Re: [HCP-Users] DeDriftAndResamplePipeline error
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
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 mailto:glass...@wustl.edu>> 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 mailto: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 mailto:mmorenoort...@icloud.com>> Date: Monday, April 15, 2019 at 8:53 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: HCP Users mailto:hcp-users@humanconnectome.org>&g
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 <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
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
mailto: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 mailto:mmorenoort...@icloud.com>>
Date: Monday, April 15, 2019 at 8:53 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: HCP Users
mailto:hcp-users@humanconnectome.org>>, Timothy
Coalson mailto:tsc...@mst.edu>>, "Brown, Tim"
mailto: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
mailto:mmorenoort...@icloud.com>> wrote:
It seams to be working now. Thanks a lot!
Leah.
On Apr 15, 2019, at 12:04 AM, Glasser, Matthew
mailto: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}
M
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.___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
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:
>>>>
>>>> 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
>>>> Date: Monday, April 15, 2019 at 8:53 AM
>>>> To: Matt Glasser
>>>> Cc: HCP Users , Timothy Coalson <
>>>> tsc...@mst.edu>, "Brown, Tim"
>>>> 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
>>>> wrote:
>>>>
>>>> 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
>>>>
>>>> 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
>>>> Date: Sunday, April 14, 2019 at 10:56 PM
>>>> To: Matt Glasser
>>>> Cc: HCP Users
>>>> Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error
>>>>
>>>> Thanks a lot for your
Re: [HCP-Users] DeDriftAndResamplePipeline error
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
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:
>>
>> 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
>> Date: Monday, April 15, 2019 at 8:53 AM
>> To: Matt Glasser
>> Cc: HCP Users , Timothy Coalson <
>> tsc...@mst.edu>, "Brown, Tim"
>> 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
>> wrote:
>>
>> 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
>>
>> Also it looks like line 124 needs an “s” on the end of the flag name to
>> read --multirun-fix-concat-names=${MRFixConcatName}
>>
>> Matt.
>>
>> From: Marta Moreno
>> Date: Sunday, April 14, 2019 at 10:56 PM
>> To: Matt Glasser
>> Cc: HCP Users
>> Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error
>>
>> Thanks a lot for your response.
>>
>> I am running v.4.0.0 now. And I have set up the script as follow:
>>
>> HighResMesh="164"
>> LowResMesh="32"
>> RegName="MSMAll_InitalReg_2_d40_WRN"
>>
>> DeDriftRegFiles="${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
>> 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: on behalf of Marta Moreno <
>> mmorenoort...@icloud.com>
>> Date: Sund
Re: [HCP-Users] DeDriftAndResamplePipeline error
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:
>
> 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
> Date: Monday, April 15, 2019 at 8:53 AM
> To: Matt Glasser
> Cc: HCP Users , Timothy Coalson <
> tsc...@mst.edu>, "Brown, Tim"
> 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
> wrote:
>
> 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
>
> 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
> Date: Sunday, April 14, 2019 at 10:56 PM
> To: Matt Glasser
> Cc: HCP Users
> 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 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: on behalf of Marta Moreno <
> mmorenoort...@icloud.com>
> Date: Sunday, April 14, 2019 at 10:06 PM
> To: HCP Users
> 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
Re: [HCP-Users] DeDriftAndResamplePipeline error
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 mailto:mmorenoort...@icloud.com>>
Date: Monday, April 15, 2019 at 8:53 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: HCP Users
mailto:hcp-users@humanconnectome.org>>, Timothy
Coalson mailto:tsc...@mst.edu>>, "Brown, Tim"
mailto: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
mailto:mmorenoort...@icloud.com>> wrote:
It seams to be working now. Thanks a lot!
Leah.
On Apr 15, 2019, at 12:04 AM, Glasser, Matthew
mailto: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=${MRFixConcatName}
Matt.
From: Marta Moreno mailto:mmorenoort...@icloud.com>>
Date: Sunday, April 14, 2019 at 10:56 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: HCP Users
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error
Thanks a lot for your response.
I am running v.4.0.0 now. And I have set up the script as follow:
HighResMesh="164"
LowResMesh="32"
RegName="MSMAll_InitalReg_2_d40_WRN"
DeDriftRegFiles="${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/R
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 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
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
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=${MRFixConcatName}
Matt.
From: Marta Moreno mailto:mmorenoort...@icloud.com>>
Date: Sunday, April 14, 2019 at 10:56 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: HCP Users
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error
Thanks a lot for your response.
I am running v.4.0.0 now. And I have set up the script as follow:
HighResMesh="164"
LowResMesh="32"
RegName="MSMAll_InitalReg_2_d40_WRN"
DeDriftRegFiles="${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
/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_MRâ€, 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,
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 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
Re: [HCP-Users] DeDriftAndResamplePipeline error
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
/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.
___
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http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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[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.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
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DeDriftAndResamplePipeline.sh.o17336
Description: Binary data
