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 on behalf of
Marta Moreno" wrote:
>Dear Experts,
>
>I am running the following script MSMAllPipelineBatch.sh
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
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"
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:
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 -
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
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
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
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:
You could try setting line 353 to NO:
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
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"
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
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.
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
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