Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

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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mri_mcsim update and FreeSurfer6
by Damien MARIE 28 Apr '17

28 Apr '17

I just read this statement : “ A newer version of mri_mcsim for linux can be obtained from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mri_mcsim.… <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mri_mcsim.…> Copy it to $FREESURFER_HOME/bin/mri_mcsim “ here: https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo <https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo> I am working with FreeSurfer6, should I update it or it was implemented in the version 6? Thank you and best, Damien MARIE

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Qdec 1.5
by Duy Nguyen 28 Apr '17

28 Apr '17

Dear FS Expert I am doing analysis from the group_analysis_tutorial data to practice and learn. However, I come across the error window like it shows on the attached picture (please see the attachment) when I press the button "Generate Stats Data Table." Please help me how can I can find the file aseg.volume.stats.dat. If the file does not exist, how can I create one? Thank you for your response. Any help would be appreciated!!! *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme(a)gmail.com <duy.nguyenbme(a)gmail.com>*

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Implement my own parcellation on aparc+aseg.mgz file
by Das S. 28 Apr '17

28 Apr '17

Hi I have create my own annot file and lookuptable for cortical parcellation. How I can implement my own parcellation in aparc+aseg.mgz file. I am also stuck on how to update the FreeSurferColorLUT.txt file? Please help. Thanks Sarbani

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debug mri_aparc2aseg
by Das S. 28 Apr '17

28 Apr '17

Hi I need to debug the issue I am facing at the moment. So I want to run the program with GDB. I could run it with gdb but no debug information/symbol is present in the current installed form. So I guess I need to recompile the mri_aparc2aseg program with in debug mode. Can you please help me in that? What is the easiest way to recompile with the debug symbols so that I can put a breakpoint in GDB? Also, if there any option to activate more logs/log levels? Thanks a lot for your help. Much appreciated. Regards, Sarbani

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Skull stripping
by John Anderson 28 Apr '17

28 Apr '17

Dear FS experts, I want to inquire if there are any threshold for the flag "gcut " in the command: recon-all -skullstrip -clean-bm -gcut -subjid <subject name> If this not available are there any tools that can help to control how much dura will be cut out Thanks in advance! John

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R: Re: Questions on fsdg file using complex study design
by stdp82＠virgilio.it 27 Apr '17

27 Apr '17

Thanks. I do not know if in the previous mail we well described our case. I repropose my question in more explicative way. In a first step we want assess the differences between 4 groups, considering a single structure (eg. right ROI). We have 4 groups (e.g. Young, Older, MCI, AD). This case is similar to the example reported on the site for Three Groups (One Factor/Three Levels), No Covariates. There you have put Older (OA), MCI, AD. Here we aim at add an other group which is Young (YA). Please could you show me the possible combination of mtx.files? Especially of group.effect and YA-OA+mci-ad.mtx? In the second step we would evaluate the differences between 4 groups in more complex design, including more than a single structure (e.g. right and left ROI1, right and left ROI2, right and left ROI3, right and left ROI4). Many thanks Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 27-apr-2017 17.40 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] Questions on fsdg file using complex study design > > > >On 04/27/2017 09:02 AM, stdp82(a)virgilio.it wrote: >> Dear list, >> >> we have several difficulty to understand how I should build fsdg file >> and we are worried to produce correct results. >> >> On FS site, it is not available an example if we would look for >> differences among 4 different groups (A, B, C, D; 4 Groups - One >> Factor/Three Levels - No Covariates). >> The proposed design with 2 levels and 2 factors is no helpful in our case. >Mathematically, it is the same. >> >> We have 4 groups (1 factor and 4 levels, no covariates) and we our >> hypothesis (in term of impaiment) is A<B<C<D. >This is not a valid linear contrast since it requires an AND operation >(A<B AND B<C AND C<D). You have to use a conjunction analysis in which >you create 3 contrasts then conjunct them (with mri_concat --conjunct) >> >> Which should be the group.effect.mtx? >> How should we look to difference between Group1, Group2, Group3 and >> Group4? >> Should we opt for G1+G3 vs G2+G4 or G1+G2 vs G3+G4? Other option? >> >> Please may you argue a rationale? >> >> e.g. Looking your example on three Groups (One Factor/Three Levels), >> No Covariates, we wonder why if Normals==MCI AND Normals==AD, then it >> MUST be the case that MCI==AD? >> >> We aim at assess differences by using more complex design (4x2x4), >> including >> 4 different structures, looking at right and left structures and >> having 4 levels (4 different groups). >> >> How should we do, please? >> >> Thank you very much. >> >> Best regards >> >> Stefano >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom it is >addressed. If you believe this e-mail was sent to you in error and the e-mail >contains patient information, please contact the Partners Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in error >but does not contain patient information, please contact the sender and properly >dispose of the e-mail. > >

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Freesurfer April 2017