Anderson just pointed a data transpose line option in PALM in an aside email. Although the online documentation says it's for CSV 2D data, apparently it works for other data input types as well. So my problem actually is not that CIFTI format concatenation is terribly more complex than I was starting to wonder... Which is a relief.
Mike Sent from my iPhone On Sep 26, 2015, at 12:05 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: wb_command -cifti-merge is the right command and you want to create a dscalar that has the dimensions 91282 grayordinates x 45 maps. It sounds like you have a simple issue of a matrix transpose not being right when the data makes it into PALM. Is it possible that you aren’t using a recent version of wb_command? dcsalar and dtseries files are very similar except that series refers to some sort of continuous mapping (like time), whereas scalar refers to named maps (e.g. Subjects 1-45). Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Stevens, Michael" <michael.stev...@hhchealth.org<mailto:michael.stev...@hhchealth.org>> Date: Saturday, September 26, 2015 at 7:07 AM To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] 4D CIFTI file for PALM random-effects analysis Hi Tim, I think I should’ve been more clear, it’s not the command itself I was missing. It’s the logic of concatenation that I was wondering if it was more complex than I would’ve naively assumed. I had tried both that and the cifti-merge-dense commands and created 4D files. However, PALM still doesn’t like them. When I attempt to run a simple PALM analysis, that software throws an error like “number of rows in the design matrix does not match the number of observations in the data. – Rows in the matrix: 45 –Observations in the data: 91282” This involves PALM vs. CIFTI, and such a problem could logically arise from a problem in either the design matrix, the PALM input code, or the CIFTI structure. It’s doubtful the design matrix is wrong (45 images, 45 rows, created using Feat, etc.). And Anderson already mentioned that PALM is looking for a different number of rows given this error. I had simply assumed there must be a way I’m not familiar with to use the cifti-merge or some other specification of wb_command to alter the structure of a concatenated CIFTI file so that the data is compatible with PALM’s input expectations. I’ve even tried changing the format from .dtseries.nii to .dscalar.nii (possibly doing that wrong, granted) in case PALM recognized these differently. Nothing I tried worked. So while I’ll keep working with Anderson if needs be about how PALM works, I was hoping to learn if anyone had already successfully prepped HCP stats modeling output in CIFTI format for PALM using a direct import of the CIFTI data. Barring that, I was hoping for some help figuring out the exact reason for the incompatibility. I’m realizing this is not as straightforward as I had hoped for. Thanks, Mike From: Timothy Coalson [mailto:tsc...@mst.edu] Sent: Saturday, September 26, 2015 1:26 AM To: Stevens, Michael Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] 4D CIFTI file for PALM random-effects analysis wb_command -cifti-merge takes the output filename first, then you repeat "-cifti <input>" for each input file (which is why in the help the -cifti option is marked as repeatable), in the order you want them concatenated. The help information for -cifti-merge includes this example and explanation: Example: wb_command -cifti-merge out.dtseries.nii -cifti first.dtseries.nii -column 1 -cifti second.dtseries.nii This example would take the first column from first.dtseries.nii, followed by all columns from second.dtseries.nii, and write these columns to out.dtseries.nii. See: http://humanconnectome.org/software/workbench-command.php?function=-cifti-merge Tim On Fri, Sep 25, 2015 at 5:12 PM, Stevens, Michael <michael.stev...@hhchealth.org<mailto:michael.stev...@hhchealth.org>> wrote: Hi folks, Today, I tried using PALM to load CIFTI files directly in order to estimate some simple 1 and 2 sample t tests on some HCP-processed data I’ve got from one of my projects. But I quickly ran into a problem. Anderson Winkler and I just talked about it via email. He pointed out that I was trying to load 45 dense-data activation map images into PALM in a way that the program interpreted as needing to have only 45 datapoints along the first dimension. In other words, PALM doesn’t like the CIFTI output from HCP’s fMRI modelling script when it’s loaded directly using the -i input specification. Anderson suggested things might work more easily if I merged these CIFTI files into a 4D file. But he also suggested I pay close attention to how the data was oriented so that PALM interprets things right. I know I could instead follow previous posts about splitting the data up into NIFTI volume vs. surface data, running stats, and ultimately recombining, but I was hoping that PALM really could do everything in one step if the CIFTI stats file data was prepped right, as that’d make it a bit easier to try out all the cool statistical options Anderson built into PALM across the various HCP datasets I’ve got at hand. Can anyone whose dealt with this or a similar problem before tell me exactly how to invoke the wb_command –cifti-merge command to collapse into 4D and to orient these CIFTI data properly for PALM group-level analyses? Thanks, Mike This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. 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