Thanks for the feedback
I found it easier to copy back the files :-)
And - YES ! It worked :-)
Thanks a lot for your help guiding me through this. Very much appreciate !
Sven
> On 17 Jan 2023, at 17:57, Matthew Webster <[log in to unmask]> wrote:
>
> Dear Sven,
> You could potentially change the `cat /Volumes/SVEN-T7/UU-ASMR/7_FMRI_FSL/ICA-20.gica/.filelist` part of the dual_regression command to:
>
> `ls -1 /Volumes/SVEN-T7/UU-ASMR/7_FMRI_FSL/Asmr*.ica/reg_standard/filtered_func_data*`
>
> To check the files will be correct, the ls command should be run without backticks, e.g.
>
> ls -1 /Volumes/SVEN-T7/UU-ASMR/7_FMRI_FSL/Asmr*.ica/reg_standard/filtered_func_data*
>
> to confirm that the input ica folder names ( e.g. the Asmr*.ica section ) match those in the original .filelist.
>
> Hope this helps,.
> Kind Regards,
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
>
>> On 17 Jan 2023, at 11:17, Sven Haller <[log in to unmask]> wrote:
>>
>> Dear Matthew
>>
>> Thanks for your message
>>
>> That is absolutely possible (do not remember 100% for sure)
>>
>> So what should I do ? Copy back the files to the old location and try again ? Or is it possible to “fix” the path ?
>>
>> Sven
>>
>>> On 16 Jan 2023, at 21:05, Matthew Webster <[log in to unmask]> wrote:
>>>
>>> Dear Sven,
>>> Is it possible the data files been moved since the original analyses? The paths from .filelist are of the form:
>>>
>>> /Users/sven/0_UU-ASMR-ANALYSIS/7_FMRI_FSL/<blah>
>>>
>>> But in the screenshot they look to be stored on a removable drive:
>>>
>>> SVEN-T7/UU-ASMR/7_FMRI_FSL/<blah>
>>>
>>> Kind Regards
>>> Matthew
>>> --------------------------------
>>> Dr Matthew Webster
>>> FMRIB Centre
>>> John Radcliffe Hospital
>>> University of Oxford
>>>
>>>> On 5 Jan 2023, at 16:14, Matthew Webster <[log in to unmask]> wrote:
>>>>
>>>> Dear Sven,
>>>> The example call looks to have a erroneous 0 in it, if you retry the dual_regression call with the 0 after the 500 removed do the error messages change? You can run dual_regression in any folder - unless their paths are fully qualified, the input <foo>.mat and <foo>.con files are expected to be in the current directory, and the the output directory ( here DUAL ) will likewise be created in the current directory. I’m not sure what is causing the "shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory” messages, normally these occur when a directory is moved/renamed etc by an actions outside of the current terminal.
>>>>
>>>> Hope this helps,
>>>> Kind Regards
>>>> Matthew
>>>> --------------------------------
>>>> Dr Matthew Webster
>>>> FMRIB Centre
>>>> John Radcliffe Hospital
>>>> University of Oxford
>>>>
>>>>> On 5 Jan 2023, at 09:53, Sven HALLER <[log in to unmask]> wrote:
>>>>>
>>>>> Dear FSL experts
>>>>>
>>>>> I want to do a dual regression on MELODIC output (I have 79 cases total 57 pat versus 22 controls)
>>>>>
>>>>> I did the Melodic group ICA
>>>>>
>>>>> now I want to run dual regression, yet I get an error message (see below)
>>>>>
>>>>> I am not a programmer, only a simple user. The instructions on the website are not very detailed for me...
>>>>>
>>>>> - in which folder so I need to start the command ?
>>>>> - in which folder should I put the desing.mat and design.con files ?
>>>>>
>>>>> Any help is highly appreciated
>>>>>
>>>>> Sven
>>>>>
>>>>> ERROR MESSAGE
>>>>> sven@Svens-MacBook-Pro ICA-20.gica % dual_regression /Volumes/SVEN-T7/UU-ASMR/7_FMRI_FSL/ICA-20.gica/groupmelodic.ica/melodic_IC.nii.gz 1 UU-design.mat UU-design.con 500 0 DUAL `cat /Volumes/SVEN-T7/UU-ASMR/7_FMRI_FSL/ICA-20.gica/.filelist`
>>>>> shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
>>>>> shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
>>>>> mkdir: .: No such file or directory
>>>>> mkdir: 0: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 148: 0/scripts+logs/command: No such file or directory
>>>>> cp: UU-design.mat: No such file or directory
>>>>> cp: UU-design.con: No such file or directory
>>>>> creating common mask
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>> /Users/sven/fsl/bin/dual_regression: line 160: 0/scripts+logs/drA: No such file or directory
>>>>>
>>>>> ########################################################################
>>>>>
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>
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