Freesurfer August 2016

freesurfer@nmr.mgh.harvard.edu

127 participants
198 discussions

September FreeSurfer Course in Boston Registration open
by Allison Moreau 05 Aug '16

05 Aug '16

The FreeSurfer group is offering a four-day FreeSurfer Tutorial and Workshop September 26th to 29th, 2016 at the Martinos Center in Charlestown, MA. You can register for the course on our course website: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription Details about the content of the course, the location, registration fees, accepted payment types, and nearby hotels is currently on the website above. Please read the above page in its entirety before registering and before sending questions. If you are not one of the first 50 to register, you will be put on a waiting list and will be notified if a spot becomes available. *Do not submit a payment or make travel arrangements until you have received an email confirmation that you successfully secured a seat in the course. *NOTE- We will hold the course even if 40 students are not registered, so you can make travel arrangements once you have received an email confirmation. -- Allison Moreau Research Technologist Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital

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Problems with QDEC
by Vikas Bandalli 05 Aug '16

05 Aug '16

Dear Freesurfers, Sorry if the question sounds too basic. 1. I am running an analysis on qdec with paired groups - normal and patients, To control for IntraCranialVolume(ICV),I am adding it as an 'nuisance factor',Is it correct? The suggested mode to add ICV to the tabled was to *demean* the ICV. But when I subtract the mean values from individual subject ICV values,I noticed that some of the subjects have a negative demeaned ICV value. My question is - How should I proceed to include the data,ignore the negative sign(because I thought a negative ICV makes no sense) and just keep the values or retain the numbers with the sign. Please correct me if I am going wrong in any of the steps. However,I ran two analysis - one with the sign retained and other with sign removed ,I noticed that both have very different results. 2. If I want to see the effect due to lithium within the patient group (Between patients with and without psychosis) how should I design the matrix in GUI. I designed the following format Fixed factor :- Diagnosis - Psychotic-pt Non-Psychotic-pt Co-variate :- Lithium use :- 1 - lithium user 0 - non user Nuisance factor :- ICV Is this design correct? If not how should I construct it ? Also what query would contain the result for anticipated question My intention is to control for Diagnosis and then see effect/change due to lithium use. Thank you very much -- Vikas B. R. Medical student Bangalore Medical College and Research Institute (BMCRI), Bangalore,India, Ph : +918904286825

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Re: [Freesurfer] Freesurfer Digest, Vol 150, Issue 6
by Caroline Beelen 05 Aug '16

05 Aug '16

My command line is: mris_label2annot --subject fsaverage --hemi lh --ctab aparc.annot.ctab --annot myaparc --l lh.fusiform.label --l lh.inferiorparietal.label (etc.) --nhits nhits.mgh (I have version 5.3) Regards, Caroline Message: 3 Date: Wed, 3 Aug 2016 09:30:48 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mapping error To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <f3f77469-16ad-6fdf-f647-80aee162dbfc(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" what is your command line? On 8/3/16 6:00 AM, Caroline Beelen wrote: > > Dear FS, > > An aparc.annot ctab file was created but I got the following error: > > Colortable:aparc.annot.ctab > > Annotname: myaparc > > Nhitsfile nhits.mgh > > Nlabels 6 > > Labeltresh 0 0.00000 > > Loading freesurfer/fsaverage/surf/lh.orig > > 1 -1 not found > > 2 -1 not found > > 3 -1 not found > > Etc? > > Mapping unhit to unknown > > Found 132101 unhit vertices > > Writing annot to freesurfer/fsaverage/lh.myaparc.annot > > I guess my ctab file is incorrect? I included an example of a label > with it. > > Thanks again for your help. > > Caroline > > -----Oorspronkelijk bericht----- Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens freesurfer-request(a)nmr.mgh.harvard.edu Verzonden: woensdag 3 augustus 2016 18:00 Aan: freesurfer(a)nmr.mgh.harvard.edu Onderwerp: Freesurfer Digest, Vol 150, Issue 6 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. Re: brain mask and T1 are not the same size (Isabelle Deschamps) 2. Re: Coordinates in TRACULA group analysis (Anri WATANABE) 3. Re: mapping error (Douglas Greve) 4. Re: Multiple Comparison Question for surface-based analyses (Douglas Greve) 5. Re: Coordinates in TRACULA group analysis (Anastasia Yendiki) 6. Re: brain mask and T1 are not the same size (Douglas N Greve) ---------------------------------------------------------------------- Message: 1 Date: Wed, 3 Aug 2016 10:50:30 +0000 From: Isabelle Deschamps <isabelle.deschamps.1(a)ulaval.ca> Subject: Re: [Freesurfer] brain mask and T1 are not the same size To: "<freesurfer(a)nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <8F31A8F6-59C6-4D12-A2A4-2EF526465775(a)ulaval.ca> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/f… ------------------------------ Message: 2 Date: Wed, 3 Aug 2016 20:19:09 +0900 From: Anri WATANABE <z2aanri(a)koto.kpu-m.ac.jp> Subject: Re: [Freesurfer] Coordinates in TRACULA group analysis To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAAw-JJEAwC33OaX6oaMeuEcT3q06Ah8ZYfD6NuuO32bn-eHgNA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Anastasia, Thank you for your kind explanation. I can be understanding how TRACULA tracts white matter pathways. At each position (in training subjects, not in new subjects of my data) probability that next goes for which direction to every labels in the aparc+aseg (not with setting a certain ROI) is computed with use of training subjects. The prior probabilities are made from training subjects (your publication in 2011) and they are based on manual labeling (the manual labeling tracts are referred to Wakana et al. 2007). Then when white matter pathways are reconstructed in my subjects, TRACULA computes anatomical priors in each subjects in my data in pre-processing and probability distributions from anatomical priors and by fitting ball-and-stick model. Is this comprehension ok? Best Regards, Anri ********************************************************************** ???????????? ???????? ?? ?? ********************************************************************** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ********************************************************************** 2016-07-31 22:49 GMT+09:00 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: > > Hi Anri - Instead of hard-coding some ROIs in the white matter that the > tract is forced to go through, TRACULA uses information like "what is the > probability that this tract goes lateral/anterior/etc to XXX", where XXX > any of the labels in the aparc+aseg. TRACULA computes these prior > probabilities from a set of training subjects, where the tracts have been > labeled manually. So it knows how likely a tract is to go through a certain > aparc+aseg label, or to he left, right, anterior, etc of a certain > aparc+aseg label. This is computed separately at each position along the > tract. It's computed from the training subjects, and then used when > reconstructing the tract in the new subject that you run TRACULA on. > > Hope this helps, > a.y > > On Sun, 31 Jul 2016, Anri WATANABE wrote: > > Thanks, AnastasiaI know that TRACULA use probabilistic tractography but if >> ROIs are not >> >> set how determine the origin and the end of a certain tract? I think that >> the first we >> have to determine the origin and the end of the tract, the second it >> constructs possible >> pathway not with the deterministic way (only 1 direction / 1 voxel) but >> with the >> probabilistic way (considering which direction should be next to). Is >> this comprehension >> wrong? >> Thank you. >> >> Anri >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University of Medicine >> ********************************************************************** >> >> 2016-07-31 13:22 GMT+09:00 Anastasia Yendiki < >> ayendiki(a)nmr.mgh.harvard.edu>: >> >> Hi Anri - TRACULA does not use deterministic ROIs. It uses a >> probabilistic >> model of how likely each tract is to go through or next to each of >> the labels >> of the freesurfer subcortical segmentation and cortical >> parcellation, as a >> function of position along the trajectory of the tract. >> >> Best, >> a.y >> >> On Sun, 31 Jul 2016, Anri WATANABE wrote: >> >> Hi Anastasia, >> Thank you! It seems work well!! >> I have another question. Are ROIs for automatic tractography >> in >> TRACULA the same ROIs >> presented in Wakana et al. 2007? >> >> Anri >> >> >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University of Medicine >> >> ********************************************************************** >> >> 2016-07-27 13:17 GMT+09:00 Anastasia Yendiki >> <ayendiki(a)nmr.mgh.harvard.edu>: >> >> Hi Anri - The problem is in this line: >> >> set cmd = ($cmd --ref $cvstempdir/$cvstemp) >> >> It should be changed to this: >> >> set cmd = ($cmd --ref >> $cvstempdir/$cvstemp/mri/norm.mgz) >> >> For this to take effect, you need to run "which >> trac-all" >> and make the change in >> the trac-all file that the which commands shows you. >> >> Hope this helps, >> >> a.y >> >> On Fri, 15 Jul 2016, Anri WATANABE wrote: >> >> Hi, AnastasiaThis is trac-all.local-copy from 1 >> subject. Thank you! >> >> Anri >> >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University >> of >> Medicine >> >> >> ********************************************************************** >> >> 2016-07-13 6:16 GMT+09:00 Anastasia Yendiki >> <ayendiki(a)nmr.mgh.harvard.edu>: >> >> Hi Anri - This may be a bug that was fixed >> at >> some point. Can >> you send me the scripts/trac-all.local-copy >> from >> one of your >> subjects? Thanks! >> >> a.y >> >> On Mon, 11 Jul 2016, Anri WATANABE wrote: >> >> Hi Anastasia,There is an error in .log >> files of left >> corticospinal tract in cvs template >> and I >> attached >> one >> of file. In addition .log files of >> right >> corticospinal tract in cvs template >> doesn't exist. >> Thanks in advance. >> >> Anri >> >> >> >> >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> >> >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural >> University of >> Medicine >> >> >> >> ********************************************************************** >> >> 2016-07-07 20:12 GMT+09:00 Anastasia >> Yendiki >> <ayendiki(a)nmr.mgh.harvard.edu>: >> >> Hi Anri - Is there an error in >> the >> stats/*.log >> files for the different tracts? >> >> a.y >> >> On Tue, 5 Jul 2016, Anri >> WATANABE >> wrote: >> >> Dear Anastasia, >> >> I use TRACULA to obtain >> diffusion >> measures at each voxel in a certain >> pathway for >> group analysis, but >> there aren't >> stats/*.path.mean.txt >> files. I found .log files >> >> (<tract>_PP.avg33_mni_bbr.log) >> which >> exist >> 1 file per 1 tract, except >> corticospinal >> tract which has 2 .log files. >> >> Command: trac-all ?stat ?c >> >> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example >> >> Error log: Loading output >> reference >> volume from >> >> >> /Applications/freesurfer/subjects/cvs_avg35 >> >> corRead(): can't open file >> >> /Applications/freesurfer/subjects/cvs_avg35/COR-.info >> >> ERROR: Could not read >> >> /Applications/freesurfer/subjects/cvs_avg35 >> >> >> I attached dmrirc.example >> (configuration >> file) and >> <subjd>/scripts/trac-all.log. >> >> >> Thanks in advance, >> Anri >> >> >> >> >> >> >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> >> >> >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto >> Prefectural >> University of Medicine >> >> >> >> >> ********************************************************************** >> >> 2016-06-03 9:51 GMT+09:00 >> Anri >> WATANABE >> <z2aanri(a)koto.kpu-m.ac.jp>: >> Hi, Anastasia. >> There aren't any .log >> files >> but text >> files like >> lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. >> I guess text >> files complete all >> pathways >> and >> measures. >> >> >> >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> >> >> >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto >> Prefectural >> University of Medicine >> >> >> >> >> ********************************************************************** >> >> 2016-06-02 3:03 GMT+09:00 >> Anastasia >> Yendiki <ayendiki(a)nmr.mgh.harvard.edu >> >: >> >> Thanks, Anri. So the >> previous >> steps seem to have run fine. Are >> there any >> .log >> files >> created in the >> stats/ >> folder, >> which is created by trac-all -stat? >> >> On Wed, 1 Jun 2016, >> Anri >> WATANABE >> wrote: >> >> Hi >> Anastasia, This >> is a >> <subjid>/scripts/trac-all.log of one >> subject of >> the group. >> >> Thanks, >> Anri >> >> >> >> >> >> ********************************************************************** >> >> ???????????? >> ???????? >> ?? ?? >> >> >> >> >> ********************************************************************** >> Anri WATANABE, >> M.D. >> Department of >> Psychiatry, >> University >> Hospital, Kyoto >> Prefectural University of Medicine >> >> >> >> >> ********************************************************************** >> >> 2016-05-31 >> 22:55 >> GMT+09:00 >> Anastasia Yendiki >> >> <ayendiki(a)nmr.mgh.harvard.edu>: >> >> Hi Anri >> - >> Can you also >> send your log file >> (scripts/trac-all.log)? >> I'll need to >> see >> what >> exactly >> was >> running >> when the error occurred. Thanks! >> >> a.y >> >> On Sat, >> 28 >> May 2016, >> Anri WATANABE wrote: >> >> >> Hello >> Anastasia,sorry for few information >> and >> let me tell >> you >> command and >> >> error >> log. >> >> Command: trac-all ?stat ?c >> >> >> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example >> >> >> Error >> log: Loading output reference volume >> from >> >> >> /Applications/freesurfer/subjects/cvs_avg35 >> >> >> corRead(): can't >> open file >> >> >> /Applications/freesurfer/subjects/cvs_avg35/COR-.info >> >> >> ERROR: >> Could not >> read >> >> >> /Applications/freesurfer/subjects/cvs_avg35 >> >> >> >> dmrirc.example (configuration file) is >> attached to >> this >> e-mail. >> >> >> Thanks >> in >> advance, >> >> Anri >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> ???????????? >> >> ???????? >> ?? >> ?? >> >> >> >> >> >> ********************************************************************** >> >> Anri >> WATANABE, >> M.D. >> >> Department of >> Psychiatry, >> >> University >> Hospital, Kyoto Prefectural >> University of >> Medicine >> >> >> >> >> >> ********************************************************************** >> >> >> 2016-05-27 22:57 >> GMT+09:00 Anastasia Yendiki >> >> <ayendiki(a)nmr.mgh.harvard.edu>: >> >> >> >> Hi Anri - >> I do not know what command line you >> ran >> and >> what your >> >> configuration >> file looks like, so it is very >> >> >> hard for >> me to suggest solutions. >> >> >> >> Best, >> >> >> a.y >> >> >> >> On Fri, 27 >> May 2016, Anri WATANABE wrote: >> >> >> >> Hi >> Anastasia, >> >> >> >> Thank you for your answer. >> >> >> >> There aren't stats/*.path.mean.txt >> files and >> terminal says >> 'Could >> >> not >> read >> >> >> >> >> /Applications/freesurfer/subjects/cvs_avg35.' I >> >> >> >> checked >> >> >> /Application/freesurfer/subjects/cvs_avg35 >> folder >> and >> >> couldn't find >> COR-.info file. >> >> >> >> Could you tell me any resolutions, >> please? >> >> >> >> >> Thanks, >> >> >> Anri >> >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> >> >> ???????????? >> >> >> >> ???????? >> >> >> ?? >> ?? >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> >> Anri >> WATANABE, M.D. >> >> >> >> Department of Psychiatry, >> >> >> >> University Hospital, Kyoto Prefectural >> University >> of Medicine >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> >> >> >> 2016-05-21 6:48 GMT+09:00 Anastasia >> Yendiki >> >> <ayendiki(a)nmr.mgh.harvard.edu>: >> >> >> >> >> Hi Anri - The FA values are >> extracted in >> the native >> space >> of >> each subject, >> which is why >> >> >> >> those are the only >> >> >> >> coordinates that you see. If you >> want to >> display the >> >> results of your >> analysis on an average >> >> >> >> path, after >> >> >> >> running trac-all -stat, you can use >> the >> >> stats/*.path.mean.txt files (see also >> the >> last part >> >> >> of >> the TRACULA >> >> >> >> tutorial). >> >> >> >> >> Best, >> >> >> >> a.y >> >> >> >> >> On Wed, 18 May 2016, Anri WATANABE >> wrote: >> >> >> >> >> Dear experts, >> >> >> >> I use TRACULA to examine a >> measure >> (FA) at each >> voxel >> >> in one >> pathway. >> >> >> >> pathstats.byvoxel.txt files >> show >> coordinates in >> >> native >> space and >> after converting >> >> >> >> those the new >> >> >> >> files don't show any >> coordinates >> which are in >> MNI >> >> space. >> >> >> >> Could you tell me how can I >> know >> MNI >> coordinate >> >> values? >> >> >> >> >> Thank you! >> >> >> >> >> >> Regards, >> >> >> >> Anri >> >> >> >> >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> >> >> ???????????? >> >> >> >> ???????? >> >> >> >> ?? ?? >> >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> >> >> Anri WATANABE, M.D. >> >> >> >> Department of Psychiatry, >> >> >> >> University Hospital, Kyoto >> Prefectural >> University of >> >> Medicine >> >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> >> >> >> >> >> _______________________________________________ >> >> >> >> 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. >> >> >> >> >> >> >> _______________________________________________ >> >> 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 >> >> > ... > > [???????????] > _______________________________________________ > 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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Spearman correlation in FreeSurfer
by martina.papmeyer＠puk.unibe.ch 05 Aug '16

05 Aug '16

Dear FS experts I would like to examine associations between cortical thickness and sum scores of a scale (ordinal scale). Accordingly, I would need to conduct Spearman rather than Pearson correlation analyses. I found the following post to this email list, indicating that the GLM model in FS is basically a generalization of Pearson: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-January/009320.h… Since the post is from 2009, I would kindly like to ask if there is currently any way to conduct a Spearman correlation based analysis in FS or if there will be a way in the near future? Thank you very much for your kind help! All best wishes, Martina Psychiatric Services University of Bern (UPD) University Hospital of Psychiatry Division of Systems Neuroscience of Psychopathology Translational Research Center Dr. Martina Papmeyer, Postdoctoral Fellow Bolligenstr. 111, CH-3000 Bern 60 Tel: ++41 0(31) 930 9599, Fax: ++41 0(31) 930 9961 Mail: Martina.Papmeyer(a)puk.unibe.ch www.puk.unibe.ch

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Re: [Freesurfer] How does Optseq2 arrange order of conditions?
by 連志浩 05 Aug '16

05 Aug '16

Dear Douglas, Thanks for your explanation. These information are helpful to me. >I'm not sure what you mean. How can it be a delay if it is after the trial is over? I’m sorry for I didn’t describe my second question well. I think I can take another situation to describe my question. If I have a experiment that present stimulus until participants response, and I know the average RT of this experiment is 1500 ms after pilot test. In this situation, should I +/- the duration of jitter/null condition in terms of the duration of each stimulus? For example, if a part of sequence Optseq2 output is “ Con1 Null(500 ms) Con2 Null(1500 ms)”, and one of participants takes 1000 ms to response for Con1. Should I add 500 ms to the first Null? or I don’t need to anything? Thanks for your reading. Best Regards, Chih-Hao

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Error using LGI script despite making suggested changes to Matlab script.
by Sam Mathias 05 Aug '16

05 Aug '16

Dear all, I'm running into the following error when running "recon-all -s <subj-id> -lgi" using the latest version of FreeSurfer and Matlab R2016a: ERROR: make_roi_paths did not complete successfully! It seems like this is a common issue when using more recent versions of Matlab, so I editted the script as documented here: http://freesurfer.net/fswiki/ReleaseNotes?highlight=%28%28LGI%29%29 However, this did not fix my problem and I get the exact same error message. Any ideas? -- Samuel R. Mathias, Ph.D. Associate Research Scientist (ARS) Neurocognition, Neurocomputation and Neurogenetics (n3) Division Yale University School of Medicine 40 Temple Street, Room 694 New Haven CT 06511 http://www.srmathias.com

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recent problems with hippocampal subfield and brainstem modules
by Iglesias, Eugenio 05 Aug '16

05 Aug '16

Dear users, Many of you have recently experienced problems with the hippocampal subfield and brainstem substructure segmentation modules. These modules have been broken in the dev version for a couple of weeks. All the problems have now been fixed internally. The updates will be incorporated to the dev version on the website as soon as possible. So, if your subfield module is not working, just wait for a few days (I would say late next week, to be on the safe side), and try downloading the dev version again. On a happier note, we have added some new features to the modules: 1. They can now segment high resolution T1s that have been processed with recon-all -cm 2. There is now a longitudinal version of the hippocampal subfield segmentation module: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields based on our recent Neuroimage paper: “Bayesian longitudinal segmentation of hippocampal substructures in brain MRI using subject-specific atlases” Apologies to everyone for the inconvenience, and special thanks to our developer Zeke Kaufman for all the work. Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

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Re: [Freesurfer] brain mask and T1 are not the same size
by Isabelle Deschamps 04 Aug '16

04 Aug '16

> Can you try running simply > freeview -v > /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/brainmask.mgz Yes, so the original brainmask has the following dimensions (as before) mri_info /Users/Isabelle/Desktop/Tryout/brainmask.mgz Volume information for /Users/Isabelle/Desktop/Tryout/brainmask.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 > > Then save to a different file name using the "Save Volume As". Does that > file have the right dimensions? > The new brainmask saved under brainmask_resaved has the wrong dimensions: Volume information for /Users/Isabelle/Desktop/Tryout/brainmask_resaved.mgz type: MGH dimensions: 256 x 256 x 255 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -127.5, zend: 127.5 > Then make an edit and then "Save Volume". Does that file have the right > dims? > The brainmask_resaved once edited keeps the wrong dimensions: Volume information for /Users/Isabelle/Desktop/Tryout/brainmask_resaved.mgz type: MGH dimensions: 256 x 256 x 255 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -127.5, zend: 127.5 > It might be a mac thing; I've been working under linux I think it might be--however it is weird that only some participants were affected by this. I do not have access to computers running linux. Is there a way to solve this problem? I cannot exclude 4 participants. Thank you again for your help, Isabelle > On 4 Aug 2016, at 12:00, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > 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. Re: mri_normalize, 110 is too dark (tvg[fs]) > 2. Re: brain mask and T1 are not the same size (Douglas N Greve) > 3. Re: mri_label2label (Douglas N Greve) > 4. Re: Coordinates in TRACULA group analysis (Anri WATANABE) > 5. mri_label2label holes (Fred Dick) > 6. Re: Labels to MNI152, SPM compatible (Maty?? Kuhn) > 7. Re: mri_label2label holes (Douglas Greve) > 8. Re: mri_label2label holes (zkaufman(a)nmr.mgh.harvard.edu) > 9. Re: mri_label2label holes (Douglas Greve) > 10. Re: mri_label2label holes (Bruce Fischl) > 11. Re: mri_label2label holes (Bruce Fischl) > 12. Re: Labels to MNI152, SPM compatible (Thomas Yeo) > 13. Re: Poor automatic segmentation of the cerebellum (Bruce Fischl) > 14. Re: Flattening the surface (Younghoon Kim) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 3 Aug 2016 17:39:56 -0400 > From: "tvg[fs]" <tvg214+fs(a)nyu.edu> > Subject: Re: [Freesurfer] mri_normalize, 110 is too dark > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Cc: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CAMBOMk8jO5qBUHJ=MDnyRFUuG3G_18Ng_1aK+rOYTSoOceTs0w(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Bruce, > >> You can't just change which peak is the WM - lots of things downstream would fail > > That is unfortunate. > > I've send you the subject files and the raw files via filedrop (per > these instructions > https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange) > > > On Fri, Jul 29, 2016 at 4:38 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Tom >> >> it's tough for us to tell without some images or the data. If you upload the >> entire subject dir of a subject that failed we will take a look. You can't >> just change which peak is the WM - lots of things downstream would fail >> >> cheers >> Bruce >> >> >> >> On Fri, 29 Jul 2016, tvg[fs] wrote: >> >>> Dear community and developers, >>> >>> I am experiencing issues during the normalization step, converting >>> NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter >>> and high intensity WM is ignored. The resulting T1.mgz collapses the >>> wrong voxels into the 110 bin. >>> >>> It seems that what mri_normalize assumes a peak in the WM intensity >>> distribution that is too low. >>> In NU.mgz WM seems centered around 140 not 110. Note that this is not >>> due to RF-field inhomogeneities. It is likely of physiological origin >>> >>> - Is there a way to explicitly tell mri_normalize to use a different >>> intensity peak? >>> >>> I realize that correction can be done with control points, however I >>> understand that does not compute a new intensity distribution, but >>> merely adds voxels around CPs. This is undesirable since I have >20 >>> scans to process. Also this will not correct the falsely tagged GM >>> voxels. >>> >>> I've tried to trick mri_normalize by adjusting NU.mgz intensity by -30 >>> (140-30 = 110). This did not give me the wished-for effect. >>> - Is it possible to bypass preprocessing steps of mri_normalize before >>> collapsing? >>> >>> - In general it would help if there is some elaboration on the options: >>> -no1d, >>> -nosnr, >>> -gentle, >>> -f vs -fonly, >>> -prune, >>> -g, >>> -monkey >>> - is [-monkey] just shorthand for [-no1d -n 1]? >>> >>> Thanks, >>> Tom >>> >>> System: >>> Mac OS X 10.10.5 >>> freesurfer-Darwin-lion-stable-pub-v5.3.0 >>>> >>>> mri_normalize --version >>> >>> stable5 >>> _______________________________________________ >>> 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. >> > > > ------------------------------ > > Message: 2 > Date: Wed, 3 Aug 2016 17:40:57 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] brain mask and T1 are not the same size > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <57A264E9.7090207(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > Can you try running simply > freeview -v > /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/brainmask.mgz > > Then save to a different file name using the "Save Volume As". Does that > file have the right dimensions? > > Then make an edit and then "Save Volume". Does that file have the right > dims? > > It might be a mac thing; I've been working under linux > > > On 08/03/2016 01:05 PM, Isabelle Deschamps wrote: >> I am using an iMAC with mountain lion (10.8.5). I have this version of >> Freesurfer: freesurfer-Darwin-lion-stable-pub-v5.3.0 >> >> I open using a terminal Freeview: >> >> freeview -v >> /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/brainmask.mgz >> \ >> -f >> /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/surf/lh.white:edgecolor=yellow >> \ >> /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/surf/lh.pial:edgecolor=red >> \ >> /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/surf/rh.white:edgecolor=yellow >> \ >> /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/surf/rh.pial:edgecolor=red >> \ >> >> Then I follow these instructions >> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview) >> >> So basically, I look for areas where the skull or meninges are >> included within the pial boundary. >> >> I use the recon edit button, making sure that the brainmask is >> highlighted (see Screen shot attached). I use the default parameters >> as it has worked well for me in the past. When I am done editing the >> brainmask, I save the changes using the save volume button. Then I run >> the following command to regenerate the pial surface. >> >> recon-all -autorecon-pial -subjid S08_FS. >> >> Let me know if I can provide other information. I am puzzled as to why >> it worked for 3/4 of the participants but it won't work for 4 of them. >> >> Thank you again for the help, >> >> Isabelle >> >> >> Sorry, I did not see that one of the volumes was 256x256x255. I cannot >> replicate here on your data using 5.3 under linux. Can you say exactly >> what you do in freeview? Also, what version of FS are you using? And >> what platform? >> >> On 3 Aug 2016, at 12:00, <freesurfer-request(a)nmr.mgh.harvard.edu >> <mailto:freesurfer-request@nmr.mgh.harvard.edu>> >> wrote: >> >>> Send Freesurfer mailing list submissions to >>> freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@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 >>> <mailto:freesurfer-request@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. Re: brain mask and T1 are not the same size (Isabelle Deschamps) >>> 2. Re: Coordinates in TRACULA group analysis (Anri WATANABE) >>> 3. Re: mapping error (Douglas Greve) >>> 4. Re: Multiple Comparison Question for surface-based analyses >>> (Douglas Greve) >>> 5. Re: Coordinates in TRACULA group analysis (Anastasia Yendiki) >>> 6. Re: brain mask and T1 are not the same size (Douglas N Greve) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Wed, 3 Aug 2016 10:50:30 +0000 >>> From: Isabelle Deschamps <isabelle.deschamps.1(a)ulaval.ca> >>> Subject: Re: [Freesurfer] brain mask and T1 are not the same size >>> To: "<freesurfer(a)nmr.mgh.harvard.edu>" >>> <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <8F31A8F6-59C6-4D12-A2A4-2EF526465775(a)ulaval.ca> >>> Content-Type: text/plain; charset="us-ascii" >>> >>> An HTML attachment was scrubbed... >>> URL: >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/f… >>> >>> ------------------------------ >>> >>> Message: 2 >>> Date: Wed, 3 Aug 2016 20:19:09 +0900 >>> From: Anri WATANABE <z2aanri(a)koto.kpu-m.ac.jp> >>> Subject: Re: [Freesurfer] Coordinates in TRACULA group analysis >>> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: >>> <CAAw-JJEAwC33OaX6oaMeuEcT3q06Ah8ZYfD6NuuO32bn-eHgNA(a)mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi Anastasia, >>> >>> Thank you for your kind explanation. I can be understanding how TRACULA >>> tracts white matter pathways. >>> At each position (in training subjects, not in new subjects of my data) >>> probability that next goes for which direction to every labels in the >>> aparc+aseg (not with setting a certain ROI) is computed with use of >>> training subjects. The prior probabilities are made from training >>> subjects >>> (your publication in 2011) and they are based on manual labeling (the >>> manual labeling tracts are referred to Wakana et al. 2007). Then when >>> white >>> matter pathways are reconstructed in my subjects, TRACULA computes >>> anatomical priors in each subjects in my data in pre-processing and >>> probability distributions from anatomical priors and by fitting >>> ball-and-stick model. >>> Is this comprehension ok? >>> >>> Best Regards, >>> Anri >>> >>> >>> >>> ********************************************************************** >>> ???????????? >>> ???????? >>> ?? ?? >>> ********************************************************************** >>> Anri WATANABE, M.D. >>> Department of Psychiatry, >>> University Hospital, Kyoto Prefectural University of Medicine >>> ********************************************************************** >>> >>> 2016-07-31 22:49 GMT+09:00 Anastasia Yendiki >>> <ayendiki(a)nmr.mgh.harvard.edu>: >>> >>>> >>>> Hi Anri - Instead of hard-coding some ROIs in the white matter that the >>>> tract is forced to go through, TRACULA uses information like "what >>>> is the >>>> probability that this tract goes lateral/anterior/etc to XXX", where XXX >>>> any of the labels in the aparc+aseg. TRACULA computes these prior >>>> probabilities from a set of training subjects, where the tracts have >>>> been >>>> labeled manually. So it knows how likely a tract is to go through a >>>> certain >>>> aparc+aseg label, or to he left, right, anterior, etc of a certain >>>> aparc+aseg label. This is computed separately at each position along the >>>> tract. It's computed from the training subjects, and then used when >>>> reconstructing the tract in the new subject that you run TRACULA on. >>>> >>>> Hope this helps, >>>> a.y >>>> >>>> On Sun, 31 Jul 2016, Anri WATANABE wrote: >>>> >>>> Thanks, AnastasiaI know that TRACULA use probabilistic tractography >>>> but if >>>>> ROIs are not >>>>> >>>>> set how determine the origin and the end of a certain tract? I >>>>> think that >>>>> the first we >>>>> have to determine the origin and the end of the tract, the second it >>>>> constructs possible >>>>> pathway not with the deterministic way (only 1 direction / 1 voxel) but >>>>> with the >>>>> probabilistic way (considering which direction should be next to). Is >>>>> this comprehension >>>>> wrong? >>>>> Thank you. >>>>> >>>>> Anri >>>>> >>>>> >>>>> ********************************************************************** >>>>> ???????????? >>>>> ???????? >>>>> ?? ?? >>>>> ********************************************************************** >>>>> Anri WATANABE, M.D. >>>>> Department of Psychiatry, >>>>> University Hospital, Kyoto Prefectural University of Medicine >>>>> ********************************************************************** >>>>> >>>>> 2016-07-31 13:22 GMT+09:00 Anastasia Yendiki < >>>>> ayendiki(a)nmr.mgh.harvard.edu>: >>>>> >>>>> Hi Anri - TRACULA does not use deterministic ROIs. It uses a >>>>> probabilistic >>>>> model of how likely each tract is to go through or next to each of >>>>> the labels >>>>> of the freesurfer subcortical segmentation and cortical >>>>> parcellation, as a >>>>> function of position along the trajectory of the tract. >>>>> >>>>> Best, >>>>> a.y >>>>> >>>>> On Sun, 31 Jul 2016, Anri WATANABE wrote: >>>>> >>>>> Hi Anastasia, >>>>> Thank you! It seems work well!! >>>>> I have another question. Are ROIs for automatic tractography >>>>> in >>>>> TRACULA the same ROIs >>>>> presented in Wakana et al. 2007? >>>>> >>>>> Anri >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> ???????????? >>>>> ???????? >>>>> ?? ?? >>>>> >>>>> ********************************************************************** >>>>> Anri WATANABE, M.D. >>>>> Department of Psychiatry, >>>>> University Hospital, Kyoto Prefectural University of >>>>> Medicine >>>>> >>>>> ********************************************************************** >>>>> >>>>> 2016-07-27 13:17 GMT+09:00 Anastasia Yendiki >>>>> <ayendiki(a)nmr.mgh.harvard.edu>: >>>>> >>>>> Hi Anri - The problem is in this line: >>>>> >>>>> set cmd = ($cmd --ref >>>>> $cvstempdir/$cvstemp) >>>>> >>>>> It should be changed to this: >>>>> >>>>> set cmd = ($cmd --ref >>>>> $cvstempdir/$cvstemp/mri/norm.mgz) >>>>> >>>>> For this to take effect, you need to run "which >>>>> trac-all" >>>>> and make the change in >>>>> the trac-all file that the which commands shows you. >>>>> >>>>> Hope this helps, >>>>> >>>>> a.y >>>>> >>>>> On Fri, 15 Jul 2016, Anri WATANABE wrote: >>>>> >>>>> Hi, AnastasiaThis is trac-all.local-copy from 1 >>>>> subject. Thank you! >>>>> >>>>> Anri >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> ???????????? >>>>> ???????? >>>>> ?? ?? >>>>> >>>>> >>>>> ********************************************************************** >>>>> Anri WATANABE, M.D. >>>>> Department of Psychiatry, >>>>> University Hospital, Kyoto Prefectural >>>>> University >>>>> of >>>>> Medicine >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> 2016-07-13 6:16 GMT+09:00 Anastasia Yendiki >>>>> <ayendiki(a)nmr.mgh.harvard.edu>: >>>>> >>>>> Hi Anri - This may be a bug that was fixed >>>>> at >>>>> some point. Can >>>>> you send me the >>>>> scripts/trac-all.local-copy >>>>> from >>>>> one of your >>>>> subjects? Thanks! >>>>> >>>>> a.y >>>>> >>>>> On Mon, 11 Jul 2016, Anri WATANABE wrote: >>>>> >>>>> Hi Anastasia,There is an error >>>>> in .log >>>>> files of left >>>>> corticospinal tract in cvs template >>>>> and I >>>>> attached >>>>> one >>>>> of file. In addition .log files of >>>>> right >>>>> corticospinal tract in cvs template >>>>> doesn't exist. >>>>> Thanks in advance. >>>>> >>>>> Anri >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> ???????????? >>>>> ???????? >>>>> ?? ?? >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> Anri WATANABE, M.D. >>>>> Department of Psychiatry, >>>>> University Hospital, Kyoto >>>>> Prefectural >>>>> University of >>>>> Medicine >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> 2016-07-07 20:12 GMT+09:00 Anastasia >>>>> Yendiki >>>>> <ayendiki(a)nmr.mgh.harvard.edu>: >>>>> >>>>> Hi Anri - Is there an error in >>>>> the >>>>> stats/*.log >>>>> files for the different tracts? >>>>> >>>>> a.y >>>>> >>>>> On Tue, 5 Jul 2016, Anri >>>>> WATANABE >>>>> wrote: >>>>> >>>>> Dear Anastasia, >>>>> >>>>> I use TRACULA to obtain >>>>> diffusion >>>>> measures at each voxel in a certain >>>>> pathway for >>>>> group analysis, but >>>>> there aren't >>>>> stats/*.path.mean.txt >>>>> files. I found .log files >>>>> >>>>> (<tract>_PP.avg33_mni_bbr.log) >>>>> which >>>>> exist >>>>> 1 file per 1 tract, >>>>> except >>>>> corticospinal >>>>> tract which has 2 .log files. >>>>> >>>>> Command: trac-all >>>>> ?stat ?c >>>>> >>>>> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example >>>>> >>>>> Error log: Loading >>>>> output >>>>> reference >>>>> volume from >>>>> >>>>> >>>>> /Applications/freesurfer/subjects/cvs_avg35 >>>>> >>>>> corRead(): can't >>>>> open file >>>>> >>>>> /Applications/freesurfer/subjects/cvs_avg35/COR-.info >>>>> >>>>> ERROR: Could not read >>>>> >>>>> /Applications/freesurfer/subjects/cvs_avg35 >>>>> >>>>> >>>>> I attached >>>>> dmrirc.example >>>>> (configuration >>>>> file) and >>>>> <subjd>/scripts/trac-all.log. >>>>> >>>>> >>>>> Thanks in advance, >>>>> Anri >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> ???????????? >>>>> ???????? >>>>> ?? ?? >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> Anri WATANABE, M.D. >>>>> Department of >>>>> Psychiatry, >>>>> University Hospital, >>>>> Kyoto >>>>> Prefectural >>>>> University of Medicine >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> 2016-06-03 9:51 >>>>> GMT+09:00 >>>>> Anri >>>>> WATANABE >>>>> <z2aanri(a)koto.kpu-m.ac.jp>: >>>>> Hi, Anastasia. >>>>> There aren't any .log >>>>> files >>>>> but text >>>>> files like >>>>> lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. >>>>> I guess text >>>>> files complete all >>>>> pathways >>>>> and >>>>> measures. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> ???????????? >>>>> ???????? >>>>> ?? ?? >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> Anri WATANABE, M.D. >>>>> Department of >>>>> Psychiatry, >>>>> University Hospital, >>>>> Kyoto >>>>> Prefectural >>>>> University of Medicine >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> 2016-06-02 3:03 >>>>> GMT+09:00 >>>>> Anastasia >>>>> Yendiki >>>>> <ayendiki(a)nmr.mgh.harvard.edu >>>>>> : >>>>> >>>>> Thanks, Anri. >>>>> So the >>>>> previous >>>>> steps seem to have run fine. Are >>>>> there any >>>>> .log >>>>> files >>>>> created in the >>>>> stats/ >>>>> folder, >>>>> which is created by trac-all -stat? >>>>> >>>>> On Wed, 1 Jun >>>>> 2016, >>>>> Anri >>>>> WATANABE >>>>> wrote: >>>>> >>>>> Hi >>>>> Anastasia, This >>>>> is a >>>>> <subjid>/scripts/trac-all.log of one >>>>> subject of >>>>> the group. >>>>> >>>>> Thanks, >>>>> Anri >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> ???????????? >>>>> ???????? >>>>> ?? ?? >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> Anri >>>>> WATANABE, >>>>> M.D. >>>>> Department >>>>> of >>>>> Psychiatry, >>>>> University >>>>> Hospital, Kyoto >>>>> Prefectural University of Medicine >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> 2016-05-31 >>>>> 22:55 >>>>> GMT+09:00 >>>>> Anastasia Yendiki >>>>> >>>>> <ayendiki(a)nmr.mgh.harvard.edu>: >>>>> >>>>> Hi >>>>> Anri >>>>> - >>>>> Can you also >>>>> send your log file >>>>> (scripts/trac-all.log)? >>>>> I'll need to >>>>> see >>>>> what >>>>> exactly >>>>> was >>>>> running >>>>> when the error occurred. Thanks! >>>>> >>>>> a.y >>>>> >>>>> On >>>>> Sat, >>>>> 28 >>>>> May 2016, >>>>> Anri WATANABE wrote: >>>>> >>>>> >>>>> Hello >>>>> Anastasia,sorry for few information >>>>> and >>>>> let me tell >>>>> you >>>>> command and >>>>> >>>>> error >>>>> log. >>>>> >>>>> Command: trac-all ?stat ?c >>>>> >>>>> >>>>> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example >>>>> >>>>> >>>>> Error >>>>> log: Loading output reference volume >>>>> from >>>>> >>>>> >>>>> /Applications/freesurfer/subjects/cvs_avg35 >>>>> >>>>> >>>>> corRead(): can't >>>>> open file >>>>> >>>>> >>>>> /Applications/freesurfer/subjects/cvs_avg35/COR-.info >>>>> >>>>> >>>>> ERROR: >>>>> Could not >>>>> read >>>>> >>>>> >>>>> /Applications/freesurfer/subjects/cvs_avg35 >>>>> >>>>> >>>>> >>>>> dmrirc.example (configuration >>>>> file) is >>>>> attached to >>>>> this >>>>> e-mail. >>>>> >>>>> >>>>> Thanks >>>>> in >>>>> advance, >>>>> >>>>> Anri >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> ???????????? >>>>> >>>>> ???????? >>>>> ?? >>>>> ?? >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> Anri >>>>> WATANABE, >>>>> M.D. >>>>> >>>>> Department of >>>>> Psychiatry, >>>>> >>>>> University >>>>> Hospital, Kyoto Prefectural >>>>> University of >>>>> Medicine >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> >>>>> 2016-05-27 22:57 >>>>> GMT+09:00 Anastasia Yendiki >>>>> >>>>> <ayendiki(a)nmr.mgh.harvard.edu>: >>>>> >>>>> >>>>> >>>>> Hi Anri - >>>>> I do not know what command line you >>>>> ran >>>>> and >>>>> what your >>>>> >>>>> configuration >>>>> file looks like, so it is very >>>>> >>>>> >>>>> hard for >>>>> me to suggest solutions. >>>>> >>>>> >>>>> >>>>> Best, >>>>> >>>>> >>>>> a.y >>>>> >>>>> >>>>> >>>>> On Fri, 27 >>>>> May 2016, Anri WATANABE wrote: >>>>> >>>>> >>>>> >>>>> Hi >>>>> Anastasia, >>>>> >>>>> >>>>> >>>>> Thank you for your answer. >>>>> >>>>> >>>>> >>>>> There aren't stats/*.path.mean.txt >>>>> files and >>>>> terminal >>>>> says >>>>> 'Could >>>>> >>>>> not >>>>> read >>>>> >>>>> >>>>> >>>>> >>>>> /Applications/freesurfer/subjects/cvs_avg35.' I >>>>> >>>>> >>>>> >>>>> checked >>>>> >>>>> >>>>> /Application/freesurfer/subjects/cvs_avg35 >>>>> folder >>>>> and >>>>> >>>>> couldn't find >>>>> COR-.info file. >>>>> >>>>> >>>>> >>>>> Could you tell me any resolutions, >>>>> please? >>>>> >>>>> >>>>> >>>>> >>>>> Thanks, >>>>> >>>>> >>>>> Anri >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> >>>>> >>>>> ???????????? >>>>> >>>>> >>>>> >>>>> ???????? >>>>> >>>>> >>>>> ?? >>>>> ?? >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> >>>>> Anri >>>>> WATANABE, M.D. >>>>> >>>>> >>>>> >>>>> Department of Psychiatry, >>>>> >>>>> >>>>> >>>>> University Hospital, Kyoto >>>>> Prefectural >>>>> University >>>>> of Medicine >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> >>>>> >>>>> >>>>> 2016-05-21 6:48 GMT+09:00 Anastasia >>>>> Yendiki >>>>> >>>>> <ayendiki(a)nmr.mgh.harvard.edu>: >>>>> >>>>> >>>>> >>>>> >>>>> Hi Anri - The FA values are >>>>> extracted in >>>>> the native >>>>> space >>>>> of >>>>> each subject, >>>>> which is why >>>>> >>>>> >>>>> >>>>> those are the only >>>>> >>>>> >>>>> >>>>> coordinates that you see. If you >>>>> want to >>>>> display the >>>>> >>>>> results of your >>>>> analysis on an average >>>>> >>>>> >>>>> >>>>> path, after >>>>> >>>>> >>>>> >>>>> running trac-all -stat, you >>>>> can use >>>>> the >>>>> >>>>> stats/*.path.mean.txt files (see >>>>> also >>>>> the >>>>> last part >>>>> >>>>> >>>>> of >>>>> the TRACULA >>>>> >>>>> >>>>> >>>>> tutorial). >>>>> >>>>> >>>>> >>>>> >>>>> Best, >>>>> >>>>> >>>>> >>>>> a.y >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, 18 May 2016, Anri WATANABE >>>>> wrote: >>>>> >>>>> >>>>> >>>>> >>>>> Dear experts, >>>>> >>>>> >>>>> >>>>> I use TRACULA to examine a >>>>> measure >>>>> (FA) at each >>>>> voxel >>>>> >>>>> in one >>>>> pathway. >>>>> >>>>> >>>>> >>>>> pathstats.byvoxel.txt files >>>>> show >>>>> coordinates >>>>> in >>>>> >>>>> native >>>>> space and >>>>> after converting >>>>> >>>>> >>>>> >>>>> those the new >>>>> >>>>> >>>>> >>>>> files don't show any >>>>> coordinates >>>>> which are in >>>>> MNI >>>>> >>>>> space. >>>>> >>>>> >>>>> >>>>> Could you tell me how can I >>>>> know >>>>> MNI >>>>> coordinate >>>>> >>>>> values? >>>>> >>>>> >>>>> >>>>> >>>>> Thank you! >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Regards, >>>>> >>>>> >>>>> >>>>> Anri >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> >>>>> >>>>> ???????????? >>>>> >>>>> >>>>> >>>>> ???????? >>>>> >>>>> >>>>> >>>>> ?? ?? >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> >>>>> >>>>> Anri WATANABE, M.D. >>>>> >>>>> >>>>> >>>>> Department of Psychiatry, >>>>> >>>>> >>>>> >>>>> University Hospital, Kyoto >>>>> Prefectural >>>>> University of >>>>> >>>>> Medicine >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ********************************************************************** >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> >>>>> >>>>> >>>>> 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. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> >>>>> 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 >>>>> >>>>> >>>> ... >>>> >>>> [???????????] >>>> _______________________________________________ >>>> 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 . 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Poor automatic segmentation of the cerebellum
by Sam Mathias 04 Aug '16

04 Aug '16

Dear list, I'm interested in measuring cerebellar volumes using freesurfer. However, the automatic segmentation (aseg) seems to be doing a poor job of capturing the whole structure for many subjects. Specifically, it is chopping off the bottom of the cerebellum. Here is an example: https://drive.google.com/open?id=0B68CY3v4cg7tS0hSNkVVMWNiZV8xYWR2eTJQQlhFe… The issue seems to be when the cerebellum is very close to the bottom of the image, as is the case in many of our scans. Has anyone encountered similar issues with cerebellum segmentation, and if so, have any advice about how to improve it? Many thanks, -- Samuel R. Mathias, Ph.D. Associate Research Scientist (ARS) Neurocognition, Neurocomputation and Neurogenetics (n3) Division Yale University School of Medicine 40 Temple Street, Room 694 New Haven CT 06511 http://www.srmathias.com

2 1

ROIs defined in MNI space and vol2surf
by Funk, Quentin 04 Aug '16

04 Aug '16

All, I have a question regarding the required registration file in mri_vol2surf. I have some spherical ROI's in MNI space produced via 3dUndump--they're volume files that show up in the correct places when loaded in with an MNI standard subject such as fsaverage. I also have some patients scans. I'd really like to compute cortical thickness for these ROI's on my patient scans, so I attempt to follow the instructions at ( https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness ), but these instructions assume that the ROI is in the native space--which produces no problems until the step : cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf \ --mov /path/to/ROI5.nii \ --reg TT_avg152T1_to_fsaverage.dat \ --projdist-max 0 1 0.1 \ --interp nearest \ --hemi lh \ --out lh.fsaverage.ROI5.mgh \ --reshape My question is then three parts: (1) Why does vol2surf require a registration file? Shouldn't it be possible to do it as a straight conversion of data types if I know that my surface is registered to the file that I want? Perhaps naive, my first intuition was to construct a TT.dat that was the identity matrix, but this fails, with the response listed in (2). (2) How can I do this without shifting my data? If I follow the instructions, when the surface is overlayed on fsaverage's lh.pial, the entire surface is included in the overlay. (3) What exactly do the numbers mean in the registration file TT.dat (as in the instructions on the website)? The 4x4 matrix is clear, and the first two numbers appear to have something to do with Voxel resolution, but I'm unable to find documentation that explains the notation in the output. Any help anyone can offer would be tremendously appreciated. -qf Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital 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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Freesurfer August 2016