.edu>>, "Brown, Tim" 
> mailto:tbbr...@wustl.edu>>
> Subject: Re: [HCP-Users] MSMAllPipeline error
> 
> Thanks for your response, and sorry to bother with this issue.
> 
> I went back to previous MSMAII version not to mix different versions but the 
> problem persists. 
> I have checked --verbose but the only line that includes it with mkdir (or 
> cp) is in line 473 of SingleSubjectConcat.sh. 
> I also checked MSMAllPipeline.sh.
> 
> Any other suggestion?
> 
> Leah.
> 
>> On Apr 14, 2019, at 10:16 AM, Glasser, Matthew > <mailto:glass...@wustl.edu>> wrote:
>> 
>> You can delete the --verbose from all the cp lines.  All these flags appear 
>> not to be compatible with mac os x built in utilities.
>> 
>> You certainly should actually download the entire pipelines 4.0.0 release 
>> and follow the instructions there.  Running code from multiple versions is 
>> likely to create problems, though the issues with mac that you have 
>> encountered thus far are likely still there.
>> 
>> Matt.
>> 
>> From: Marta Moreno > <mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, April 14, 2019 at 2:17 AM
>> To: Matt Glasser mailto:glass...@wustl.edu>>
>> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users 
>> mailto:hcp-users@humanconnectome.org>>, 
>> Timothy Coalson mailto:tsc...@mst.edu>>
>> Subject: Re: [HCP-Users] MSMAllPipeline error
>> 
>> I downloaded the last version of MSMAll to see if is a version problem. The 
>> script now gives me the following error:
>> Sun Apr 14 03:11:18 EDT 2019 - MSMAllPipeline.sh - HCPPIPEDIR: 
>> /usr/local/bin/HCP/Connectome_Project_3_22/Pipelines
>> Sun Apr 14 03:11:18 EDT 2019 - MSMAllPipeline.sh - ABORTING: MSMCONFIGDIR 
>> environment variable must be set
>> 
>> How should i configure the environment variable: MSMCONFIGDIR?
>> 
>> Thanks!
>> 
>> Leah.
>> 
>>> On Apr 14, 2019, at 2:54 AM, Marta Moreno >> <mailto:mmorenoort...@icloud.com>> wrote:
>>> 
>>> Thanks for your response!
>>> 
>>> Sorry to bother you but still I am getting an error. Now it says:
>>> cp: illegal option -- -
>>> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file
>>>cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file … 
>>> target_directory
>>> 
>>> In cat MSMAllPipeline.sh.o31773, says:
>>> (…)
>>> un Apr 14 02:52:14 EDT 2019 - MSMAll.sh - RSNTargetFile: 
>>> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/melodic_oIC.dscalar.nii
>>> Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - File: 
>>> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/melodic_oIC.dscalar.nii
>>>  EXISTS
>>> Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - RSNCostWeights: 
>>> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt
>>> Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - File: 
>>> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt
>>>  EXISTS
>>> 
>>> Leah.
>>> 
>>> 
>>>> On Apr 13, 2019, at 4:45 PM, Glasser, Matthew >>&

Re: [HCP-Users] MSMAllPipeline error

[Marta Moreno]

Thanks for your response, and sorry to bother with this issue.

I went back to previous MSMAII version not to mix different versions but the 
problem persists. 
I have checked --verbose but the only line that includes it with mkdir (or cp) 
is in line 473 of SingleSubjectConcat.sh. 
I also checked MSMAllPipeline.sh.

Any other suggestion?

Leah.

> On Apr 14, 2019, at 10:16 AM, Glasser, Matthew  wrote:
> 
> You can delete the --verbose from all the cp lines.  All these flags appear 
> not to be compatible with mac os x built in utilities.
> 
> You certainly should actually download the entire pipelines 4.0.0 release and 
> follow the instructions there.  Running code from multiple versions is likely 
> to create problems, though the issues with mac that you have encountered thus 
> far are likely still there.
> 
> Matt.
> 
> From: Marta Moreno  <mailto:mmorenoort...@icloud.com>>
> Date: Sunday, April 14, 2019 at 2:17 AM
> To: Matt Glasser mailto:glass...@wustl.edu>>
> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users 
> mailto:hcp-users@humanconnectome.org>>, 
> Timothy Coalson mailto:tsc...@mst.edu>>
> Subject: Re: [HCP-Users] MSMAllPipeline error
> 
> I downloaded the last version of MSMAll to see if is a version problem. The 
> script now gives me the following error:
> Sun Apr 14 03:11:18 EDT 2019 - MSMAllPipeline.sh - HCPPIPEDIR: 
> /usr/local/bin/HCP/Connectome_Project_3_22/Pipelines
> Sun Apr 14 03:11:18 EDT 2019 - MSMAllPipeline.sh - ABORTING: MSMCONFIGDIR 
> environment variable must be set
> 
> How should i configure the environment variable: MSMCONFIGDIR?
> 
> Thanks!
> 
> Leah.
> 
>> On Apr 14, 2019, at 2:54 AM, Marta Moreno > <mailto:mmorenoort...@icloud.com>> wrote:
>> 
>> Thanks for your response!
>> 
>> Sorry to bother you but still I am getting an error. Now it says:
>> cp: illegal option -- -
>> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file
>>cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file … 
>> target_directory
>> 
>> In cat MSMAllPipeline.sh.o31773, says:
>> (…)
>> un Apr 14 02:52:14 EDT 2019 - MSMAll.sh - RSNTargetFile: 
>> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/melodic_oIC.dscalar.nii
>> Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - File: 
>> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/melodic_oIC.dscalar.nii
>>  EXISTS
>> Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - RSNCostWeights: 
>> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt
>> Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - File: 
>> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt
>>  EXISTS
>> 
>> Leah.
>> 
>> 
>>> On Apr 13, 2019, at 4:45 PM, Glasser, Matthew >> <mailto:glass...@wustl.edu>> wrote:
>>> 
>>> https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/SingleSubjectConcat.sh
>>>  
>>> <https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/SingleSubjectConcat.sh>
>>> 
>>> Line 473 apparently has to be -p on a mac
>>> 
>>> Matt.
>>> 
>>> From: Marta Moreno >> <mailto:mmorenoort...@icloud.com>>
>>> Date: Saturday, April 13, 2019 at 3:32 PM
>>> To: Matt Glasser mailto:glass...@wustl.edu>>
>>> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP 
>>> Users mailto:hcp-users@humanconnectome.org>>
>>> Subject: Re: [HCP-Users] MSMAllPipeline error
>>> 
>>> Thanks for your response.
>>> 
>>> I changed line 353 to NO. Now I am getting a different error:
>>> mkdir: illegal option -- -
>>> usage: mkdir [-pv] [-m mode] directory …
>>> 
>>> In cat MSMAllPipeline.sh.o9037, it stops in:
>>> (…)
>>> Operating System: Apple OSX
>>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Using named 
>>> parameters
>>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Study Folder: 
>>> /Volumes/data/data3/NTTMS/NTTMS_s002
>>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectCo

Re: [HCP-Users] MSMAllPipeline error

[Marta Moreno]

I downloaded the last version of MSMAll to see if is a version problem. The 
script now gives me the following error:
Sun Apr 14 03:11:18 EDT 2019 - MSMAllPipeline.sh - HCPPIPEDIR: 
/usr/local/bin/HCP/Connectome_Project_3_22/Pipelines
Sun Apr 14 03:11:18 EDT 2019 - MSMAllPipeline.sh - ABORTING: MSMCONFIGDIR 
environment variable must be set

How should i configure the environment variable: MSMCONFIGDIR?

Thanks!

Leah.

> On Apr 14, 2019, at 2:54 AM, Marta Moreno  wrote:
> 
> Thanks for your response!
> 
> Sorry to bother you but still I am getting an error. Now it says:
> cp: illegal option -- -
> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file
>cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file … 
> target_directory
> 
> In cat MSMAllPipeline.sh.o31773, says:
> (…)
> un Apr 14 02:52:14 EDT 2019 - MSMAll.sh - RSNTargetFile: 
> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/melodic_oIC.dscalar.nii
> Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - File: 
> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/melodic_oIC.dscalar.nii
>  EXISTS
> Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - RSNCostWeights: 
> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt
> Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - File: 
> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt
>  EXISTS
> 
> Leah.
> 
> 
>> On Apr 13, 2019, at 4:45 PM, Glasser, Matthew > <mailto:glass...@wustl.edu>> wrote:
>> 
>> https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/SingleSubjectConcat.sh
>>  
>> <https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/SingleSubjectConcat.sh>
>> 
>> Line 473 apparently has to be -p on a mac
>> 
>> Matt.
>> 
>> From: Marta Moreno > <mailto:mmorenoort...@icloud.com>>
>> Date: Saturday, April 13, 2019 at 3:32 PM
>> To: Matt Glasser mailto:glass...@wustl.edu>>
>> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users 
>> mailto:hcp-users@humanconnectome.org>>
>> Subject: Re: [HCP-Users] MSMAllPipeline error
>> 
>> Thanks for your response.
>> 
>> I changed line 353 to NO. Now I am getting a different error:
>> mkdir: illegal option -- -
>> usage: mkdir [-pv] [-m mode] directory …
>> 
>> In cat MSMAllPipeline.sh.o9037, it stops in:
>> (…)
>> Operating System: Apple OSX
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Using named 
>> parameters
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Study Folder: 
>> /Volumes/data/data3/NTTMS/NTTMS_s002
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Subject ID: 
>> NTTMS_s002_170812
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRI name list: 
>> RS_fMRI_MR
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - ICA+FIX highpass 
>> setting: 0
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Output fMRI Name: 
>> RS_fMRI_MR
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRI Proc String: 
>> _Atlas_hp0_clean
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Output Proc String: 
>> _vn
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Demean: YES
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Variance 
>> Normalization: NO
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Compute Variance 
>> Normalization: YES
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Revert Bias Field: NO
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - MATLAB run mode: 1
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - StudyFolder: 
>> /Volumes/data/data3/NTTMS/NTTMS_s002
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Subject: 
>> NTTMS_s002_170812
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRINames: RS_fMRI_MR
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - HighPass: 0
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - OutputfMRIName: 
>> RS_fMRI_MR
>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRIProcSTRING: 
>> _Atlas_hp0_clean
>> Sat 

Re: [HCP-Users] MSMAllPipeline error

[Marta Moreno]

Thanks for your response!

Sorry to bother you but still I am getting an error. Now it says:
cp: illegal option -- -
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file
   cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file … target_directory

In cat MSMAllPipeline.sh.o31773, says:
(…)
un Apr 14 02:52:14 EDT 2019 - MSMAll.sh - RSNTargetFile: 
/usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/melodic_oIC.dscalar.nii
Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - File: 
/usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/melodic_oIC.dscalar.nii
 EXISTS
Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - RSNCostWeights: 
/usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt
Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - File: 
/usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt
 EXISTS

Leah.


> On Apr 13, 2019, at 4:45 PM, Glasser, Matthew  wrote:
> 
> https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/SingleSubjectConcat.sh
>  
> <https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/SingleSubjectConcat.sh>
> 
> Line 473 apparently has to be -p on a mac
> 
> Matt.
> 
> From: Marta Moreno  <mailto:mmorenoort...@icloud.com>>
> Date: Saturday, April 13, 2019 at 3:32 PM
> To: Matt Glasser mailto:glass...@wustl.edu>>
> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users 
> mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] MSMAllPipeline error
> 
> Thanks for your response.
> 
> I changed line 353 to NO. Now I am getting a different error:
> mkdir: illegal option -- -
> usage: mkdir [-pv] [-m mode] directory …
> 
> In cat MSMAllPipeline.sh.o9037, it stops in:
> (…)
> Operating System: Apple OSX
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Using named parameters
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Study Folder: 
> /Volumes/data/data3/NTTMS/NTTMS_s002
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Subject ID: 
> NTTMS_s002_170812
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRI name list: 
> RS_fMRI_MR
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - ICA+FIX highpass 
> setting: 0
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Output fMRI Name: 
> RS_fMRI_MR
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRI Proc String: 
> _Atlas_hp0_clean
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Output Proc String: 
> _vn
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Demean: YES
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Variance 
> Normalization: NO
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Compute Variance 
> Normalization: YES
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Revert Bias Field: NO
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - MATLAB run mode: 1
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - StudyFolder: 
> /Volumes/data/data3/NTTMS/NTTMS_s002
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Subject: 
> NTTMS_s002_170812
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRINames: RS_fMRI_MR
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - HighPass: 0
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - OutputfMRIName: 
> RS_fMRI_MR
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRIProcSTRING: 
> _Atlas_hp0_clean
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - OutputProcSTRING: _vn
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Demean: YES
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - 
> VarianceNormalization: NO
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - 
> ComputeVarianceNormalization: YES
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - RevertBiasField: NO
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - MatlabRunMode: 1
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRINames: RS_fMRI_MR
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - OutputProcSTRING: _vn
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - AtlasFolder: 
> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear
> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Outp

Re: [HCP-Users] MSMAllPipeline error

[Marta Moreno]

Thanks for your response.

I changed line 353 to NO. Now I am getting a different error:
mkdir: illegal option -- -
usage: mkdir [-pv] [-m mode] directory …

In cat MSMAllPipeline.sh.o9037, it stops in:
(…)
Operating System: Apple OSX
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Using named parameters
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Study Folder: 
/Volumes/data/data3/NTTMS/NTTMS_s002
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Subject ID: 
NTTMS_s002_170812
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRI name list: 
RS_fMRI_MR
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - ICA+FIX highpass 
setting: 0
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Output fMRI Name: 
RS_fMRI_MR
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRI Proc String: 
_Atlas_hp0_clean
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Output Proc String: _vn
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Demean: YES
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Variance Normalization: 
NO
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Compute Variance 
Normalization: YES
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Revert Bias Field: NO
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - MATLAB run mode: 1
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - StudyFolder: 
/Volumes/data/data3/NTTMS/NTTMS_s002
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Subject: 
NTTMS_s002_170812
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRINames: RS_fMRI_MR
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - HighPass: 0
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - OutputfMRIName: 
RS_fMRI_MR
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRIProcSTRING: 
_Atlas_hp0_clean
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - OutputProcSTRING: _vn
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Demean: YES
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - VarianceNormalization: 
NO
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - 
ComputeVarianceNormalization: YES
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - RevertBiasField: NO
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - MatlabRunMode: 1
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRINames: RS_fMRI_MR
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - OutputProcSTRING: _vn
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - AtlasFolder: 
/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - OutputFolder: 
/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Caret7_Command: 
/Applications/workbench/bin_macosx64//wb_command
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRIName: RS_fMRI_MR
Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - ResultsFolder: 
/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR
Sat Apr 13 16:29:46 EDT 2019 - SingleSubjectConcat.sh - MATH: ((TCS - Mean))
parsed '((TCS - Mean))' as '(TCS-Mean)'

Leah.

> On Apr 13, 2019, at 4:10 PM, Glasser, Matthew  wrote:
> 
> You could try setting line 353 to NO: 
> 
> https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/MSMAllPipeline.sh
>  
> <https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/MSMAllPipeline.sh>
> 
> For more recent versions of FIX and MR+FIX, variance normalization is always 
> already computed.  That said, it isn’t clear to me why it is failing to 
> compute it again.  Perhaps you are not reporting the first error that occurs. 
>  
> 
> Matt.
> 
> From: Marta Moreno  <mailto:mmorenoort...@icloud.com>>
> Date: Saturday, April 13, 2019 at 2:55 PM
> To: Matt Glasser mailto:glass...@wustl.edu>>
> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users 
> mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] MSMAllPipeline error
> 
> Thanks for your response.
> 
> I am using now the concatenated name, called “RS_fMRI_MR” when I run MR 
> ICA+FIX:
> fMRINames="RS_fMRI_MR"
> OutfMRIName=“RS_fMRI_MR"
> (…)
> 
> but still getting same error:
> While running:
> /Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command
>  -cifti-math '((TCS - Mean)) / max(VN,0.001)' 
> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn.dtseries.nii
>  -var TCS 
> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean.dtseries.nii
>  -var Mean 
> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s

Re: [HCP-Users] MSMAllPipeline error

[Marta Moreno]

Thanks for your response.

I am using now the concatenated name, called “RS_fMRI_MR” when I run MR ICA+FIX:
fMRINames="RS_fMRI_MR"
OutfMRIName=“RS_fMRI_MR"
(…)

but still getting same error:
While running:
/Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command
 -cifti-math '((TCS - Mean)) / max(VN,0.001)' 
/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn.dtseries.nii
 -var TCS 
/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean.dtseries.nii
 -var Mean 
/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_mean.dscalar.nii
 -select 1 1 -repeat -var VN 
/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii
 -select 1 1 -repeat

ERROR: failed to open file 
'/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii',
 file does not exist, or folder permissions prevent seeing it

Leah.

***
Leah Moreno, PhD
Research Scientist
Division of Experimental Therapeutics
Department of Psychiatry
Columbia University Medical Center
1051 Riverside Drive, Unit 21
New York, NY 10032
phone: (914) 218-7311
email: mm4...@cumc.columbia.edu

> On Apr 13, 2019, at 3:39 PM, Glasser, Matthew  wrote:
> 
> If you ran MR+FIX, your data are already concatenated for MSMAll, so just 
> provide the concatenated fMRIName from the MR+FIX run.  It should work then.
> 
> Matt.
> 
> From: Marta Moreno  <mailto:mmorenoort...@icloud.com>>
> Date: Saturday, April 13, 2019 at 2:37 PM
> To: Matt Glasser mailto:glass...@wustl.edu>>
> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users 
> mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] MSMAllPipeline error
> 
> Thanks for your response!
> 
> I changed the set up as follow:
> fMRINames="RS_fMRI_1@RS_fMRI_2"
> OutfMRIName="RS_fMRI_1@RS_fMRI_2"
> HighPass="0"
> fMRIProcSTRING="_Atlas_hp0_clean"
> MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
> RegName="MSMAll_InitalReg"
> HighResMesh="164"
> LowResMesh="32"
> InRegName="MSMSulc"
> MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab
> 
> but still getting same error:
> While running:
> /Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command
>  -cifti-math '((TCS - Mean)) / max(VN,0.001)' 
> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean_vn.dtseries.nii
>  -var TCS 
> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean.dtseries.nii
>  -var Mean 
> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean_mean.dscalar.nii
>  -select 1 1 -repeat -var VN 
> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean_vn_tempcompute.dscalar.nii
>  -select 1 1 -repeat
> 
> ERROR: failed to open file 
> '/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean_vn_tempcompute.dscalar.nii',
>  file does not exist, or folder permissions prevent seeing it
> 
> Leah.
> 
>> On Apr 13, 2019, at 3:22 PM, Glasser, Matthew > <mailto:glass...@wustl.edu>> wrote:
>> 
>> You can just put your MR+FIX concatenated name in for the fMRIName and 
>> OutfMRIName.  
>> 
>> Matt.
>> 
>> From: Marta Moreno > <mailto:mmorenoort...@icloud.com>>
>> Date: Saturday, April 13, 2019 at 2:15 PM
>> To: Matt Glasser mailto:glass...@wustl.edu>>
>> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users 
>> mailto:hcp-users@humanconnectome.org>>
>> Subject: Re: [HCP-Users] MSMAllPipeline error
>> 
>> Thanks for your response!
>> 
>> I am running the following script MSMAllPipelineBatch.sh from 
>> ${StudyFolder}/${Subject}/scripts after running MR ICA+FIX with success
>> 
>> I set up the script as follow:
>> fMRINames="RS_fMRI_MR"
>> OutfMRIName="RS_fMRI_MR_REST"
>> HighPass=“0"
>> fMRIProcSTRING="_Atlas_hp0_clean"
>> MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
>> RegName="MSMAll_InitalReg"
>> HighResMesh="164"
&

Re: [HCP-Users] MSMAllPipeline error

[Marta Moreno]

Thanks for your response!

I changed the set up as follow:
fMRINames="RS_fMRI_1@RS_fMRI_2"
OutfMRIName="RS_fMRI_1@RS_fMRI_2"
HighPass="0"
fMRIProcSTRING="_Atlas_hp0_clean"
MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
RegName="MSMAll_InitalReg"
HighResMesh="164"
LowResMesh="32"
InRegName="MSMSulc"
MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab

but still getting same error:
While running:
/Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command
 -cifti-math '((TCS - Mean)) / max(VN,0.001)' 
/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean_vn.dtseries.nii
 -var TCS 
/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean.dtseries.nii
 -var Mean 
/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean_mean.dscalar.nii
 -select 1 1 -repeat -var VN 
/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean_vn_tempcompute.dscalar.nii
 -select 1 1 -repeat

ERROR: failed to open file 
'/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean_vn_tempcompute.dscalar.nii',
 file does not exist, or folder permissions prevent seeing it

Leah.

> On Apr 13, 2019, at 3:22 PM, Glasser, Matthew  wrote:
> 
> You can just put your MR+FIX concatenated name in for the fMRIName and 
> OutfMRIName.  
> 
> Matt.
> 
> From: Marta Moreno  <mailto:mmorenoort...@icloud.com>>
> Date: Saturday, April 13, 2019 at 2:15 PM
> To: Matt Glasser mailto:glass...@wustl.edu>>
> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users 
> mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] MSMAllPipeline error
> 
> Thanks for your response!
> 
> I am running the following script MSMAllPipelineBatch.sh from 
> ${StudyFolder}/${Subject}/scripts after running MR ICA+FIX with success
> 
> I set up the script as follow:
> fMRINames="RS_fMRI_MR"
> OutfMRIName="RS_fMRI_MR_REST"
> HighPass=“0"
> fMRIProcSTRING="_Atlas_hp0_clean"
> MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
> RegName="MSMAll_InitalReg"
> HighResMesh="164"
> LowResMesh="32"
> InRegName="MSMSulc"
> MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab
> 
> In "cat MSMAllPipeline.sh.o3905", it does not complete the following step:
> Sat Apr 13 15:09:36 EDT 2019 - SingleSubjectConcat.sh - OutputVN: 
> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii
> 
> (…)
> 
> And stops in:
> >> Sat Apr 13 15:09:44 EDT 2019 - SingleSubjectConcat.sh - 
> >> ComputeVN('/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean.dtseries.nii','NONE','/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_hp0.ica/filtered_func_data.ica/melodic_mix','/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_hp0.ica/.fix','/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii','/Applications/workbench/bin_macosx64//wb_command');
> Sat Apr 13 15:09:44 EDT 2019 - SingleSubjectConcat.sh - MATH: ((TCS - Mean)) 
> / max(VN,0.001)
> 
> Leah.
> 
> 
>> On Apr 13, 2019, at 3:02 PM, Glasser, Matthew > <mailto:glass...@wustl.edu>> wrote:
>> 
>> I guess specify how you called the MSMAll pipeline and perhaps that will 
>> provide a clue to the error if there are no other errors.
>> 
>> Matt.
>> 
>> From: Marta Moreno > <mailto:mmorenoort...@icloud.com>>
>> Date: Saturday, April 13, 2019 at 1:58 PM
>> To: "Harms, Michael" mailto:mha...@wustl.edu>>
>> Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP Users 
>> mailto:hcp-users@humanconnectome.org>>
>> Subject: Re: [HCP-Users] MSMAllPipeline error
>> 
>> Dear Experts,
>> 
>> I re-run MR ICA+FIX with hp=0 without errors but I am getting same error as 
>> before when running MSMAll; i.e. the file “*vn_tempcompute.dscalar.nii" does 
>> not exist. Please advice.
>> 
>> ERROR: failed to open file 
>> '/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean

Re: [HCP-Users] MSMAllPipeline error

[Marta Moreno]

Thanks for your response!

I am running the following script MSMAllPipelineBatch.sh from 
${StudyFolder}/${Subject}/scripts after running MR ICA+FIX with success

I set up the script as follow:
fMRINames="RS_fMRI_MR"
OutfMRIName="RS_fMRI_MR_REST"
HighPass=“0"
fMRIProcSTRING="_Atlas_hp0_clean"
MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
RegName="MSMAll_InitalReg"
HighResMesh="164"
LowResMesh="32"
InRegName="MSMSulc"
MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab

In "cat MSMAllPipeline.sh.o3905", it does not complete the following step:
Sat Apr 13 15:09:36 EDT 2019 - SingleSubjectConcat.sh - OutputVN: 
/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii

(…)

And stops in:
>> Sat Apr 13 15:09:44 EDT 2019 - SingleSubjectConcat.sh - 
>> ComputeVN('/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean.dtseries.nii','NONE','/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_hp0.ica/filtered_func_data.ica/melodic_mix','/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_hp0.ica/.fix','/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii','/Applications/workbench/bin_macosx64//wb_command');
Sat Apr 13 15:09:44 EDT 2019 - SingleSubjectConcat.sh - MATH: ((TCS - Mean)) / 
max(VN,0.001)

Leah.


> On Apr 13, 2019, at 3:02 PM, Glasser, Matthew  wrote:
> 
> I guess specify how you called the MSMAll pipeline and perhaps that will 
> provide a clue to the error if there are no other errors.
> 
> Matt.
> 
> From: Marta Moreno  <mailto:mmorenoort...@icloud.com>>
> Date: Saturday, April 13, 2019 at 1:58 PM
> To: "Harms, Michael" mailto:mha...@wustl.edu>>
> Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP Users 
> mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] MSMAllPipeline error
> 
> Dear Experts,
> 
> I re-run MR ICA+FIX with hp=0 without errors but I am getting same error as 
> before when running MSMAll; i.e. the file “*vn_tempcompute.dscalar.nii" does 
> not exist. Please advice.
> 
> ERROR: failed to open file 
> '/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii',
>  file does not exist, or folder permissions prevent seeing it
> 
> The file that exists is: RS_fMRI_MR_Atlas_hp0_clean_vn.dscalar.nii
> 
> Thanks!,
> 
> Leah.
> 
> 
> 
>> On Apr 13, 2019, at 12:33 PM, Harms, Michael > <mailto:mha...@wustl.edu>> wrote:
>> 
>> 
>> We extended that feature such that it should be an accepted option for all 
>> the "ICAFIX"-related scripts, but we haven't had a chance yet to extend it 
>> to the context of MSMAll and TaskAnalysis.  Hopefully in the near future...
>> 
>> --
>> 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 
>> <mailto:mha...@wustl.edu>
>> 
>> On 4/13/19, 11:28 AM, "hcp-users-boun...@humanconnectome.org 
>> <mailto:hcp-users-boun...@humanconnectome.org> on behalf of Glasser, 
>> Matthew" > <mailto:hcp-users-boun...@humanconnectome.org> on behalf of 
>> glass...@wustl.edu <mailto:glass...@wustl.edu>> wrote:
>> 
>> I wouldn¹t use hp=pd2 unless you know what you are doing, as that option
>> has not been fully tested.  I run with hp=0.
>> 
>> Matt.
>> 
>> On 4/13/19, 10:41 AM, "hcp-users-boun...@humanconnectome.org 
>> <mailto:hcp-users-boun...@humanconnectome.org> on behalf of
>> Marta Moreno" > <mailto:hcp-users-boun...@humanconnectome.org> on behalf of
>> mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>> wrote:
>> 
>>> Dear Experts,
>>> 
>>> I am running the following script MSMAllPipelineBatch.sh from
>>> ${StudyFolder}/${Subject}/scripts after running MR ICA+FIX with success,
>>> and I am getting the following error:
>>> 
>>> ERROR: failed to open file
>>> '/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s

Re: [HCP-Users] MSMAllPipeline error

[Marta Moreno]

Dear Experts,

I re-run MR ICA+FIX with hp=0 without errors but I am getting same error as 
before when running MSMAll; i.e. the file “*vn_tempcompute.dscalar.nii" does 
not exist. Please advice.

ERROR: failed to open file 
'/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii',
 file does not exist, or folder permissions prevent seeing it

The file that exists is: RS_fMRI_MR_Atlas_hp0_clean_vn.dscalar.nii

Thanks!,

Leah.



> On Apr 13, 2019, at 12:33 PM, Harms, Michael  wrote:
> 
> 
> We extended that feature such that it should be an accepted option for all 
> the "ICAFIX"-related scripts, but we haven't had a chance yet to extend it to 
> the context of MSMAll and TaskAnalysis.  Hopefully in the near future...
> 
> --
> 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 
> <mailto:mha...@wustl.edu>
> 
> On 4/13/19, 11:28 AM, "hcp-users-boun...@humanconnectome.org 
> <mailto:hcp-users-boun...@humanconnectome.org> on behalf of Glasser, Matthew" 
>  <mailto:hcp-users-boun...@humanconnectome.org> on behalf of 
> glass...@wustl.edu <mailto:glass...@wustl.edu>> wrote:
> 
> I wouldn¹t use hp=pd2 unless you know what you are doing, as that option
> has not been fully tested.  I run with hp=0.
> 
> Matt.
> 
> On 4/13/19, 10:41 AM, "hcp-users-boun...@humanconnectome.org 
> <mailto:hcp-users-boun...@humanconnectome.org> on behalf of
> Marta Moreno"  <mailto:hcp-users-boun...@humanconnectome.org> on behalf of
> mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>> wrote:
> 
>> Dear Experts,
>> 
>> I am running the following script MSMAllPipelineBatch.sh from
>> ${StudyFolder}/${Subject}/scripts after running MR ICA+FIX with success,
>> and I am getting the following error:
>> 
>> ERROR: failed to open file
>> '/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Resul
>> ts/RS_fMRI_MR/RS_fMRI_MR_Atlas_hppd2_clean_vn_tempcompute.dscalar.nii',
>> file does not exist, or folder permissions prevent seeing it
>> 
>> I set up the script as follow:
>> 
>> fMRINames="RS_fMRI_MR"
>> OutfMRIName="RS_fMRI_MR_REST"
>> HighPass="pd2"
>> fMRIProcSTRING="_Atlas_hppd2_clean"
>> MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
>> RegName="MSMAll_InitalReg"
>> HighResMesh="164"
>> LowResMesh="32"
>> InRegName="MSMSulc"
>> MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab
>> 
>> I checked and the file called: *tempcompute.dscalar.nii¹, is not there.
>> 
>> What am I doing wrong? Something went wrong in the previous step while
>> running MR ICA+FIX that I am not aware of?
>> 
>> Thanks a lot!
>> 
>> Leah.
>> 
>> 
>> 
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 
> 
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
> 
> 
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] MSMAllPipeline error

[Marta Moreno]

Thanks for your response. 

I am re-running MR ICA+FIX with hp=0. Will confirm if problem running MSMAll 
with hp=0 is solved.

Leah.


> On Apr 13, 2019, at 12:33 PM, Harms, Michael  wrote:
> 
> 
> We extended that feature such that it should be an accepted option for all 
> the "ICAFIX"-related scripts, but we haven't had a chance yet to extend it to 
> the context of MSMAll and TaskAnalysis.  Hopefully in the near future...
> 
> --
> 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 
> <mailto:mha...@wustl.edu>
> 
> On 4/13/19, 11:28 AM, "hcp-users-boun...@humanconnectome.org 
> <mailto:hcp-users-boun...@humanconnectome.org> on behalf of Glasser, Matthew" 
>  <mailto:hcp-users-boun...@humanconnectome.org> on behalf of 
> glass...@wustl.edu <mailto:glass...@wustl.edu>> wrote:
> 
> I wouldn¹t use hp=pd2 unless you know what you are doing, as that option
> has not been fully tested.  I run with hp=0.
> 
> Matt.
> 
> On 4/13/19, 10:41 AM, "hcp-users-boun...@humanconnectome.org 
> <mailto:hcp-users-boun...@humanconnectome.org> on behalf of
> Marta Moreno"  <mailto:hcp-users-boun...@humanconnectome.org> on behalf of
> mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>> wrote:
> 
>> Dear Experts,
>> 
>> I am running the following script MSMAllPipelineBatch.sh from
>> ${StudyFolder}/${Subject}/scripts after running MR ICA+FIX with success,
>> and I am getting the following error:
>> 
>> ERROR: failed to open file
>> '/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Resul
>> ts/RS_fMRI_MR/RS_fMRI_MR_Atlas_hppd2_clean_vn_tempcompute.dscalar.nii',
>> file does not exist, or folder permissions prevent seeing it
>> 
>> I set up the script as follow:
>> 
>> fMRINames="RS_fMRI_MR"
>> OutfMRIName="RS_fMRI_MR_REST"
>> HighPass="pd2"
>> fMRIProcSTRING="_Atlas_hppd2_clean"
>> MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
>> RegName="MSMAll_InitalReg"
>> HighResMesh="164"
>> LowResMesh="32"
>> InRegName="MSMSulc"
>> MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab
>> 
>> I checked and the file called: *tempcompute.dscalar.nii¹, is not there.
>> 
>> What am I doing wrong? Something went wrong in the previous step while
>> running MR ICA+FIX that I am not aware of?
>> 
>> Thanks a lot!
>> 
>> Leah.
>> 
>> 
>> 
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 
> 
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
> 
> 
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] MSMAllPipeline error

[Marta Moreno]

Dear Experts,

I am running the following script MSMAllPipelineBatch.sh from 
${StudyFolder}/${Subject}/scripts after running MR ICA+FIX with success, and I 
am getting the following error:

ERROR: failed to open file 
'/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hppd2_clean_vn_tempcompute.dscalar.nii',
 file does not exist, or folder permissions prevent seeing it

I set up the script as follow:

fMRINames="RS_fMRI_MR"
OutfMRIName="RS_fMRI_MR_REST"
HighPass="pd2"
fMRIProcSTRING="_Atlas_hppd2_clean"
MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
RegName="MSMAll_InitalReg"
HighResMesh="164"
LowResMesh="32"
InRegName="MSMSulc"
MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab

I checked and the file called: *tempcompute.dscalar.nii’, is not there.

What am I doing wrong? Something went wrong in the previous step while running 
MR ICA+FIX that I am not aware of?

Thanks a lot!

Leah.



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] MR ICA+FIX error

[Marta Moreno]

Thanks for your response, problem solved!

Leah.


> On Apr 6, 2019, at 4:18 PM, Harms, Michael  wrote:
> 
>  
> This indicates that you aren’t using the version of hcp_fix_multi_run from 
> the v4.0.0 pipelines, which supports the use of all 3 matlab modes.
>  
> -- 
> 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 
> <mailto:mha...@wustl.edu>
>  
> From:  on behalf of "Glasser, Matthew" 
> 
> Date: Saturday, April 6, 2019 at 2:57 PM
> To: Marta Moreno , NEUROSCIENCE tim 
> Cc: HCP Users 
> Subject: Re: [HCP-Users] MR ICA+FIX error
>  
> I would use mode=1
>  
> Matt.
>  
> From:  <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
> mailto:mmorenoort...@icloud.com>>
> Date: Saturday, April 6, 2019 at 2:46 PM
> To: Timothy Coalson mailto:tsc...@mst.edu>>
> Cc: HCP Users  <mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] MR ICA+FIX error
>  
> Dear Tim, 
>  
> I am getting the following error:
>  
> hcp_fix_multi_run - ABORTING: Unsupported MATLAB run mode value 
> (FSL_FIX_MATLAB_MODE) in 
> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/ICAFIX/hcp_fix_multi_run/settings.sh:
>  
> 
> 
> In settings.sh, I have set up the following:
>  
> # Part III General settings
> # =
> # This variable selects how we run the MATLAB portions of FIX.
> # It takes the values 0-2:
> #   0 - Try running the compiled version of the function
> #   1 - Use the MATLAB script version
> #   2 - Use Octave script version
> if [ -z "${FSL_FIX_MATLAB_MODE}" ]; then
> FSL_FIX_MATLAB_MODE=0
> fi
> if [[ ${FSL_FIX_MATLAB_MODE} = 2 && -z ${FSL_FIX_OCTAVE} ]]; then
> echo "ERROR in $0: Can't find Octave command"
> exit 1
> fi
> 
> 
>  Not sure if this is needed but FSL_FIX_OCTAVE is disabled in my settings.sh 
> since I tried to install octave via MacPorts and am getting the following 
> errors:
> 
> 
> Error: Failed to build mpich-default: command execution failed
> Error: See 
> /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_mpich/mpich-default/main.log
>  for details.
> Error: Follow https://guide.macports.org/#project.tickets 
> <https://guide.macports.org/#project.tickets> to report a bug.
> Error: Processing of port octave failed
> 
> 
> Thanks a lot,
> 
> 
> Leah.
> 
> 
>  
>  
>> On Apr 1, 2019, at 2:58 PM, Timothy Coalson > <mailto:tsc...@mst.edu>> wrote:
>>  
>> I have pushed a change (it launched the matlab part without error, which is 
>> where that path is used), try the latest master.
>>  
>> Tim
>>  
>>  
>> On Mon, Apr 1, 2019 at 1:49 PM Marta Moreno > <mailto:mmorenoort...@icloud.com>> wrote:
>>> Thanks for your response, Tim. 
>>> What should I do specifically to make it work. I am not sure I am following 
>>> the steps as written.
>>>  
>>> Thanks again,
>>> Leah.
>>> 
>>> Sent from my iPhone
>>> 
>>> On Apr 1, 2019, at 2:40 PM, Timothy Coalson >> <mailto:tsc...@mst.edu>> wrote:
>>> 
>>>> Looks like mac's readlink is incapable of being easily useful for this - 
>>>> without -f, it doesn't even output anything if it isn't a symlink, while 
>>>> the point is to find the real location whether it is a symlink or not 
>>>> (because it needs other files from that directory). 
>>>>  
>>>> I guess I will make it test whether "$0" is a symlink first.
>>>>  
>>>> Tim
>>>>  
>>>>  
>>>> On Mon, Apr 1, 2019 at 9:31 AM Harms, Michael >>> <mailto:mha...@wustl.edu>> wrote:
>>>>> Tim will have to comment on the ‘readlink -f’ issue, since I think he 
>>>>> introduced that particular syntax.
>>>>>  
>>>>> Please keep posts cc’ed to the HCP-User list, so that we can archive the 
>>>>> discussion, and other users can benefit from it.
>>>>>  
>>>>> -- 
>>>>> Michael Harms, Ph.D.
>>>>> ---
>>>>> Associate Prof

Re: [HCP-Users] MR ICA+FIX error

[Marta Moreno]

Dear Tim,

I am getting the following error:

hcp_fix_multi_run - ABORTING: Unsupported MATLAB run mode value 
(FSL_FIX_MATLAB_MODE) in 
/usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/ICAFIX/hcp_fix_multi_run/settings.sh:
 

In settings.sh, I have set up the following:

# Part III General settings
# =
# This variable selects how we run the MATLAB portions of FIX.
# It takes the values 0-2:
#   0 - Try running the compiled version of the function
#   1 - Use the MATLAB script version
#   2 - Use Octave script version
if [ -z "${FSL_FIX_MATLAB_MODE}" ]; then
FSL_FIX_MATLAB_MODE=0
fi
if [[ ${FSL_FIX_MATLAB_MODE} = 2 && -z ${FSL_FIX_OCTAVE} ]]; then
echo "ERROR in $0: Can't find Octave command"
exit 1
fi

 Not sure if this is needed but FSL_FIX_OCTAVE is disabled in my settings.sh 
since I tried to install octave via MacPorts and am getting the following 
errors:

Error: Failed to build mpich-default: command execution failed
Error: See 
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_mpich/mpich-default/main.log
 for details.
Error: Follow https://guide.macports.org/#project.tickets to report a bug.
Error: Processing of port octave failed

Thanks a lot,

Leah.



> On Apr 1, 2019, at 2:58 PM, Timothy Coalson  wrote:
> 
> I have pushed a change (it launched the matlab part without error, which is 
> where that path is used), try the latest master.
> 
> Tim
> 
> 
> On Mon, Apr 1, 2019 at 1:49 PM Marta Moreno  <mailto:mmorenoort...@icloud.com>> wrote:
> Thanks for your response, Tim. 
> What should I do specifically to make it work. I am not sure I am following 
> the steps as written.
> 
> Thanks again,
> Leah.
> 
> Sent from my iPhone
> 
> On Apr 1, 2019, at 2:40 PM, Timothy Coalson  <mailto:tsc...@mst.edu>> wrote:
> 
>> Looks like mac's readlink is incapable of being easily useful for this - 
>> without -f, it doesn't even output anything if it isn't a symlink, while the 
>> point is to find the real location whether it is a symlink or not (because 
>> it needs other files from that directory).
>> 
>> I guess I will make it test whether "$0" is a symlink first.
>> 
>> Tim
>> 
>> 
>> On Mon, Apr 1, 2019 at 9:31 AM Harms, Michael > <mailto:mha...@wustl.edu>> wrote:
>> Tim will have to comment on the ‘readlink -f’ issue, since I think he 
>> introduced that particular syntax.
>> 
>>  
>> 
>> Please keep posts cc’ed to the HCP-User list, so that we can archive the 
>> discussion, and other users can benefit from it.
>> 
>>  
>> 
>> -- 
>> 
>> Michael Harms, Ph.D.
>> 
>> ---
>> 
>> Associate Professor of Psychiatry
>> 
>> Washington University School of Medicine
>> 
>> Department of Psychiatry, Box 8134
>> 
>> 660 South Euclid Ave.Tel: 314-747-6173
>> 
>> St. Louis, MO  63110  Email: mha...@wustl.edu 
>> <mailto:mha...@wustl.edu>
>>  
>> 
>> From: Marta Moreno > <mailto:mmorenoort...@icloud.com>>
>> Date: Monday, April 1, 2019 at 9:21 AM
>> To: "Harms, Michael" mailto:mha...@wustl.edu>>
>> Subject: Re: [HCP-Users] ICA+FIX error
>> 
>>  
>> 
>> Thanks for your response, Michael. The issue with single ICA+ FIX is solved 
>> after running fMRISurface again.
>> 
>>  
>> 
>> The problem is now with MR ICA+FIX. I am copying the error below for your 
>> convenience. Matt said is probably related to the fact that I am using a MAC.
>> 
>>  
>> 
>> bash-3.2$ hcp_fix_multi_run 
>> RS_fMRI_1/RS_fMRI_1.nii.gz@RS_fMRI_2/RS_fMRI_2.nii.gz RS_fMRI_MR 2000 TRUE
>> 
>> Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - HCPPIPEDIR: 
>> /usr/local/bin/HCP/Pipelines
>> 
>> Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - CARET7DIR: 
>> /Applications/workbench/bin_macosx64/
>> 
>> Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - FSLDIR: /usr/local/fsl
>> 
>> Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - FSL_FIXDIR: 
>> /usr/local/bin/HCP/Pipelines/ICAFIX/hcp_fix_multi_run
>> 
>> readlink: illegal option -- f
>> 
>> usage: readlink [-n] [file …]
>> 
>>  
>> 
>> Thanks!,
>> 
>> Leah.
>> 
>> 
>> On Apr 1, 2019, at 9:29 AM, Harms, Michael > <mailto:mha...@wustl.edu>> wrote:
>> 
>>  
>> 
>> Check RS_fMRI_2_hp2000.ica/.fix.l

Re: [HCP-Users] ICA+FIX error

[Marta Moreno]

Thanks for your response, Michael. The issue with single ICA+ FIX is solved 
after running fMRISurface again.

The problem is now with MR ICA+FIX. I am copying the error below for your 
convenience. Matt said is probably related to the fact that I am using a MAC.

bash-3.2$ hcp_fix_multi_run 
RS_fMRI_1/RS_fMRI_1.nii.gz@RS_fMRI_2/RS_fMRI_2.nii.gz RS_fMRI_MR 2000 TRUE
Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - HCPPIPEDIR: 
/usr/local/bin/HCP/Pipelines
Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - CARET7DIR: 
/Applications/workbench/bin_macosx64/
Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - FSLDIR: /usr/local/fsl
Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - FSL_FIXDIR: 
/usr/local/bin/HCP/Pipelines/ICAFIX/hcp_fix_multi_run
readlink: illegal option -- f
usage: readlink [-n] [file …]

Thanks!,
Leah.



> On Apr 1, 2019, at 9:29 AM, Harms, Michael  wrote:
> 
>  
> Check RS_fMRI_2_hp2000.ica/.fix.log for clues.  Also, what’s in the stderr 
> output from the run?
>  
>  
> -- 
> 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 Marta Moreno 
> 
> Date: Sunday, March 31, 2019 at 6:44 PM
> To: HCP Users 
> Subject: [HCP-Users] ICA+FIX error
>  
> Dear Experts,
>  
> I am running hip_fix and getting the following error with just one of my 
> subjects, please see below. It seams the script stoped at the end, in section 
> "Rename some files (relative to the default names coded in fix_3_clean)”, 
> first line: "$FSLDIR/bin/immv ${fmrihp}.ica/filtered_func_data_clean 
> ${fmrihp}_clean”, which could not find a supported file with prefix 
> ".ica/filtered_func_data_clean”
>  
> (…)
> Sun Mar 31 19:18:12 EDT 2019 - hcp_fix - Done running FIX
> Sun Mar 31 19:18:13 EDT 2019 - hcp_fix - ABORTING: Something went wrong;  
> RS_fMRI_2_hp2000.ica/Atlas_clean.dtseries.nii wasn't created
>  
> How can I solve this problem?
>  
> Thanks,
>  
> Leah.
>  
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 
>  
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] ICA+FIX error

[Marta Moreno]

Dear Experts,

I am running hip_fix and getting the following error with just one of my 
subjects, please see below. It seams the script stoped at the end, in section 
"Rename some files (relative to the default names coded in fix_3_clean)”, first 
line: "$FSLDIR/bin/immv ${fmrihp}.ica/filtered_func_data_clean 
${fmrihp}_clean”, which could not find a supported file with prefix 
".ica/filtered_func_data_clean”

(…)
Sun Mar 31 19:18:12 EDT 2019 - hcp_fix - Done running FIX
Sun Mar 31 19:18:13 EDT 2019 - hcp_fix - ABORTING: Something went wrong;  
RS_fMRI_2_hp2000.ica/Atlas_clean.dtseries.nii wasn't created

How can I solve this problem?

Thanks,

Leah.



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] ICA+FIX not running

[Marta Moreno]

Dear Experts,

I downloaded the ICAFIX HCPpipelines v4.0.0  and installed fsl 6.0.1. 

I am running the hcp_fix_multi_run option and getting the following message 
(see below). What am I doing wrong?

bash-3.2$ hcp_fix_multi_run 
RS_fMRI_1/RS_fMRI_1.nii.gz@RS_fMRI_2/RS_fMRI_2.nii.gz RS_fMRI_MR 2000 TRUE
Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - HCPPIPEDIR: 
/usr/local/bin/HCP/Pipelines
Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - CARET7DIR: 
/Applications/workbench/bin_macosx64/
Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - FSLDIR: /usr/local/fsl
Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - FSL_FIXDIR: 
/usr/local/bin/HCP/Pipelines/ICAFIX/hcp_fix_multi_run
readlink: illegal option -- f
usage: readlink [-n] [file …]

Thanks!,

Leah.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] Question on fsl 6.0.1

[Marta Moreno]

Dear Experts,

Is FSL 6.0.1 ready for MR ICA+FIX and MSMAII? I have not seen any post yet in 
here.

Thanks,

Leah.

Sent from my iPhone

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] question on fsl 6.0.1

[Marta Moreno]

Dear Experts,

Is FSL 6.0.1 ready for MR ICA+FIX and MSMAII? I have not seen any post.

Thanks,

Leah.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Topup_AP dimension issue

[Marta Moreno]

Thanks, problem solved!

Leah.

> On Mar 25, 2019, at 2:35 PM, Timothy Coalson  wrote:
> 
> That looks like you cut off some brain tissue.  I'm not really sure what your 
> goal is here, but if you have images with different voxel sizes, what you may 
> actually need to do is to resample an image (flirt, applywarp, or wb_command 
> -volume-*-resample), and not crop it.
> 
> Tim
> 
> 
> On Sun, Mar 24, 2019 at 10:22 PM Marta Moreno  <mailto:mmorenoort...@icloud.com>> wrote:
> Thanks for your response. The image is now cropped, image attached.
> 
> Leah.
> 
> 
> 
> ***
> Leah Moreno, PhD
> Research Scientist
> Division of Experimental Therapeutics
> Department of Psychiatry
> Columbia University Medical Center
> 1051 Riverside Drive, Unit 21
> New York, NY 10032
> phone: (914) 218-7311
> email: mm4...@cumc.columbia.edu <mailto:mm4...@cumc.columbia.edu>
> 
>> On Mar 24, 2019, at 10:58 PM, Glasser, Matthew > <mailto:glass...@wustl.edu>> wrote:
>> 
>> 0 66 to include all slices and probably 0 1 for timepoints tacked onto the 
>> end.
>> 
>> Matt.
>> 
>> From: Marta Moreno > <mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, March 24, 2019 at 9:54 PM
>> To: Matt Glasser mailto:glass...@wustl.edu>>
>> Cc: HCP Users > <mailto:hcp-users@humanconnectome.org>>
>> Subject: Re: [HCP-Users] Topup_AP dimension issue
>> 
>> Thanks for your response. Still seams to be empty. I have attached both 
>> files into this email in case it helps. 
>> 
>> Leah.
>> 
>> 
>> 
>> ***
>> Leah Moreno, PhD
>> Research Scientist
>> Division of Experimental Therapeutics
>> Department of Psychiatry
>> Columbia University Medical Center
>> 1051 Riverside Drive, Unit 21
>> New York, NY 10032
>> phone: (914) 218-7311
>> email: mm4...@cumc.columbia.edu <mailto:mm4...@cumc.columbia.edu>
>> 
>>> On Mar 24, 2019, at 10:47 PM, Glasser, Matthew >> <mailto:glass...@wustl.edu>> wrote:
>>> 
>>> Not negative.
>>> 
>>> Matt.
>>> 
>>> From: Marta Moreno >> <mailto:mmorenoort...@icloud.com>>
>>> Date: Sunday, March 24, 2019 at 9:45 PM
>>> To: Matt Glasser mailto:glass...@wustl.edu>>
>>> Cc: HCP Users >> <mailto:hcp-users@humanconnectome.org>>
>>> Subject: Re: [HCP-Users] Topup_AP dimension issue
>>> 
>>> Thanks for your response. Do you mean running this?: fslroi 
>>> NTTMS_s037_181015_3T_SpinEchoFieldMap_AP_1.nii.gz test.nii.gz -16 96 -16 96 
>>> 66 66
>>> 
>>> If that is the case the test file seams to be empty.
>>> 
>>> Leah.
>>> 
>>> 
>>> 
>>>> On Mar 24, 2019, at 8:25 PM, Glasser, Matthew >>> <mailto:glass...@wustl.edu>> wrote:
>>>> 
>>>> Subtract 128 from 96 and then take half of that as your start and 96 as 
>>>> your length.
>>>> 
>>>> Matt.
>>>> 
>>>> From: >>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
>>>> mailto:mmorenoort...@icloud.com>>
>>>> Date: Sunday, March 24, 2019 at 6:40 PM
>>>> To: HCP Users >>> <mailto:hcp-users@humanconnectome.org>>
>>>> Subject: [HCP-Users] Topup_AP dimension issue
>>>> 
>>>> Dear Experts,
>>>> 
>>>> Maybe a trivial question but how can I change the Topup_AP dimension' size 
>>>> from 128 128 66 to 96 96 66? Using fslroi I am cutting the brain. 
>>>> 
>>>> Thanks,
>>>> 
>>>> Leah.
>>>> 
>>>> ___
>>>> HCP-Users mailing list
>>>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
>>>> <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

Re: [HCP-Users] Topup_AP dimension issue

[Marta Moreno]

Thanks for your response. The image is now cropped, image attached.

Leah.



***
Leah Moreno, PhD
Research Scientist
Division of Experimental Therapeutics
Department of Psychiatry
Columbia University Medical Center
1051 Riverside Drive, Unit 21
New York, NY 10032
phone: (914) 218-7311
email: mm4...@cumc.columbia.edu

> On Mar 24, 2019, at 10:58 PM, Glasser, Matthew  wrote:
> 
> 0 66 to include all slices and probably 0 1 for timepoints tacked onto the 
> end.
> 
> Matt.
> 
> From: Marta Moreno  <mailto:mmorenoort...@icloud.com>>
> Date: Sunday, March 24, 2019 at 9:54 PM
> To: Matt Glasser mailto:glass...@wustl.edu>>
> Cc: HCP Users  <mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] Topup_AP dimension issue
> 
> Thanks for your response. Still seams to be empty. I have attached both files 
> into this email in case it helps. 
> 
> Leah.
> 
> 
> 
> ***
> Leah Moreno, PhD
> Research Scientist
> Division of Experimental Therapeutics
> Department of Psychiatry
> Columbia University Medical Center
> 1051 Riverside Drive, Unit 21
> New York, NY 10032
> phone: (914) 218-7311
> email: mm4...@cumc.columbia.edu <mailto:mm4...@cumc.columbia.edu>
> 
>> On Mar 24, 2019, at 10:47 PM, Glasser, Matthew > <mailto:glass...@wustl.edu>> wrote:
>> 
>> Not negative.
>> 
>> Matt.
>> 
>> From: Marta Moreno > <mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, March 24, 2019 at 9:45 PM
>> To: Matt Glasser mailto:glass...@wustl.edu>>
>> Cc: HCP Users > <mailto:hcp-users@humanconnectome.org>>
>> Subject: Re: [HCP-Users] Topup_AP dimension issue
>> 
>> Thanks for your response. Do you mean running this?: fslroi 
>> NTTMS_s037_181015_3T_SpinEchoFieldMap_AP_1.nii.gz test.nii.gz -16 96 -16 96 
>> 66 66
>> 
>> If that is the case the test file seams to be empty.
>> 
>> Leah.
>> 
>> 
>> 
>>> On Mar 24, 2019, at 8:25 PM, Glasser, Matthew >> <mailto:glass...@wustl.edu>> wrote:
>>> 
>>> Subtract 128 from 96 and then take half of that as your start and 96 as 
>>> your length.
>>> 
>>> Matt.
>>> 
>>> From: >> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
>>> mailto:mmorenoort...@icloud.com>>
>>> Date: Sunday, March 24, 2019 at 6:40 PM
>>> To: HCP Users >> <mailto:hcp-users@humanconnectome.org>>
>>> Subject: [HCP-Users] Topup_AP dimension issue
>>> 
>>> Dear Experts,
>>> 
>>> Maybe a trivial question but how can I change the Topup_AP dimension' size 
>>> from 128 128 66 to 96 96 66? Using fslroi I am cutting the brain. 
>>> 
>>> Thanks,
>>> 
>>> Leah.
>>> 
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
>>> 
>>>  
>>> The materials in this message are private and may contain Protected 
>>> Healthcare Information or other information of a sensitive nature. If you 
>>> are not the intended recipient, be advised that any unauthorized use, 
>>> disclosure, copying or the taking of any action in reliance on the contents 
>>> of this information is strictly prohibited. If you have received this email 
>>> in error, please immediately notify the sender via telephone or return mail.
>> 
>> 
>>  
>> The materials in this message are private and may contain Protected 
>> Healthcare Information or other information of a sensitive nature. If you 
>> are not the intended recipient, be advised that any unauthorized use, 
>> disclosure, copying or the taking of any action in reliance on the contents 
>> of this information is strictly prohibited. If you have received this email 
>> in error, please immediately notify the sender via telephone or return mail.
> 
> 
>  
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Topup_AP dimension issue

[Marta Moreno]

Thanks for your response. Do you mean running this?: fslroi 
NTTMS_s037_181015_3T_SpinEchoFieldMap_AP_1.nii.gz test.nii.gz -16 96 -16 96 66 
66

If that is the case the test file seams to be empty.

Leah.



> On Mar 24, 2019, at 8:25 PM, Glasser, Matthew  wrote:
> 
> Subtract 128 from 96 and then take half of that as your start and 96 as your 
> length.
> 
> Matt.
> 
> From:  <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
> mailto:mmorenoort...@icloud.com>>
> Date: Sunday, March 24, 2019 at 6:40 PM
> To: HCP Users  <mailto:hcp-users@humanconnectome.org>>
> Subject: [HCP-Users] Topup_AP dimension issue
> 
> Dear Experts,
> 
> Maybe a trivial question but how can I change the Topup_AP dimension' size 
> from 128 128 66 to 96 96 66? Using fslroi I am cutting the brain. 
> 
> Thanks,
> 
> Leah.
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
> 
>  
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] Topup_AP dimension issue

[Marta Moreno]

Dear Experts,

Maybe a trivial question but how can I change the Topup_AP dimension' size from 
128 128 66 to 96 96 66? Using fslroi I am cutting the brain. 

Thanks,

Leah.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] related parcellation

[Marta Moreno]

Thanks so much!

Leah.

> On Mar 24, 2019, at 3:54 PM, Timothy Coalson  wrote:
> 
> The labels are used in the order of their keys, which is also how the 
> exported label table is ordered.  If your dlabel file has more label names 
> than there ended up being parcels, you can first use 
> -cifti-parcel-mapping-to-label to get a minimal dlabel file that exactly 
> matches the parcels mapping:
> 
> https://www.humanconnectome.org/software/workbench-command/-cifti-parcel-mapping-to-label
>  
> <https://www.humanconnectome.org/software/workbench-command/-cifti-parcel-mapping-to-label>
> 
> I believe -file-information will also print the parcel names in the order 
> they occur.
> 
> Tim
> 
> 
> On Sun, Mar 24, 2019 at 1:15 PM Glasser, Matthew  <mailto:glass...@wustl.edu>> wrote:
> You can use wb_command -cifti-label-export-table or look inside the Workbench 
> GUI.
> 
> Matt.
> 
> From:  <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
> mailto:mmorenoort...@icloud.com>>
> Date: Sunday, March 24, 2019 at 11:59 AM
> To: HCP Users  <mailto:hcp-users@humanconnectome.org>>
> Subject: [HCP-Users] related parcellation
> 
> Dear Experts,
> 
> If I create a ‘pconn.nii’ from each subject through the commands wb_command 
> -cifti-parcellate and -cifti-correlation to generate correlation matrix 
> between parcels (struct 360*360). How can I know which number in raw and 
> column correspond to parcel’s name in the dlabel.nii from 
> Q1-Q6_RelatedParcellation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii?
>  p.e., correlation value between parcels 46 and a24.
> 
> Thanks,
> 
> Leah
> 
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
> 
>  
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] related parcellation

[Marta Moreno]

Dear Experts,

If I create a ‘pconn.nii’ from each subject through the commands wb_command 
-cifti-parcellate and -cifti-correlation to generate correlation matrix between 
parcels (struct 360*360). How can I know which number in raw and column 
correspond to parcel’s name in the dlabel.nii from 
Q1-Q6_RelatedParcellation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii?
 p.e., correlation value between parcels 46 and a24.

Thanks,

Leah



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] MSMAll, missing _vn file

[Marta Moreno]

Dear experts,

I am running MSMAllPipelineBatch.sh after hcp_fix on a 10min run (rsfMRI) and 
getting an error saying that the file: 
"RS_fMRI_1_Atlas_hp2000_clean_vn_tempcompute.dscalar.nii" does not exist. I am 
using fsl 5.0.11 and fix 1.067. 

Any help?

Thanks,

Leah






___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] error running hcp_fix

[Marta Moreno]

 94 # Set this to the location of the HCP Workbench command for your platform
 95 FSL_FIX_WBC='/Applications/workbench/bin_macosx64';
 96 export FSL_FIX_CIFTIRW FSL_FIX_WBC

Thanks!

***
Leah Moreno, PhD
Associate Research Scientist
Division of Experimental Therapeutics
Department of Psychiatry
Columbia University Medical Center
1051 Riverside Drive, Unit 21
New York, NY 10032
phone: (914) 218-7311
email: mm4...@cumc.columbia.edu
email: mmor...@nyspi.columbia.edu

> On Jun 5, 2018, at 1:32 PM, Glasser, Matthew  wrote:
> 
> What do you have on line 94 of the FIX settings.sh?
> 
> Matt.
> 
> From: Marta Moreno  <mailto:mmorenoort...@icloud.com>>
> Date: Tuesday, June 5, 2018 at 12:28 PM
> To: Matt Glasser mailto:glass...@wustl.edu>>
> Cc: "st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>" 
> mailto:st...@fmrib.ox.ac.uk>>, HCP Users 
> mailto:hcp-users@humanconnectome.org>>, 
> Timothy Coalson mailto:tsc...@mst.edu>>, "Harwell, John" 
> mailto:jharw...@wustl.edu>>
> Subject: Re: [HCP-Users] error running hcp_fix
> 
> Dear Matt and all,
> 
> R version 3.4. Matlab version 2017b. Workbench version 1.3. I am using a 
> macOS Sierra version 10.12.6.  
> 
> I have installed all required versions from packages kernlab, party, etc. in 
> R successfully, but after running hcp_fix I get the following error in 
> .fix.log. Please advice (see below):
> 
> /bin/bash: /Applications/workbench/bin_macosx64: is a directory
> Error using read_gifti_file_standalone (line 20)
> [GIFTI] Loading of XML file
> /private/var/folders/j2/__433pcd02l1cw9qkydkqs5hgn/T/tp8475904261983465.gii
> failed.
> 
> Error in gifti (line 71)
> this = read_gifti_file_standalone(varargin{1},giftistruct);
> 
> Error in ciftiopen (line 31)
> cifti = gifti([tmpfile '.gii']);
> 
> Error in fix_3_clean (line 46)
>   BO=ciftiopen('Atlas.dtseries.nii',WBC);
> 
> Thanks,
> 
> -L
> ***
> Leah Moreno, PhD
> Associate Research Scientist
> Division of Experimental Therapeutics
> Department of Psychiatry
> Columbia University Medical Center
> 1051 Riverside Drive, Unit 21
> New York, NY 10032
> phone: (914) 218-7311
> email: mm4...@cumc.columbia.edu <mailto:mm4...@cumc.columbia.edu>
> email: mmor...@nyspi.columbia.edu <mailto:mmor...@nyspi.columbia.edu>
>> On May 27, 2018, at 4:24 PM, Glasser, Matthew > <mailto:glass...@wustl.edu>> wrote:
>> 
>> There is no relationship between R and Workbench (or R and matlab).  As to a 
>> Workbench/matlab incompatibility, we would need to know what version of 
>> Workbench and matlab to debug this.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: Marta Moreno > <mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, May 27, 2018 at 3:22 PM
>> To: "st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>" 
>> mailto:st...@fmrib.ox.ac.uk>>
>> Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP Users 
>> mailto:hcp-users@humanconnectome.org>>
>> Subject: Re: [HCP-Users] error running hcp_fix
>> 
>> Thanks, but with newer versions is not working either because R software 
>> packages  such as 'kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' 
>> version 1.6.7 or  'randomForest' version 4.6.12, are incompatible with R 3.3 
>> or 3.5. At least based on my experience. So could you please let me know 
>> which is the R version I need to install to have it compatible with 
>> workbench and also compatible with R software packages listed above that are 
>> needed to run hcp_fix? I am using a MAC pro, with workbench v1.3.
>> 
>> This is becoming a nightmare so I would really appreciate your help.
>> 
>> Thanks!,
>> 
>> -L
>> 
>>> On May 27, 2018, at 3:04 AM, st...@fmrib.ox.ac.uk 
>>> <mailto:st...@fmrib.ox.ac.uk> wrote:
>>> 
>>> Hi - we've seen this in the past with specific combinations of matlab 
>>> version and workbench version.  I'm not quite sure if the very latest 
>>> versions of both have the issue or not.
>>> Cheers.
>>> 
>>> 
>>>> On 27 May 2018, at 02:32, Marta Moreno >>> <mailto:mmorenoort...@icloud.com>> wrote:
>>>> 
>>>> I found the following error, please advice: (before is giving me some 
>>>> warnings about different functions that has same name as a Matlab builtin, 
>>>> I have pasted the output from last warning and first error). 
>>>> 
>>>> Which a

Re: [HCP-Users] error running hcp_fix

[Marta Moreno]

Dear Matt and all,

R version 3.4. Matlab version 2017b. Workbench version 1.3. I am using a macOS 
Sierra version 10.12.6.  

I have installed all required versions from packages kernlab, party, etc. in R 
successfully, but after running hcp_fix I get the following error in .fix.log. 
Please advice (see below):

/bin/bash: /Applications/workbench/bin_macosx64: is a directory
Error using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file
/private/var/folders/j2/__433pcd02l1cw9qkydkqs5hgn/T/tp8475904261983465.gii
failed.

Error in gifti (line 71)
this = read_gifti_file_standalone(varargin{1},giftistruct);

Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);

Error in fix_3_clean (line 46)
  BO=ciftiopen('Atlas.dtseries.nii',WBC);

Thanks,

-L
***
Leah Moreno, PhD
Associate Research Scientist
Division of Experimental Therapeutics
Department of Psychiatry
Columbia University Medical Center
1051 Riverside Drive, Unit 21
New York, NY 10032
phone: (914) 218-7311
email: mm4...@cumc.columbia.edu
email: mmor...@nyspi.columbia.edu

> On May 27, 2018, at 4:24 PM, Glasser, Matthew  wrote:
> 
> There is no relationship between R and Workbench (or R and matlab).  As to a 
> Workbench/matlab incompatibility, we would need to know what version of 
> Workbench and matlab to debug this.
> 
> Peace,
> 
> Matt.
> 
> From: Marta Moreno  <mailto:mmorenoort...@icloud.com>>
> Date: Sunday, May 27, 2018 at 3:22 PM
> To: "st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>" 
> mailto:st...@fmrib.ox.ac.uk>>
> Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP Users 
> mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] error running hcp_fix
> 
> Thanks, but with newer versions is not working either because R software 
> packages  such as 'kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' 
> version 1.6.7 or  'randomForest' version 4.6.12, are incompatible with R 3.3 
> or 3.5. At least based on my experience. So could you please let me know 
> which is the R version I need to install to have it compatible with workbench 
> and also compatible with R software packages listed above that are needed to 
> run hcp_fix? I am using a MAC pro, with workbench v1.3.
> 
> This is becoming a nightmare so I would really appreciate your help.
> 
> Thanks!,
> 
> -L
> 
>> On May 27, 2018, at 3:04 AM, st...@fmrib.ox.ac.uk 
>> <mailto:st...@fmrib.ox.ac.uk> wrote:
>> 
>> Hi - we've seen this in the past with specific combinations of matlab 
>> version and workbench version.  I'm not quite sure if the very latest 
>> versions of both have the issue or not.
>> Cheers.
>> 
>> 
>>> On 27 May 2018, at 02:32, Marta Moreno >> <mailto:mmorenoort...@icloud.com>> wrote:
>>> 
>>> I found the following error, please advice: (before is giving me some 
>>> warnings about different functions that has same name as a Matlab builtin, 
>>> I have pasted the output from last warning and first error). 
>>> 
>>> Which are the files that needs to be included in ‘CIFTIMatlabReaderWriter’ 
>>> for the settings.sh?
>>> 
>>> Warning: Function subsref has the same name as a MATLAB builtin. We suggest 
>>> you
>>> rename the function to avoid a potential name conflict. 
>>> > In path (line 109)
>>>   In fix_3_clean (line 45) 
>>> /bin/bash: /usr/local/workbench/bin_macosx64: is a directory
>>> Error using read_gifti_file_standalone (line 20)
>>> [GIFTI] Loading of XML file
>>> /private/var/folders/j2/__433pcd02l1cw9qkydkqs5hgn/T/tp6555679429695603.gii
>>> failed.
>>> 
>>> Error in gifti (line 71)
>>> this = read_gifti_file_standalone(varargin{1},giftistruct);
>>> 
>>> Error in ciftiopen (line 31)
>>> cifti = gifti([tmpfile '.gii']);
>>> 
>>> Error in fix_3_clean (line 46)
>>>   BO=ciftiopen('Atlas.dtseries.nii',WBC);
>>> 
>>> Thanks!
>>> 
>>> -L
>>> 
>>> 
>>>> On May 26, 2018, at 6:55 PM, Marta Moreno >>> <mailto:mmorenoort...@icloud.com>> wrote:
>>>> 
>>>> You were right, now the problem is gone but still cannot find my 
>>>> clean.dtseries
>>>> 
>>>> Here is the output, I could not find any error in .ica folder:
>>>> hcp_fix RS_fMRI_1.nii.gz 2000
>>>> processing FMRI file RS_fMRI_1 with highpass 2000
>>>> running highpass
>>>> running MELODIC
>>>> running FIX
>>>> FIX Feature extr

[HCP-Users] hcp_fix question

[Marta Moreno]

Dear Experts,

I have installed all required versions from packages kernlab, party, etc. in R 
successfully, but after running hcp_fix I found the following error in 
.fix.log. Please advice (see below):

/bin/bash: /Applications/workbench/bin_macosx64: is a directory
Error using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file
/private/var/folders/j2/__433pcd02l1cw9qkydkqs5hgn/T/tp8475904261983465.gii
failed.

Error in gifti (line 71)
this = read_gifti_file_standalone(varargin{1},giftistruct);

Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);

Error in fix_3_clean (line 46)
  BO=ciftiopen('Atlas.dtseries.nii',WBC);

Thanks,

-L


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] error running hcp_fix

[Marta Moreno]

Thanks. I can install randomForest_4.6-14 instead. IS there any specific reason 
for needing version 4.6-12 to run hip_fix?



***
Leah Moreno, PhD
Associate Research Scientist
Division of Experimental Therapeutics
Department of Psychiatry
Columbia University Medical Center
1051 Riverside Drive, Unit 21
New York, NY 10032
phone: (914) 218-7311
email: mm4...@cumc.columbia.edu
email: mmor...@nyspi.columbia.edu

> On May 30, 2018, at 7:52 PM, Timothy Coalson  wrote:
> 
> That is the same line I used to install randomForest in a docker container.  
> I would guess that those look like assembly directives.  Based on that, I 
> would guess that either randomForest uses some assembly code, and it doesn't 
> support the OS X compiler you are using, or that you somehow have a broken 
> compiler setup (less likely).
> 
> The main possibilities I see:
> 
> 1) do your processing using linux instead of OS X (VM, container, or a native 
> install)
> 2) try installing gcc and gfortran on OS X, and getting R to use them to 
> build packages (probably messy, may need to rebuild R itself, we haven't 
> tested it)
> 
> Tim
> 
> 
> On Wed, May 30, 2018 at 8:59 AM, Marta Moreno  <mailto:mmorenoort...@icloud.com>> wrote:
> Dear Tim,
> 
>  How did you install randomForest' version 4.6.12? I am getting the following 
> error (see below). Do I need R-devel as well to install randomForest? Please 
> advice this should be the last step before having hcp_fix running properly. 
> 
> install_version("randomForest", version = "4.6-12", repos = 
> "http://cran.us.r-project.org <http://cran.us.r-project.org/>”)
> 
> (…)
> 
> /var/tmp//ccP5LbYW.s:2671:2: error: unknown directive
> .stabn  224,0,0,LBE141
> ^
> /var/tmp//ccP5LbYW.s:2673:9: error: unsupported directive '.stabs'
> .stabs  "",36,0,0,Lscope8-LFBB8
> ^
> /var/tmp//ccP5LbYW.s:2697:9: error: unsupported directive '.stabs'
> .stabs  "",100,0,0,Letext0
> ^
> /var/tmp//ccP5LbYW.s:2835:11: warning: section "__textcoal_nt" is deprecated
> .section __TEXT,__textcoal_nt,coalesced,pure_instructions
>  ^  ~
> /var/tmp//ccP5LbYW.s:2835:11: note: change section name to "__text"
> .section __TEXT,__textcoal_nt,coalesced,pure_instructions
>  ^  ~
> make: *** [rfsub.o] Error 1
> ERROR: compilation failed for package ‘randomForest’
> * removing 
> ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/randomForest’
> Installation failed: Command failed (1)
> 
> Thanks a lot!
> 
> -L
> 
> ***
> Leah Moreno, PhD
> Associate Research Scientist
> Division of Experimental Therapeutics
> Department of Psychiatry
> Columbia University Medical Center
> 1051 Riverside Drive, Unit 21 
> <https://maps.google.com/?q=1051+Riverside+Drive,+Unit+21+New+York,+NY+10032=gmail=g>
> New York, NY 10032 
> <https://maps.google.com/?q=1051+Riverside+Drive,+Unit+21+New+York,+NY+10032=gmail=g>
> phone: (914) 218-7311
> email: mm4...@cumc.columbia.edu <mailto:mm4...@cumc.columbia.edu>
> email: mmor...@nyspi.columbia.edu <mailto:mmor...@nyspi.columbia.edu>
> 
>> On May 27, 2018, at 11:20 PM, Marta Moreno > <mailto:mmorenoort...@icloud.com>> wrote:
>> 
>> Thanks, Tim! I followed your advice and I am almost there… How did you 
>> install randomForest' version 4.6.12? I am getting the following error: 
>> 
>> install_version("randomForest", version = "4.6-12", repos = 
>> "http://cran.us.r-project.org <http://cran.us.r-project.org/>”)
>> 
>> (…)
>> 
>> /var/tmp//ccP5LbYW.s:2671:2: error: unknown directive
>> .stabn  224,0,0,LBE141
>> ^
>> /var/tmp//ccP5LbYW.s:2673:9: error: unsupported directive '.stabs'
>> .stabs  "",36,0,0,Lscope8-LFBB8
>> ^
>> /var/tmp//ccP5LbYW.s:2697:9: error: unsupported directive '.stabs'
>> .stabs  "",100,0,0,Letext0
>> ^
>> /var/tmp//ccP5LbYW.s:2835:11: warning: section "__textcoal_nt" is deprecated
>> .section __TEXT,__textcoal_nt,coalesced,pure_instructions
>>  ^  ~
>> /var/tmp//ccP5LbYW.s:2835:11: note: change section name to "__text"
>> .section __TEXT,__textcoal_nt,coalesced,pure_instructions
>>  ^  ~
>> make: *** [rfsub.o] Error 1
>> ERROR: compilation failed for package 

Re: [HCP-Users] error running hcp_fix

[Marta Moreno]

Dear Tim,

 How did you install randomForest' version 4.6.12? I am getting the following 
error (see below). Do I need R-devel as well to install randomForest? Please 
advice this should be the last step before having hcp_fix running properly. 

install_version("randomForest", version = "4.6-12", repos = 
"http://cran.us.r-project.org <http://cran.us.r-project.org/>”)

(…)

/var/tmp//ccP5LbYW.s:2671:2: error: unknown directive
.stabn  224,0,0,LBE141
^
/var/tmp//ccP5LbYW.s:2673:9: error: unsupported directive '.stabs'
.stabs  "",36,0,0,Lscope8-LFBB8
^
/var/tmp//ccP5LbYW.s:2697:9: error: unsupported directive '.stabs'
.stabs  "",100,0,0,Letext0
^
/var/tmp//ccP5LbYW.s:2835:11: warning: section "__textcoal_nt" is deprecated
.section __TEXT,__textcoal_nt,coalesced,pure_instructions
 ^  ~
/var/tmp//ccP5LbYW.s:2835:11: note: change section name to "__text"
.section __TEXT,__textcoal_nt,coalesced,pure_instructions
 ^  ~
make: *** [rfsub.o] Error 1
ERROR: compilation failed for package ‘randomForest’
* removing 
‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/randomForest’
Installation failed: Command failed (1)

Thanks a lot!

-L

***
Leah Moreno, PhD
Associate Research Scientist
Division of Experimental Therapeutics
Department of Psychiatry
Columbia University Medical Center
1051 Riverside Drive, Unit 21
New York, NY 10032
phone: (914) 218-7311
email: mm4...@cumc.columbia.edu
email: mmor...@nyspi.columbia.edu

> On May 27, 2018, at 11:20 PM, Marta Moreno  wrote:
> 
> Thanks, Tim! I followed your advice and I am almost there… How did you 
> install randomForest' version 4.6.12? I am getting the following error: 
> 
> install_version("randomForest", version = "4.6-12", repos = 
> "http://cran.us.r-project.org <http://cran.us.r-project.org/>”)
> 
> (…)
> 
> /var/tmp//ccP5LbYW.s:2671:2: error: unknown directive
> .stabn  224,0,0,LBE141
> ^
> /var/tmp//ccP5LbYW.s:2673:9: error: unsupported directive '.stabs'
> .stabs  "",36,0,0,Lscope8-LFBB8
> ^
> /var/tmp//ccP5LbYW.s:2697:9: error: unsupported directive '.stabs'
> .stabs  "",100,0,0,Letext0
> ^
> /var/tmp//ccP5LbYW.s:2835:11: warning: section "__textcoal_nt" is deprecated
> .section __TEXT,__textcoal_nt,coalesced,pure_instructions
>  ^  ~
> /var/tmp//ccP5LbYW.s:2835:11: note: change section name to "__text"
> .section __TEXT,__textcoal_nt,coalesced,pure_instructions
>  ^  ~
> make: *** [rfsub.o] Error 1
> ERROR: compilation failed for package ‘randomForest’
> * removing 
> ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/randomForest’
> Installation failed: Command failed (1)
> 
> Thanks!
> 
> -L
> 
>> On May 27, 2018, at 9:12 PM, Timothy Coalson > <mailto:tsc...@mst.edu>> wrote:
>> 
>> The way I solved this was to use the very latest R version (cran mirrors 
>> contain debian and ubuntu packages, see 
>> http://cran.wustl.edu/bin/linux/ubuntu/ 
>> <http://cran.wustl.edu/bin/linux/ubuntu/> , and they also have OS X 
>> binaries: http://cran.wustl.edu/bin/macosx/ 
>> <http://cran.wustl.edu/bin/macosx/> ), then install devtools (this is the 
>> main reason for installing the latest R, as getting devtools installed in 
>> older R is an even bigger pain), and then use "install_version": 
>> https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages
>>  
>> <https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages>
>> 
>> Tim
>> 
>> 
>> On Sun, May 27, 2018 at 3:32 PM, Marta Moreno > <mailto:mmorenoort...@icloud.com>> wrote:
>> I am using workbench v1.3. I have used R v3.3, R v3.4.and R v3.5. None of 
>> them allowed me to install specified software packages versions required to 
>> run hcp_fix: ('kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' 
>> version 1.6.7 or  'randomForest' version 4.6.12), so I guess the error I am 
>> getting now is regarding this issue. I have pasted the error below: 
>> 
>> Error in ctreefit(object = object, controls = controls, weights = weights,  
>> : 
>>   no slot of name "remove_weights" for this object of class "TreeGrowControl"
>> Calls: eval -> eval ->  -> ctreefit
>> Execution halte

Re: [HCP-Users] error running hcp_fix

[Marta Moreno]

Thanks, Tim! I followed your advice and I am almost there… How did you install 
randomForest' version 4.6.12? I am getting the following error: 

install_version("randomForest", version = "4.6-12", repos = 
"http://cran.us.r-project.org”)

(…)

/var/tmp//ccP5LbYW.s:2671:2: error: unknown directive
.stabn  224,0,0,LBE141
^
/var/tmp//ccP5LbYW.s:2673:9: error: unsupported directive '.stabs'
.stabs  "",36,0,0,Lscope8-LFBB8
^
/var/tmp//ccP5LbYW.s:2697:9: error: unsupported directive '.stabs'
.stabs  "",100,0,0,Letext0
^
/var/tmp//ccP5LbYW.s:2835:11: warning: section "__textcoal_nt" is deprecated
.section __TEXT,__textcoal_nt,coalesced,pure_instructions
 ^  ~
/var/tmp//ccP5LbYW.s:2835:11: note: change section name to "__text"
.section __TEXT,__textcoal_nt,coalesced,pure_instructions
 ^  ~
make: *** [rfsub.o] Error 1
ERROR: compilation failed for package ‘randomForest’
* removing 
‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/randomForest’
Installation failed: Command failed (1)

Thanks!

-L

> On May 27, 2018, at 9:12 PM, Timothy Coalson <tsc...@mst.edu> wrote:
> 
> The way I solved this was to use the very latest R version (cran mirrors 
> contain debian and ubuntu packages, see 
> http://cran.wustl.edu/bin/linux/ubuntu/ 
> <http://cran.wustl.edu/bin/linux/ubuntu/> , and they also have OS X binaries: 
> http://cran.wustl.edu/bin/macosx/ <http://cran.wustl.edu/bin/macosx/> ), then 
> install devtools (this is the main reason for installing the latest R, as 
> getting devtools installed in older R is an even bigger pain), and then use 
> "install_version": 
> https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages
>  
> <https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages>
> 
> Tim
> 
> 
> On Sun, May 27, 2018 at 3:32 PM, Marta Moreno <mmorenoort...@icloud.com 
> <mailto:mmorenoort...@icloud.com>> wrote:
> I am using workbench v1.3. I have used R v3.3, R v3.4.and R v3.5. None of 
> them allowed me to install specified software packages versions required to 
> run hcp_fix: ('kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' 
> version 1.6.7 or  'randomForest' version 4.6.12), so I guess the error I am 
> getting now is regarding this issue. I have pasted the error below: 
> 
> Error in ctreefit(object = object, controls = controls, weights = weights,  : 
>   no slot of name "remove_weights" for this object of class "TreeGrowControl"
> Calls: eval -> eval ->  -> ctreefit
> Execution halted
> 
> Please advice on which R version should I have installed to make it to work. 
> I have downloaded software packages and installing them in R as root as 
> follow:
> > install.packages('/Users/alayar/Downloads/kernlab_0.9-24.tar', 
> > dependencies=TRUE)
> Warning message:
> package ‘/Users/alayar/Downloads/kernlab_0.9-24.tar’ is not available (for R 
> version 3.3.3)
> 
> Thanks!
> 
> -L
> 
>> On May 27, 2018, at 4:24 PM, Glasser, Matthew <glass...@wustl.edu 
>> <mailto:glass...@wustl.edu>> wrote:
>> 
>> There is no relationship between R and Workbench (or R and matlab).  As to a 
>> Workbench/matlab incompatibility, we would need to know what version of 
>> Workbench and matlab to debug this.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: Marta Moreno <mmorenoort...@icloud.com 
>> <mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, May 27, 2018 at 3:22 PM
>> To: "st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>" 
>> <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>>
>> Cc: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>, HCP Users 
>> <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
>> Subject: Re: [HCP-Users] error running hcp_fix
>> 
>> Thanks, but with newer versions is not working either because R software 
>> packages  such as 'kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' 
>> version 1.6.7 or  'randomForest' version 4.6.12, are incompatible with R 3.3 
>> or 3.5. At least based on my experience. So could you please let me know 
>> which is the R version I need to install to have it compatible with 
>> workbench and also compatible with R software packages listed above that are 
>> needed to run hcp_fix? I am using a MAC pro, with workbench v1.3.
>> 
>> This is becoming a nightmare so I would really appreciate your

Re: [HCP-Users] error running hcp_fix

[Marta Moreno]

I am using workbench v1.3. I have used R v3.3, R v3.4.and R v3.5. None of them 
allowed me to install specified software packages versions required to run 
hcp_fix: ('kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' version 
1.6.7 or  'randomForest' version 4.6.12), so I guess the error I am getting now 
is regarding this issue. I have pasted the error below: 

Error in ctreefit(object = object, controls = controls, weights = weights,  : 
  no slot of name "remove_weights" for this object of class "TreeGrowControl"
Calls: eval -> eval ->  -> ctreefit
Execution halted

Please advice on which R version should I have installed to make it to work. I 
have downloaded software packages and installing them in R as root as follow:
> install.packages('/Users/alayar/Downloads/kernlab_0.9-24.tar', 
> dependencies=TRUE)
Warning message:
package ‘/Users/alayar/Downloads/kernlab_0.9-24.tar’ is not available (for R 
version 3.3.3)

Thanks!

-L

> On May 27, 2018, at 4:24 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
> 
> There is no relationship between R and Workbench (or R and matlab).  As to a 
> Workbench/matlab incompatibility, we would need to know what version of 
> Workbench and matlab to debug this.
> 
> Peace,
> 
> Matt.
> 
> From: Marta Moreno <mmorenoort...@icloud.com 
> <mailto:mmorenoort...@icloud.com>>
> Date: Sunday, May 27, 2018 at 3:22 PM
> To: "st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>" 
> <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>>
> Cc: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>, HCP Users 
> <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] error running hcp_fix
> 
> Thanks, but with newer versions is not working either because R software 
> packages  such as 'kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' 
> version 1.6.7 or  'randomForest' version 4.6.12, are incompatible with R 3.3 
> or 3.5. At least based on my experience. So could you please let me know 
> which is the R version I need to install to have it compatible with workbench 
> and also compatible with R software packages listed above that are needed to 
> run hcp_fix? I am using a MAC pro, with workbench v1.3.
> 
> This is becoming a nightmare so I would really appreciate your help.
> 
> Thanks!,
> 
> -L
> 
>> On May 27, 2018, at 3:04 AM, st...@fmrib.ox.ac.uk 
>> <mailto:st...@fmrib.ox.ac.uk> wrote:
>> 
>> Hi - we've seen this in the past with specific combinations of matlab 
>> version and workbench version.  I'm not quite sure if the very latest 
>> versions of both have the issue or not.
>> Cheers.
>> 
>> 
>>> On 27 May 2018, at 02:32, Marta Moreno <mmorenoort...@icloud.com 
>>> <mailto:mmorenoort...@icloud.com>> wrote:
>>> 
>>> I found the following error, please advice: (before is giving me some 
>>> warnings about different functions that has same name as a Matlab builtin, 
>>> I have pasted the output from last warning and first error). 
>>> 
>>> Which are the files that needs to be included in ‘CIFTIMatlabReaderWriter’ 
>>> for the settings.sh?
>>> 
>>> Warning: Function subsref has the same name as a MATLAB builtin. We suggest 
>>> you
>>> rename the function to avoid a potential name conflict. 
>>> > In path (line 109)
>>>   In fix_3_clean (line 45) 
>>> /bin/bash: /usr/local/workbench/bin_macosx64: is a directory
>>> Error using read_gifti_file_standalone (line 20)
>>> [GIFTI] Loading of XML file
>>> /private/var/folders/j2/__433pcd02l1cw9qkydkqs5hgn/T/tp6555679429695603.gii
>>> failed.
>>> 
>>> Error in gifti (line 71)
>>> this = read_gifti_file_standalone(varargin{1},giftistruct);
>>> 
>>> Error in ciftiopen (line 31)
>>> cifti = gifti([tmpfile '.gii']);
>>> 
>>> Error in fix_3_clean (line 46)
>>>   BO=ciftiopen('Atlas.dtseries.nii',WBC);
>>> 
>>> Thanks!
>>> 
>>> -L
>>> 
>>> 
>>>> On May 26, 2018, at 6:55 PM, Marta Moreno <mmorenoort...@icloud.com 
>>>> <mailto:mmorenoort...@icloud.com>> wrote:
>>>> 
>>>> You were right, now the problem is gone but still cannot find my 
>>>> clean.dtseries
>>>> 
>>>> Here is the output, I could not find any error in .ica folder:
>>>> hcp_fix RS_fMRI_1.nii.gz 2000
>>>> processing FMRI file RS_fMRI_1 with highpass 2000
>>>> running highpas

Re: [HCP-Users] error running hcp_fix

[Marta Moreno]

Thanks, but with newer versions is not working either because R software 
packages  such as 'kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' 
version 1.6.7 or  'randomForest' version 4.6.12, are incompatible with R 3.3 or 
3.5. At least based on my experience. So could you please let me know which is 
the R version I need to install to have it compatible with workbench and also 
compatible with R software packages listed above that are needed to run 
hcp_fix? I am using a MAC pro, with workbench v1.3.

This is becoming a nightmare so I would really appreciate your help.

Thanks!,

-L

> On May 27, 2018, at 3:04 AM, st...@fmrib.ox.ac.uk wrote:
> 
> Hi - we've seen this in the past with specific combinations of matlab version 
> and workbench version.  I'm not quite sure if the very latest versions of 
> both have the issue or not.
> Cheers.
> 
> 
>> On 27 May 2018, at 02:32, Marta Moreno <mmorenoort...@icloud.com 
>> <mailto:mmorenoort...@icloud.com>> wrote:
>> 
>> I found the following error, please advice: (before is giving me some 
>> warnings about different functions that has same name as a Matlab builtin, I 
>> have pasted the output from last warning and first error). 
>> 
>> Which are the files that needs to be included in ‘CIFTIMatlabReaderWriter’ 
>> for the settings.sh?
>> 
>> Warning: Function subsref has the same name as a MATLAB builtin. We suggest 
>> you
>> rename the function to avoid a potential name conflict. 
>> > In path (line 109)
>>   In fix_3_clean (line 45) 
>> /bin/bash: /usr/local/workbench/bin_macosx64: is a directory
>> Error using read_gifti_file_standalone (line 20)
>> [GIFTI] Loading of XML file
>> /private/var/folders/j2/__433pcd02l1cw9qkydkqs5hgn/T/tp6555679429695603.gii
>> failed.
>> 
>> Error in gifti (line 71)
>> this = read_gifti_file_standalone(varargin{1},giftistruct);
>> 
>> Error in ciftiopen (line 31)
>> cifti = gifti([tmpfile '.gii']);
>> 
>> Error in fix_3_clean (line 46)
>>   BO=ciftiopen('Atlas.dtseries.nii',WBC);
>> 
>> Thanks!
>> 
>> -L
>> 
>> 
>>> On May 26, 2018, at 6:55 PM, Marta Moreno <mmorenoort...@icloud.com 
>>> <mailto:mmorenoort...@icloud.com>> wrote:
>>> 
>>> You were right, now the problem is gone but still cannot find my 
>>> clean.dtseries
>>> 
>>> Here is the output, I could not find any error in .ica folder:
>>> hcp_fix RS_fMRI_1.nii.gz 2000
>>> processing FMRI file RS_fMRI_1 with highpass 2000
>>> running highpass
>>> running MELODIC
>>> running FIX
>>> FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica
>>>  create edge masks
>>>  run FAST
>>>  registration of standard space masks
>>>  extract features
>>> FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica using 
>>> training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and 
>>> threshold 10
>>> FIX Applying cleanup using cleanup file: 
>>> RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup 
>>> set to 1
>>> 
>>>  Please advice.
>>> 
>>> Thanks!
>>> 
>>> -L
>>> 
>>> 
>>>> On May 26, 2018, at 2:52 PM, Glasser, Matthew <glass...@wustl.edu 
>>>> <mailto:glass...@wustl.edu>> wrote:
>>>> 
>>>> Perhaps you are running out of memory.
>>>> 
>>>> Peace,
>>>> 
>>>> Matt.
>>>> 
>>>> From: <hcp-users-boun...@humanconnectome.org 
>>>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
>>>> <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>>
>>>> Date: Saturday, May 26, 2018 at 1:50 PM
>>>> To: HCP Users <hcp-users@humanconnectome.org 
>>>> <mailto:hcp-users@humanconnectome.org>>
>>>> Subject: [HCP-Users] error running hcp_fix
>>>> 
>>>> Dear experts,
>>>> 
>>>> I am getting the following error. Please advice:
>>>> 
>>>> hcp_fix RS_fMRI_1.nii.gz 2000
>>>> processing FMRI file RS_fMRI_1 with highpass 2000
>>>> running highpass
>>>> running MELODIC
>>>> running FIX
>>>> FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica
>>>>  create edge masks
>>>>  run FAST
>>>>  registration of standard spa

Re: [HCP-Users] error running hcp_fix

[Marta Moreno]

I found the following error, please advice: (before is giving me some warnings 
about different functions that has same name as a Matlab builtin, I have pasted 
the output from last warning and first error). 

Which are the files that needs to be included in ‘CIFTIMatlabReaderWriter’ for 
the settings.sh?

Warning: Function subsref has the same name as a MATLAB builtin. We suggest you
rename the function to avoid a potential name conflict. 
> In path (line 109)
  In fix_3_clean (line 45) 
/bin/bash: /usr/local/workbench/bin_macosx64: is a directory
Error using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file
/private/var/folders/j2/__433pcd02l1cw9qkydkqs5hgn/T/tp6555679429695603.gii
failed.

Error in gifti (line 71)
this = read_gifti_file_standalone(varargin{1},giftistruct);

Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);

Error in fix_3_clean (line 46)
  BO=ciftiopen('Atlas.dtseries.nii',WBC);

Thanks!

-L


> On May 26, 2018, at 6:55 PM, Marta Moreno <mmorenoort...@icloud.com> wrote:
> 
> You were right, now the problem is gone but still cannot find my 
> clean.dtseries
> 
> Here is the output, I could not find any error in .ica folder:
> hcp_fix RS_fMRI_1.nii.gz 2000
> processing FMRI file RS_fMRI_1 with highpass 2000
> running highpass
> running MELODIC
> running FIX
> FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica
>  create edge masks
>  run FAST
>  registration of standard space masks
>  extract features
> FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica using 
> training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and 
> threshold 10
> FIX Applying cleanup using cleanup file: 
> RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set 
> to 1
> 
>  Please advice.
> 
> Thanks!
> 
> -L
> 
> 
>> On May 26, 2018, at 2:52 PM, Glasser, Matthew <glass...@wustl.edu 
>> <mailto:glass...@wustl.edu>> wrote:
>> 
>> Perhaps you are running out of memory.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: <hcp-users-boun...@humanconnectome.org 
>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
>> <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>>
>> Date: Saturday, May 26, 2018 at 1:50 PM
>> To: HCP Users <hcp-users@humanconnectome.org 
>> <mailto:hcp-users@humanconnectome.org>>
>> Subject: [HCP-Users] error running hcp_fix
>> 
>> Dear experts,
>> 
>> I am getting the following error. Please advice:
>> 
>> hcp_fix RS_fMRI_1.nii.gz 2000
>> processing FMRI file RS_fMRI_1 with highpass 2000
>> running highpass
>> running MELODIC
>> running FIX
>> FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica
>>  create edge masks
>>  run FAST
>>  registration of standard space masks
>>  extract features
>> FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica using 
>> training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and 
>> threshold 10
>> FIX Applying cleanup using cleanup file: 
>> RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set 
>> to 1
>> sh: line 1: 10513 Killed: 9   
>> /Applications/MATLAB_R2017b.app/bin/matlab -nojvm -nodisplay -nodesktop 
>> -nosplash -r "addpath('/usr/local/fix1.065'); 
>> addpath('/usr/local/fsl/etc/matlab'); fix_3_clean('.fix',0,1,2000)" >> 
>> .fix.log 2>&1
>> 
>> Thanks,
>> 
>> -L
>> 
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
> ___
> 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

Re: [HCP-Users] error running hcp_fix

[Marta Moreno]

You were right, now the problem is gone but still cannot find my clean.dtseries

Here is the output, I could not find any error in .ica folder:
hcp_fix RS_fMRI_1.nii.gz 2000
processing FMRI file RS_fMRI_1 with highpass 2000
running highpass
running MELODIC
running FIX
FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica
 create edge masks
 run FAST
 registration of standard space masks
 extract features
FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica using 
training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and 
threshold 10
FIX Applying cleanup using cleanup file: 
RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set to 
1

 Please advice.

Thanks!

-L


> On May 26, 2018, at 2:52 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
> 
> Perhaps you are running out of memory.
> 
> Peace,
> 
> Matt.
> 
> From: <hcp-users-boun...@humanconnectome.org 
> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
> <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>>
> Date: Saturday, May 26, 2018 at 1:50 PM
> To: HCP Users <hcp-users@humanconnectome.org 
> <mailto:hcp-users@humanconnectome.org>>
> Subject: [HCP-Users] error running hcp_fix
> 
> Dear experts,
> 
> I am getting the following error. Please advice:
> 
> hcp_fix RS_fMRI_1.nii.gz 2000
> processing FMRI file RS_fMRI_1 with highpass 2000
> running highpass
> running MELODIC
> running FIX
> FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica
>  create edge masks
>  run FAST
>  registration of standard space masks
>  extract features
> FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica using 
> training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and 
> threshold 10
> FIX Applying cleanup using cleanup file: 
> RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set 
> to 1
> sh: line 1: 10513 Killed: 9   
> /Applications/MATLAB_R2017b.app/bin/matlab -nojvm -nodisplay -nodesktop 
> -nosplash -r "addpath('/usr/local/fix1.065'); 
> addpath('/usr/local/fsl/etc/matlab'); fix_3_clean('.fix',0,1,2000)" >> 
> .fix.log 2>&1
> 
> Thanks,
> 
> -L
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] error running hcp_fix

[Marta Moreno]

Dear experts,

I am getting the following error. Please advice:

hcp_fix RS_fMRI_1.nii.gz 2000
processing FMRI file RS_fMRI_1 with highpass 2000
running highpass
running MELODIC
running FIX
FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica
 create edge masks
 run FAST
 registration of standard space masks
 extract features
FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica using 
training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and 
threshold 10
FIX Applying cleanup using cleanup file: 
RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set to 
1
sh: line 1: 10513 Killed: 9   
/Applications/MATLAB_R2017b.app/bin/matlab -nojvm -nodisplay -nodesktop 
-nosplash -r "addpath('/usr/local/fix1.065'); 
addpath('/usr/local/fsl/etc/matlab'); fix_3_clean('.fix',0,1,2000)" >> .fix.log 
2>&1

Thanks,

-L


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] wb_view crashes after 1 day of using it

[Marta Moreno]

Dear experts,

My wb_view crashes after 1 day of using it, what happens is that the next day I 
cannot keep loading more images with setting created for illustration of brain 
results and need to restart all over -even it requires to restart the computer 
to have it working properly. I have installed last version in Applications, and 
I am using a Mac Pro (Late 2013). What specs are needed to diagnose this 
problem and solve it?

Thanks,

L




___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] workbench crashes - Namespace SIGNAL, Code 0xb

[Marta Moreno]

Thanks.

What details do you need to help? 

It crashes anytime I try to open a new file. I am running macOS Sierra version 
10.12.5 on a Mac Pro (Late 2013). Could it be related to memory? My Mac 
contains 4 memory slots, and all memory slots are currently in use.

Here I pasted the entire problem report for wb_view.:

Process:   wb_view [25125]
Path:  
/usr/local/workbench/bin_macosx64/../macosx64_apps/wb_view.app/Contents/MacOS/wb_view
Identifier:workbench
Version:   1.1.1 (1.1.1)
Code Type: X86-64 (Native)
Parent Process:??? [25123]
Responsible:   wb_view [25125]
User ID:   501

Date/Time: 2017-12-26 15:14:16.054 -0500
OS Version:Mac OS X 10.12.5 (16F73)
Report Version:12
Anonymous UUID:D5FF43E5-1CCA-5E9C-C5AF-22ACAE67AFE8


Time Awake Since Boot: 95 seconds

System Integrity Protection: enabled

Crashed Thread:0  Dispatch queue: com.apple.main-thread

Exception Type:EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:   KERN_INVALID_ADDRESS at 0x
Exception Note:EXC_CORPSE_NOTIFY

Termination Signal:Segmentation fault: 11
Termination Reason:Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [0]

VM Regions Near 0:
--> 
__TEXT 0001-000101965000 [ 25.4M] r-x/rwx 
SM=COW  /usr/local/workbench/macosx64_apps/wb_view.app/Contents/MacOS/wb_view

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   QtGui   0x000101f8c678 
QMacInputContext::reset() + 872
1   com.apple.AppKit0x7fff9f95d19f 
-[NSTextInputContext(NSInputContext_WithCompletion) 
selectedRangeWithCompletionHandler:] + 66
2   com.apple.AppKit0x7fffa006f16f -[NSTextInputContext 
tryHandleTSMEvent_offsetToPos_markedOrSelRange_withContext:markedOrSelRangeDispatchCondition:markedRangeContinuation:selectedRangeContinuation:continuation:]
 + 181
3   com.apple.AppKit0x7fffa0072b0f 
__55-[NSTextInputContext handleTSMEvent:completionHandler:]_block_invoke.564 + 
320
4   com.apple.AppKit0x7fff9f836ec2 -[NSTextInputContext 
handleTSMEvent:completionHandler:] + 1488
5   com.apple.AppKit0x7fff9f836883 _NSTSMEventHandler + 
321
6   com.apple.HIToolbox 0x7fffa10dfd85 
DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 
1708
7   com.apple.HIToolbox 0x7fffa10deff6 
SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, 
HandlerCallRec*) + 428
8   com.apple.HIToolbox 0x7fffa10dee3f 
SendEventToEventTargetWithOptions + 43
9   com.apple.HIToolbox 0x7fffa11366d6 
SendTSMEvent_WithCompletionHandler + 408
10  com.apple.HIToolbox 0x7fffa12ea61c 
__SendTextInputEvent_WithCompletionHandler_block_invoke + 584
11  com.apple.HIToolbox 0x7fffa12e892d 
SendTextInputEvent_WithCompletionHandler + 1154
12  com.apple.HIToolbox 0x7fffa135a5b5 -[IMKInputSession 
_postEvent:completionHandler:] + 176
13  com.apple.HIToolbox 0x7fffa135a47f -[IMKInputSession 
_createAndSendOffsetToPointEvent:completionHandler:] + 281
14  com.apple.HIToolbox 0x7fffa136f157 -[IMKInputSession 
attributesForCharacterIndex_andLineRect:completionHandler:] + 591
15  com.apple.HIToolbox 0x7fffa136fde3 -[IMKInputSession 
attributesForCharacterIndex:completionHandler:] + 80
16  com.apple.HIToolbox 0x7fffa135c2f5 
__60-[IMKInputSession imkxpc_attributesForCharacterIndex:reply:]_block_invoke + 
505
17  com.apple.CoreFoundation0x7fffa1bc722c 
__CFRUNLOOP_IS_CALLING_OUT_TO_A_BLOCK__ + 12
18  com.apple.CoreFoundation0x7fffa1ba83c4 __CFRunLoopDoBlocks 
+ 356
19  com.apple.CoreFoundation0x7fffa1ba7b35 __CFRunLoopRun + 917
20  com.apple.CoreFoundation0x7fffa1ba7544 CFRunLoopRunSpecific 
+ 420
21  com.apple.HIToolbox 0x7fffa134419e 
-[IMKInputSessionXPCInvocation invocationAwaitXPCReply] + 606
22  com.apple.HIToolbox 0x7fffa1348a7c -[IMKInputSession 
deactivate] + 2969
23  com.apple.HIToolbox 0x7fffa12fa7db 
IMKInputSessionDeactivate + 36
24  com.apple.HIToolbox 0x7fffa12f9ba9 
DeactivateInputMethodInstance + 100
25  com.apple.HIToolbox 0x7fffa12ee66d 
utDeactivateAllSelectedIMInDocIterator + 87
26  com.apple.CoreFoundation0x7fffa1b6b944 CFArrayApplyFunction 
+ 68
27  com.apple.HIToolbox 0x7fffa113c13b 
utDeactivateAllSelectedIMInDoc + 131
28  com.apple.HIToolbox 0x7fffa113bba0 
MyDeactivateTSMDocument + 351
29  com.apple.HIToolbox 0x7fffa113ba1f 

[HCP-Users] workbench crashes - Namespace SIGNAL, Code 0xb

[Marta Moreno]

Dear experts,

My workbench crashes anytime I upload a new file. I am using version 1.2.3. 
Please advice, below problem details.

Process:   wb_view [81425]
Path:  
/usr/local/workbench/bin_macosx64/../macosx64_apps/wb_view.app/Contents/MacOS/wb_view
Identifier:workbench
Version:   1.1.1 (1.1.1)
Code Type: X86-64 (Native)
Parent Process:sh [81419]
Responsible:   wb_view [81425]
User ID:   501

Date/Time: 2017-12-26 11:43:03.522 -0500
OS Version:Mac OS X 10.12.5 (16F73)
Report Version:12
Anonymous UUID:D5FF43E5-1CCA-5E9C-C5AF-22ACAE67AFE8


Time Awake Since Boot: 94 seconds

System Integrity Protection: enabled

Crashed Thread:0  Dispatch queue: com.apple.main-thread

Exception Type:EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:   KERN_INVALID_ADDRESS at 0x
Exception Note:EXC_CORPSE_NOTIFY

Termination Signal:Segmentation fault: 11
Termination Reason:Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [0]

VM Regions Near 0:

Thanks,

-L
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] error open file in wb_view

[Marta Moreno]

Thanks a lot. Problem solved.


> On Dec 12, 2017, at 2:28 PM, Harwell, John <jharw...@wustl.edu> wrote:
> 
> It is possible the file is corrupted.  Please try to run “wb_command 
> -file-information  ” on the file and see if that works.
> 
>> On Dec 12, 2017, at 12:20 PM, Marta Moreno <mmorenoort...@icloud.com 
>> <mailto:mmorenoort...@icloud.com>> wrote:
>> 
>> Thanks.
>> 
>> Yes, I can load spec files but when trying to see functional connectivity 
>> maps for the specific subject it crashes. I can load other type of files, 
>> i.e., seed used. This is the first time I cannot see this file, before I was 
>> able to do so without crashing. I have downloaded workbench v1.2.3. now but 
>> the problem persists. The only change I had these past weeks was the 
>> MATLAB_R2017b.
>> 
>> 
>>> On Dec 12, 2017, at 1:12 PM, Harwell, John <jharw...@wustl.edu 
>>> <mailto:jharw...@wustl.edu>> wrote:
>>> 
>>> 
>>> Hi Marta,
>>> 
>>> Does wb_view start up if you do not try to load any files?  Is this the 
>>> first time you have run wb_view on this Mac?  
>>> 
>>> Do you know which file is causing the crash?  You could use File Menu —> 
>>> Open File and try opening just a surface file.  
>>> 
>>> 
>>> John Harwell
>>> 
>>> 
>>>> On Dec 12, 2017, at 11:25 AM, Marta Moreno <mmorenoort...@icloud.com 
>>>> <mailto:mmorenoort...@icloud.com>> wrote:
>>>> 
>>>> Dear experts,
>>>> 
>>>> I am getting an error any time I am trying to open file in wb_view. Any 
>>>> idea how to solve this problem? 
>>>> 
>>>> Thanks,
>>>> 
>>>> -L
>>>> 
>>>> Error attached below:
>>>> 
>>>> Process:   wb_view [56364]
>>>> Path:  
>>>> /usr/local/workbench-new/bin_macosx64/../macosx64_apps/wb_view.app/Contents/MacOS/wb_view
>>>> Identifier:workbench
>>>> Version:   1.1.1 (1.1.1)
>>>> Code Type: X86-64 (Native)
>>>> Parent Process:??? [56362]
>>>> Responsible:   wb_view [56364]
>>>> User ID:   501
>>>> 
>>>> Date/Time: 2017-12-12 12:21:10.852 -0500
>>>> OS Version:Mac OS X 10.12.5 (16F73)
>>>> Report Version:12
>>>> Anonymous UUID:D5FF43E5-1CCA-5E9C-C5AF-22ACAE67AFE8
>>>> 
>>>> 
>>>> Time Awake Since Boot: 270 seconds
>>>> 
>>>> System Integrity Protection: enabled
>>>> 
>>>> Crashed Thread:0  Dispatch queue: com.apple.main-thread
>>>> 
>>>> Exception Type:EXC_BAD_ACCESS (SIGSEGV)
>>>> Exception Codes:   KERN_INVALID_ADDRESS at 0x
>>>> Exception Note:EXC_CORPSE_NOTIFY
>>>> 
>>>> Termination Signal:Segmentation fault: 11
>>>> Termination Reason:Namespace SIGNAL, Code 0xb
>>>> Terminating Process:   exc handler [0]
>>>> 
>>>> 
>>>> ___
>>>> HCP-Users mailing list
>>>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
>>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
>>> 
>> 
> 


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] error open file in wb_view

[Marta Moreno]

Thanks.

Yes, I can load spec files but when trying to see functional connectivity maps 
for the specific subject it crashes. I can load other type of files, i.e., seed 
used. This is the first time I cannot see this file, before I was able to do so 
without crashing. I have downloaded workbench v1.2.3. now but the problem 
persists. The only change I had these past weeks was the MATLAB_R2017b.


> On Dec 12, 2017, at 1:12 PM, Harwell, John <jharw...@wustl.edu> wrote:
> 
> 
> Hi Marta,
> 
> Does wb_view start up if you do not try to load any files?  Is this the first 
> time you have run wb_view on this Mac?  
> 
> Do you know which file is causing the crash?  You could use File Menu —> Open 
> File and try opening just a surface file.  
> 
> 
> John Harwell
> 
> 
>> On Dec 12, 2017, at 11:25 AM, Marta Moreno <mmorenoort...@icloud.com> wrote:
>> 
>> Dear experts,
>> 
>> I am getting an error any time I am trying to open file in wb_view. Any idea 
>> how to solve this problem? 
>> 
>> Thanks,
>> 
>> -L
>> 
>> Error attached below:
>> 
>> Process:   wb_view [56364]
>> Path:  
>> /usr/local/workbench-new/bin_macosx64/../macosx64_apps/wb_view.app/Contents/MacOS/wb_view
>> Identifier:workbench
>> Version:   1.1.1 (1.1.1)
>> Code Type: X86-64 (Native)
>> Parent Process:??? [56362]
>> Responsible:   wb_view [56364]
>> User ID:   501
>> 
>> Date/Time: 2017-12-12 12:21:10.852 -0500
>> OS Version:Mac OS X 10.12.5 (16F73)
>> Report Version:12
>> Anonymous UUID:D5FF43E5-1CCA-5E9C-C5AF-22ACAE67AFE8
>> 
>> 
>> Time Awake Since Boot: 270 seconds
>> 
>> System Integrity Protection: enabled
>> 
>> Crashed Thread:0  Dispatch queue: com.apple.main-thread
>> 
>> Exception Type:EXC_BAD_ACCESS (SIGSEGV)
>> Exception Codes:   KERN_INVALID_ADDRESS at 0x
>> Exception Note:EXC_CORPSE_NOTIFY
>> 
>> Termination Signal:Segmentation fault: 11
>> Termination Reason:Namespace SIGNAL, Code 0xb
>> Terminating Process:   exc handler [0]
>> 
>> 
>> ___
>> 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

[HCP-Users] error open file in wb_view

[Marta Moreno]

Dear experts,

I am getting an error any time I am trying to open file in wb_view. Any idea 
how to solve this problem? 

Thanks,

-L

Error attached below:

Process:   wb_view [56364]
Path:  
/usr/local/workbench-new/bin_macosx64/../macosx64_apps/wb_view.app/Contents/MacOS/wb_view
Identifier:workbench
Version:   1.1.1 (1.1.1)
Code Type: X86-64 (Native)
Parent Process:??? [56362]
Responsible:   wb_view [56364]
User ID:   501

Date/Time: 2017-12-12 12:21:10.852 -0500
OS Version:Mac OS X 10.12.5 (16F73)
Report Version:12
Anonymous UUID:D5FF43E5-1CCA-5E9C-C5AF-22ACAE67AFE8


Time Awake Since Boot: 270 seconds

System Integrity Protection: enabled

Crashed Thread:0  Dispatch queue: com.apple.main-thread

Exception Type:EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:   KERN_INVALID_ADDRESS at 0x
Exception Note:EXC_CORPSE_NOTIFY

Termination Signal:Segmentation fault: 11
Termination Reason:Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [0]


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] mcflirt_acc in ABCD

[Marta Moreno]

Is the version 3.4.0 the latest version of the pipelines which default to FSL 
mcflirt?

Thanks,

-L

Sent from my iPhone

> On Nov 8, 2017, at 4:55 PM, Glasser, Matthew  wrote:
> 
> I would use the latest version of the pipelines which default to FSL mcflirt 
> because some folks had been seeing this issue.
> 
> Peace,
> 
> Matt.
> 
> From:  on behalf of "Sanchez, Juan 
> (NYSPI)" 
> Date: Wednesday, November 8, 2017 at 3:41 PM
> To: "hcp-users@humanconnectome.org" , 
> "hcp-users@humanconnectome.org" , 
> "hcp-users@humanconnectome.org" , 
> "hcp-users@humanconnectome.org" , 
> "hcp-users@humanconnectome.org" , 
> "hcp-users@humanconnectome.org" , 
> "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] mcflirt_acc in ABCD
> 
> Dear all,
> 
> We are using pipelines version 3.4. Using the TOPUP distortion correction we 
> are getting very good Epi to T1 co-registration, however it seems that there 
> is intermittent motion in the processed data  that is not present in the raw 
> data.
> 
>  
> 
> This is occuring during MotionCorrection_FLIRTbased.sh
> 
> the fMRI_gdc.nii.gz shows no motion between volumes, however the fMRI_mc 
> shows motion in the entire brain (around a 1mm shift)  see attached qc png
> 
> This error was present using both mcflirt.sh and mcflirt_acc.sh
> 
> I used fsl mcflirt with these inputs and the motion error was gone.
> 
> Any suggestions on how to edit the mcflirt_acc.sh or why this may be 
> happening?
> 
> thanks
> Juan Sanchez-Pena
> ___
> 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

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] HCP_hp2000.RData

[Marta Moreno]

Thanks. I did and they helped. 

The problem seams to be the required version for packages:
'kernlab' version 0.9.24
'ROCR' version 1.0.7
'class' version 7.3.14
'party' version 1.0.25
'e1071' version 1.6.7
'randomForest' version 4.6.12


> On Nov 6, 2017, at 9:34 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
> 
> I would ask specifically on the FSL list again as they are the primary 
> support for FIX.
> 
> Matt.
> 
> From: Marta Moreno <mmorenoort...@icloud.com 
> <mailto:mmorenoort...@icloud.com>>
> Date: Monday, November 6, 2017 at 8:31 PM
> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>
> Cc: HCP Users <hcp-users@humanconnectome.org 
> <mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] HCP_hp2000.RData
> 
> Thanks, Matt.
> 
> I am still getting the same problem. What version of R and package party are 
> you using or is recommended? 
> I checked also in the FSL list and this problem has been posted but not 
> solution was provided. 
> 
> Thank you,
> -L
> 
>> On Nov 6, 2017, at 11:54 AM, Glasser, Matthew <glass...@wustl.edu 
>> <mailto:glass...@wustl.edu>> wrote:
>> 
>> I’m not an expert in R, so I’m not sure.  I think that it does some 
>> compiling and other things on my machine, but perhaps if you don’t compile 
>> that is all that is needed.  You could test ICA+FIX again and see if the 
>> error is resolved.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: Marta Moreno <mmorenoort...@icloud.com 
>> <mailto:mmorenoort...@icloud.com>>
>> Date: Monday, November 6, 2017 at 10:51 AM
>> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>
>> Cc: HCP Users <hcp-users@humanconnectome.org 
>> <mailto:hcp-users@humanconnectome.org>>
>> Subject: Re: [HCP-Users] HCP_hp2000.RData
>> 
>> Thanks again, Matt. 
>> 
>> I went through required packages again as suggested, a common output in R is 
>> the following (for all packages): as root,
>> "> install.packages("randomForest", dependencies=TRUE)
>> trying URL 
>> 'https://cran.cnr.berkeley.edu/bin/macosx/el-capitan/contrib/3.4/randomForest_4.6-12.tgz
>>  
>> <https://cran.cnr.berkeley.edu/bin/macosx/el-capitan/contrib/3.4/randomForest_4.6-12.tgz>'
>> Content type 'application/x-gzip' length 176377 bytes (172 KB)
>> ==
>> downloaded 172 KB
>> The downloaded binary packages are in
>> /tmp/RtmpP65gVF/downloaded_packages”
>> 
>> Should I go over each package to install it or this message includes 
>> installation? 
>> 
>> Thank you,
>> 
>> -L
>> 
>> 
>>> On Nov 6, 2017, at 10:31 AM, Glasser, Matthew <glass...@wustl.edu 
>>> <mailto:glass...@wustl.edu>> wrote:
>>> 
>>> You could ask on the FSL list, but I think it would make sense to go 
>>> through the setup instructions again and make sure you aren’t missing any 
>>> of the required R packages.
>>> 
>>> Peace,
>>> 
>>> Matt.
>>> 
>>> From: Marta Moreno <mmorenoort...@icloud.com 
>>> <mailto:mmorenoort...@icloud.com>>
>>> Date: Monday, November 6, 2017 at 9:29 AM
>>> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>
>>> Cc: HCP Users <hcp-users@humanconnectome.org 
>>> <mailto:hcp-users@humanconnectome.org>>
>>> Subject: Re: [HCP-Users] HCP_hp2000.RData
>>> 
>>> Thank you, Matt. I found the only one and following error in 
>>> Results/RS_fMRI_2/RS_fMRI_2_hp2000.ica:
>>> 
>>> "Error in ctreefit(object = object, controls = controls, weights = weights, 
>>>  : 
>>>   no slot of name "remove_weights" for this object of class 
>>> "TreeGrowControl"
>>> Calls: eval -> eval ->  -> ctreefit -> .Call
>>> Execution halted”
>>> 
>>> Any idea what should I do to fix this problem? I do not have R-devel 
>>> installed, is this required and/or related to this problem?
>>> 
>>> Thank you,
>>> 
>>> -L
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> On Nov 4, 2017, at 4:55 PM, Glasser, Matthew <glass...@wustl.edu 
>>>> <mailto:glass...@wustl.edu>> wrote:
>>>> 
>>>> You will need to look into the logs more carefully (i.e. in subfolders of 
>>>> the FIX folder) and you will likely find some issue with the

Re: [HCP-Users] HCP_hp2000.RData

[Marta Moreno]

Thanks again, Matt. 

I went through required packages again as suggested, a common output in R is 
the following (for all packages): as root,
"> install.packages("randomForest", dependencies=TRUE)
trying URL 
'https://cran.cnr.berkeley.edu/bin/macosx/el-capitan/contrib/3.4/randomForest_4.6-12.tgz'
Content type 'application/x-gzip' length 176377 bytes (172 KB)
==
downloaded 172 KB
The downloaded binary packages are in
/tmp/RtmpP65gVF/downloaded_packages”

Should I go over each package to install it or this message includes 
installation? 

Thank you,

-L


> On Nov 6, 2017, at 10:31 AM, Glasser, Matthew <glass...@wustl.edu> wrote:
> 
> You could ask on the FSL list, but I think it would make sense to go through 
> the setup instructions again and make sure you aren’t missing any of the 
> required R packages.
> 
> Peace,
> 
> Matt.
> 
> From: Marta Moreno <mmorenoort...@icloud.com 
> <mailto:mmorenoort...@icloud.com>>
> Date: Monday, November 6, 2017 at 9:29 AM
> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>
> Cc: HCP Users <hcp-users@humanconnectome.org 
> <mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] HCP_hp2000.RData
> 
> Thank you, Matt. I found the only one and following error in 
> Results/RS_fMRI_2/RS_fMRI_2_hp2000.ica:
> 
> "Error in ctreefit(object = object, controls = controls, weights = weights,  
> : 
>   no slot of name "remove_weights" for this object of class "TreeGrowControl"
> Calls: eval -> eval ->  -> ctreefit -> .Call
> Execution halted”
> 
> Any idea what should I do to fix this problem? I do not have R-devel 
> installed, is this required and/or related to this problem?
> 
> Thank you,
> 
> -L
> 
> 
> 
> 
> 
>> On Nov 4, 2017, at 4:55 PM, Glasser, Matthew <glass...@wustl.edu 
>> <mailto:glass...@wustl.edu>> wrote:
>> 
>> You will need to look into the logs more carefully (i.e. in subfolders of 
>> the FIX folder) and you will likely find some issue with the R packages you 
>> have installed.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: <hcp-users-boun...@humanconnectome.org 
>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
>> <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>>
>> Date: Saturday, November 4, 2017 at 3:28 PM
>> To: HCP Users <hcp-users@humanconnectome.org 
>> <mailto:hcp-users@humanconnectome.org>>
>> Subject: [HCP-Users] HCP_hp2000.RData
>> 
>> Dear experts,
>> 
>> I am getting the following error running hip_fix, my RSfMRI data is similar 
>> to HCP data but I am getting the following error running hcp_fix 
>> RS_fMRI_2/RS_fMRI_2.nii.gz 2000:
>> 
>> "FIX Classifying components in Melodic directory: RS_fMRI_2_hp2000.ica using 
>> training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and 
>> threshold 10
>> No valid labelling file specified"
>> 
>> I checked the settings and everything looks good. I do not see errors in 
>> /.fix.log. Any idea what might be the problem? 
>> 
>> Thank you,
>> 
>> -L
>> 
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] HCP_hp2000.RData

[Marta Moreno]

Dear experts,

I am getting the following error running hip_fix, my RSfMRI data is similar to 
HCP data but I am getting the following error running hcp_fix 
RS_fMRI_2/RS_fMRI_2.nii.gz 2000:

"FIX Classifying components in Melodic directory: RS_fMRI_2_hp2000.ica using 
training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and 
threshold 10
No valid labelling file specified"

I checked the settings and everything looks good. I do not see errors in 
/.fix.log. Any idea what might be the problem? 

Thank you,

-L


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] hcp_fix script and settings

[Marta Moreno]

Dear experts,

I want to use the “hcp_fix" script for clean up of resting state data after HCP 
pipelines. I am editing “settings.sh" and wanted to know if I have to edit 
these lines copied below:

# Settings file for FIX
# Modify these settings based on your system setup
FIXVERSION=1.065
#   (actually this version is 1.065 - see wiki page for details)

# Get the OS and CPU type
FSL_FIX_OS=`uname -s`
FSL_FIX_ARCH=`uname -m`

if [ -z "${FSL_FIXDIR}" ]; then
FSL_FIXDIR=$( cd $(dirname $0) ; pwd)
export FSL_FIXDIR
fi

Thank you very much,

Leah


> On Oct 30, 2017, at 10:29 AM, Marta Moreno <mmorenoort...@icloud.com> wrote:
> 
> Great. Thank you very much.
> 
>> On Oct 29, 2017, at 4:44 PM, Glasser, Matthew <glass...@wustl.edu 
>> <mailto:glass...@wustl.edu>> wrote:
>> 
>> Yes that is what we do.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: Marta Moreno <mmorenoort...@icloud.com 
>> <mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, October 29, 2017 at 12:03 PM
>> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>
>> Cc: HCP Users <hcp-users@humanconnectome.org 
>> <mailto:hcp-users@humanconnectome.org>>
>> Subject: Re: [HCP-Users] ICA+FIX cleanup scripts
>> 
>> Thanks for your answer. I just want to use the “hcp_fix" script for clean up 
>> of resting state data after HCP pipelines. I only need to know if I just 
>> need to run the “hcp_fix" on data already preprocessed with HCP pipelines, 
>> after which I get my clean dtseries.nii ready for FC analyses.
>> 
>> Much appreciation.
>> 
>> 
>> 
>> 
>>> On Oct 29, 2017, at 11:41 AM, Glasser, Matthew <glass...@wustl.edu 
>>> <mailto:glass...@wustl.edu>> wrote:
>>> 
>>> I think there is a readme with instructions on set up.  If you have 
>>> specific questions about those, ICA+FIX questions might be best asked on 
>>> the FSL list, as the FSL programmers don’t watch this list.  Here we can 
>>> answer questions about CIFTI or approaching clean up of resting state data.
>>> 
>>> Peace,
>>> 
>>> Matt.
>>> 
>>> From: <hcp-users-boun...@humanconnectome.org 
>>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
>>> <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>>
>>> Date: Sunday, October 29, 2017 at 9:11 AM
>>> To: HCP Users <hcp-users@humanconnectome.org 
>>> <mailto:hcp-users@humanconnectome.org>>
>>> Subject: [HCP-Users] ICA+FIX cleanup scripts
>>> 
>>> Dear experts,
>>> 
>>> I would like to use  ICA+FIX cleanup after HCP minimal preprocessing 
>>> pipelines on high quality resting-state data acquired with a GE scanner. 
>>> HCP minimal preprocessing is working fine and installed locally. I have 
>>> downloaded now the tar file with ICA+FIX cleanup scripts. Could you please 
>>> give me some guidelines on what are the steps to follow to have them 
>>> running? I am using a MacPro.
>>> 
>>> Much appreciation for your help.
>>> 
>>> 
>>> 
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
>> 
>> 
> 


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] ICA+FIX cleanup scripts

[Marta Moreno]

Great. Thank you very much.

> On Oct 29, 2017, at 4:44 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
> 
> Yes that is what we do.
> 
> Peace,
> 
> Matt.
> 
> From: Marta Moreno <mmorenoort...@icloud.com 
> <mailto:mmorenoort...@icloud.com>>
> Date: Sunday, October 29, 2017 at 12:03 PM
> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>
> Cc: HCP Users <hcp-users@humanconnectome.org 
> <mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] ICA+FIX cleanup scripts
> 
> Thanks for your answer. I just want to use the “hcp_fix" script for clean up 
> of resting state data after HCP pipelines. I only need to know if I just need 
> to run the “hcp_fix" on data already preprocessed with HCP pipelines, after 
> which I get my clean dtseries.nii ready for FC analyses.
> 
> Much appreciation.
> 
> 
> 
> 
>> On Oct 29, 2017, at 11:41 AM, Glasser, Matthew <glass...@wustl.edu 
>> <mailto:glass...@wustl.edu>> wrote:
>> 
>> I think there is a readme with instructions on set up.  If you have specific 
>> questions about those, ICA+FIX questions might be best asked on the FSL 
>> list, as the FSL programmers don’t watch this list.  Here we can answer 
>> questions about CIFTI or approaching clean up of resting state data.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: <hcp-users-boun...@humanconnectome.org 
>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
>> <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, October 29, 2017 at 9:11 AM
>> To: HCP Users <hcp-users@humanconnectome.org 
>> <mailto:hcp-users@humanconnectome.org>>
>> Subject: [HCP-Users] ICA+FIX cleanup scripts
>> 
>> Dear experts,
>> 
>> I would like to use  ICA+FIX cleanup after HCP minimal preprocessing 
>> pipelines on high quality resting-state data acquired with a GE scanner. HCP 
>> minimal preprocessing is working fine and installed locally. I have 
>> downloaded now the tar file with ICA+FIX cleanup scripts. Could you please 
>> give me some guidelines on what are the steps to follow to have them 
>> running? I am using a MacPro.
>> 
>> Much appreciation for your help.
>> 
>> 
>> 
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
> 
> 


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] ICA+FIX cleanup scripts

[Marta Moreno]

Thanks for your answer. I just want to use the “hcp_fix" script for clean up of 
resting state data after HCP pipelines. I only need to know if I just need to 
run the “hcp_fix" on data already preprocessed with HCP pipelines, after which 
I get my clean dtseries.nii ready for FC analyses.

Much appreciation.




> On Oct 29, 2017, at 11:41 AM, Glasser, Matthew <glass...@wustl.edu> wrote:
> 
> I think there is a readme with instructions on set up.  If you have specific 
> questions about those, ICA+FIX questions might be best asked on the FSL list, 
> as the FSL programmers don’t watch this list.  Here we can answer questions 
> about CIFTI or approaching clean up of resting state data.
> 
> Peace,
> 
> Matt.
> 
> From: <hcp-users-boun...@humanconnectome.org 
> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
> <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>>
> Date: Sunday, October 29, 2017 at 9:11 AM
> To: HCP Users <hcp-users@humanconnectome.org 
> <mailto:hcp-users@humanconnectome.org>>
> Subject: [HCP-Users] ICA+FIX cleanup scripts
> 
> Dear experts,
> 
> I would like to use  ICA+FIX cleanup after HCP minimal preprocessing 
> pipelines on high quality resting-state data acquired with a GE scanner. HCP 
> minimal preprocessing is working fine and installed locally. I have 
> downloaded now the tar file with ICA+FIX cleanup scripts. Could you please 
> give me some guidelines on what are the steps to follow to have them running? 
> I am using a MacPro.
> 
> Much appreciation for your help.
> 
> 
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] ICA+FIX cleanup scripts

[Marta Moreno]

Dear experts,

I would like to use  ICA+FIX cleanup after HCP minimal preprocessing pipelines 
on high quality resting-state data acquired with a GE scanner. HCP minimal 
preprocessing is working fine and installed locally. I have downloaded now the 
tar file with ICA+FIX cleanup scripts. Could you please give me some guidelines 
on what are the steps to follow to have them running? I am using a MacPro.

Much appreciation for your help.




___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] NEWMAT::SingularException

[Marta Moreno]

Dear experts,

After running all preprocessing steps using the HCP pipeline and not getting 
any error, I am getting the following error message with the motion correction 
script, last step (power et al.), on the resting data:

libc++abi.dylib: terminating with uncaught exception of type 
NEWMAT::SingularException
Abort

Any idea how to fix this? This is only happening in one subject.

Thanks a lot,

Leah
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] map data between FreeSurfer and HCP

[Marta Moreno]

Thank you, Dona. I tried that too but I am getting similar pictures. Any other 
recommendation? I got very nice results from analyses and need nice pictures.

Thanks, 
-L


> On Jan 15, 2017, at 10:40 AM, Dierker, Donna  wrote:
> 
> 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
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> 
>> 
> 
> 
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Freesurfer to Workbench (Marta Moreno)

[Marta Moreno]

Thank you very much, Alex.


> On Nov 14, 2016, at 10:54 AM, Alex Cohen  wrote:
> 
> You could take a look at this as well:
> https://www.ncbi.nlm.nih.gov/pubmed/27655470/ 
> 
> https://github.com/alexlicohen/script-toolbox 
> 
> https://youtu.be/bvqgg7ZFeI8 
> 
> It won't give you MNI-space files and isn't intended for cross-subject 
> comparison, but the scripts could get you started converting from FS files...
> 
> -Alex
> 
> 
> Alexander Li Cohen, M.D., Ph.D.
> E-mail: alexander.coh...@childrens.harvard.edu 
>  (Medical/Science Email)
> E-mail: alexco...@gmail.com  (Lifetime Email)
> 
> ___
> 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

Re: [HCP-Users] Freesurfer to Workbench

[Marta Moreno]

Thank you very much, Matt.

Leah


> On Nov 13, 2016, at 7:16 AM, Glasser, Matthew <glass...@wustl.edu> wrote:
> 
> You can use mris_convert to convert FreeSurfer formatted surface files to
> GIFTI.
> 
> Peace,
> 
> Matt.
> 
> On 11/12/16, 7:33 PM, "hcp-users-boun...@humanconnectome.org on behalf of
> Marta Moreno" <hcp-users-boun...@humanconnectome.org on behalf of
> mmorenoort...@icloud.com> wrote:
> 
>> Dear HCP users,
>> 
>> I want to convert individual surfaces obtained with Freesurfer to
>> Workbench format to be able to upload them into Workbench and run the
>> wb_commands with them. Is there any public script available for this?
>> 
>> Thank you,
>> 
>> Leah
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 
> 
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] geodesic-distance

[Marta Moreno]

I tried but still is empty

***
Leah Moreno, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons
1051 Riverside Dr., Unit 21
New York, NY 10032



> On May 29, 2016, at 7:06 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
> 
> Try without the commas.  
> 
> Peace,
> 
> Matt.
> 
> From: Marta Moreno <mmorenoort...@icloud.com 
> <mailto:mmorenoort...@icloud.com>>
> Date: Sunday, May 29, 2016 at 6:04 PM
> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>
> Cc: HCP Users <hcp-users@humanconnectome.org 
> <mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] geodesic-distance
> 
> ?44, 40, 29
> 
> ***
> Leah Moreno, Ph.D.
> Postdoctoral Research Fellow
> Division of Experimental Therapeutics
> New York State Psychiatric Institute
> Department of Psychiatry
> Columbia University College of Physicians and Surgeons
> 1051 Riverside Dr., Unit 21
> New York, NY 10032
> 
> 
> 
>> On May 29, 2016, at 6:59 PM, Glasser, Matthew <glass...@wustl.edu 
>> <mailto:glass...@wustl.edu>> wrote:
>> 
>> How did you call the command?
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: Marta Moreno <mmorenoort...@icloud.com 
>> <mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, May 29, 2016 at 5:58 PM
>> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>
>> Cc: HCP Users <hcp-users@humanconnectome.org 
>> <mailto:hcp-users@humanconnectome.org>>
>> Subject: Re: [HCP-Users] geodesic-distance
>> 
>> Thanks for answering!
>> No error message but vertex-list-out is empty
>> 
>> ***
>> Leah Moreno, Ph.D.
>> Postdoctoral Research Fellow
>> Division of Experimental Therapeutics
>> New York State Psychiatric Institute
>> Department of Psychiatry
>> Columbia University College of Physicians and Surgeons
>> 1051 Riverside Dr., Unit 21
>> New York, NY 10032
>> 
>> 
>> 
>>> On May 29, 2016, at 6:57 PM, Glasser, Matthew <glass...@wustl.edu 
>>> <mailto:glass...@wustl.edu>> wrote:
>>> 
>>> What is the error message?
>>> 
>>> Peace,
>>> 
>>> Matt.
>>> 
>>> From: <hcp-users-boun...@humanconnectome.org 
>>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
>>> <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>>
>>> Date: Sunday, May 29, 2016 at 5:54 PM
>>> To: HCP Users <hcp-users@humanconnectome.org 
>>> <mailto:hcp-users@humanconnectome.org>>
>>> Subject: [HCP-Users] geodesic-distance
>>> 
>>> Dear users,
>>> 
>>> I want to compute the geodesic distance in mm between two vertices using 
>>> MNI coordinates as input. I was planing to do:
>>>  wb_command -surface-closest-vertex
>>>  wb_commands -surface-geodesic-distance
>>> But the first command is not working.
>>> What am I doing wrong? Also, is there any other way?
>>> 
>>> Thanks,
>>> 
>>> Leah
>>> ***
>>> Leah Moreno, Ph.D.
>>> Postdoctoral Research Fellow
>>> Division of Experimental Therapeutics
>>> New York State Psychiatric Institute
>>> Department of Psychiatry
>>> Columbia University College of Physicians and Surgeons
>>> 1051 Riverside Dr., Unit 21
>>> New York, NY 10032
>>> 
>>> 
>>> 
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
>>> <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.
>> 
>> 
>&

Re: [HCP-Users] geodesic-distance

[Marta Moreno]

−44, 40, 29

***
Leah Moreno, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons
1051 Riverside Dr., Unit 21
New York, NY 10032



> On May 29, 2016, at 6:59 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
> 
> How did you call the command?
> 
> Peace,
> 
> Matt.
> 
> From: Marta Moreno <mmorenoort...@icloud.com 
> <mailto:mmorenoort...@icloud.com>>
> Date: Sunday, May 29, 2016 at 5:58 PM
> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>
> Cc: HCP Users <hcp-users@humanconnectome.org 
> <mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] geodesic-distance
> 
> Thanks for answering!
> No error message but vertex-list-out is empty
> 
> ***
> Leah Moreno, Ph.D.
> Postdoctoral Research Fellow
> Division of Experimental Therapeutics
> New York State Psychiatric Institute
> Department of Psychiatry
> Columbia University College of Physicians and Surgeons
> 1051 Riverside Dr., Unit 21
> New York, NY 10032
> 
> 
> 
>> On May 29, 2016, at 6:57 PM, Glasser, Matthew <glass...@wustl.edu 
>> <mailto:glass...@wustl.edu>> wrote:
>> 
>> What is the error message?
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: <hcp-users-boun...@humanconnectome.org 
>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
>> <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, May 29, 2016 at 5:54 PM
>> To: HCP Users <hcp-users@humanconnectome.org 
>> <mailto:hcp-users@humanconnectome.org>>
>> Subject: [HCP-Users] geodesic-distance
>> 
>> Dear users,
>> 
>> I want to compute the geodesic distance in mm between two vertices using MNI 
>> coordinates as input. I was planing to do:
>>  wb_command -surface-closest-vertex
>>  wb_commands -surface-geodesic-distance
>> But the first command is not working.
>> What am I doing wrong? Also, is there any other way?
>> 
>> Thanks,
>> 
>> Leah
>> ***
>> Leah Moreno, Ph.D.
>> Postdoctoral Research Fellow
>> Division of Experimental Therapeutics
>> New York State Psychiatric Institute
>> Department of Psychiatry
>> Columbia University College of Physicians and Surgeons
>> 1051 Riverside Dr., Unit 21
>> New York, NY 10032
>> 
>> 
>> 
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
>> 
>>  
>> The materials in this message are private and may contain Protected 
>> Healthcare Information or other information of a sensitive nature. If you 
>> are not the intended recipient, be advised that any unauthorized use, 
>> disclosure, copying or the taking of any action in reliance on the contents 
>> of this information is strictly prohibited. If you have received this email 
>> in error, please immediately notify the sender via telephone or return mail.
> 
> 
>  
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] HCP_S500_R468_MIGPd4500ROW.dconn.nii

[Marta Moreno]

Hi users,

I have downloaded the HCP_S500_R468_MIGPd4500ROW.dconn.nii and want to seed in 
a particular vertex based on MNI coordinates to use the the seed-map as my 
mask. 
How could I get the functional connectivity matrix for particular vertex in 
whole brain and corresponding in time series?

Thanks,

Leah
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons
1051 Riverside Dr., Unit 21
New York, NY 10032

office# 5700
phone: (646) 774-5428
email: mm4...@cumc.columbia.edu




___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] T1w/wmparc_1mm

[Marta Moreno]

Hi Matt,

wmparc.mgz file does not exist. I run FreeSurfer pipeline again as I did not 
have gradunwarp installed but still I am not getting this file. Any idea, 
please?

Best wishes,

Leah
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons
1051 Riverside Dr., Unit 21
New York, NY 10032

office# 5700
phone: (646) 774-5428
email: mm4...@cumc.columbia.edu



On Jun 26, 2015, at 8:22 AM, Glasser, Matthew glass...@wusm.wustl.edu wrote:

 It sounds like the FreeSurfer pipeline might not have finished okay.  Does
 the ${StudyFolder}/${Subject}/T1w/${Subject}/mri/wmparc.mgz file exist?
 
 Peace,
 
 Matt.
 
 On 6/25/15, 9:14 PM, hcp-users-boun...@humanconnectome.org on behalf of
 Marta Moreno hcp-users-boun...@humanconnectome.org on behalf of
 mmorenoort...@icloud.com wrote:
 
 Hi users,
 
 I run PostfreesurferPipeline script and I am getting the next error: ³can
 not open T1w/wmparc_1mm for reading². I checked and the file is not
 there.
 I am running Freesurfer v5.3.0, not the HCP version. Any help, please?
 
 Thanks,
 
 Leah
 ___
 HCP-Users mailing list
 HCP-Users@humanconnectome.org
 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
 
 
 
 The materials in this message are private and may contain Protected 
 Healthcare Information or other information of a sensitive nature. If you are 
 not the intended recipient, be advised that any unauthorized use, disclosure, 
 copying or the taking of any action in reliance on the contents of this 
 information is strictly prohibited. If you have received this email in error, 
 please immediately notify the sender via telephone or return mail.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] fc maps in subject native volume space

[Marta Moreno]

Dear Users,

I have an ROI created in the surface, how could I map it to the native volume 
subject space?

Also, I have my fc map from that ROI (dscalar.nii), how could I map it to the 
native volume subject space?

Please help.

Thank you,

Leah 
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons
1051 Riverside Dr., Unit 21
New York, NY 10032

office# 5700
phone: (646) 774-5428
email: mm4...@cumc.columbia.edu




___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] from volume to gifti file to cifti roi

[Marta Moreno]

Thank you Timothy, I found your email very useful. I followed it and is done!!

Also thanks to Donna and Jo!

Best wishes always,

Leah
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons
1051 Riverside Dr., Unit 21
New York, NY 10032

phone: (646) 774-5428
email: mm4...@cumc.columbia.edu



On Apr 21, 2015, at 5:04 PM, Timothy Coalson tsc...@mst.edu wrote:

 You can always get help for an individual command by running it without any 
 arguments, and you can list the commands and only a short description with 
 -list-commands.  You can also browse the commands here:
 
 http://www.humanconnectome.org/software/workbench-command.php
 
 In this case, you will want to start with -volume-to-surface-mapping and 
 -metric-label-import, then either -cifti-create-label if you have the 
 Atlas_ROIs.2.nii.gz file handy, or else -cifti-replace-structure (potentially 
 with -cifti-math, -cifti-merge, and -cifti-label-import commands to create an 
 empty single-map cifti label file from an existing cifti file).  This will 
 get you a cifti label file, and you can then use -cifti-label-to-roi or 
 -cifti-all-labels-to-rois to get a label as an ROI.
 
 We are working on a way to make it easier to get volume and surface data into 
 cifti format, matching the brainordinate space of an existing file.
 
 Tim
 
 
 On Tue, Apr 21, 2015 at 9:27 AM, do...@brainvis.wustl.edu wrote:
 Hi Marta,
 
 You will probably end up using wb_command to do what you need to do.
 There are a bunch of tools that might be able to help.  The usage is huge,
 so do something like this to write it to a text file:
 
 wb_command -all-commands-help  ~/Desktop/wb_command.help.txt
 
 Then open ~/Desktop/wb_command.help.txt in a text editor and have a look
 at the help for these commands:
 
 -cifti-all-labels-to-rois
 -cifti-create-label
 -cifti-find-clusters
 -cifti-label-import
 -cifti-label-to-roi
 -volume-to-surface-mapping
 
 You won't use all of them, but this will narrow the focus.
 
 Donna
 
 
  Dear Users,
 
  I am generating ROIs in subject volume space and need to know how to
  create a gifti label file when I map from volume to surface and how to
  convert that label gifti file to cifti roi?
 
  Best wishes always,
 
  Leah
  ___
  Marta Moreno-Ortega, Ph.D.
  Postdoctoral Research Fellow
  Division of Experimental Therapeutics
  New York State Psychiatric Institute
  Department of Psychiatry
  Columbia University College of Physicians and Surgeons
  1051 Riverside Dr., Unit 21
  New York, NY 10032
 
  phone: (646) 774-5428
  email: mm4...@cumc.columbia.edu
 
 
 
 
  ___
  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
 


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] from volume to gifti file to cifti roi

[Marta Moreno]

Dear Users,

I am generating ROIs in subject volume space and need to know how to create a 
gifti label file when I map from volume to surface and how to convert that 
label gifti file to cifti roi? 

Best wishes always,

Leah
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons
1051 Riverside Dr., Unit 21
New York, NY 10032

phone: (646) 774-5428
email: mm4...@cumc.columbia.edu




___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] creati cifti from nifti1

[Marta Moreno]

Hi users,

I am working on 7 T data doing some testing for fc analyses and would like to 
to create a cifti file from nifti1 (my nifti1 fc t-map was created with SPM). 

I am using wb_command -volume-to-surface-mapping and wb_command 
-cifti-create-dense-scalar to have my cifti file but when loading into 
workbench my subcortical data is not separated from my surface t-map. 
What am I doing wrong?

Thanks,

Leah
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons





___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] 7 tesla MRI

[Marta Moreno]

Hi Joseph,

Thanks for your recommendation! 

All the best,
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons




On Feb 24, 2015, at 1:41 PM, An Vu j...@umn.edu wrote:

 Hi Marta,
 
 Matt has the right idea here. To get the 1.6-2mm at 7T, I would recommend 
 using IPAT 2, partial fourier 6/8, TE ~20ms. Use the smallest MB factor that 
 will give you TR = 1 second (should be MB = 5).
 
 Joseph
 
 On Feb 23, 2015, at 10:01 AM, hcp-users-requ...@humanconnectome.org wrote:
 
 Send HCP-Users mailing list submissions to
  hcp-users@humanconnectome.org
 
 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
  hcp-users-requ...@humanconnectome.org
 
 You can reach the person managing the list at
  hcp-users-ow...@humanconnectome.org
 
 When replying, please edit your Subject line so it is more specific
 than Re: Contents of HCP-Users digest...
 
 
 Today's Topics:
 
  1. 7 tesla MRI (Marta Moreno)
  2. Re: 7 tesla MRI (Glasser, Matthew)
  3. Re: 7 tesla MRI (Marta Moreno)
  4. Re: Processing Diffusion MRI Data (Archer,Derek B)
  5. Re: Processing Diffusion MRI Data (Satrajit Ghosh)
 
 
 --
 
 Message: 1
 Date: Sun, 22 Feb 2015 20:26:29 -0500
 From: Marta Moreno mmorenoort...@icloud.com
 Subject: [HCP-Users] 7 tesla MRI
 To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Message-ID: 68a764ca-d62d-42cf-87ed-c9eb4be92...@icloud.com
 Content-Type: text/plain; charset=us-ascii
 
 Hi users,
 
 I am going to start acquiring data from 7 Tesla MRI (Siemens) and would like 
 to know best option for resting state (carrying out whole brain shimming up 
 to 2nd order). Which would be best protocol in your expert opinion? 
 
 Thanks!
 ___
 Marta Moreno-Ortega, Ph.D.
 Postdoctoral Research Fellow 
 Division of Experimental Therapeutics
 New York State Psychiatric Institute
 Department of Psychiatry
 Columbia University College of Physicians and Surgeons
 
 
 
 
 -- next part --
 An HTML attachment was scrubbed...
 URL: 
 http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150222/66144559/attachment-0001.html
  
 
 --
 
 Message: 2
 Date: Mon, 23 Feb 2015 01:37:22 +
 From: Glasser, Matthew glass...@wusm.wustl.edu
 Subject: Re: [HCP-Users] 7 tesla MRI
 To: Marta Moreno mmorenoort...@icloud.com,
  hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Message-ID: d10fe02a.e8a88%glass...@wusm.wustl.edu
 Content-Type: text/plain; charset=us-ascii
 
 An HTML attachment was scrubbed...
 URL: 
 http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150223/7d35a7c7/attachment-0001.html
  
 
 --
 
 Message: 3
 Date: Sun, 22 Feb 2015 21:35:37 -0500
 From: Marta Moreno mmorenoort...@icloud.com
 Subject: Re: [HCP-Users] 7 tesla MRI
 To: Glasser, Matthew glass...@wusm.wustl.edu
 Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Message-ID: 0b4de77d-556c-4ca4-99c1-50f830a4a...@icloud.com
 Content-Type: text/plain; charset=windows-1252
 
 Thank you very much, Matt! I am going to test both this week and chose best. 
 Is there any other information I should be aware of in order to acquire my 
 data best way and establish a final protocol? Will have this week for 
 testing.
 ___
 Marta Moreno-Ortega, Ph.D.
 Postdoctoral Research Fellow
 Division of Experimental Therapeutics
 New York State Psychiatric Institute
 Department of Psychiatry
 Columbia University College of Physicians and Surgeons
 
 
 
 
 On Feb 22, 2015, at 8:37 PM, Glasser, Matthew glass...@wusm.wustl.edu 
 wrote:
 
 I?d get the best spatial resolution you can (e.g. 2mm-1.6mm) while keeping 
 the TR under 1 second (with multi-band EPI).  
 
 Peace,
 
 Matt.
 
 From: Marta Moreno mmorenoort...@icloud.com
 Date: Sunday, February 22, 2015 at 7:26 PM
 To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: [HCP-Users] 7 tesla MRI
 
 Hi users,
 
 I am going to start acquiring data from 7 Tesla MRI (Siemens) and would 
 like to know best option for resting state (carrying out whole brain 
 shimming up to 2nd order). Which would be best protocol in your expert 
 opinion? 
 
 Thanks!
 ___
 Marta Moreno-Ortega, Ph.D.
 Postdoctoral Research Fellow 
 Division of Experimental Therapeutics
 New York State Psychiatric Institute
 Department of Psychiatry
 Columbia University College of Physicians and Surgeons
 
 
 
 
 ___
 HCP-Users mailing list
 HCP-Users@humanconnectome.org
 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
 
 
 The materials in this message

[HCP-Users] 7 tesla MRI

[Marta Moreno]

Hi users,

I am going to start acquiring data from 7 Tesla MRI (Siemens) and would like to 
know best option for resting state (carrying out whole brain shimming up to 2nd 
order). Which would be best protocol in your expert opinion? 

Thanks!
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow 
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons





___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] requirements for HCP pipeline?

[Marta Moreno]

Thanks to everybody, you are being very helpful. Much appreciation.
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons




On Feb 3, 2015, at 12:20 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote:

 You also need a T2w scan unless you want to do major hacking on the pipelines.
 
 Peace,
 
 Matt.
 
 From: Jennifer Elam el...@pcg.wustl.edu
 Date: Tuesday, February 3, 2015 at 11:25 AM
 To: Harms, Michael mha...@wustl.edu, 'Marta Moreno' 
 mmorenoort...@icloud.com, hcp-users@humanconnectome.org 
 hcp-users@humanconnectome.org
 Subject: Re: [HCP-Users] requirements for HCP pipeline?
 
 Hi Marta,
 As a reminder, there’s also lots of good documentation on the pipelines at 
 https://github.com/Washington-University/Pipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage.
  Might be particularly useful for you methods write up.
  
 Best,
 Jenn
  
 Jennifer Elam, Ph.D.
 Outreach Coordinator, Human Connectome Project
 Washington University School of Medicine
 Department of Anatomy and Neurobiology, Box 8108
 660 South Euclid Avenue
 St. Louis, MO 63110
 314-362-9387
 el...@pcg.wustl.edu
 www.humanconnectome.org
  
 From: hcp-users-boun...@humanconnectome.org 
 [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Harms, Michael
 Sent: Tuesday, February 03, 2015 8:41 AM
 To: Marta Moreno; hcp-users@humanconnectome.org
 Subject: Re: [HCP-Users] requirements for HCP pipeline?
  
  
 Hi,
 I'm not sure what those numbers for your T1w scan refer to.  For fMRI data, 
 you will need either a traditional gradient echo field map, or a 
 phase-encoding reversed pair of scans for distortion correction.
  
 Glasser et al. 2013 is the published reference for the HCP pipelines.
  
 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: Marta Moreno mmorenoort...@icloud.com
 Date: Monday, February 2, 2015 10:45 PM
 To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: [HCP-Users] requirements for HCP pipeline?
  
 Hi users,
  
 I am going to analyze some data acquired before the HCP pipeline was 
 established here at PI and I am wondering which would be the minimum 
 requisites I need. I had collected 2T1w (512, 512, 236), 1T2 and resting 
 state (3x3x3mm; TR=2).
  
 Also would need some boiler plate documentation to write the methods from 
 another data set already analyzed through the HCP pipeline. Any 
 recommendation, please?
  
 Thanks,
 ___
 Marta Moreno-Ortega, Ph.D.
 Postdoctoral Research Fellow
 Division of Experimental Therapeutics
 New York State Psychiatric Institute
 Department of Psychiatry
 Columbia University College of Physicians and Surgeons
 
 
 
  
 ___
 HCP-Users mailing list
 HCP-Users@humanconnectome.org
 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
  
 The materials in this message are private and may contain Protected 
 Healthcare Information or other information of a sensitive nature. If you are 
 not the intended recipient, be advised that any unauthorized use, disclosure, 
 copying or the taking of any action in reliance on the contents of this 
 information is strictly prohibited. If you have received this email in error, 
 please immediately notify the sender via telephone or return mail.
 ___
 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
 
  
 The materials in this message are private and may contain Protected 
 Healthcare Information or other information of a sensitive nature. If you are 
 not the intended recipient, be advised that any unauthorized use, disclosure, 
 copying or the taking of any action in reliance on the contents of this 
 information is strictly prohibited. If you have received this email in error, 
 please immediately notify the sender via telephone or return mail.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] 7 RSN Netoworks label file

[Marta Moreno]

It works using the map index number 1, thanks Tim!

___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons




On Jan 26, 2015, at 2:37 AM, Timothy Coalson tsc...@mst.edu wrote:

 The map name/number is not a label name, it is the map index or name that you 
 select in the overlays toolbox in the gui, use 1 and it will probably give 
 you what you want.  A single map usually has multiple labels, specifically 
 all the ones that get displayed at the same time in the gui.
 
 Tim
 
 
 On Sat, Jan 24, 2015 at 10:20 PM, Marta Moreno mmorenoort...@icloud.com 
 wrote:
 I was doing: wb_command -cifti-label-export-table but the map from 
 RSN-netwoks.32k was not recognized.
 I did what Donna suggested and I got the information that way so the problem 
 is resolved, but still can not find which is the map from RSN just in case 
 someone has that information.
 
 I want to extract the connectivity from my seed to different networks, that 
 is why I needed the table to know which networks to extract in matlab. I did 
 it that way and is working.
 
 Thanks,
 ___
 Marta Moreno-Ortega, Ph.D.
 Postdoctoral Research Fellow
 Division of Experimental Therapeutics
 New York State Psychiatric Institute
 Department of Psychiatry
 Columbia University College of Physicians and Surgeons
 
 
 
 
 On Jan 23, 2015, at 12:03 AM, Glasser, Matthew glass...@wusm.wustl.edu 
 wrote:
 
 You can also use the map number if that is the issue.  Else perhaps we
 need more info on what you are trying to do.
 
 Peace,
 
 Matt.
 
 On 1/22/15, 9:20 PM, Marta Moreno mmorenoort...@icloud.com wrote:
 
 Hi users,
 
 I am trying to get the labels from 7 RSN Networks but map on export
 table command is not recognized and I am not sure if frontoparietal is 6
 and DMN 7. Any idea?
 
 Thanks
 
 Sent from my iPhone
 ___
 HCP-Users mailing list
 HCP-Users@humanconnectome.org
 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
 
 
 
 The materials in this message are private and may contain Protected 
 Healthcare Information or other information of a sensitive nature. If you 
 are not the intended recipient, be advised that any unauthorized use, 
 disclosure, copying or the taking of any action in reliance on the contents 
 of this information is strictly prohibited. If you have received this email 
 in error, please immediately notify the sender via telephone or return mail.
 
 ___
 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

Re: [HCP-Users] 7 RSN Netoworks label file

[Marta Moreno]

I was doing: wb_command -cifti-label-export-table but the map from 
RSN-netwoks.32k was not recognized.
I did what Donna suggested and I got the information that way so the problem is 
resolved, but still can not find which is the map from RSN just in case someone 
has that information.

I want to extract the connectivity from my seed to different networks, that is 
why I needed the table to know which networks to extract in matlab. I did it 
that way and is working.

Thanks,
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons




On Jan 23, 2015, at 12:03 AM, Glasser, Matthew glass...@wusm.wustl.edu 
wrote:

 You can also use the map number if that is the issue.  Else perhaps we
 need more info on what you are trying to do.
 
 Peace,
 
 Matt.
 
 On 1/22/15, 9:20 PM, Marta Moreno mmorenoort...@icloud.com wrote:
 
 Hi users,
 
 I am trying to get the labels from 7 RSN Networks but map on export
 table command is not recognized and I am not sure if frontoparietal is 6
 and DMN 7. Any idea?
 
 Thanks
 
 Sent from my iPhone
 ___
 HCP-Users mailing list
 HCP-Users@humanconnectome.org
 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
 
 
 
 The materials in this message are private and may contain Protected 
 Healthcare Information or other information of a sensitive nature. If you are 
 not the intended recipient, be advised that any unauthorized use, disclosure, 
 copying or the taking of any action in reliance on the contents of this 
 information is strictly prohibited. If you have received this email in error, 
 please immediately notify the sender via telephone or return mail.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] 7 RSN Netoworks label file

[Marta Moreno]

Hi users,

I am trying to get the labels from 7 RSN Networks but map on export table 
command is not recognized and I am not sure if frontoparietal is 6 and DMN 7. 
Any idea?

Thanks

Sent from my iPhone
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] grey matter volume

[Marta Moreno]

Great I could find it, much appreciation.
Are those measures reliable or should I do VBM? I overly aparc.a2009s+aseg to 
T1w_restore and it fits perfectly. Is that enough quality check?

Thanks!,
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons




On Jan 20, 2015, at 9:21 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote:

 That should be in ${StudyFolder}/${Subject}/T1w/${Subject}/stats
 
 Peace,
 
 Matt.
 
 From: Marta Moreno mmorenoort...@icloud.com
 Date: Tuesday, January 20, 2015 at 7:59 PM
 To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: [HCP-Users] grey matter volume
 
 Hi users,
 
 Where to find grey matter volume from subcortical structures same way you can 
 find them in freesurfer/subects/'subject_id'/stats/aseg.stats?
 
 Thanks,
 ___
 Marta Moreno-Ortega, Ph.D.
 Postdoctoral Research Fellow
 Division of Experimental Therapeutics
 New York State Psychiatric Institute
 Department of Psychiatry
 Columbia University College of Physicians and Surgeons
 
 
 
 
 ___
 HCP-Users mailing list
 HCP-Users@humanconnectome.org
 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
 
  
 The materials in this message are private and may contain Protected 
 Healthcare Information or other information of a sensitive nature. If you are 
 not the intended recipient, be advised that any unauthorized use, disclosure, 
 copying or the taking of any action in reliance on the contents of this 
 information is strictly prohibited. If you have received this email in error, 
 please immediately notify the sender via telephone or return mail.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] grey matter volume

[Marta Moreno]

Hi users,

Where to find grey matter volume from subcortical structures same way you can 
find them in freesurfer/subects/'subject_id'/stats/aseg.stats?

Thanks,
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons





___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] -cifti-separate

[Marta Moreno]

wb_command cifti-in COLUMN -metric CORTEX_RIGHT metric-out

Thanks,
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons




On Jan 12, 2015, at 10:54 PM, Glasser, Matthew glass...@wusm.wustl.edu 
wrote:

 Please post your wb_command -cifti-separate command line.
 
 Peace,
 
 Matt.
 
 From: Marta Moreno mmorenoort...@icloud.com
 Date: Monday, January 12, 2015 at 9:52 PM
 To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: [HCP-Users] -cifti-separate
 
 Hi users,
 
 I am using the -cifti-separate command to generate a surface (i.e. CORTEX 
 RIGHT) to use as right surface input to the -cifti-find-clusters command.
 The output from cifti-separate is not recognized. How do I convert it to a 
 format that will work with cifti-find-clusters? I tried -metric-convert but 
 to no avail. 
 
 Thank you,
 
 ___
 Marta Moreno-Ortega, Ph.D.
 Postdoctoral Research Fellow
 Division of Experimental Therapeutics
 New York State Psychiatric Institute
 Department of Psychiatry
 Columbia University College of Physicians and Surgeons
 
 
 
 
 ___
 HCP-Users mailing list
 HCP-Users@humanconnectome.org
 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
 
  
 The materials in this message are private and may contain Protected 
 Healthcare Information or other information of a sensitive nature. If you are 
 not the intended recipient, be advised that any unauthorized use, disclosure, 
 copying or the taking of any action in reliance on the contents of this 
 information is strictly prohibited. If you have received this email in error, 
 please immediately notify the sender via telephone or return mail.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] -cifti-separate

[Marta Moreno]

Hi users,

I am using the -cifti-separate command to generate a surface (i.e. CORTEX 
RIGHT) to use as right surface input to the -cifti-find-clusters command.
The output from cifti-separate is not recognized. How do I convert it to a 
format that will work with cifti-find-clusters? I tried -metric-convert but to 
no avail. 

Thank you,

___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons





___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] -cifti-separate

[Marta Moreno]

Thank you I appreciate your help!

All the best,
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons




On Jan 12, 2015, at 11:19 PM, Glasser, Matthew glass...@wusm.wustl.edu 
wrote:

 Use 
 ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.midthickness.32k_fs_LR.surf.gii
 
 Peace,
 
 Matt.
 
 From: Marta Moreno mmorenoort...@icloud.com
 Date: Monday, January 12, 2015 at 10:15 PM
 To: Matt Glasser glass...@wusm.wustl.edu
 Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: Re: [HCP-Users] -cifti-separate
 
 Is data created by the HCP pipeline.
 I made a t-map and saved it as a cifti file with 91K brain ordinates and I 
 would like to cluster extent thresholding using the -cifti-fiind-clusters 
 command but I am not sure what to use as the surface inputs files.
 
 Thanks,
 ___
 Marta Moreno-Ortega, Ph.D.
 Postdoctoral Research Fellow
 Division of Experimental Therapeutics
 New York State Psychiatric Institute
 Department of Psychiatry
 Columbia University College of Physicians and Surgeons
 
 
 
 
 On Jan 12, 2015, at 11:09 PM, Glasser, Matthew glass...@wusm.wustl.edu 
 wrote:
 
 Is this HCP data or your own data?
 
 Matt.
 
 From: Marta Moreno mmorenoort...@icloud.com
 Date: Monday, January 12, 2015 at 10:06 PM
 To: Matt Glasser glass...@wusm.wustl.edu
 Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: Re: [HCP-Users] -cifti-separate
 
 What is the required surface input for -cifti-find-clusters?
 
 Thanks,
 ___
 Marta Moreno-Ortega, Ph.D.
 Postdoctoral Research Fellow
 Division of Experimental Therapeutics
 New York State Psychiatric Institute
 Department of Psychiatry
 Columbia University College of Physicians and Surgeons
 
 
 
 
 On Jan 12, 2015, at 11:01 PM, Glasser, Matthew glass...@wusm.wustl.edu 
 wrote:
 
 I didn’t read your question closely enough.  You cannot make a surface from 
 -cifti-separate (you can make data that you can display and analyze on a 
 surface however).
 
 Peace,
 
 Matt.
 
 From: Marta Moreno mmorenoort...@icloud.com
 Date: Monday, January 12, 2015 at 9:59 PM
 To: Matt Glasser glass...@wusm.wustl.edu
 Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: Re: [HCP-Users] -cifti-separate
 
 wb_command cifti-in COLUMN -metric CORTEX_RIGHT metric-out
 
 Thanks,
 ___
 Marta Moreno-Ortega, Ph.D.
 Postdoctoral Research Fellow
 Division of Experimental Therapeutics
 New York State Psychiatric Institute
 Department of Psychiatry
 Columbia University College of Physicians and Surgeons
 
 
 
 
 On Jan 12, 2015, at 10:54 PM, Glasser, Matthew glass...@wusm.wustl.edu 
 wrote:
 
 Please post your wb_command -cifti-separate command line.
 
 Peace,
 
 Matt.
 
 From: Marta Moreno mmorenoort...@icloud.com
 Date: Monday, January 12, 2015 at 9:52 PM
 To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: [HCP-Users] -cifti-separate
 
 Hi users,
 
 I am using the -cifti-separate command to generate a surface (i.e. CORTEX 
 RIGHT) to use as right surface input to the -cifti-find-clusters command.
 The output from cifti-separate is not recognized. How do I convert it to a 
 format that will work with cifti-find-clusters? I tried -metric-convert 
 but to no avail. 
 
 Thank you,
 
 ___
 Marta Moreno-Ortega, Ph.D.
 Postdoctoral Research Fellow
 Division of Experimental Therapeutics
 New York State Psychiatric Institute
 Department of Psychiatry
 Columbia University College of Physicians and Surgeons
 
 
 
 
 ___
 HCP-Users mailing list
 HCP-Users@humanconnectome.org
 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
 
  
 The materials in this message are private and may contain Protected 
 Healthcare Information or other information of a sensitive nature. If you 
 are not the intended recipient, be advised that any unauthorized use, 
 disclosure, copying or the taking of any action in reliance on the 
 contents of this information is strictly prohibited. If you have received 
 this email in error, please immediately notify the sender via telephone or 
 return mail.
 
 
  
 The materials in this message are private and may contain Protected 
 Healthcare Information or other information of a sensitive nature. If you 
 are not the intended recipient, be advised that any unauthorized use, 
 disclosure, copying or the taking of any action in reliance on the contents 
 of this information is strictly prohibited. If you have received this email 
 in error, please immediately notify the sender via telephone or return mail.
 
 
  
 The materials in this message are private and may contain Protected 
 Healthcare Information or other information of a sensitive nature. If you 
 are not the intended recipient, be advised

Re: [HCP-Users] cluster extent thresholding on surface

[Marta Moreno]

Ok, thanks for the answer. 
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons




On Jan 11, 2015, at 10:20 PM, Harms, Michael mha...@wustl.edu wrote:

 
 We are working on developing a script that will use randomise and permutation 
 testing to accomplish that, but don't have anything to share at this time.
 
 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: Marta Moreno mmorenoort...@icloud.com
 Date: Sunday, January 11, 2015 7:38 PM
 To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: [HCP-Users] cluster extent thresholding on surface
 
 Hi users,
 
 For cluster extent thresholding on surface I am using wb_command 
 -cifti-find-clusters. How to find surface area to have corrected  p value of 
 0.05? 
 
 Thanks,
 ___
 Marta Moreno-Ortega, Ph.D.
 Postdoctoral Research Fellow
 Division of Experimental Therapeutics
 New York State Psychiatric Institute
 Department of Psychiatry
 Columbia University College of Physicians and Surgeons
 
 
 
 
 On Jan 9, 2015, at 3:24 PM, Glasser, Matthew glass...@wusm.wustl.edu 
 wrote:
 
 This line in the pipelines deals with either case:
 
 ${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude
 
 
 On 1/9/15, 2:17 PM, Greg Burgess gcburg...@gmail.com wrote:
 
 I think (but am not 100% certain) that the magnitude image should be a
 single volume (dim4 = 1), whereas your magnitude image appears to be two
 volumes (dim4 = 2). That could be the mismatching dimension.
 
 --Greg
 
 
 Greg Burgess, Ph.D.
 Staff Scientist, Human Connectome Project
 Washington University School of Medicine
 Department of Anatomy and Neurobiology
 Phone: 314-362-7864
 Email: gburg...@wustl.edu
 
 On Jan 9, 2015, at 1:59 PM, Glasser, Matthew glass...@wusm.wustl.edu
 wrote:
 
 Can you check that the headers of these files look okay:
 
 
 ${StudyFolder}/${Subject}/${fMRIName}/DistortionCorrectionAndEPIToT1wReg_
 FLIRTBBRAndFreeSurferBBRbased/FieldMap/Phase.nii.gz
 
 ${StudyFolder}/${Subject}/${fMRIName}/DistortionCorrectionAndEPIToT1wReg_
 FLIRTBBRAndFreeSurferBBRbased/FieldMap/Magnitude_brain
 
 The first file is directly copied from the input location
 
 ${FSLDIR}/bin/imcp ${PhaseInputName} ${WD}/Phase
 
 And the second one has had the following done to it (initial fslmaths
 command reads from input location):
 
 ${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude
 ${FSLDIR}/bin/bet ${WD}/Magnitude ${WD}/Magnitude_brain -f 0.35 -m
 #Brain extract the magnitude image
 
 If all those files look okay, then the issue is with the
 fsl_prepare_fieldmap script, which is a part of the FSL distribution and
 is supported by the FSL team:
 
 ${FSLDIR}/bin/fsl_prepare_fieldmap SIEMENS ${WD}/Phase
 ${WD}/Magnitude_brain ${WD}/FieldMap ${DeltaTE}
 
 Peace,
 
 Matt.
 
 From: Book, Gregory gregory.b...@hhchealth.org
 Date: Friday, January 9, 2015 at 1:26 PM
 To: Matt Glasser glass...@wusm.wustl.edu,
 hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: RE: [HCP-Users] fieldmap processing error
 
 Digging deeper into it, I think the fieldmap voxel sizes may be changed
 or misreported inside the HCP script.
 
 In the analysis/unprocessed directory, the headers look like this:
 [Gbook@compute31 T1w_MPR1]$ fslinfo
 analysis_3T_FieldMap_Magnitude.nii.gz
 data_type  INT16
 dim1   80
 dim2   80
 dim3   48
 dim4   2
 datatype   4
 pixdim13.00
 pixdim23.00
 pixdim33.00
 pixdim40.731000
 cal_max0.
 cal_min0.
 file_type  NIFTI-1+
 [Gbook@compute31 T1w_MPR1]$ fslinfo analysis_3T_FieldMap_Phase.nii.gz
 data_type  INT16
 dim1   80
 dim2   80
 dim3   48
 dim4   1
 datatype   4
 pixdim13.00
 pixdim23.00
 pixdim33.00
 pixdim40.731000
 cal_max0.
 cal_min0.
 file_type  NIFTI-1+
 
 Then, when running the HCP pipeline, it reports this error (found
 through grep):
 
 ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log:Phase and Magnitude images
 must have the same number of voxels and voxel dimensions
 ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log-Current dimensions are:
 ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log-  Phase image: 80  x
 80  x 48  with dims of 3.00  x 3.00  x 3.01  mm
 ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log-  Magnitude image: 80  x
 80  x 48  with dims of 3.00  x 3.00  x 3.00

[HCP-Users] cluster extent thresholding on surface

[Marta Moreno]

Hi users,

For cluster extent thresholding on surface I am using wb_command 
-cifti-find-clusters. How to find surface area to have corrected  p value of 
0.05? 

Thanks,
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons




On Jan 9, 2015, at 3:24 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote:

 This line in the pipelines deals with either case:
 
 ${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude
 
 
 On 1/9/15, 2:17 PM, Greg Burgess gcburg...@gmail.com wrote:
 
 I think (but am not 100% certain) that the magnitude image should be a
 single volume (dim4 = 1), whereas your magnitude image appears to be two
 volumes (dim4 = 2). That could be the mismatching dimension.
 
 --Greg
 
 
 Greg Burgess, Ph.D.
 Staff Scientist, Human Connectome Project
 Washington University School of Medicine
 Department of Anatomy and Neurobiology
 Phone: 314-362-7864
 Email: gburg...@wustl.edu
 
 On Jan 9, 2015, at 1:59 PM, Glasser, Matthew glass...@wusm.wustl.edu
 wrote:
 
 Can you check that the headers of these files look okay:
 
 
 ${StudyFolder}/${Subject}/${fMRIName}/DistortionCorrectionAndEPIToT1wReg_
 FLIRTBBRAndFreeSurferBBRbased/FieldMap/Phase.nii.gz
 
 ${StudyFolder}/${Subject}/${fMRIName}/DistortionCorrectionAndEPIToT1wReg_
 FLIRTBBRAndFreeSurferBBRbased/FieldMap/Magnitude_brain
 
 The first file is directly copied from the input location
 
 ${FSLDIR}/bin/imcp ${PhaseInputName} ${WD}/Phase
 
 And the second one has had the following done to it (initial fslmaths
 command reads from input location):
 
 ${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude
 ${FSLDIR}/bin/bet ${WD}/Magnitude ${WD}/Magnitude_brain -f 0.35 -m
 #Brain extract the magnitude image
 
 If all those files look okay, then the issue is with the
 fsl_prepare_fieldmap script, which is a part of the FSL distribution and
 is supported by the FSL team:
 
 ${FSLDIR}/bin/fsl_prepare_fieldmap SIEMENS ${WD}/Phase
 ${WD}/Magnitude_brain ${WD}/FieldMap ${DeltaTE}
 
 Peace,
 
 Matt.
 
 From: Book, Gregory gregory.b...@hhchealth.org
 Date: Friday, January 9, 2015 at 1:26 PM
 To: Matt Glasser glass...@wusm.wustl.edu,
 hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: RE: [HCP-Users] fieldmap processing error
 
 Digging deeper into it, I think the fieldmap voxel sizes may be changed
 or misreported inside the HCP script.
 
 In the analysis/unprocessed directory, the headers look like this:
 [Gbook@compute31 T1w_MPR1]$ fslinfo
 analysis_3T_FieldMap_Magnitude.nii.gz
 data_type  INT16
 dim1   80
 dim2   80
 dim3   48
 dim4   2
 datatype   4
 pixdim13.00
 pixdim23.00
 pixdim33.00
 pixdim40.731000
 cal_max0.
 cal_min0.
 file_type  NIFTI-1+
 [Gbook@compute31 T1w_MPR1]$ fslinfo analysis_3T_FieldMap_Phase.nii.gz
 data_type  INT16
 dim1   80
 dim2   80
 dim3   48
 dim4   1
 datatype   4
 pixdim13.00
 pixdim23.00
 pixdim33.00
 pixdim40.731000
 cal_max0.
 cal_min0.
 file_type  NIFTI-1+
 
 Then, when running the HCP pipeline, it reports this error (found
 through grep):
 
 ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log:Phase and Magnitude images
 must have the same number of voxels and voxel dimensions
 ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log-Current dimensions are:
 ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log-  Phase image: 80  x
 80  x 48  with dims of 3.00  x 3.00  x 3.01  mm
 ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log-  Magnitude image: 80  x
 80  x 48  with dims of 3.00  x 3.00  x 3.00  mm
 ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log-Fix this (probably in
 reconstruction stage) before re-running this script
 
 From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
 Sent: Thursday, January 08, 2015 2:07 PM
 To: Book, Gregory; hcp-users@humanconnectome.org
 Subject: Re: [HCP-Users] fieldmap processing error
 
 Probably the easiest thing to do would be to fix the outlying image
 dimension by editing the NIFTI header.  What program are you using to
 convert from scanner format to NIFTI?  We use dcm2nii in the HCP.
 
 Peace,
 
 Matt.
 
 From: Book, Gregory gregory.b...@hhchealth.org
 Date: Thursday, January 8, 2015 at 12:18 PM
 To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: [HCP-Users] fieldmap processing error
 
 We¹ve noticed an error while processing some fMRI data through the HCP
 pipeline. Several series are failing with the following message:
 
 Phase and Magnitude images must have the same number of voxels and
 voxel dimensions
 Current dimensions are:
  Phase image: 80  x 80  x 48

[HCP-Users] Fwd: question

[Marta Moreno Ortega]

Hi Users,

Just to say I resolved the problem I was having and now I can see my matrix and 
pconn so no problem!

Thanks,
___
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons

Begin forwarded message:

 From: Marta Moreno Ortega mm4...@columbia.edu
 Subject: question
 Date: December 25, 2014 12:17:33 AM EST
 To: hcp-users@humanconnectome.org
 
 Hi users,
 
 I am doing a paired t-test on matlab with rs-fc-MRI data using the 
 17Network_ContiguosParcels_32K (100*100) from the workbench tutorial as my 
 ROIs file to look at changes in connectivity between each pair of parcels.
 I am using wb_command -cifti-parcellate to generate the average time series 
 data within parcels and -cifti-correlation to determine the fc between time 
 series of parcels. 
 
 I want to save my results as gifti file to convert back to cifti and use 
 workbench to display my matrix but I am getting an error in my conversion 
 back to cifti (ERROR: dimensions of input gift array do not match dimensions 
 in the embedded cifti XML). Also would like to know how to visualize my 
 matrix in workbench as I tried with one of my subjects without success (I can 
 see it in matlab).
 
 Thank you,
 ___
 Marta Moreno-Ortega, Ph.D.
 Postdoctoral Research Fellow
 Division of Experimental Therapeutics
 New York State Psychiatric Institute
 Department of Psychiatry
 Columbia University College of Physicians and Surgeons
 


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users