Re: [HCP-Users] Error using PALM for Group study

I've just replied to this in the FSL mailing list. Looks like a bug, hopefully fixable soon... On 6 December 2017 at 07:10, Dev vasu wrote: > Dear all , > > > I am using PALM in order to perform Two sample Unpaired T test for my > group study . > > I followed the instructions provided in PA

Re: [HCP-Users] Group comparison of Myelin maps

Hi Donatas, The surface file, that correspond to one particular subject, is probably fine as far as it has the same geometry (number of vertices and faces) as all other subjects. For the area file, PALM expects it to be the average area across all subjects, as opposed to the actual areas for all

Re: [HCP-Users] group comparison

Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173> > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: on behalf of "Glasser, > Matthew" > Date: Wednesday, November 30, 2016 at 12:43 PM > To: nailin yao , &qu

Re: [HCP-Users] Palm with TFCE on Cifti data

robably >> be: results_dpv_tstat_m1_c1.gii instead of results_tfce_tstat_mfwep_m1_c1.gii >> ,and the same for the other inputs. Maybe I am wrong, but I think that >> naming would have resulted from a call of palm with TFCE. >> >> >> Thanks, >> >> Michae

Re: [HCP-Users] Palm and Variance

Hi Michael, I'm afraid that this isn't possible yet, sorry. However, this has been for a while in the to-do list, and will eventually become available. All the best, Anderson On 20 September 2016 at 17:10, Michael F.W. Dreyfuss < mid2...@med.cornell.edu> wrote: > Hello, > > > Is there anyway

Re: [HCP-Users] Palm with TFCE on Cifti data

tex area if I can as that seems more appropriate. > Do you think that is important? > > As for the previous errors, I had left out the -ise flag, so I'm not sure > what the program was putting out (I guess nothing). > > Thank you again for all your help, > Michael >

Re: [HCP-Users] Palm with TFCE on Cifti data

:1060 voxels > > PutamenRight: 1010 voxels > > ThalamusLeft: 1288 voxels > > ThalamusRight: 1248 voxels > > > Map Minimum MaximumMean Sample Dev % Positive % Negative > Inf/NaN Map N

Re: [HCP-Users] Palm with TFCE on Cifti data

commend a local group average, what would be > the wb_command to do that on the midthickness data? > > > Sorry, I wasn't sure what you were referring to about compiling and > skipping the conversion. What is that in reference to? > > > Thank you again, > > Mi

Re: [HCP-Users] Palm with TFCE on Cifti data

ael > -- > *From:* Timothy Coalson > *Sent:* Thursday, September 15, 2016 4:46:12 PM > > *To:* Michael F.W. Dreyfuss > *Cc:* Anderson M. Winkler; hcp-users@humanconnectome.org; Dierker, Donna > *Subject:* Re: [HCP-Users] Palm with TFCE on Cifti data &g

Re: [HCP-Users] Palm with TFCE on Cifti data

options. Hope this helps! All the best, Anderson On 15 September 2016 at 07:21, Anderson M. Winkler wrote: > Hi Michael, > > TFCE needs to be run separately for the surface-based and for the > volume-based parts of the CIFTI file. This means that the input file has to > be

Re: [HCP-Users] Palm with TFCE on Cifti data

Hi Michael, TFCE needs to be run separately for the surface-based and for the volume-based parts of the CIFTI file. This means that the input file has to be separated using wb_command, then PALM be executed, then the results need to be corrected via Bonferroni or Šidák. I will add hopefully today

Re: [HCP-Users] PALM with cifti files

ded for identifying clusters of activation? > > > Thank you, > > Michael > -- > *From:* Michael F.W. Dreyfuss > *Sent:* Tuesday, September 13, 2016 12:25:03 PM > *To:* Burgess, Gregory > > *Cc:* hcp-users@humanconnectome.org; Anderson M. W

Re: [HCP-Users] PALM with cifti files

Hi Michael, In the first case the option "-transposedata" should fix the problem. In the second case, with "-evperdat", it seems the dimensions of the input and of the voxelwise EV don't match. Please, when quoting, send the full error message, including particularly those seemingly cryptical lin

Re: [HCP-Users] PALM Errors

Hi Michael, The -transposedata should solve the problem for a 1-sample t-test (there should be no need for -evperdat for this design). That said, indeed, as you observed, -transposedata transposes only the input data entered with -i, not the one entered with -eveperdat. This can be changed for th

Re: [HCP-Users] Cluster Thresholding

Hi Michael, PALM can be used either in place of FEAT at higher levels, or together it, using as inputs the COPEs from lower levels. As Michael Harms said earlier, this is exactly one of the practicals of the upcoming HCP course. The course materials will be available online for download shortly af

Re: [HCP-Users] PALM and cifti

o (at least) dscalar. It might work with other types, but these hasn't been tested yet. Hope this helps. All the best, Anderson On 22 April 2016 at 18:33, Anderson M. Winkler wrote: > Hi Jarek, > > Thanks for sending the file. It's a dscalar, which sadly isn't currently &g

Re: [HCP-Users] PALM and cifti

Hi Jarek, Thanks for sending the file. It's a dscalar, which sadly isn't currently supported. You'd have to save the data from the pipeline as dtseries. In fact, from what I can see in the file, although it has extension dscalar, internally it can be interpreted as a 6D vector field. Saving as a d

Re: [HCP-Users] PALM and cifti

Hi all, It seems it's reading the input as if having 59412 subjects, when the design matrix has only 6 rows. If the -transposedata doesn't work, I'd kindly ask if you could send the file then. Sorry for the issue. All the best, Anderson On 21 April 2016 at 01:42, Glasser, Matthew wrote: > P

Re: [HCP-Users] Cluster-extent thresholding of CIFTI data

ay in which you post-process the gradient map to > make boundaries clearer? Maybe I should take a look at the methods > published by the Petersen group for RS based parcellation using gradients? > Matt, please let me know the pipeline you would suggest. > Thanks for your help! > -

Re: [HCP-Users] Cluster-extent thresholding of CIFTI data

Hi Julien, Indeed, as Matt said, you can use PALM, which does then a permutation test (it is superior to Monte Carlo tests in that MC don't bypass the usual assumptions of parametric tests). Of course, if MC tests were better, PALM would surely be using them :-) Currently there are some difficult

Re: [HCP-Users] Fwd: Difficulties reading cifti into matlab with ft_read_cifti or ciftiopen

Hi all, I just would like to comment that I receive the exact same error message when I try to open one of the CIFTI test data examples available in NITRC: >> x = ft_read_cifti('Conte69.parcellations_VGD11b.32k_fs_LR.dlabel.nii'); reading CORTEX_LEFT surface from Conte69.L.inflated.32k_fs_LR.surf

Re: [HCP-Users] freesurfer directory structure for 32k average

act timeline for the patch, but I'd think sometime in the coming > weeks. > > -Dan > > From: "Anderson M. Winkler" > Date: Thursday, September 4, 2014 9:26 AM > > Cc: "hcp-users@humanconnectome.org" > Subject: Re: [HCP-Users] freesurfer directory s

Re: [HCP-Users] freesurfer directory structure for 32k average

Hi Michael, I'd second Satra's request: it'd be great to have the original FS directory structure available somewhere -- many of us have scripts that expect that file structure, and also those same file formats that are very easy to read. Thanks! All the best, Anderson On 4 September 2014 15:23,