Oh, sorry, I did not include that as a possibility. FSL codes F-contrasts differently than t-contrasts (FS codes them in the same way, just a matrix). If you want to do it this way, you'll have to use PALM by itself without the fspalm frontend. fspalm should still create files that can be conveniently used in PALM, you'll just have to create the FSL-related files needed to run that contrast.
On 12/21/2020 6:56 AM, Marina Fernández wrote:
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Dear experts,
To correct multiple comparisons on the surface I'm using fspalm. I know that this command internally transforms the design contrast and desing matrix from the Freesurfer format to the fsl format so that FSL-PALM understands the input.
When the freesurfer contrasts include only one line, I can run permutations with fspalm without errors. The problem arises when the contrast has two lines (e.g., when including a three-level factor like in the example "Contrast 4: group.effect.mtx" from the link MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0Vhttps://secure-web.cisco.com/1zRPseSPjbEGgbMXbZRKYmGKkEKOP342L-FeUKM_km6ilBsfbfQJ_8-GKG0ysjrbni7SSqZSiRJEwGoNdTaDT7odDRtL4P8fXeJYKwJhPkQkrvUtYk6NsdQmQbrH5peBojO-GhYGC4fJBL8oiTjdRUnWElMzVNTDVVzcpeyhF4J-oNKoDjCnw7KeXyN6LJukL1rX7L9IjS4gmANZHEgbA8LyjIyhGxboT3lU_JSnWQGXoN93TpE-Th6Kv5ZIGHRensM51F7oceekuHSwqwMzpsQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdf3G0V; or when including a two-way interaction between a dichotomic factor and two covariates of interest). You can see below the error. How can I solve this problem?
Thank you in advance.
Marina
**ERROR:**
Loading surface 1/1: /usr/local/freesurfer/subjects/amyloid74_thickness_average/surf/lh.white
Reading input 1/1: /usr/local/freesurfer/subjects/amyloid74_thickness_stats/smoothing/gaussians/lh.fsgd_subj_gauss003.mgh
Reading design matrix and contrasts.
Error using palm_vestread (line 56)
File not in the correct format: design.con
Error in palm_miscread (line 110)
[X.data,X.extra.PPH] = palm_vestread(X.filename);
Error in palm_takeargs (line 2111)
tmp = palm_miscread(opts.t{t},[],[],opts.precision);
Error in palm_core (line 33)
[opts,plm] = palm_takeargs(varargin{:});
Error in palm (line 81)
palm_core(varargin{:});
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