Re: [HCP-Users] CMRR vs MGH multiband/SMS sequences
Hi, It's best seen on tStd and tSnr images. Depending on sequence parameters it can very subtle. I've tried different coils and sites. These are with CMRR. Just a few (20 I think) volumes demonstrating the artifact. https://ibb.co/cPAwEa https://ibb.co/cmu6Ea > On Jul 14, 2017, at 6:08 PM, Harms, Michael <mha...@wustl.edu> wrote: > > > What banding artifact are you referring to? Could you post a picture to a > sharing site? > > thx > -- > 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. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: <hcp-users-boun...@humanconnectome.org> on behalf of A R > <aruls...@gmail.com> > Date: Friday, July 14, 2017 at 8:25 AM > To: "Juranek, Jenifer" <jenifer.jura...@uth.tmc.edu> > Cc: "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org> > Subject: Re: [HCP-Users] CMRR vs MGH multiband/SMS sequences > > In my experience they both suffer from the same banding artifact affecting > the middle 25% of slices. > > > On Jul 11, 2017, at 5:34 PM, Juranek, Jenifer <jenifer.jura...@uth.tmc.edu> > wrote: > >> Just curious if anyone is aware of head-to-head comparisons of CMRR and MGH >> MB/SMS sequences? >> Someone recently mentioned to me that “the general consensus is that MGH >> outperforms CMRR”. >> Is there a “general consensus” in the research community on this issue? Any >> differences between dMRI and fMRI applications? >> I’m interested in using an HCP-style acquisition protocol for a 5yr study >> about to start…from what I can tell, CMRR MB sequences have been selected >> across the board for HCP-style studies currently funded by NIH. >> Does anyone have any thoughts they can share? >> Many Thanks, >> Jenifer >> ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ >> Jenifer Juranek, PhD >> Associate Professor >> Department of Pediatrics >> UTHealth >> Houston, TX 77030 >> 713.500.8233 >> >> ___ >> 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 > > > 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] Split dtseries
Dear HCP users, How to split/trim a dtseries or ptseries file by number of time points? Basically an equivalent of fslroi... Thanks for any info ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] fix error, vn maps
Hi Micheal, Thanks for the speedy response. I look forward to the update. Cheers, Aaron > On Dec 6, 2018, at 5:41 PM, Harms, Michael wrote: > > > ciftisavereset wasn’t compiled in to the existing 1.067 compiled matlab. I > just tested a new compiled in which this is fixed. Waiting for Oxford to > either update the fix1.067 package, or release a new fix version. > > Cheers, > -MH > > -- > Michael Harms, Ph.D. > --- > Associate Professor of Psychiatry > Washington University 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 Aaron R > > Date: Thursday, December 6, 2018 at 10:29 AM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] fix error, vn maps > > Dear HCP users, > > I'm getting an error with fix 1.067, the cifti variance normalization field > is not created. The file filtered_func_data_clean_vn.nii.gz is created > however, and everything else is ok. In .fix.log, i see: > > The file >'/usr/local/gifti/ciftisavereset.m' >is not in the application's expanded CTF archive at > '/home/aaron/.mcrCache8.3/fix_3_1'. > This is typically caused by calls to ADDPATH in your startup.m or matlabrc.m > files. Please see the compiler documentation and use the ISDEPLOYED function > to ensure ADDPATH commands are not executed by deployed applications. > Previously accessible file "/usr/local/gifti/ciftisavereset.m" is now > inaccessible. > > Error in fix_3_clean (line 131) > > I'm using the compiled matlab option. Any ideas? > > Thanks in advance, > Aaron > ___ > 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] CIFTIMatlabReaderWriter
Dear Matt, Thanks for the info. I've been trying to get hcp_fix working, but no luck so far. I'm not sure if I should post here or on the fsl list, but hopefully someone will respond here. With the compiled route, I get a seg fault when this file is not found: mc/prefiltered_func_data_mcf_conf_hp The errors seem related to two paths that don't exist. They must be set in the compiled scripts, I can't find them anywhere else: Warning: Name is nonexistent or not a directory: /usr/local/fsl/etc/matlab Warning: Name is nonexistent or not a directory: /usr/local/fmrib/fmt This first one I solved with a symlink, the second I have no idea what it should point to. With octave, the log isn't very helpful: Segmentation fault fslmeants: symbol lookup error: fslmeants: undefined symbol: _ZN9Utilities12OptionParser18parse_command_lineEjPPci load: unable to find file rsa_hp2000.ica/fix/hr2exfTMP.txt Any insight would be appreciated :) On Sun, Oct 18, 2015 at 2:00 AM, Glasser, Matthew <glass...@wustl.edu> wrote: > Use option B from #2 on this webpage: > https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Aaron R < > aaro...@gmail.com> > Date: Saturday, October 17, 2015 at 4:30 PM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] CIFTIMatlabReaderWriter > > Dear HCPers, > > Can anyone tell me what 'CIFTIMatlabReaderWriter' is - required by > ICA-FIX? Is it a binary, directory, file.. ? I definitely don't have it on > my computer. Is it only distributed with the data? > > Thanks, > A. > > ___ > 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] combining cortical and subcortical parcellations
Never mind, I managed to figure it out. The command label-modify-keys doesn't seem to work however, which makes fixing the key values a bit more cumbersome. Cheers, Aaron On Sun, May 20, 2018 at 12:21 AM, Aaron R <aaro...@gmail.com> wrote: > I've attempted to combine cortical and subcortical parcellations on a few > occasions without any luck, I'm hoping someone here can help me out. > > #make some subcortical labels > wb_command -cifti-create-label subcortical.dlabel.nii -volume > Atlas_ROIs.2.nii.gz Atlas_ROIs.2.nii.gz > > #combine with cortical > wb_command -cifti-create-dense-from-template 91282_Greyordinates.dscalar.nii > TEST.dlabel.nii -cifti glasser_cort.dlabel.nii -cifti > subcortical.dlabel.nii > > ... seg fault > > #try -cifti-merge-dense > wb_command -cifti-merge-dense COLUMN TEST.dlabel.nii -cifti > glasser_cort.dlabel.nii -cifti subcortical.dlabel.nii > > #check > wb_command -file-information TEST.dlabel.nii > > ... everything looks ok.. > > #try to use it, look at the output after running through task pipeline > wb_command -file-information subject_TEST.pscalar.nii > > And parcellations are incorrectly merged, exactly like described here: > https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03217.html > > I also apparently created a dlabel file another way, I don't remember how, > but the parcellations were incorrectly merged as above. I extracted the > labels to text, manually edited the key values in vi and reimported them.. > it looked ok then (dlabel.nii), however the output (pscalar.nii) again was > incorrectly merged as above. > > Can anyone tell me how to do this? > > Thank you, > Aaron > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] combining cortical and subcortical parcellations
Hi Tim, Thanks for the reply. Yep, I was trying to use label-modify-keys on a cifiti file, so that explains it. Cheers, Aaron On Tue, May 22, 2018 at 6:28 AM, Timothy Coalson <tsc...@mst.edu> wrote: > Oh, I have a guess as to what you encountered: the -label-modify-keys > command is only for gifti label files, not cifti, so it probably told you > something like "parse error on line 1". It looks like I didn't implement > equivalents for other formats, probably related to the fact that label > tables are separate per map in volume and cifti label files, but only one > for the whole file in gifti label files. > > Tim > > > On Mon, May 21, 2018 at 11:18 PM, Timothy Coalson <tsc...@mst.edu> wrote: > >> I think you must be using an older version of workbench, the recent 1.3.0 >> release appears to do those commands correctly. Do "wb_command -version" >> to check. I'll take a look at the -label-modify-keys command, can you be >> more specific about what it did? >> >> Note that Neurodebian has not yet updated workbench, we have a few things >> to work out with them. Hopefully it will be ready soon. >> >> Tim >> >> >> On Mon, May 21, 2018 at 10:33 AM, Aaron R <aaro...@gmail.com> wrote: >> >>> Never mind, I managed to figure it out. The command label-modify-keys >>> doesn't seem to work however, which makes fixing the key values a bit more >>> cumbersome. >>> >>> Cheers, >>> Aaron >>> >>> On Sun, May 20, 2018 at 12:21 AM, Aaron R <aaro...@gmail.com> wrote: >>> >>>> I've attempted to combine cortical and subcortical parcellations on a >>>> few occasions without any luck, I'm hoping someone here can help me out. >>>> >>>> #make some subcortical labels >>>> wb_command -cifti-create-label subcortical.dlabel.nii -volume >>>> Atlas_ROIs.2.nii.gz Atlas_ROIs.2.nii.gz >>>> >>>> #combine with cortical >>>> wb_command -cifti-create-dense-from-template >>>> 91282_Greyordinates.dscalar.nii TEST.dlabel.nii -cifti >>>> glasser_cort.dlabel.nii -cifti subcortical.dlabel.nii >>>> >>>> ... seg fault >>>> >>>> #try -cifti-merge-dense >>>> wb_command -cifti-merge-dense COLUMN TEST.dlabel.nii -cifti >>>> glasser_cort.dlabel.nii -cifti subcortical.dlabel.nii >>>> >>>> #check >>>> wb_command -file-information TEST.dlabel.nii >>>> >>>> ... everything looks ok.. >>>> >>>> #try to use it, look at the output after running through task pipeline >>>> wb_command -file-information subject_TEST.pscalar.nii >>>> >>>> And parcellations are incorrectly merged, exactly like described here: >>>> https://www.mail-archive.com/hcp-users@humanconnectome.org/m >>>> sg03217.html >>>> >>>> I also apparently created a dlabel file another way, I don't remember >>>> how, but the parcellations were incorrectly merged as above. I extracted >>>> the labels to text, manually edited the key values in vi and reimported >>>> them.. it looked ok then (dlabel.nii), however the output (pscalar.nii) >>>> again was incorrectly merged as above. >>>> >>>> Can anyone tell me how to do this? >>>> >>>> Thank you, >>>> Aaron >>>> >>> >>> ___ >>> 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] list of significant parcels
Dear HCP users, I would like to know which parcels survived thresholding (using wb_command -cifti-math on ptseries) - just a list of parcel names, e.g. L_p10p_ROI, L_p47r_ROI, L_TGv_ROI, AMYGDALA_LEFT, etc. I've converting to ROI, cifti-reduce, cifti-restrict-dense-map, etc. No luck. Is there any way to do this, besides clicking on everything in the GUI? Thanks, Aaron ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] list of significant parcels
Ah yes, of course. Thank you for the replies. Aaron On Thu, Jun 28, 2018 at 9:45 AM, Timothy Coalson wrote: > You can export the data from the parcellated cifti file with wb_command > -cifti-convert -to-text, but that doesn't contain the parcel names. The > -file-information command will tell you the parcel names, in the order they > are in the file, giving you the missing piece. > > Tim > > > On Thu, Jun 28, 2018, 8:37 AM Aaron R wrote: > >> Hi Matt, >> >> Thanks for the reply, but unfortunately wb_command -file-information >> doesn't help. It shows all of the parcels of the original parcellation. >> Presumably they're all still there, but some now have a zero value after >> thresholding. >> >> Thanks, >> Aaron >> >> >> On Wed, Jun 27, 2018 at 11:56 PM, Glasser, Matthew >> wrote: >> >>> wb_command -file-information might be able to help with this. >>> >>> Matt. >>> >>> From: on behalf of Aaron R < >>> aaro...@gmail.com> >>> Date: Wednesday, June 27, 2018 at 8:19 AM >>> To: "hcp-users@humanconnectome.org" >>> Subject: [HCP-Users] list of significant parcels >>> >>> Dear HCP users, >>> >>> I would like to know which parcels survived thresholding (using >>> wb_command -cifti-math on ptseries) - just a list of parcel names, e.g. >>> L_p10p_ROI, L_p47r_ROI, L_TGv_ROI, AMYGDALA_LEFT, etc. >>> >>> I've converting to ROI, cifti-reduce, cifti-restrict-dense-map, etc. No >>> luck. Is there any way to do this, besides clicking on everything in the >>> GUI? >>> >>> Thanks, >>> Aaron >>> >>> >>> >>> ___ >>> 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 mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] list of significant parcels
Hi Matt, Thanks for the reply, but unfortunately wb_command -file-information doesn't help. It shows all of the parcels of the original parcellation. Presumably they're all still there, but some now have a zero value after thresholding. Thanks, Aaron On Wed, Jun 27, 2018 at 11:56 PM, Glasser, Matthew wrote: > wb_command -file-information might be able to help with this. > > Matt. > > From: on behalf of Aaron R < > aaro...@gmail.com> > Date: Wednesday, June 27, 2018 at 8:19 AM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] list of significant parcels > > Dear HCP users, > > I would like to know which parcels survived thresholding (using wb_command > -cifti-math on ptseries) - just a list of parcel names, e.g. L_p10p_ROI, > L_p47r_ROI, L_TGv_ROI, AMYGDALA_LEFT, etc. > > I've converting to ROI, cifti-reduce, cifti-restrict-dense-map, etc. No > luck. Is there any way to do this, besides clicking on everything in the > GUI? > > Thanks, > Aaron > > > > ___ > 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] fix error, vn maps
Dear HCP users, I'm getting an error with fix 1.067, the cifti variance normalization field is not created. The file filtered_func_data_clean_vn.nii.gz is created however, and everything else is ok. In .fix.log, i see: The file '/usr/local/gifti/ciftisavereset.m' is not in the application's expanded CTF archive at '/home/aaron/.mcrCache8.3/fix_3_1'. This is typically caused by calls to ADDPATH in your startup.m or matlabrc.m files. Please see the compiler documentation and use the ISDEPLOYED function to ensure ADDPATH commands are not executed by deployed applications. Previously accessible file "/usr/local/gifti/ciftisavereset.m" is now inaccessible. Error in fix_3_clean (line 131) I'm using the compiled matlab option. Any ideas? Thanks in advance, Aaron ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] beta bias correction
Dear HCP Users, Regarding bias field correction of fMRI data, in Glasser et al. (Supplementary Methods For A Multi-modal Parcellation of Human Cerebral Cortex), it states: "The scaled [bias] field was used as a reference BOLD intensity image when computing bias free beta effect size maps" Was this done only on RS data, or also task HCP betas released? Where in the processing and how was this accomplished? I didn't find anything in the Pipelines. Thank you, Aaron ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] matlab cifti io
Dear HCP users, What's the current link for the matlab cifti i/o tools? The link in the readme here (and everywhere else) is dead: https://github.com/Washington-University/cifti-matlab Thanks, Aaron ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] tractography
hi HCP, we are trying to do tractography using FSL and HCP data. i have some questions -- i suspect they have been answered already, but couldn't find those answers: 1. is there a file containing the grayordinate coordinates in the diffusion space for a particular subject, both subcortical voxels and cortical vertices? 2. if i want to use some cortical and subcortical voxels from the list of grayordinates as targets, do i have to run probtrackx2 twice (i.e. once for the cortical surface vertices and once for the subcortical voxels), or can i run it just once? 3. where is the label file for the grayordinate vertices/voxels for a given subject? thanks in advance. -dh ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Resting fMRI Cortex Vertices Indices
Hi matt, One other thing. I understand that if you take the grayordinate locations of the vertices and apply the appropriate spatial transform, one gets the vertex locations in subject space, along with labels, so you have corresponding cortical points across subjects, with the same vertex having the same label across subjects. How does this work for the subcortical voxels? If you apply the same transform to the set of grayordinate voxel locations, you don't wind up with a consistent set across subjects. The points in subject space won't always be in different voxels. They can't be, because the volume of the subcortical structures varies across subjects. Is it possible to get a set of consistently labelled points in subcortical structures, or can this only be done at the level of subcortical structures (20 or so, rather than 30K, per subject)? -dh From: hcp-users-boun...@humanconnectome.org hcp-users-boun...@humanconnectome.org on behalf of Glasser, Matthew glass...@wusm.wustl.edu Sent: Sunday, May 31, 2015 11:51:41 AM To: Chao Liu; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Resting fMRI Cortex Vertices Indices Yes they are and they have correspondence across subjects. That is the point of being on standard meshes and a standard atlas set of subcortical voxels in the 2mm CIFTI grayordinates space. The reason that not all surface vertices are included is because the medial wall is not cortical grey matter. Peace, Matt. From: Chao Liu chao@brunel.ac.ukmailto:chao@brunel.ac.uk Date: Sunday, May 31, 2015 at 1:46 PM To: hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: [HCP-Users] Resting fMRI Cortex Vertices Indices Dear Experts, In resting state fMRI dtseries file, by using wb_command -file-information xxx.dtseries.nii, we could see: CortexLeft: 29696 out of 32492 vertices CortexRight: 29716 out of 32492 vertices ... And by using wb_command -nifti-information xxx.dtseries.nii -print-xml we could see: BrainModel IndexOffset=0 IndexCount=29696 BrainStructure=CIFTI_STRUCTURE_CORTEX_LEFT ModelType=CIFTI_MODEL_TYPE_SURFACE SurfaceNumberOfVertices=32492 VertexIndices0 1 2 3 4 5 6 8 9 10 11 12 13 14 15 16 17 18 19 20 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 ... which tells us which 29696 vertices (CortexLeft) out of 32492 are included. And for CortexRight, it tells which 29716 vertices out of 32492 are included. My question is are all the vertices indices in CortexLeft (29696) and CortexRight (29716) the SAME for all the subjects? Thank you very much for your time! Cheers, Chao ___ HCP-Users mailing list HCP-Users@humanconnectome.orgmailto: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
