Re: [HCP-Users] group comparison in myelin maps

.@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "Ho, Wilson Christopher" <w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>>

Re: [HCP-Users] group comparison in myelin maps

Hi Matt, We concatenated the myelin maps into one .dscalar.nii map for each group. I cannot open them, however, I think I am missing other files that I need. Which other files do I need to generate? A volume file? Thanks, Jodi Jodi Gilman, Ph.D. Assistant Professor, Harvard Medical School

Re: [HCP-Users] group comparison in myelin maps

rs@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] group comparison in myelin maps Thank you, Matt. Do you have an example of a -cifti-concatenate script? I keep getting errors, I don’

Re: [HCP-Users] group comparison in myelin maps

That would be reasonable. I would probably use the myelin maps without _BC if you are looking for differences in myelin content across groups. Peace, Matt. From: > on behalf of "Gilman, Jodi"

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

Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173> > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: nailin yao <ynai...@gmail.com> > Date: Thursday, December 15, 2016 at 12:45 PM > To: Michael Harms <mha...@wustl.edu> > Subject: Re: [HCP-Users] group

Re: [HCP-Users] group comparison

ber 15, 2016 at 4:20 PM To: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users]

Re: [HCP-Users] group comparison

.edu<mailto:mha...@wustl.edu>> Subject: Re: [HCP-Users] group comparison Hi MH, How can I generate the mean midthickness.surf.gii for my subjects? I tried cifti-merge, but the error says: ERROR: error reading NIfTI file /home/fas/glahn/ny87/scratch60/Connectivity_Study/S0039JRF/MNIN

Re: [HCP-Users] group comparison

lto:hcp-users@humanconnectome.org>>, "Dierker, Donna" <do...@wustl.edu<mailto:do...@wustl.edu>> Subject: Re: [HCP-Users] group comparison Hi Tim, Do you know where can I find midthickness.surf.gii file for palm CIFTI usage? Thanks! Best, Nailin 2016-12-09 16:00

Re: [HCP-Users] group comparison

ension names >>> for wb_view to know what kind of file it is. Do you actually need to do >>> the CIFTI separate part though? I thought PALM supported CIFTI files >>> natively now. >>> >>> Peace, >>> >>> Matt. >>> >>> F

Re: [HCP-Users] group comparison

t; To: Matt Glasser <glass...@wustl.edu> > Cc: "Dierker, Donna" <do...@wustl.edu>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org> > > Subject: Re: [HCP-Users] group comparison > > Hi Matt, > > The result is generated by

Re: [HCP-Users] group comparison

t; > Date: Wednesday, November 30, 2016 at 12:43 PM > To: nailin yao <ynai...@gmail.com>, "Anderson M. Winkler" < > wink...@fmrib.ox.ac.uk> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, > "Dierker, Donna" <do..

Re: [HCP-Users] group comparison

"Dierker, Donna" <do...@wustl.edu<mailto:do...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] group comparison Hi Matt, The result

Re: [HCP-Users] group comparison

@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] group comparison Hi Matt, The result is generated by the command: wb_command -cifti-separate data.dtseries.nii COLUMN (-volume-all data_sub.nii) -metric

Re: [HCP-Users] group comparison

uot; <do...@wustl.edu> > > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] group comparison > > Hi, > > I have successfully generated statistic result from palm, files are > results_dpv_tstat_mfwep_m1_c1.g

Re: [HCP-Users] group comparison

>> Date: Wednesday, November 30, 2016 at 11:24 AM To: "Dierker, Donna" <do...@wustl.edu<mailto:do...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org&g

Re: [HCP-Users] group comparison

Date: Tuesday, November 29, 2016 at 1:41 PM > > To: Michael Harms <mha...@wustl.edu> > > Cc: "Glasser, Matthew" <glass...@wustl.edu>, " > hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > > Subject: Re: [HCP-Users] group comparison &g

Re: [HCP-Users] group comparison

"Glasser, Matthew" <glass...@wustl.edu>, "hcp-users@humanconnectome.org" > <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] group comparison > > Because I need to do group comparison here , and met this error when running > palm: > Error us

Re: [HCP-Users] group comparison

org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] group comparison Because I need to do group comparison here , and met this error when running palm: Error using palm_takeargs (line 2003) The number of rows in the des

Re: [HCP-Users] group comparison

CIFTI you don't need to mask the data/can use a CIFTI >> file of all ones. >> >> Peace, >> >> Matt. >> >> >> Sent from my Verizon, Samsung Galaxy smartphone >> >> >> ---- Original message >> From: nailin yao <yn

Re: [HCP-Users] group comparison

OSCIENCE tim <tsc...@mst.edu<mailto:tsc...@mst.edu>>, hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] group comparison So how do I deal with the two hemispheres when comparing ${subj}.MyelinMap.32k_fs_LR.dscalar.nii if the mask is onl

Re: [HCP-Users] group comparison

ssage > From: nailin yao <ynai...@gmail.com> > Date: 11/29/16 11:33 AM (GMT-06:00) > To: "Glasser, Matthew" <glass...@wustl.edu> > Cc: NEUROSCIENCE tim <tsc...@mst.edu>, hcp-users@humanconnectome.org > Subject: Re: [HCP-Users] gr

Re: [HCP-Users] group comparison

hew" <glass...@wustl.edu> Cc: NEUROSCIENCE tim <tsc...@mst.edu>, hcp-users@humanconnectome.org Subject: Re: [HCP-Users] group comparison So how do I deal with the two hemispheres when comparing ${subj}.MyelinMap.32k_fs_LR.dscalar.nii if the mask is only for one hemisphere? Thank yo

Re: [HCP-Users] group comparison

To: Timothy Coalson <tsc...@mst.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] group comparison > > Thank you Tim! I have now concatenated the myelin maps and going to do > the permutation test with Palm. I plan

Re: [HCP-Users] group comparison

mha...@wustl.edu<mailto:mha...@wustl.edu> From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>> Date: Tuesday, November 22, 2016 at 2:14 PM To: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-user

Re: [HCP-Users] group comparison

ail: mha...@wustl.edu >> >> From: nailin yao <ynai...@gmail.com> >> Date: Tuesday, November 22, 2016 at 2:14 PM >> To: Michael Harms <mha...@wustl.edu> >> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subje

Re: [HCP-Users] group comparison

yao <ynai...@gmail.com> > Date: Tuesday, November 22, 2016 at 2:14 PM > To: Michael Harms <mha...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] group comparison > > Hi Michael, > > I

Re: [HCP-Users] group comparison

umanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] group comparison Hi Michael, I tried the command: ./wb_command -cifti-merge L.SmoothedMyelinMap.32k_fs_LR.out.func.gii -cifti *.L.SmoothedMyelinMap.32k_fs_LR.f

Re: [HCP-Users] group comparison

Hi Michael, I tried the command: ./wb_command -cifti-merge L.SmoothedMyelinMap.32k_fs_LR.out.func.gii -cifti *.L.SmoothedMyelinMap.32k_fs_LR.func.gii, but comes the error: ERROR: error reading NIfTI file

Re: [HCP-Users] group comparison

Thank you MH! Best, Nailin 2016-11-22 13:30 GMT-05:00 Harms, Michael : > > By “compress” do you mean merge into a single file? If so, you can use > wb_command > -cifti-merge, or wb_shortcuts -cifti-concatenate. (The latter is a > wrapper that simplifies the merge call).

Re: [HCP-Users] group comparison

By “compress” do you mean merge into a single file? If so, you can use wb_command -cifti-merge, or wb_shortcuts -cifti-concatenate. (The latter is a wrapper that simplifies the merge call). And you can use FSL’s PALM to do a permutation test. If 164k is too dense a sampling, there are 32k