Hi,
I think the problem here is related to the first error message, which is:
Cannot access column number 4 in matrix /mnt/hgfs/shared_folder/TO/PNM/cardiac_resp_TRtriggers.txt
So I'd check that file. I'd say that either the columns are wrongly specified or that it might contain non-unix end-of-line characters, which you can check by running "file /mnt/hgfs/shared_folder/TO/PNM/cardiac_resp_TRtriggers.txt" and if it says anything more than "ASCII text" then you probably need to fix it with dos2unix or similar.
If the file seems to have the right number of columns and the result of "file" is just "ASCII text" then let us know as we'll have to dig deeper.
All the best,
Mark
On 4 Jul 2013, at 06:06, Eiji Takasawa <[log in to unmask]> wrote:
> Dear FSL experts,
>
>
> I ran PNM_GUI for my fMRI data, but failed as shown below (/usr/local/fsl/bin/pnm_stage1: line 97: 7112 Segmentation fault (core dumped)).
> I couldn't find reason of this trouble, although I checked the script of "pnm_stage1".
>
> Could anyone give me some advice ?
> Is this system problem or something else like a bad txt file of physiological recordings ?
>
>
> Thanks,
>
>
>
> /usr/local/fsl/bin/pnm_stage1 -i /mnt/hgfs/shared_folder/TO/PNM/cardiac_resp_TRtriggers.txt -o /mnt/hgfs/shared_folder/TO/PNM -s 100 --tr=2.6 --smoothcard=0.1 --smoothresp=0.1 --resp=3 --cardiac=2 --trigger=4
> /usr/local/fsl/bin/pnm_evs -i /mnt/hgfs/shared_folder/TO/3HZ/4Dar3HZ.nii -c /mnt/hgfs/shared_folder/TO/PNM_card.txt -r /mnt/hgfs/shared_folder/TO/PNM_resp.txt -o /mnt/hgfs/shared_folder/TO/PNM --tr=2.6 --oc=4 --or=4 --multc=2 --multr=2 --sliceorder=up --csfmask=/mnt/hgfs/shared_folder/TO/CSF_IC7
>
> /usr/local/fsl/bin/pnm_stage1 -i /mnt/hgfs/shared_folder/TO/PNM/cardiac_resp_TRtriggers.txt -o /mnt/hgfs/shared_folder/TO/PNM -s 100 --tr=2.6 --smoothcard=0.1 --smoothresp=0.1 --resp=3 --cardiac=2 --trigger=4
> /usr/local/fsl/bin/popp -i /mnt/hgfs/shared_folder/TO/PNM/cardiac_resp_TRtriggers.txt -o /mnt/hgfs/shared_folder/TO/PNM -s 100 --tr=2.6 --smoothcard=0.1 --smoothresp=0.1 --resp=3 --cardiac=2 --trigger=4
> Cannot access column number 4 in matrix /mnt/hgfs/shared_folder/TO/PNM/cardiac_resp_TRtriggers.txt
> Done
> /usr/local/fsl/bin/pnm_stage1 -i /mnt/hgfs/shared_folder/TO/PNM/cardiac_resp_TRtriggers.txt -o /mnt/hgfs/shared_folder/TO/PNM -s 100 --tr=2.6 --smoothcard=0.1 --smoothresp=0.1 --resp=2 --cardiac=1 --trigger=3
> /usr/local/fsl/bin/pnm_evs -i /mnt/hgfs/shared_folder/TO/3HZ/4Dar3HZ.nii -c /mnt/hgfs/shared_folder/TO/PNM_card.txt -r /mnt/hgfs/shared_folder/TO/PNM_resp.txt -o /mnt/hgfs/shared_folder/TO/PNM --tr=2.6 --oc=4 --or=4 --multc=2 --multr=2 --sliceorder=up
>
> /usr/local/fsl/bin/pnm_stage1 -i /mnt/hgfs/shared_folder/TO/PNM/cardiac_resp_TRtriggers.txt -o /mnt/hgfs/shared_folder/TO/PNM -s 100 --tr=2.6 --smoothcard=0.1 --smoothresp=0.1 --resp=2 --cardiac=1 --trigger=3
> /usr/local/fsl/bin/popp -i /mnt/hgfs/shared_folder/TO/PNM/cardiac_resp_TRtriggers.txt -o /mnt/hgfs/shared_folder/TO/PNM -s 100 --tr=2.6 --smoothcard=0.1 --smoothresp=0.1 --resp=2 --cardiac=1 --trigger=3
>
> /usr/local/fsl/bin/pnm_stage1: line 97: 7112 Segmentation fault (core dumped)
>
> $FSLDIR/bin/popp $args
> Done
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