Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

Check not only your standard output file, but also your standard error. Do either indicate whether it is finding matlab/octave? > On Nov 2, 2018, at 3:02 PM, Jayasekera, Dinal > wrote: > > Dear Michael and Matt, > > I reconfigured R, updated sICA+FIX and FSL but I still continue to get the >

Re: [HCP-Users] drawing borders

: Tuesday, October 9, 2018 11:50 AM To: Dierker, Donna Cc: Gaurav Patel; hcp-users@humanconnectome.org Users Subject: Re: [HCP-Users] drawing borders In the borders menu? Changing that changes the size of the final border, but not the border as I draw it _ gaurav patel

Re: [HCP-Users] drawing borders

Check the diameter of your sphere, Gaurav. From: hcp-users-boun...@humanconnectome.org on behalf of Gaurav Patel Sent: Tuesday, October 9, 2018 11:37 AM To: hcp-users@humanconnectome.org Users Subject: [HCP-Users] drawing borders Hi—when I am drawing borders

Re: [HCP-Users] map names | wb_command

See this page: https://www.humanconnectome.org/software/workbench-command/-all-commands-help wb_command -set-map-names - the file to set the map names of [-name-file] - use a text file to replace all map names - text file containing map names, one per line

Re: [HCP-Users] Cerebellum surface

Maybe also have a look at Joern Diedrichsen’s page: http://www.diedrichsenlab.org/imaging/propatlas.htm > On Sep 19, 2017, at 9:42 AM, Glasser, Matthew wrote: > > This is built into the CIFTI format for the future, however we do not yet > have an algorithm for making

Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

Many of the HCP experts are at OHBM, so replies might take longer. I know from my own experience with HCP output to look here for the Freesurfer subject directories: subject-id/T1w/subject-id/label/* subject-id/T1w/subject-id/mri/* subject-id/T1w/subject-id/surf/* … Also see page 21 here:

Re: [HCP-Users] Position of vertices in myelin maps and 164k sphere

Nicola, It is possible to generate a grid on a spherical surface like Alex Cohen did in this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705206/ … and then fold those coordinates back up into midthickness configuration. The 164k_fs_LR vertex-wise correspondence is as good as can be

Re: [HCP-Users] Questions regarding coordinates infomation of vertex

Hi Qinqin, As Matt said, the file named like *midthickness*.surf.gii contains the vertex-to-3D coordinate mapping that you seek. This could be an individual’s surface, if the cifti data pertains to a particular subject, or it could be a mean midthickness (e.g., HCP500) if it is group data.

Re: [HCP-Users] Making a movie in connectome workbench

Jonathan Power’s tools might be worth a look: http://www.jonathanpower.net/resources.html … depending on what you are doing. > On Feb 28, 2017, at 10:31 AM, Harwell, John wrote: > > > Hello Kristian, > > * Load your files into Workbench and select the first map in your

Re: [HCP-Users] map data between FreeSurfer and HCP

Hi Leah, I wonder if you need to apply an affine transform to your white/pial surfaces to adjust for the offset between Freesurfer’s origin and your orig.mgz volume’s origin. See this script:

Re: [HCP-Users] Threshold p value in workbench view

See if you can read this link, Xavier: https://wustl.box.com/s/uuxn06pjlnn6ts7nhak0zww53l33fxzf People also use metric- or cifti-math to convert to log p or 1-p. Whatever works for you. > On Dec 27, 2016, at 10:39 AM, Xavier Guell Paradis wrote: > > Dear Sir or Madam, >

Re: [HCP-Users] thresholding the data to p-value

TimH - you mean this one? On Jul 7, 2016, at 10:26 AM, Dierker, Donna <do...@wustl.edu<mailto:do...@wustl.edu>> wrote: You need to adjust your overlay settings; see attached capture. Make sure Threshold Type is set to On. [cid:B7646768-2537-4828-8045-A6B646996AD8@wustl.edu] On

Re: [HCP-Users] group comparison

Try the -transposedata option. > On Nov 29, 2016, at 1:49 PM, Harms, Michael wrote: > > > Sounds like your design.mat file isn’t set up correctly, or you haven’t > supplied a necessary flag to PALM. Read the PALM documentation carefully. I > believe that there are now

Re: [HCP-Users] Glasser nature atlas

If you can’t do MSMAll, then consider using just sulc, rather than sulc+curv. See figure 4, row B, in Emma Robinson’s paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190319/figure/F4/ I have heard David describe curvature as capturing more local folding, sulc global folding. In my

Re: [HCP-Users] PALM Errors

Did you try using the -transposedata option? > On Sep 8, 2016, at 4:54 PM, Michael F.W. Dreyfuss > wrote: > > Hello, > > I am trying to run PALM on subject level betas in cifti to get group means > and identify clusters of significant activation. I have tried two

Re: [HCP-Users] create cortical thickness maps for multiple subjects in the same template space

?. > > > Thanks > Vasudev > > On 11 July 2016 at 17:25, Dierker, Donna <do...@wustl.edu> wrote: > Hi Vasudev, > > This question confuses me a bit, I confess, but I would use Freesurfer to > generate cortical thickness measurements from T1w volumes: >

Re: [HCP-Users] thresholding the data to p-value

com> Sent: Thursday, July 7, 2016 10:03:28 AM To: Dierker, Donna Cc: <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] thresholding the data to p-value Dear madam, I don't want to write to an ROI volume, i just want to observe activation levels with a threshold of p<0.05. Thanks Va

Re: [HCP-Users] thresholding the data to p-value

Hi Vasudev, I'm pretty sure wb_view can display voxels within a range of values (inside upper and lower limit), but I think you mean threshold and write a ROI volume. For that, try: wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x ${PstatFile} Donna

Re: [HCP-Users] Extracting ROI data from HCP resting state data

Hi David, I hope this publication answers your questions about HCP rfMRI preprocessing: Resting-state fMRI in the Human Connectome Project. Smith SM1, Beckmann CF, Andersson J, Auerbach EJ, Bijsterbosch J, Douaud G, Duff E, Feinberg DA, Griffanti L, Harms MP, Kelly M, Laumann T, Miller KL,

Re: [HCP-Users] Define the ROI and signal extraction in ROI

you please let me know how to register the images ( both volume and > surface ) to Jue-lich histological (cyto- and myelo-architectonic) atlas. > > > Thanks > Vasudev > > > > > On 29 June 2016 at 16:25, Dierker, Donna <do...@wustl.edu> wrote: > Vasud

Re: [HCP-Users] Define the ROI and signal extraction in ROI

of all the > data now i would like to perform analysis. > > If you have any other better way to map vestibular thalamic connectivity , i > would really appreciate your suggestions. > > > Thanks > Vasudev > > > On 28 June 2016 at 15:50, Dierker, Donna

Re: [HCP-Users] Location of CIFTI vertices in standard space

Tom has a volumetric parcellation in MNI space that he has used for other analyses, so he needs to use the same parcellation for comparison with the dconn and dscalar fancy graph stuff. It might be possible to map the parcellation volume to the S900 midthickness and use the mapped parcellation

Re: [HCP-Users] [SPAM] ERROR: mpr2mni305 failed in FreesurferPipelineBatch.sh

Hi Barbara, It looks like there was a problem with a runtime library Freesurfer needs. Have a look at this similar issue: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40092.html I'd report your issue to the Freesurfer mailing list: