Re: [HCP-Users] stat output of pipeline

What FSL version?  I don’t think that error is important and is related to whether the variable POSIXLY_CORRECT is set or not (have a google search about it in relation to FreeSurfer and being queued by the fsl_sub command).   As for the stats differences, FreeSurfer isn’t expected to give ide

[HCP-Users] stat output of pipeline

Dear Human Connectome project experts, I ran PreFreeSurfer & FreeSurfer shell scripts. As input data I used the second set of Example data on which gradient distortion correction has already been performed. Both PreFreeSurferPipelineBatch.sh and FreeSurferPipelineBatch.sh finished successfully.

Re: [HCP-Users] Problem with wb_command -volume-parcel-resampling? dimension mismatch?

Your data is RPI, but both label volumes are LPI. The -generic version doesn't accept that either, the current labels must be in the same volume space as the data. Maybe when you pulled the first volume off the data, it changed something? Use -volume-reorient to get them to match, and it works.

Re: [HCP-Users] Problem with wb_command -volume-parcel-resampling? dimension mismatch?

I would suspect an orientation problem between the current and new parcel volumes, one volume being LPI and the other being RPI, or similar. Do -file-information on all the input files, and look at the orientation fields (or -nifti-information -print-header and compare the sforms). It has been a

Re: [HCP-Users] Problem with wb_command -volume-parcel-resampling? dimension mismatch?

Here's a tar with the relevant data (only 1.6MB ... truncated the fmri to a single volume): https://drive.google.com/folderview?id=0B-jUIqj-goJ9cVJWcGM5d05RTUk&usp=sharing -Keith On Thu, Apr 23, 2015 at 3:25 PM, Glasser, Matthew wrote: > That seems like it shouldn’t be happening. Tim C. migh

Re: [HCP-Users] Problem with wb_command -volume-parcel-resampling? dimension mismatch?

That seems like it shouldn’t be happening.  Tim C. might need you to upload that data somewhere so that he can debug.   There isn’t any downside to using the generic command, but in your situation it should not be necessary. Peace, Matt. From: Keith Jamison Date: Thu

[HCP-Users] Problem with wb_command -volume-parcel-resampling? dimension mismatch?

Hi HCPers I'm running into an error when running SubcorticalProcessing.sh in the fMRISurface pipeline. Specifically, when it tries to run: wb_command -volume-parcel-resampling .nii.gz ROIs/ROIs..nii.gz ROIs/Atlas_ROIs..nii.gz I get an error saying "volume spacing or dimension mismatch". I

Re: [HCP-Users] help for identifying MNI atlas in the fMRI pipeline

What we use is based on FSL¹s nonlinear MNI templates, but was made using Conte69 data registered to these templates. Peace, Matt. On 4/23/15, 8:34 AM, "Alpay Özcan" wrote: >Hello, >I would appreciate if anyone can help me identify the atlas used >in fMRI pipeline. > >I believe FLIRT-FNIRT com

Re: [HCP-Users] from volume to gifti file to cifti roi

Thank you Timothy, I found your email very useful. I followed it and is done!! Also thanks to Donna and Jo! Best wishes always, Leah ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Ps

[HCP-Users] help for identifying MNI atlas in the fMRI pipeline

Hello, I would appreciate if anyone can help me identify the atlas used in fMRI pipeline. I believe FLIRT-FNIRT combination uses MNI152 nonlinear 6th generation (http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6) which has the dimensions: 193 x 229 x 193 HCP fMRI timeseries has the image