Re: [HCP-Users] requirements for HCP pipeline?

Thanks to everybody, you are being very helpful. Much appreciation. ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons

[HCP-Users] 7 RSN Netoworks label file

Hi users, I am trying to get the labels from 7 RSN Networks but map on export table command is not recognized and I am not sure if frontoparietal is 6 and DMN 7. Any idea? Thanks Sent from my iPhone ___ HCP-Users mailing list

Re: [HCP-Users] grey matter volume

Great I could find it, much appreciation. Are those measures reliable or should I do VBM? I overly aparc.a2009s+aseg to T1w_restore and it fits perfectly. Is that enough quality check? Thanks!, ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental

[HCP-Users] grey matter volume

Hi users, Where to find grey matter volume from subcortical structures same way you can find them in freesurfer/subects/'subject_id'/stats/aseg.stats? Thanks, ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric

Re: [HCP-Users] 7 RSN Netoworks label file

It works using the map index number 1, thanks Tim! ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons On Jan 26, 2015

Re: [HCP-Users] 7 RSN Netoworks label file

to extract the connectivity from my seed to different networks, that is why I needed the table to know which networks to extract in matlab. I did it that way and is working. Thanks, ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New

Re: [HCP-Users] cluster extent thresholding on surface

Ok, thanks for the answer. ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons On Jan 11, 2015, at 10:20 PM, Harms

[HCP-Users] cluster extent thresholding on surface

Hi users, For cluster extent thresholding on surface I am using wb_command -cifti-find-clusters. How to find surface area to have corrected p value of 0.05? Thanks, ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State

Re: [HCP-Users] -cifti-separate

wb_command cifti-in COLUMN -metric CORTEX_RIGHT metric-out Thanks, ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons

[HCP-Users] -cifti-separate

-metric-convert but to no avail. Thank you, ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons

Re: [HCP-Users] -cifti-separate

Thank you I appreciate your help! All the best, ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons On Jan 12, 2015

[HCP-Users] creati cifti from nifti1

loading into workbench my subcortical data is not separated from my surface t-map. What am I doing wrong? Thanks, Leah ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia

[HCP-Users] 7 tesla MRI

Hi users, I am going to start acquiring data from 7 Tesla MRI (Siemens) and would like to know best option for resting state (carrying out whole brain shimming up to 2nd order). Which would be best protocol in your expert opinion? Thanks! ___ Marta Moreno-Ortega, Ph.D

Re: [HCP-Users] 7 tesla MRI

Hi Joseph, Thanks for your recommendation! All the best, ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons On Feb

[HCP-Users] from volume to gifti file to cifti roi

Dear Users, I am generating ROIs in subject volume space and need to know how to create a gifti label file when I map from volume to surface and how to convert that label gifti file to cifti roi? Best wishes always, Leah ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow

Re: [HCP-Users] from volume to gifti file to cifti roi

Thank you Timothy, I found your email very useful. I followed it and is done!! Also thanks to Donna and Jo! Best wishes always, Leah ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department

[HCP-Users] fc maps in subject native volume space

Dear Users, I have an ROI created in the surface, how could I map it to the native volume subject space? Also, I have my fc map from that ROI (dscalar.nii), how could I map it to the native volume subject space? Please help. Thank you, Leah ___ Marta Moreno-Ortega, Ph.D

Re: [HCP-Users] T1w/wmparc_1mm

Hi Matt, wmparc.mgz file does not exist. I run FreeSurfer pipeline again as I did not have gradunwarp installed but still I am not getting this file. Any idea, please? Best wishes, Leah ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental

[HCP-Users] HCP_S500_R468_MIGPd4500ROW.dconn.nii

? Thanks, Leah ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons 1051 Riverside Dr., Unit 21 New York, NY 10032 office

Re: [HCP-Users] geodesic-distance

May 29, 2016, at 6:59 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > > How did you call the command? > > Peace, > > Matt. > > From: Marta Moreno <mmorenoort...@icloud.com > <mailto:mmorenoort...@icloud.com>> > Date: Sunday, May 29, 201

Re: [HCP-Users] geodesic-distance

10032 > On May 29, 2016, at 7:06 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > > Try without the commas. > > Peace, > > Matt. > > From: Marta Moreno <mmorenoort...@icloud.com > <mailto:mmorenoort...@icloud.com>> > Date: Sunday

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

Thank you, Dona. I tried that too but I am getting similar pictures. Any other recommendation? I got very nice results from analyses and need nice pictures. Thanks, -L > On Jan 15, 2017, at 10:40 AM, Dierker, Donna wrote: > > Hi Leah, > > I wonder if you need to apply an

Re: [HCP-Users] Freesurfer to Workbench (Marta Moreno)

Thank you very much, Alex. > On Nov 14, 2016, at 10:54 AM, Alex Cohen wrote: > > You could take a look at this as well: > https://www.ncbi.nlm.nih.gov/pubmed/27655470/ > > https://github.com/alexlicohen/script-toolbox >

Re: [HCP-Users] Freesurfer to Workbench

ers-boun...@humanconnectome.org on behalf of > Marta Moreno" <hcp-users-boun...@humanconnectome.org on behalf of > mmorenoort...@icloud.com> wrote: > >> Dear HCP users, >> >> I want to convert individual surfaces obtained with Freesurfer to >> Workbench

[HCP-Users] NEWMAT::SingularException

Dear experts, After running all preprocessing steps using the HCP pipeline and not getting any error, I am getting the following error message with the motion correction script, last step (power et al.), on the resting data: libc++abi.dylib: terminating with uncaught exception of type

Re: [HCP-Users] error open file in wb_view

Thanks a lot. Problem solved. > On Dec 12, 2017, at 2:28 PM, Harwell, John <jharw...@wustl.edu> wrote: > > It is possible the file is corrupted. Please try to run “wb_command > -file-information ” on the file and see if that works. > >> On Dec 12, 2017, at 12:20 P

[HCP-Users] error open file in wb_view

Dear experts, I am getting an error any time I am trying to open file in wb_view. Any idea how to solve this problem? Thanks, -L Error attached below: Process: wb_view [56364] Path:

Re: [HCP-Users] error open file in wb_view

rst > time you have run wb_view on this Mac? > > Do you know which file is causing the crash? You could use File Menu —> Open > File and try opening just a surface file. > > > John Harwell > > >> On Dec 12, 2017, at 11:25 AM, Marta Moreno <mmorenoort

[HCP-Users] HCP_hp2000.RData

Dear experts, I am getting the following error running hip_fix, my RSfMRI data is similar to HCP data but I am getting the following error running hcp_fix RS_fMRI_2/RS_fMRI_2.nii.gz 2000: "FIX Classifying components in Melodic directory: RS_fMRI_2_hp2000.ica using training file:

[HCP-Users] hcp_fix script and settings

t 30, 2017, at 10:29 AM, Marta Moreno <mmorenoort...@icloud.com> wrote: > > Great. Thank you very much. > >> On Oct 29, 2017, at 4:44 PM, Glasser, Matthew <glass...@wustl.edu >> <mailto:glass...@wustl.edu>> wrote: >> >> Yes that is wh

Re: [HCP-Users] mcflirt_acc in ABCD

Is the version 3.4.0 the latest version of the pipelines which default to FSL mcflirt? Thanks, -L Sent from my iPhone > On Nov 8, 2017, at 4:55 PM, Glasser, Matthew wrote: > > I would use the latest version of the pipelines which default to FSL mcflirt > because some

Re: [HCP-Users] HCP_hp2000.RData

;glass...@wustl.edu> wrote: > > I would ask specifically on the FSL list again as they are the primary > support for FIX. > > Matt. > > From: Marta Moreno <mmorenoort...@icloud.com > <mailto:mmorenoort...@icloud.com>> > Date: Monday, November 6, 2017 a

Re: [HCP-Users] HCP_hp2000.RData

uired R packages. > > Peace, > > Matt. > > From: Marta Moreno <mmorenoort...@icloud.com > <mailto:mmorenoort...@icloud.com>> > Date: Monday, November 6, 2017 at 9:29 AM > To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>&g

[HCP-Users] ICA+FIX cleanup scripts

Dear experts, I would like to use ICA+FIX cleanup after HCP minimal preprocessing pipelines on high quality resting-state data acquired with a GE scanner. HCP minimal preprocessing is working fine and installed locally. I have downloaded now the tar file with ICA+FIX cleanup scripts. Could

Re: [HCP-Users] ICA+FIX cleanup scripts

Great. Thank you very much. > On Oct 29, 2017, at 4:44 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > > Yes that is what we do. > > Peace, > > Matt. > > From: Marta Moreno <mmorenoort...@icloud.com > <mailto:mmorenoort...@icloud.com>&

Re: [HCP-Users] ICA+FIX cleanup scripts

the FSL programmers don’t watch this list. Here we can answer questions > about CIFTI or approaching clean up of resting state data. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org>> on beh

[HCP-Users] error running hcp_fix

Dear experts, I am getting the following error. Please advice: hcp_fix RS_fMRI_1.nii.gz 2000 processing FMRI file RS_fMRI_1 with highpass 2000 running highpass running MELODIC running FIX FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica create edge masks run FAST

Re: [HCP-Users] error running hcp_fix

> Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno > <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>> > Date: Saturday, May 26, 2018 at 1:50 PM &

Re: [HCP-Users] error running hcp_fix

y, we would need to know what version of > Workbench and matlab to debug this. > > Peace, > > Matt. > > From: Marta Moreno <mmorenoort...@icloud.com > <mailto:mmorenoort...@icloud.com>> > Date: Sunday, May 27, 2018 at 3:22 PM > To: "st...@fmrib.

Re: [HCP-Users] error running hcp_fix

ror in fix_3_clean (line 46) BO=ciftiopen('Atlas.dtseries.nii',WBC); Thanks! -L > On May 26, 2018, at 6:55 PM, Marta Moreno <mmorenoort...@icloud.com> wrote: > > You were right, now the problem is gone but still cannot find my > clean.dtseries > > Here is the output,

Re: [HCP-Users] error running hcp_fix

> > Tim > > > On Wed, May 30, 2018 at 8:59 AM, Marta Moreno <mailto:mmorenoort...@icloud.com>> wrote: > Dear Tim, > > How did you install randomForest' version 4.6.12? I am getting the following > error (see below). Do I need R-devel as well to install

[HCP-Users] hcp_fix question

Dear Experts, I have installed all required versions from packages kernlab, party, etc. in R successfully, but after running hcp_fix I found the following error in .fix.log. Please advice (see below): /bin/bash: /Applications/workbench/bin_macosx64: is a directory Error using

Re: [HCP-Users] error running hcp_fix

ote: > > There is no relationship between R and Workbench (or R and matlab). As to a > Workbench/matlab incompatibility, we would need to know what version of > Workbench and matlab to debug this. > > Peace, > > Matt. > > From: Marta Moreno <mailto:mmorenoort...@icloud.com>&g

Re: [HCP-Users] error running hcp_fix

n line 94 of the FIX settings.sh? > > Matt. > > From: Marta Moreno <mailto:mmorenoort...@icloud.com>> > Date: Tuesday, June 5, 2018 at 12:28 PM > To: Matt Glasser mailto:glass...@wustl.edu>> > Cc: "st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>&qu

Re: [HCP-Users] error running hcp_fix

eutics Department of Psychiatry Columbia University Medical Center 1051 Riverside Drive, Unit 21 New York, NY 10032 phone: (914) 218-7311 email: mm4...@cumc.columbia.edu email: mmor...@nyspi.columbia.edu > On May 27, 2018, at 11:20 PM, Marta Moreno wrote: > > Thanks, Tim! I followed your advi

Re: [HCP-Users] error running hcp_fix

en bigger pain), and then use > "install_version": > https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages > > <https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages> > > Tim > &g

Re: [HCP-Users] error running hcp_fix

;> On 27 May 2018, at 02:32, Marta Moreno <mmorenoort...@icloud.com >> <mailto:mmorenoort...@icloud.com>> wrote: >> >> I found the following error, please advice: (before is giving me some >> warnings about different functions that has same name as a Matlab

[HCP-Users] wb_view crashes after 1 day of using it

Dear experts, My wb_view crashes after 1 day of using it, what happens is that the next day I cannot keep loading more images with setting created for illustration of brain results and need to restart all over -even it requires to restart the computer to have it working properly. I have

[HCP-Users] workbench crashes - Namespace SIGNAL, Code 0xb

Dear experts, My workbench crashes anytime I upload a new file. I am using version 1.2.3. Please advice, below problem details. Process: wb_view [81425] Path: /usr/local/workbench/bin_macosx64/../macosx64_apps/wb_view.app/Contents/MacOS/wb_view Identifier:

Re: [HCP-Users] workbench crashes - Namespace SIGNAL, Code 0xb

Thanks. What details do you need to help? It crashes anytime I try to open a new file. I am running macOS Sierra version 10.12.5 on a Mac Pro (Late 2013). Could it be related to memory? My Mac contains 4 memory slots, and all memory slots are currently in use. Here I pasted the entire

[HCP-Users] Question on fsl 6.0.1

Dear Experts, Is FSL 6.0.1 ready for MR ICA+FIX and MSMAII? I have not seen any post yet in here. Thanks, Leah. Sent from my iPhone ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] question on fsl 6.0.1

Dear Experts, Is FSL 6.0.1 ready for MR ICA+FIX and MSMAII? I have not seen any post. Thanks, Leah. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] ICA+FIX error

Dear Experts, I am running hip_fix and getting the following error with just one of my subjects, please see below. It seams the script stoped at the end, in section "Rename some files (relative to the default names coded in fix_3_clean)”, first line: "$FSLDIR/bin/immv

Re: [HCP-Users] Topup_AP dimension issue

8 from 96 and then take half of that as your start and 96 as your > length. > > Matt. > > From: <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno > mailto:mmorenoort...@icloud.com>> > Date: Sunday, March 24, 2019 at 6:40 PM > To:

Re: [HCP-Users] Topup_AP dimension issue

10032 phone: (914) 218-7311 email: mm4...@cumc.columbia.edu > On Mar 24, 2019, at 10:58 PM, Glasser, Matthew wrote: > > 0 66 to include all slices and probably 0 1 for timepoints tacked onto the > end. > > Matt. > > From: Marta Moreno <mailto:mmorenoort...@icloud.

Re: [HCP-Users] related parcellation

abel-export-table or look inside the Workbench > GUI. > > Matt. > > From: <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno > mailto:mmorenoort...@icloud.com>> > Date: Sunday, March 24, 2019 at 11:59 AM > To: HCP Users <m

[HCP-Users] related parcellation

Dear Experts, If I create a ‘pconn.nii’ from each subject through the commands wb_command -cifti-parcellate and -cifti-correlation to generate correlation matrix between parcels (struct 360*360). How can I know which number in raw and column correspond to parcel’s name in the dlabel.nii from

[HCP-Users] Topup_AP dimension issue

Dear Experts, Maybe a trivial question but how can I change the Topup_AP dimension' size from 128 128 66 to 96 96 66? Using fslroi I am cutting the brain. Thanks, Leah. ___ HCP-Users mailing list HCP-Users@humanconnectome.org

[HCP-Users] ICA+FIX not running

Dear Experts, I downloaded the ICAFIX HCPpipelines v4.0.0 and installed fsl 6.0.1. I am running the hcp_fix_multi_run option and getting the following message (see below). What am I doing wrong? bash-3.2$ hcp_fix_multi_run RS_fMRI_1/RS_fMRI_1.nii.gz@RS_fMRI_2/RS_fMRI_2.nii.gz RS_fMRI_MR

Re: [HCP-Users] ICA+FIX error

sity School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave.Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: on behalf of Marta Moreno > > Date: Sunday, March 31, 2019 at 6:44 PM > To

Re: [HCP-Users] MR ICA+FIX error

63110 Email: mha...@wustl.edu > <mailto:mha...@wustl.edu> > > From: on behalf of "Glasser, Matthew" > > Date: Saturday, April 6, 2019 at 2:57 PM > To: Marta Moreno , NEUROSCIENCE tim > Cc: HCP Users > Subject: Re: [HCP-Users] MR

Re: [HCP-Users] MR ICA+FIX error

s used), try the latest master. > > Tim > > > On Mon, Apr 1, 2019 at 1:49 PM Marta Moreno <mailto:mmorenoort...@icloud.com>> wrote: > Thanks for your response, Tim. > What should I do specifically to make it work. I am not sure I am following > the steps as w

Re: [HCP-Users] Topup_AP dimension issue

sample an image (flirt, applywarp, or wb_command > -volume-*-resample), and not crop it. > > Tim > > > On Sun, Mar 24, 2019 at 10:22 PM Marta Moreno <mailto:mmorenoort...@icloud.com>> wrote: > Thanks for your response. The im

[HCP-Users] MSMAll, missing _vn file

Dear experts, I am running MSMAllPipelineBatch.sh after hcp_fix on a 10min run (rsfMRI) and getting an error saying that the file: "RS_fMRI_1_Atlas_hp2000_clean_vn_tempcompute.dscalar.nii" does not exist. I am using fsl 5.0.11 and fix 1.067. Any help? Thanks, Leah

Re: [HCP-Users] MSMAllPipeline error

> > <https://github.com/Washington-University/HCPpipelines/tree/master/global/matlab> > to your matlab path. > > Matt. > > From: Matt Glasser mailto:glass...@wustl.edu>> > Date: Sunday, April 14, 2019 at 1:16 PM > To: Marta Moreno mailto:mmorenoor

[HCP-Users] DeDriftAndResamplePipeline error

Dear Experts,I have run DeDriftAndResamplePipelineBatch.sh from from ${StudyFolder}/${Subject}/scripts after running MSMAII and getting the following error:While running:/Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command -metric-resample

Re: [HCP-Users] DeDriftAndResamplePipeline error

you do run it with the individual fMRI names and that doesn’t look like the version 4.0.0 example script... Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of Marta Moreno <mmorenoort...@icloud.com> Date: Sunday, April 14, 2019 at 10:06 PM To: HCP Users <hcp-users@

Re: [HCP-Users] DeDriftAndResamplePipeline error

tAndResamplePipelineBatch.sh> > > Also it looks like line 124 needs an “s” on the end of the flag name to read > --multirun-fix-concat-names=${MRFixConcatName} > > Matt. > > From: Marta Moreno <mailto:mmorenoort...@icloud.com>> > Date: Sunday, April 14, 2019 at

Re: [HCP-Users] DeDriftAndResamplePipeline error

DeDriftAndResamplePipeline.sh.o40867 Description: Binary data On Apr 15, 2019, at 12:19 AM, Marta Moreno <mmorenoort...@icloud.com> wrote:It seams to be working now. Thanks a lot!Leah. On Apr 15, 2019, at 12:04 AM, Glasser, Matthew <glass...@wustl.edu> wrote: If you ran MR+FIX, you need to set these a

Re: [HCP-Users] MSMAllPipeline error

e: > > I wouldn¹t use hp=pd2 unless you know what you are doing, as that option > has not been fully tested. I run with hp=0. > > Matt. > > On 4/13/19, 10:41 AM, "hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org> on beh

Re: [HCP-Users] MSMAllPipeline error

0_clean_vn_tempcompute.dscalar.nii','/Applications/workbench/bin_macosx64//wb_command'); Sat Apr 13 15:09:44 EDT 2019 - SingleSubjectConcat.sh - MATH: ((TCS - Mean)) / max(VN,0.001) Leah. > On Apr 13, 2019, at 3:02 PM, Glasser, Matthew wrote: > > I guess specify how you called the MSMAll

Re: [HCP-Users] MSMAllPipeline error

recent versions of FIX and MR+FIX, variance normalization is always > already computed. That said, it isn’t clear to me why it is failing to > compute it again. Perhaps you are not reporting the first error that occurs. > > > Matt. > > From: Marta Moreno <mailto:mm

Re: [HCP-Users] MSMAllPipeline error

> on behalf of > glass...@wustl.edu <mailto:glass...@wustl.edu>> wrote: > > I wouldn¹t use hp=pd2 unless you know what you are doing, as that option > has not been fully tested. I run with hp=0. > > Matt. > > On 4/13/19, 10:41 AM, "hcp-users-boun..

Re: [HCP-Users] MSMAllPipeline error

t; On Apr 13, 2019, at 3:39 PM, Glasser, Matthew wrote: > > If you ran MR+FIX, your data are already concatenated for MSMAll, so just > provide the concatenated fMRIName from the MR+FIX run. It should work then. > > Matt. > > From: Marta Moreno <mailto:mmorenoort...@icl

Re: [HCP-Users] MSMAllPipeline error

it Leah. > On Apr 13, 2019, at 3:22 PM, Glasser, Matthew wrote: > > You can just put your MR+FIX concatenated name in for the fMRIName and > OutfMRIName. > > Matt. > > From: Marta Moreno <mailto:mmorenoort...@icloud.com>> > Date: Saturday, April 13, 2019 a

[HCP-Users] MSMAllPipeline error

Dear Experts, I am running the following script MSMAllPipelineBatch.sh from ${StudyFolder}/${Subject}/scripts after running MR ICA+FIX with success, and I am getting the following error: ERROR: failed to open file

Re: [HCP-Users] MSMAllPipeline error

https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/SingleSubjectConcat.sh> > > Line 473 apparently has to be -p on a mac > > Matt. > > From: Marta Moreno <mailto:mmorenoort...@icloud.com>> > Date: Saturday, April 13, 2019 at 3:32 PM

Re: [HCP-Users] MSMAllPipeline error

: MSMCONFIGDIR environment variable must be set How should i configure the environment variable: MSMCONFIGDIR? Thanks! Leah. > On Apr 14, 2019, at 2:54 AM, Marta Moreno wrote: > > Thanks for your response! > > Sorry to bother you but still I am getting an error. Now it says: >

Re: [HCP-Users] MSMAllPipeline error

actually download the entire pipelines 4.0.0 release and > follow the instructions there. Running code from multiple versions is likely > to create problems, though the issues with mac that you have encountered thus > far are likely still there. > > Matt. > > From: Marta Moreno &l

Re: [HCP-Users] MSMAllPipeline error

ngton-University/HCPpipelines/blob/master/MSMAll/scripts/MSMAll.sh> > > Matt. > > From: Marta Moreno <mailto:mmorenoort...@icloud.com>> > Date: Sunday, April 14, 2019 at 9:49 AM > To: Matt Glasser mailto:glass...@wustl.edu>> > Cc: "Harms, Michael" m

Re: [HCP-Users] MSMAllPipeline error

r/Native/MSMAll_InitalReg_2_d40_WRN/Params.txt','NO',0,'NO','NO'); Sun Apr 14 11:35:35 EDT 2019 - MSMAll.sh - Resample the individual maps so they are in the correct space Thanks a lot!, Leah. > On Apr 14, 2019, at 11:13 AM, Marta Moreno wrote: > > Now it seams to be working! Thanks a lot

[HCP-Users] DeDriftAndResamplePipelineBatch.sh

Dear Experts, If I run MR ICAFIX regressing motion parameters as part of the cleaning, do I need to set DeDriftAndResamplePipelineBatch.sh as MotionRegression=TRUE? Thanks, Leah. ___ HCP-Users mailing list HCP-Users@humanconnectome.org

Re: [HCP-Users] DeDriftAndResamplePipelineBatch.sh

OK. Thanks! Leah. > On May 27, 2019, at 12:59 PM, Glasser, Matthew wrote: > > Yes. > > Matt. > > From: on behalf of Marta Moreno > > Date: Monday, May 27, 2019 at 11:15 AM > To: HCP Users > Subject: [HCP-Users] DeDriftAndResamplePipelineBatch.sh >

[HCP-Users] table for parcellation

Dear experts, After running: 1. PreFreeSurfer 2. FreeSurfer 3. PostFreeSurfer 4. fMRIVolume 5. fMRISurface 6. ICA+FIX (MR+FIX) 7. MSMAll (Do MSM Surface Registration) 8. dedrift and resample pipeline 2 questions: (i) I used wb_command -cifti-parcellate and wb_command

Re: [HCP-Users] DeDriftAndResamplePipeline error

llegal option -- f usage: readlink [-n] [file ...] I believe Tim already gave you instructions for this.   Also, the log_Warn line is again concerning as to whether you followed the installation instructions and all version 4.0.0 files here. Matt. From: Marta Moreno <mmorenoort...@icloud.com>

Re: [HCP-Users] DeDriftAndResamplePipeline error

4.0.0 version when running things from 4.0.0.  The log_Warn function is defined inside global/scripts, and it should get sourced automatically based on HCPPIPEDIR, so make sure that is set correctly (pointed to the 4.0.0 version).TimOn Thu, Apr 18, 2019 at 1:39 PM Marta Moreno <mmorenoort...@i

Re: [HCP-Users] DeDriftAndResamplePipeline error

if “case” doesn’t work > the same on Mac? > > Matt. > > From: Marta Moreno <mailto:mmorenoort...@icloud.com>> > Date: Thursday, April 18, 2019 at 11:19 PM > To: Timothy Coalson mailto:tsc...@mst.edu>> > Cc: Matt Glasser mailto:glass...@wustl.edu>>, &qu

Re: [HCP-Users] DeDriftAndResamplePipeline error

ouis, MO 63110 Email: mha...@wustl.edu > > From: on behalf of Marta Moreno > > Date: Saturday, April 20, 2019 at 12:02 PM > To: "Glasser, Matthew" > Cc: HCP Users > Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error > >

[HCP-Users] Fwd: question

Hi Users, Just to say I resolved the problem I was having and now I can see my matrix and pconn so no problem! Thanks, ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry