[HCP-Users] was behavior testing performed before the first fMRI scan or the re-test fMRI scan
Hello HCPers, I wonder when was the battery testing performed? especially in relative to the two rfMRI scans. Also what is the time interval between the two sessions of rfMRI scans (I didn't mean the within session LR and RL scans but the REST1 and REST2). Thanks -- Ze Wang, PhD ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii
Was the MSMAll one cleaned? Thanks Ze On Fri, Feb 23, 2018 at 9:43 AM, Harms, Michael <mha...@wustl.edu> wrote: > I guess, if you never plan on using the MSMSulc registered output from the > preprocessing output. But the CIFTI files are small compared to the volume > files, so I wouldn’t. Also, if you haven’t already cleaned the data (using > FIX), you’ll need that file. > > > > -- > > Michael Harms, Ph.D. > > --- > > Conte Center for the Neuroscience of Mental Disorders > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave > <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>. > Tel: 314-747-6173 <(314)%20747-6173> > > St. Louis, MO 63110 Email: > mha...@wustl.edu > > > > *From: *redhatw <redh...@gmail.com> > *Date: *Friday, February 23, 2018 at 8:03 AM > *To: *"Glasser, Matthew" <glass...@wustl.edu> > *Cc: *"Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.org" > <hcp-users@humanconnectome.org> > > *Subject: *Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii > > > > Thanks Michael and Matt. Does that mean I can delete > rfMRI_REST1_LR_Atlas.dtseries.nii to save some space? > > Ze > > > > On Thu, Feb 22, 2018 at 7:18 PM, Glasser, Matthew <glass...@wustl.edu> > wrote: > > These are both aligned to the FS_LR spherical surface geographic > convention. > > > > Peace, > > > > Matt. > > > > *From: *<hcp-users-boun...@humanconnectome.org> on behalf of "Harms, > Michael" <mha...@wustl.edu> > *Date: *Thursday, February 22, 2018 at 3:54 PM > *To: *redhatw <redh...@gmail.com>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org> > *Subject: *Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii > > > > > > The files without any “registration suffix” came first temporally and were > generated using “MSMSulc” registration. When the “MSMAll” registration was > added later, we then added “MSMAll” as part of the file name. > > > > Cheers, > > -MH > > > > -- > > Michael Harms, Ph.D. > > --- > > Conte Center for the Neuroscience of Mental Disorders > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave > <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>. > Tel: 314-747-6173 <(314)%20747-6173> > > St. Louis, MO 63110 Email: > mha...@wustl.edu > > > > *From: *<hcp-users-boun...@humanconnectome.org> on behalf of redhatw < > redh...@gmail.com> > *Date: *Thursday, February 22, 2018 at 2:06 PM > *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > *Subject: *[HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii > > > > Dear HCPers, > > In the preprocessed data, I found two dtseries data. What is > rfMRI_REST1_LR_Atlas.dtseries.nii? does it differ from > rfMRI_REST1_LR_Atlas_MSMall.dtseries.nii only by the MSM align method? > Which atlas it is based? > > Sorry I couldn't find details in the documents. > > thanks > > Ze > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii
Thanks Michael and Matt. Does that mean I can delete rfMRI_REST1_LR_Atlas.dtseries.nii to save some space? Ze On Thu, Feb 22, 2018 at 7:18 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > These are both aligned to the FS_LR spherical surface geographic > convention. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of "Harms, > Michael" <mha...@wustl.edu> > Date: Thursday, February 22, 2018 at 3:54 PM > To: redhatw <redh...@gmail.com>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii > > > > The files without any “registration suffix” came first temporally and were > generated using “MSMSulc” registration. When the “MSMAll” registration was > added later, we then added “MSMAll” as part of the file name. > > > > Cheers, > > -MH > > > > -- > > Michael Harms, Ph.D. > > --- > > Conte Center for the Neuroscience of Mental Disorders > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave > <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>. > Tel: 314-747-6173 <(314)%20747-6173> > > St. Louis, MO 63110 Email: > mha...@wustl.edu > > > > *From: *<hcp-users-boun...@humanconnectome.org> on behalf of redhatw < > redh...@gmail.com> > *Date: *Thursday, February 22, 2018 at 2:06 PM > *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > *Subject: *[HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii > > > > Dear HCPers, > > In the preprocessed data, I found two dtseries data. What is > rfMRI_REST1_LR_Atlas.dtseries.nii? does it differ from > rfMRI_REST1_LR_Atlas_MSMall.dtseries.nii only by the MSM align method? > Which atlas it is based? > > Sorry I couldn't find details in the documents. > > thanks > > Ze > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] hcp preprocessed data in MNI space
Hi Matt, Thanks for sharing. Does that mean I have to download the data again (the extended package)? what is the file " rfMRI_REST1_LR.nii.gz "? Best Ze On Mon, Feb 19, 2018 at 2:20 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > This is available in the extended packages, however in general it is not > recommended to compare cortical data across subjects or studies in MNI > space or to smooth the data in the volume. The reasons why are covered > here: > > https://www.biorxiv.org/content/early/2018/01/29/255620 > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of redhatw < > redh...@gmail.com> > Date: Monday, February 19, 2018 at 1:11 PM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] hcp preprocessed data in MNI space > > Dear HCPers, > I'm looking for a way to get the preprocessed rsfMRI data in the MNI > space. I have only downloaded the preprocessed data, are there any tool to > generate that or back-project the MSMAll.dtseries.nii into MNI space? > Also, is this file > rfMRI_REST1_LR.nii.gz > already preprocessed? I noticed that it is in the MNI space. > > Thanks > Ze > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] hcp preprocessed data in MNI space
Dear HCPers, I'm looking for a way to get the preprocessed rsfMRI data in the MNI space. I have only downloaded the preprocessed data, are there any tool to generate that or back-project the MSMAll.dtseries.nii into MNI space? Also, is this file rfMRI_REST1_LR.nii.gz already preprocessed? I noticed that it is in the MNI space. Thanks Ze ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] setting up hcp protocols in Prisma
Dear HCPers, Are there any recommended documents listing the exact parameters for each sequence or the required changes? Thanks Ze Wang ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] data downloading issues with aspera
Dear HCPers, Could you take a look at the following errors and let me know how to solve them? Aspera never consistently finished downloading for one zip file without being disconnected and reconnecting many times. More often I have to restart it after it eventually tried out the allowed number of reconnections. Thanks Ze The errors in the log file were (just copied a small piece of them): 2017-03-08 17:17:06 [1ae0-13dc] ERR fasp_sock_send() failed, err:10035, len:1436 2017-03-08 17:17:06 [1ae0-13dc] ERR Non-fatal feedback sending error=10035 len=1436 2017-03-08 17:17:06 [1ae0-13dc] ERR fasp_sock_send() failed, err:10035, len:1436 2017-03-08 17:17:06 [1ae0-13dc] ERR Non-fatal feedback sending error=10035 len=1436 2017-03-08 17:17:06 [1ae0-13dc] ERR fasp_sock_send() failed, err:10035, len:716 2017-03-08 17:17:06 [1ae0-13dc] ERR Non-fatal feedback sending error=10035 len=716 2017-03-08 17:17:06 [1ae0-156c] LOG File exists and has the same checksum [D:/HCPrest/102816_3T_rfMRI_REST1_preproc.zip.md5] src csum [07e30352ceb75d1ea9aa8f36c5c3d221] dst csum [07e30352ceb75d1ea9aa8f36c5c3d221] 2017-03-08 17:17:06 [1ae0-156c] LOG Receiver: skipping D:/HCPrest/102816_3T_rfMRI_REST1_preproc.zip.md5, overwrite_policy=1 2017-03-08 17:17:06 [1ae0-1958] LOG FASP Transfer Stop uuid=de0ef88f-412b-4426-9ed2-1271d5900fd8 op=recv status=success file="D:/HCPrest/102816_3T_rfMRI_REST1_preproc.zip.md5" size=68 start_byte=68 rate=0.00Kbps elapsed=0.00s loss=0.00 rexreqs=0 overhead=0 2017-03-08 17:17:06 [1ae0-156c] LOG File exists and has the same checksum [D:/HCPrest/103010_3T_rfMRI_REST1_preproc.zip.md5] src csum [7ea2fad33ae6ffa4136e70c9e3cfcdfe] dst csum [7ea2fad33ae6ffa4136e70c9e3cfcdfe] 2017-03-08 17:17:06 [1ae0-156c] LOG Receiver: skipping D:/HCPrest/103010_3T_rfMRI_REST1_preproc.zip.md5, overwrite_policy=1 2017-03-08 17:17:06 [1ae0-1958] LOG FASP Transfer Stop uuid=de0ef88f-412b-4426-9ed2-1271d5900fd8 op=recv status=success file="D:/HCPrest/103010_3T_rfMRI_REST1_preproc.zip.md5" size=68 start_byte=68 rate=0.00Kbps elapsed=0.00s loss=0.00 rexreqs=0 overhead=0 2017-03-08 17:17:06 [1ae0-13dc] ERR fasp_sock_send() failed, err:10022, len:1436 2017-03-08 17:17:06 [1ae0-13dc] ERR Re-transmit fatal error sending feedback len=1436 (10022): An invalid argument was supplied. 2017-03-08 17:17:06 [1ae0-13dc] LOG Receiver bl t/o/r/d/ts/c/h=19817/18709/1108/0/42411/497/45317 rex_rtt l/h/s/o=227/351/313/314 ooo_rtt l/h/s/o=154/319/133/645 rate_rtt b/l/h/s/r/f=37/38/357/315/0/1 ctl bm/bs=0/0 rex n/s/q/v/a/r=26124/23575/108/4/0/0 bl l/d/o/r/a/x/dl/df/dm/ds=26612/624/5/0/0/0/0/0/0/0 disk l/h/b=0/2/0 vlink lq/lo/rq/ro=0/0/0/0 rate t/m/c/n/vl/vr/r=100/0/1052971437/1052971437/100/100/100 prog t/f/e=27023744/30653469348/1329204 rcvD=0 2017-03-08 17:17:06 [1ae0-13dc] LOG Receiver DS Qs ds/n/rq/ao/ap/rd/ru/no/po/pc/do/tv/sv=27/0/0/0/0/0/27/0/0/0/0/0/0 Rs i/o=37/37 mgmt backlog i/s/n = 0/408/0 2017-03-08 17:17:06 [1ae0-156c] ERR Sink-work aborting since receiver shutdown (shutdown 1 aborted 10)! 2017-03-08 17:17:06 [1ae0-156c] ERR Receiver Aborted. Stopping data receiver 2017-03-08 17:17:06 [1ae0-156c] ERR Stopped data receiver 2017-03-08 17:17:06 [1ae0-156c] ERR LOCAL ABORT: Shutting down sink/receiver, abort reason FASP_ABORT_LOCAL 2017-03-08 17:17:06 [1ae0-156c] ERR sink_send_abort: sent sesserr_pdu reason 3 (total len 0) 2017-03-08 17:17:06 [1ae0-156c] LOG Session notification: type=19 len=100 reason=3 (FASP_ABORT_LOCAL) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] HCP_TFMRI_scripts.zip not exist
Could anyone post a correct link for the eprime scripts? I got an error of "No such file or directory (code 4)" when I trie to download it from HCP. Thanks Ze [image: Inline image 1] ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
