Hi Jenn, Thanks for your advice about the structural extended preprocessed data packages. Precisely what we needed. Is this data available as part of Connectome in a Box? i.e., Can we request this data to be included when we order a copy of the 900 subjects release?
Thank you, Simon On 16 November 2015 at 11:09, Jennifer Elam <[email protected]> wrote: > Hi Simon, > > The HCP Structural Extended Preprocessed packages for each subject > (available from the Download packages page with the Processing level filter > set to Preprocessed) includes the FreeSurfer v5.3.0-HCP output directory > created by the HCP Structural pipeline. These are intermediate files that > are not in NIFTI/GIFTI/CIFTI format. > > > > Best, > > Jenn > > > > Jennifer Elam, Ph.D. > Outreach Coordinator, Human Connectome Project > Washington University School of Medicine > Department of Anatomy and Neurobiology, Box 8108 > 660 South Euclid Avenue > St. Louis, MO 63110 > 314-362-9387 > [email protected] > www.humanconnectome.org > > > > *From:* [email protected] [mailto: > [email protected]] *On Behalf Of *Simon Baker > *Sent:* Sunday, November 15, 2015 5:41 PM > *To:* [email protected] > > *Subject:* Re: [HCP-Users] Custom parcellation for HCP data > > > > Thanks for your email Matt. > > > > Do you happen to know the names of those packages? > > > > Given that our custom parcellation is in the form of an annotation file > (rather than a gifti file), can you suggest a way to get our custom > parcellation from an atlas surface to a subject's volume using Connectome > Workbench? > > > > Alternatively, is there a way to generate a custom parcellation using > Connectome Workbench? > > > > Simon > > > > > > On 12 November 2015 at 03:33, Glasser, Matthew <[email protected]> wrote: > > I think this might be way more complicated than is needed. I believe > there are structural extended packages that would allow you to run a > FreeSurfer command without needing to replicate FreeSurfer files. As for > how to get a parcellation from an atlas surface to a subject’s volume, I > could tell you how to do that using Connectome Workbench tools, file > formats, and our atlas, but I don’t know the details for FreeSurfer. > > > > Peace, > > > > Matt. > > > > *From: *Simon Baker <[email protected]> > *Date: *Tuesday, November 10, 2015 at 11:34 PM > *To: *"[email protected]" <[email protected]> > *Cc: *"Harms, Michael" <[email protected]>, Timothy Coalson <[email protected]>, > Matt Glasser <[email protected]> > > > *Subject: *Re: [HCP-Users] Custom parcellation for HCP data > > > > Thanks for the pointers Michael, Tim, and Matt. We've tried a range of > approaches but we're still having trouble creating the custom parcellation. > Below describes the updated version of our pipeline. Although this version > improves the spatial alignment between the custom parcellation and the T1w > volume, the quality of the parcellation is still lacking compared to e.g. > ribbon.nii.gz. > > > > -- > > > > 1. Create a high-resolution annotation (parcellation) by randomly > parcellating the fsaverage surface into N regions of approximately equal > volume. > > > > 2. Map the annotation from the source subject (fsaverage) to the target > subject using mri_surf2surf. > > > > mri_surf2surf --srcsubject fsaverage --hemi xh --sval-annot highres.annot > --trgsubject ${SUBJECTID} --srcsurfreg sphere.reg --trgsurfreg > /MNINonLinear/Native/${SUBJECTID}.X.sphere.native.surf.gii --tval > xh.highres.annot > > > > 3. Obtain vertices and faces data from > /MNINonLinear/Native/${SUBJECTID}.X.white.native.surf.gii > > > > 4. Using the vertices and faces data obtained in step 3 as inputs for the > write_surf Matlab function, create the xh.white surface file. > > > > 5. Obtain thickness data from > /MNINonLinear/Native/${SUBJECTID}.X.thickness.native.shape.gii > > > > 6. Using T1wImage = /T1w/T1w_acpc_dc_restore.nii.gz and T1wImageBrain = > /T1w/T1w_acpc_dc_restore_brain.nii.gz, we replicate some of the steps found > in HCP's FreeSurferPipeline.sh in order to generate /mri/orig.mgz. > Specifically: > > > > #Make Spline Interpolated Downsample to 1mm > > Mean=`fslstats T1wImageBrain -M` > > > > flirt -interp spline -in T1wImage -ref T1wImage -applyisoxfm 1 -out > T1wImage_1mm > > > > applywarp --rel --interp=spline -i T1wImage -r T1wImage_1mm > --premat=/usr/local/fsl/etc/flirtsch/ident.mat -o T1wImage_1mm > > > > applywarp --rel --interp=nn -i T1wImageBrain -r T1wImage_1mm > --premat=/usr/local/fsl/etc/flirtsch/ident.mat -o T1wImageBrain_1mm > > > > fslmaths T1wImage_1mm -div $Mean -mul 150 -abs T1wImage_1mm > > > > mri_convert T1wImage_1mm /mri/orig/001.mgz > > > > #Initial Recon-all Steps > > recon-all -subjid ${SUBJECTID} -sd ${SUBJECTS_DIR} -motioncor -talairach > -nuintensitycor -normalization > > > > 7. Convert the custom parcellation annotation into a custom parcellation > volume using mri_label2vol, with /mri/orig.mgz serving as the output > template volume. > > > > mri_label2vol --annot xh.custom.annot --temp /mri/orig.mgz --identity > --proj frac 0 1 .1 --subject ${SUBJECTID} --hemi xh --o xh_custom_vol.mgz > > > > 8. Resample and reslice the custom parcellation volume. > > > > mri_convert --resample_type nearest --reslice_like T1wImage > xh_custom_vol.mgz xh_custom_vol.nii > > > > 9. Combine the resampled and resliced custom parcellation volume from each > hemisphere to create a single custom parcellation volume (custom_vol.nii). > > > > 10. Find c_ras offset and generate matrix > > > > MatrixX=$(mri_info --cras T1wImage | cut -d " " -f 1) > > MatrixY=$(mri_info --cras T1wImage | cut -d " " -f 2) > > MatrixZ=$(mri_info --cras T1wImage | cut -d " " -f 3) > > echo "1 0 0 ""$MatrixX" > c_ras_xfm.mat > > echo "0 1 0 ""$MatrixY" >> c_ras_xfm.mat > > echo "0 0 1 ""$MatrixZ" >> c_ras_xfm.mat > > echo "0 0 0 1" >> c_ras_xfm.mat > > > > 11. Invert the c_ras offset matrix > > > > convert_xfm -omat c_ras_xfm_inv.mat -inverse c_ras_xfm.mat > > > > 12. Apply the inverted c_ras offset matrix to the custom parcellation > volume (custom_vol.nii) > > > > flirt -in custom_vol.nii -applyxfm -init c_ras_xfm_inv.mat -out > parcellation.nii -paddingsize 0.0 -interp nearestneighbour -ref T1wImage > > > > 13. [Not sure why, but then we had to] Warp the output from the previous > step in order to align the parcellation with T1wImage (i.e., > /T1w/T1w_acpc_dc_restore.nii.gz). > > > > applywarp --rel --interp=nn -i parcellation.nii -r T1wImage -w > /MNINonLinear/xfms/standard2acpc_dc.nii.gz -o parcellation_native.nii > > > > 14. See attached screenshot2.jpeg showing /T1w/T1w_acpc_dc_restore, > /T1w/ribbon (blue), and parcellation_native (yellow). > > > > -- > > > > The alignment of parcellation_native is a bit off and it appears to be > grainy/pixelated. Do you have any suggestions as to why this is the case? > > > > Kind regards, > > > > Simon Baker > > Brain & Mental Health Laboratory > > Institute of Cognitive & Clinical Neuroscience > > Monash University > > > > > > On 20 October 2015 at 09:20, Glasser, Matthew <[email protected]> wrote: > > FreeSurfer might do it if you simply specify the correct extension, but if > not, mris_convert will do the conversion. > > > > Peace, > > > > Matt. > > > > *From: *<[email protected]> on behalf of Timothy > Coalson <[email protected]> > *Date: *Monday, October 19, 2015 at 4:44 PM > *To: *"Harms, Michael" <[email protected]> > *Cc: *"[email protected]" <[email protected]>, > Simon Baker <[email protected]> > *Subject: *Re: [HCP-Users] Custom parcellation for HCP data > > > > Additionally, if you generate a cortex-only parcellation, you shouldn't > need to put it into a volume to use it with the HCP CIFTI data. However, > I'm not sure how to get freesurfer to write GIFTI label files, and unless > you generate it on the fs_LR 32k mesh, you'll need to resample it (via > registered sphere surfaces). If you can get the label data into matlab, > though, you can write it as .func.gii files, and use wb_command to turn it > into label.gii, and then to .dlabel.nii for use with CIFTI data. Some care > may be needed to keep the right and left labels separate. > > > > Tim > > > > > > On Mon, Oct 19, 2015 at 10:08 AM, Harms, Michael <[email protected]> wrote: > > > > Hi, > > Did you see this recent thread on the list: > > http://www.mail-archive.com/hcp-users%40humanconnectome.org/msg01910.html > > > > 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. Tel: 314-747-6173 > > St. Louis, MO 63110 Email: [email protected] > > > > *From: *Simon Baker <[email protected]> > *Date: *Sunday, October 18, 2015 8:16 PM > *To: *"[email protected]" <[email protected]> > *Subject: *[HCP-Users] Custom parcellation for HCP data > > > > Hi all, > > > > We want to create a custom parcellation for use with the connectome > project data. However, we have not been able to achieve accurate spatial > alignment between the random parcellation volume and the T1w volume. > Specifically, there appears to be an "offset," possibly due to a mismatch > between the origin of these volumes. In the following we describe the > relevant steps of our pipeline. Please suggest any changes that might help > to resolve the issue. > > > > 1. Create a high-resolution annotation (parcellation) by randomly > parcellating the fsaverage surface into N regions of approximately equal > volume. > > > > 2. Map the annotation from the source subject (fsaverage) to the target > subject using mri_surf2surf. > > > > mri_surf2surf --srcsubject fsaverage --hemi lh --sval-annot highres.annot > --trgsubject ${SUBJECTID} --srcsurfreg sphere.reg --trgsurfreg > ${SUBJECTS_DIR}/${SUBJECTID}/MNINonLinear/Native/${SUBJECTID}.L.sphere.native.surf.gii > --tval lh.highres.annot > > > > [repeat for rh] > > > > 3. Obtain vertices and faces data from > ${SUBJECTS_DIR}/${SUBJECTID}/MNINonLinear/Native/${SUBJECTID}.L.white.native.surf.gii > > > > [repeat for rh] > > > > 4. Using the vertices and faces data obtained in step 3 as inputs for the > write_surf Matlab function, create the lh.white surface file. > > > > [repeat for rh] > > > > 5. Obtain thickness data from > ${SUBJECTS_DIR}/${SUBJECTID}/MNINonLinear/Native/${SUBJECTID}.L.thickness.native.shape.gii > > > > [repeat for rh] > > > > 6. Convert the annotation into a volume using mri_label2vol. > > > > mri_label2vol --annot lh.highres.annot --temp > ${SUBJECTS_DIR}/${SUBJECTID}/T1w/T1w_acpc_dc_restore.nii.gz --identity > --proj frac 0 1 .1 --subject ${SUBJECTID} --hemi lh --o vol_lh.nii > > > > [repeat for rh] > > > > 7. Configure the volume (remove unwanted ROIs). > > > > [repeat for rh] > > > > 8. Combine the configured volumes from each hemisphere to create the > random parcellation volume. > > > > 9. Overlay the random parcellation volume on the template volume. > > > > See attached screenshot.jpeg showing the misalignment between the random > parcellation volume and the template volume. > > > > Kind regards, > > > > Simon Baker > > Brain & Mental Health Laboratory > > Institute of Cognitive & Clinical Neuroscience > > Monash University > > > > _______________________________________________ > HCP-Users mailing list > [email protected] > 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. 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