Freesurfer

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30132 discussions

Hippo-subfiled Need Help
by Ramesh Babu 01 May '17

01 May '17

Dear Experts, I ave done hippocampal subfield segmentation by using 1x1x1 t1 scan. Please see the attached image and give your suggestions. It took nearly 7 hrs 10 min. to complete hippo-subfield segmentation for one scan by using the command recon-all -i grp205_t1.nii -s grp205 -sd grp205 -all Started at Wed Apr 26 11:03:34 IST 2017 Ended at Wed Apr 26 17:17:35 IST 2017 #@#%# recon-all-run-time-hours 6.234 recon-all -s grp205 finished without error at Wed Apr 26 17:17:35 IST 2017 done Then for hipposubfield, recon-all -s grp205 -sd grp205 -hippocampal-subfields-T1 I want to run for 40 scans grp-1 20 scans and grp-2 20 scans. How to modify in the command. Since it is taking long time I want to run 10 scans n give rest again 10 scans. Can I do so? I am15.6 GiB ram, Intel® Core™ i7-4790 CPU @ 3.60GHz × 8 processor, GeForce GT 610/PCIe/SSE2 graphic card.It is octa core processor. Can I run 8 analysis simultaneously (in 8 separate terminal?). Your suggestion will be helpful to me to proceed further. Thanks RB

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Re: [Freesurfer] recon-all with error (mris_curvature -w lh.white.preaparc)
by Antonin Skoch 30 Apr '17

30 Apr '17

Dear fwd9707, see these threads: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52560.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html Antonin Skoch Dear all I performed the recon all in virtualbox (with centos 7), and there error and can not continue,the error information is that :#@# Curv .H and .K lh Sat Apr 29 21:06:24 CST 2017 /media/sf_VM_ShareFolders/Freesurfer_results/Sub_001/surf mris_curvature -w lh.white.preaparc total integrated curvature = 2.136*4pi (26.843) --> -1 handles ICI = 184.8, FI = 2061.6, variation=32051.104 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Sub_001 exited with ERRORS at Sat Apr 29 21:06:26 CST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting need your help ,thank you very much

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recon-all with error (mris_curvature -w lh.white.preaparc)
by fwd9707＠sina.com 30 Apr '17

30 Apr '17

Dear all I performed the recon all in virtualbox (with centos 7), and there error and can not continue,the error information is that :#@# Curv .H and .K lh Sat Apr 29 21:06:24 CST 2017 /media/sf_VM_ShareFolders/Freesurfer_results/Sub_001/surf mris_curvature -w lh.white.preaparc total integrated curvature = 2.136*4pi (26.843) --> -1 handles ICI = 184.8, FI = 2061.6, variation=32051.104 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Sub_001 exited with ERRORS at Sat Apr 29 21:06:26 CST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting need your help ,thank you very much

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perform group analysis on user defined maps
by Ladan Shahshahani 29 Apr '17

29 Apr '17

Dear experts, I have preprocessed my functional data using FSFAST. I have calculated an index for each of my ROIs' vertices in matlab, and then created a map for each hemisphere and subcortical regions using MRIwrite. I want to perform group analysis on these maps. I also want to apply cluster-wise multiple comparison correction. Since I have not defined an analysis using mkanalysis-sess, I do not know how to use isxconcat-sess and mri_glmfit. How should I perform this analysis? Bests, Ladan

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FS-Fast's 'subject to fsaverage' registration files?
by Patrycja Naumczyk 29 Apr '17

29 Apr '17

Hello FS experts, I have a question regarding FS-Fast processing. I have performed (successfully!) an FS-Fast single subject analysis. The results look fine in the fsaverage space, but I'm interested in viewing them in the subject space. Are the registration files used along the processing pipeline (EPI->T1->fsaverage) stored anywhere (so far I only found the EPI->T1 and T1->talairach files), so I can use them? Or do I need to create new registration files (bbregister/tkregister2)? Best regards, Patrycja

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How to get SUVR images with cerebellar GM reference?
by Shane Schofield 29 Apr '17

29 Apr '17

Hello PetSurfer and Freesurfer Developers, I am using PetSurfer to obtain PVC SUVR images . I have already used mri_concat to derive the mean images over three acquisitions (template image). After gtmseg amd mri_coreg, I want to get the SUVR map with whole cerebellum as the reference (instead of the pons). How could this be done? What can I modify in mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output to achieve this goal? Thank you.

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Re: [Freesurfer] TRACULA anterior/posterior
by Funk, Quentin 28 Apr '17

28 Apr '17

Anastasia- This is super helpful! Thank you! I wrote a script to do exactly this and got something close (or exactly) to what I'm looking for, I think. However, there are very few voxels in the voxelwise file--I traced them out and they're essentially the hottest voxels stored in path.pd.nii--it seems like I'm missing a large part of the probabalistic tract by doing this. Maybe I'm a bit confused as to what exactly I'm doing. -qf Message: 8 Date: Thu, 27 Apr 2017 20:21:29 +0000 From: "Yendiki, Anastasia" <AYENDIKI(a)mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA anterior/posterior {Disarmed} To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <AF49D39E2A7A3142903EC64E43DC0FAB889289ED(a)PHSX10MB10.partners.org> Content-Type: text/plain; charset="windows-1252" Hi Quentin - Yes, this is possible! You can use the info in the pathstats.byvoxel.txt files to do that. The -stat step of TRACULA (see last part of tutorial) will put together all the point-wise, along-the-tract stats of all the subjects into a table. Each element in the table will be one position along the tract for one subject. You can then average, say, the FA values from the first 1/3 of the positions and the last 1/3 of the positions, or something like that, to get the two endings of the tract that you care about. Hope this helps, a.y ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Funk, Quentin [qfunk(a)houstonmethodist.org] Sent: Thursday, April 27, 2017 11:24 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA anterior/posterior Freesurfer experts: I'm interested in comparing anterior and posterior pieces of a tract generated by TRACULA. Ideally, I'd like to take the probabilistic map (i.e. the path.pd.nii.gz from one of the folders in SUBJECT/dpath) and obtain a "posterior part" and an "anterior part" by masking. Then I'd like to extract stats similar to the stats found in pathstats.overall.txt Is this at all possible? I can produce the poster/anterior mask by hand for each individual subject, (although if there were an automated way to do this that I'm unaware of it would be great) but getting the stats out is something I can't quite figure out from the tutorials I've looked through. Thanks for any help! Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Using multiple MEMPRAGE scans as input to recon-all: which echos to use for dura correction?
by Jared Saletin 28 Apr '17

28 Apr '17

Hi Freesurfer Experts! I have two scans for each subject in a new experiment—taken on subsequent days, each using the MEMPRAGE protocol. I’ve successfully implemented DURA correction using the 4 echos when I’ve reconstructed each scan separately. However, since I have 2 scans for each subject, I was thinking rather than reconstruct the brain twice and average the thickness measurements, it would be better to feed both MEMPRAGE scans to recon-all. My question is if I do this, which echos should I use for Dura correction: day 1 or day 2 or is there a way to combine them into an average? Is this (feeding both days’ scans to recon-all) a reasonable strategy, or am I better to reconstruct the data separately? Thanks so much! Jared

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the voxel in apar+aseg.mgh does not showing value from my parcellation table
by Das S. 28 Apr '17

28 Apr '17

Dear Freesurfer Developer, I am using freesurfer to create a equal zone parcellation on cortical surface. I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done. Here are steps that I have followed: 1. Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........ 2. Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere. mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/left Content of ColorLUT.txt 801 node-lh-1 70 130 180 0 802 node-lh-2 245 245 245 0 803 node-lh-3 205 62 78 0..... 3. Then I am using the mris_ca_train to create the .gcs file. mris_ca_train -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs mris_ca_train -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs 4. then I am following the recon-all steps and call the mris_ca_label command as below: mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs 100307/label/rh.aparc.annot mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs 100307/label/lh.aparc.annot 5. Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307 I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated. Thanks Sarbani Das

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Re: [Freesurfer] Freesurfer Digest, Vol 158, Issue 53
by Xenia Kobeleva 28 Apr '17

28 Apr '17

help ________________________________ Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Gesendet: Donnerstag, 27. April 2017 19:24:57 An: freesurfer(a)nmr.mgh.harvard.edu Betreff: Freesurfer Digest, Vol 158, Issue 53 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Last weeks to register for HCP Course 2017 (Jennifer Elam) 2. the voxel in apar+aseg.mgh does not showing value from my parcellation table (Das S.) ---------------------------------------------------------------------- Message: 1 Date: Thu, 27 Apr 2017 12:16:42 -0500 From: Jennifer Elam <elam4hcp(a)gmail.com> Subject: [Freesurfer] Last weeks to register for HCP Course 2017 To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAJbMWh5GQ8zLtDdWHcnd2b=FvWbFMKteReS2YxiFvk3MGfu7Ow(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" It's not too late to register for the 2017 HCP Course: "Exploring the Human Connectome" <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstore.huma…>, to be held June 19-23 at the Djavad Mowafagian Centre for Brain Health at University of British Columbia (UBC) in Vancouver, BC, Canada! FreeSurfer is a major part of the HCP structural processing pipeline and has been critical to the processing of the project's over 1100 released high quality imaging datasets. Spaces for the course are limited and registration is on a first come, first served basis. May 17, 2017 is the deadline to reserve discounted UBC accommodations within walking distance to the course venue: https://reserve.ubcconferences.com/vancouver/availability.asp?hotelCode=%2A… The 5-day intensive HCP course is a great opportunity to learn directly from HCP investigators and designed for those interested in: - using data collected and distributed from the HCP young adult study - acquiring and analyzing HCP-style imaging and behavioral data at your own institution - processing your own non-HCP data using HCP pipelines and methods - using Connectome Workbench tools and sharing data using the BALSA imaging database - learning HCP multimodal neuroimaging analysis methods, including those that combine MEG and MRI data - exploring the HCP MMP 1.0 multimodal parcellation brain map and learning about how it can be used in your analyses - positioning yourself to capitalize on HCP-style data being distributed by the Connectome Coordinating Facility (CCF) from HCP development (healthy subjects ages 5-21) and aging (healthy subjects ages 35-90+) and Connectomes Related to Human Disease projects See https://store.humanconnectome.org/courses/2017/exploring-the-human-connecto… for more info. If you have any questions, please contact us at: hcpcourse(a)humanconnectome.org We look forward to seeing you in Vancouver! Best, 2017 HCP Course Staff

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