Hi,
I am getting the error below running verbena on OSX 10.11.6.
Any hints?
Thanks a million,
cheers-
Andreas
verbena -i perf.nii.gz -m mask.nii.gz -tr 1.17 -te 0.03 -modelfreeinit
Ouput being placed in
/Users/andreas/Desktop/ENGELHAUPT_ROBIN_149198/KOPF_ROUTINE_20180605_161515
_984000/verbena
Creating output directory:
/Users/andreas/Desktop/ENGELHAUPT_ROBIN_149198/KOPF_ROUTINE_20180605_161515
_984000/verbena
Usage:
imcp <file1> <file2>
imcp <file1> <directory>
imcp <file1> <file2> ... <fileN> <directory>
Copy images from <file1> to <file2>, or copy all <file>s to <directory>
NB: filenames can be basenames or include an extension.
Recognised file extensions: .nii.gz, .nii, .img, .hdr, .img.gz, .hdr.gz
Cannot open volume aif for reading!
Cannot open volume szero_aif for reading!
Cannot open volume aif for reading!
Begin model-free analysis
ASL_MFREE (1.0)
Loading data
Image Exception : #22 :: ERROR: Could not open image concaif
An exception has been thrown
ERROR: Could not open image concaifTrace: read_volume4DROI.
Cannot open volume concaif for reading!
Image Exception : #22 :: ERROR: Could not open image aifsum
libc++abi.dylib: terminating with uncaught exception of type
RBD_COMMON::BaseException
/usr/local/fsl/bin/verbena: line 235: 1019 Abort trap: 6
fslmaths concsum -div aifsum cbv
Cannot open volume cbv for reading!
Cannot open volume /tmp/fsl_9OedFp_verbena/modfree_magntiude for reading!
Cannot open volume /tmp/fsl_9OedFp_verbena/cbv for reading!
Cannot open volume /tmp/fsl_9OedFp_verbena/mtt for reading!
Begin VM analysis
rm: init*: No such file or directory
------------------
Welcome to FABBER v2.0
Logfile started: init/logfile
Start time: Wed Jun 6 23:54:56 2018
FABBER release v2.0
Forward Model version:
$Id: fwdmodel_dsc.cc,v 1.14 2015/09/08 14:07:51 mwebster Exp $
Loading mask data from 'mask'
Loading supplementary data from 'aif'
Image Exception : #22 :: ERROR: Could not open image aif
NEWMAT exception caught in fabber:
An exception has been thrown
ERROR: Could not open image aifTrace: read_volume4DROI; LoadData; FABBER
main(); FABBER main (outer).
Logfile was: init/logfile
FABBER: MVNtool
Reading MVNs from init/finalMVN
Reading MVNs from init/finalMVN
Image Exception : #22 :: ERROR: Could not open image init/finalMVN
An exception has been thrown
ERROR: Could not open image init/finalMVNTrace: read_volume4DROI;
MVNDist::Load (static).
Cannot open volume mtt for reading!
FABBER: MVNtool
Reading MVNs from init_MVN
Reading MVNs from init_MVN
Image Exception : #22 :: ERROR: Could not open image init_MVN
An exception has been thrown
ERROR: Could not open image init_MVNTrace: read_volume4DROI; MVNDist::Load
(static).
FABBER: MVNtool
Reading MVNs from init_MVN
Reading MVNs from init_MVN
Image Exception : #22 :: ERROR: Could not open image init_MVN
An exception has been thrown
ERROR: Could not open image init_MVNTrace: read_volume4DROI; MVNDist::Load
(static).
FABBER: MVNtool
Reading MVNs from init_MVN
Reading MVNs from init_MVN
Image Exception : #22 :: ERROR: Could not open image init_MVN
An exception has been thrown
ERROR: Could not open image init_MVNTrace: read_volume4DROI; MVNDist::Load
(static).
FABBER: MVNtool
Reading MVNs from init_MVN
Reading MVNs from init_MVN
Image Exception : #22 :: ERROR: Could not open image init_MVN
An exception has been thrown
ERROR: Could not open image init_MVNTrace: read_volume4DROI; MVNDist::Load
(static).
rm: vm*: No such file or directory
------------------
Welcome to FABBER v2.0
Logfile started: vm/logfile
Start time: Wed Jun 6 23:54:56 2018
FABBER release v2.0
Forward Model version:
$Id: fwdmodel_dsc.cc,v 1.14 2015/09/08 14:07:51 mwebster Exp $
Expanded, --param-spatial-priors=NNNNM
Loading mask data from 'mask'
Loading supplementary data from 'aif'
Image Exception : #22 :: ERROR: Could not open image aif
NEWMAT exception caught in fabber:
An exception has been thrown
ERROR: Could not open image aifTrace: read_volume4DROI; LoadData; FABBER
main(); FABBER main (outer).
Logfile was: vm/logfile
Could not find a supported file with prefix
"/tmp/fsl_9OedFp_verbena/vm/mean_cbf"
Cannot open volume /tmp/fsl_9OedFp_verbena/vm/mean_transitm for reading!
Cannot open volume /tmp/fsl_9OedFp_verbena/vm/mean_lambda for reading!
Tidying up
Verbena done
Am 02.03.17, 10:37 schrieb "FSL - FMRIB's Software Library on behalf of
Michael Chappell" unter <[log in to unmask] on behalf of
[log in to unmask]>:
>The igamc underflow errorı isnıt a problem - this can happen naturally
>when parameters go out of bounds internally, but doesnıt normally mean
>the analysis fails (it is an error I have been unable to suppress thus
>far). I take it that it is working in some cases, but that you donıt have
>an obvious reason why some are going wrong? From memory we have sometimes
>had trouble where the mask has isolated voxels - so that might be worth
>checking, do you have log files to examine?
>
>Michael
>
>
>> On 1 Mar 2017, at 21:08, SUBSCRIBE FSL Ping-Hong Yeh
>><[log in to unmask]> wrote:
>>
>> Hello FSL users,
>>
>> Some of my attempts using verbena for DSC processing have failed; and i
>>have noticed the "igamc underflow error" message shown on the terminal,
>>but not sure if that is the cause. There is no outputs in the vm and
>>vm_mv folders, but the modelfree results seem fine.
>>
>> Here is the command i used,
>>
>> verbena -i ${out_dir}/$sub/unwarp/unwarp.nii.gz -m
>>${out_dir}/$sub/unwarp/unwarpbrain_mask.nii.gz -a
>>${out_dir}/$sub/unwarp/aif.nii.gz -aifconc -tr 1.59 -te 0.0146
>>-modelfreeinit -mv -o ${out_dir}/$sub/unwarp
>>
>> , where the unwarp.nii.gz is the 4D dsc data.
>>
>>
>> Thank you,
>>
>> Ping
>
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