I was having the same problem with the 3_22
FreeSurfer2CaretConvertAndRegisterNonlinear.sh
and was able to download the msm binaried and the params file from
https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v1/
however I am runinng into a problem with the script at
${MSMBin}/msm --levels=4 --conf=${MSMBin}/allparameterssulcDRconf
--inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii
--trans="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii
--refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
--indata="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii
--refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii
--out="$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}. --verbose
cd $DIR
cp
"$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.HIGHRES_transformed.surf.gii
"$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii
The HIGHRES file does not exist.
________________________________
From: [email protected]
<[email protected]> on behalf of Timothy Hendrickson
<[email protected]>
Sent: Tuesday, January 9, 2018 12:11:20 PM
To: Glasser, Matthew
Cc: [email protected]
Subject: Re: [HCP-Users] Resting State processing
ATTENTION: This email came from an external source. Do not open attachments or
click on links from unknown senders or unexpected emails.
Hi Matthew,
The file does not exist. I see now that the PostFreeSurfer pipeline I have
locally is different than the latest version found on github (specifically
FreeSurfer2CaretConvertAndRegisterNonlinear.sh). I see that the line
referencing allparameterssulcDRconf has been commented out in favor of
MSMSulcStrainFinalconf, however, this file does not appear to exist either.
Which version of MSM HOCR is the most recent that should be used? I am using
version 2)
On a completely other note why aren't these configuration files already
included in the HCP pipelines? It seems very burdensome to require each user to
mimic the exact version of the MSM binaries that
FreeSurfer2CaretConvertAndRegisterNonlinear.sh expects.
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
On Mon, Jan 8, 2018 at 7:16 PM, Glasser, Matthew
<[email protected]<mailto:[email protected]>> wrote:
Does the file exist? That might be the old config file it is looking for
suggesting that you don’t have the latest master.
Peace,
Matt.
From: Timothy Hendrickson <[email protected]<mailto:[email protected]>>
Date: Monday, January 8, 2018 at 9:15 AM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Cc: Matt Glasser <[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] Resting State processing
Hello all,
Despite having the most recent version of the hcp pipeline (3.22) and
downloading the MSM configuration binaries, however, I am still receiving an
error when I attempt to run the PreFreeSurfer pipeline with RegName="MSMSulc".
This is the error message I receive:
/opt/local/hcp-pipelines-3.22.0/Pipelines-3.22.0/MSMBinaries/allparameterssulcDRconf:
Couldn't open the file!
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441<tel:(612)%20624-6441>
Mobile: 507-259-3434<tel:(507)%20259-3434> (texts okay)
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