Freesurfer June 2016

freesurfer@nmr.mgh.harvard.edu

152 participants
213 discussions

aseg.stats and aparc.stats reliability
by Greenberg, Jonathan 08 Jun '16

08 Jun '16

Hello Are the volume and thickness measures in FreeSurfer's aseg.stats and aparc.stats accurate and reliable enough to assess changes in volume and thickness longitudinally? I have heard there have been some accuracy/reliability issues in these files in older versions of FreeSurfer. Is the data in these files strong enough to base a publication on? Thanks! Jonathan

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Break 3D volume
by John Anderson 08 Jun '16

08 Jun '16

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CM_Group_analysis_Create tha contrast and design matrix by myself
by Hao wen 08 Jun '16

08 Jun '16

Hello, freesurfers: I am doing group analysis, with two diff groups, so I want to know that how to create my own Contrast and Design matrix, because that I know in QDEC and CMline, in the freesurfer wiki, You just give the example for the DODS & DOSS, but it is not so flexible! I know that we should define --X in the command mris_glmfit, but I got some problems, here is my work flow: #set the SUBJECTS_DIR export SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/ cd $SUBJECTS_DIR/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version mris_preproc --fsgd AD_CN_COVARIATES_AGE_GENDER.fsgd \ --cache-in thickness.fwhm15.fsaverage \ --target fsaverage \ --hemi lh \ --out lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh mri_glmfit \ --glmdir lh.AD_CN_COVARIAETS_AGE_GENDER.glmdir --y lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh \ --C AD_CN_COVARIATS_AGE_GENDER.mtx \ or --C contrast.mat --X X.mat --surf fsaverage lh \ --cortex \ so, after I run the mri_glmfit, i got the errors, like, you should define the --X or without --C, or cant find command --surf, --cortex, i dont really understand what is the problem, and I create the design matrix and contrast matrix in Matlab Actually, I run the DODS, it works well, and the workflow, I dont change for the command mris_preproc, I just change the flags in mri_glmfit, someone could help me for this? Thanks in advance! Hao

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Re: [Freesurfer] Freesurfer program for 7 Tesla
by konasale prasad 08 Jun '16

08 Jun '16

No. not really. This paper should be useful. Thanks for sending this along. From: Alan Francis [mailto:alandarkenergy@gmail.com] Sent: Tuesday, May 24, 2016 9:47 AM To: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu>; pnucleos(a)gmail.com Subject: Re: [Freesurfer] Freesurfer program for 7 Tesla Hi Prasad: Hope all is well. Has someone replied to you on this question? I have enclosed an interesting article that compares 3T vs 7T that might be useful in guiding your analysis. best, Alan On Mon, May 16, 2016 at 12:01 PM, konasale prasad <pnucleos(a)gmail.com <mailto:pnucleos@gmail.com> > wrote: Dear FSL experts, We are trying to run freesurfer volume measurements, primarily subcortical regions along with cortical surface area and thickness. We are also interested in hippocampal subfields and shape analysis. I was wondering whether the program would be reliable compared to 3T (that we have done quite a few). Are there any known problems? If there are, please let me know the work arounds. Thanks, _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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. -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| Alan N. Francis PhD Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <mailto:ezra_wegbreit@brown.edu> afrancis(a)mclean.harvard.edu <mailto:afrancis@mclean.harvard.edu> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header
by Aloi, Joseph 07 Jun '16

07 Jun '16

Hi Doug, I do not believe the files have changed in any way since I started using them; I uploaded some dicoms for you to look at and the recon-all log to the file drop a few minutes ago (with more details). Thank you for all your help! Joseph Aloi Graduate Student, MD/PhD Scholars Program Department of Pharmacology and Experimental Neuroscience University of Nebraska Medical Center Neurobehavioral Research Assistant, Center For Neurobehavioral Research Boys Town National Research Hospital Have the dicom files changed in any way? In the failure, the problem maybe that it thinks that the series is truncated (the header thing is not a problem). Do you still have perms to all the files in that folder? I noticed in the analysis that succeeded had a bunch of these statements (never seen it before): Agreeing to the Xcode/iOS license requires admin privileges, please re-run as root via sudo. Feel free to tar up the dicom folder and send it to me at our file drop. On 05/23/2016 06:35 PM, Aloi, Joseph wrote: > Hi Doug, > > I've attached the recon-all log for an analysis on a research subject > that I successfully ran a few weeks ago and then the recon-all log > when I try to run the exact same analysis on the exact same subject > now. Thanks so much for taking a look at these. > > The log files you can just attach to the email to the list (or to me > directly if there is something in there that you don't want to post) > On 05/20/2016 04:02 PM, Aloi, Joseph wrote: > > Excellent, thank you! To do that, do I send an e-mail to the listserv > > with the log files attached or do I use the filedrop? > > > > yea, can you post the log file of both the successful and failing runs? > > > > On 05/19/2016 11:28 AM, Aloi, Joseph wrote: > > > > > > Hi Doug, > > > > > > No that’s not how I usually store my files- I have a folder for the > > > particular study that I am working on then the dicoms for each subject > > > in that study are stored in individual subject folders within the > > > study folder. > > > > > > I got a chance to look around the recon-all logs this morning for a > > > subject that I had successfully processed in the past (but that I get > > > the error when I try to process this same dataset now). From > > > comparing the recon-all log from when recon-all ran successfully > > > versus now, things are running fine up until it gets to MRI_convert. > > > However, it looks like things are actually starting to go haywire > > > during MRI_convert even before I get the warning about the ASCII > > > header and recon-all exits. It appears that MRI_convert is having > > > some trouble with extracting some of the information it needs from the > > > dicom file, resulting in the error that I posted. I know you guys are > > > busy, but would you be able to take a look at the log files? I’ve > > > only been using freesurfer a few weeks, so I would definitely > > > appreciate any insights you might have from looking at the log files. > > > > > > Thank you! > > > > > > I don't have any idea what is going wrong. I noticed that the file > > > that it is having problems with is here > > > /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm > > > Do you really keep all your dicom files in that location? > > > > > > > > > > > > On 05/17/2016 11:47 PM, Aloi, Joseph wrote: > > > > Hi Doug, > > > > Sorry- I've added entire correspondence onto the end of this > > > e-mail. I don't think the disk filled up as I am on a 3 TB hard drive > > > and I still have ~2 TB of free space on my disk. Anything else you > > > think it could be? > > > > Thanks! > > > > Joseph Aloi > > > > Please remember to include previous correspondence otherwise we can't > > > > keep track of the problem! > > > > Eg, I don't have the previous email to see what the error was. Is it > > > > possible that the disk filled up? > > > > On 05/17/2016 09:49 AM, Aloi, Joseph wrote: > > > > > Hi Doug, > > > > > > > > > > Yes, you are correct- data I have previously processed without any > > > > > problems is no longer being processed. > > > > > > > > > > My version of freesurfer is 5.3.0; I only downloaded it a few weeks > > > > > ago so I have not changed my freesurfer version recently. > > > > > > > > > > Thanks! > > > > > > > > > > Joseph Aloi > > > > > Graduate Student, MD/PhD Scholars Program > > > > > Department of Pharmacology and Experimental Neuroscience > > > > > University of Nebraska Medical Center > > > > > > > > > > Neurobehavioral Research Assistant, Center For Neurobehavioral > > > Research > > > > > Boys Town National Research Hospital > > > > So the exact same data set is now generating an error whereas it ran > > > > smoothly before? What version of FS are you using? Did you change > > > versions? > > > > doug > > > > On 05/16/2016 09:49 AM, Aloi, Joseph wrote: > > > > > > > > > > Hi freesurfer experts, > > > > > > > > > > I have recently begun to use freesurfer to do structural MRI > > > > > analyses. I have been able to successfully process about 40 > > > > > structural scans with recon-all thus far, but starting a few days ago, > > > > > I started getting this error whenever I run recon-all: > > > > > > > > > > WARNING: file > > > > > /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm does not > > > > > contain a Siemens ASCII header > > > > > > > > > > has this file been anonymized? > > > > > > > > > > ERROR: cannot unpack mosiacs without ASCII header > > > > > > > > > > Darwin nerc130622.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan > > > > > 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 > > > > > > > > > > recon-all -s sub_9999 exited with ERRORS at Mon May 16 08:43:24 > > > CDT 2016 > > > > > > > > > > Here are a few of the troubleshooting steps I’ve tried to track down > > > > > the cause of the error: > > > > > > > > > > -- Re-run recon-all with a couple of scans from my dataset that I have > > > > > already successfully processed > > > > > > > > > > - - Re-run recon-all the same datasets but on a different computer > > > > > > > > > > - - Re-convert the scans from .ima files to dicoms in osirix, then > > > > > run recon-all > > > > > > > > > > > > > > > For all of these steps, I have gotten the exact same error message. > > > > > The files should be anonymized, since I used osirix’s “anonymize and > > > > > convert” function to generate the dicom files (the scans were given to > > > > > me as .ima files). > > > > > > > > > > Any suggestions on what to try next? > > > > > > > > > > Thank you! > > > > > > > > > > > > > > > Joseph Aloi > > > > > > > > > > The information in this e-mail may be privileged and confidential, > > > > > intended only for the use of the addressee(s) above. Any unauthorized > > > > > use or disclosure of this information is prohibited. If you have > > > > > received this e-mail by mistake, please delete it and immediately > > > > > contact the sender. > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > The information in this e-mail may be privileged and confidential, > > > > intended only for the use of the addressee(s) above. Any unauthorized > > > > use or disclosure of this information is prohibited. If you have > > > > received this e-mail by mistake, please delete it and immediately > > > > contact the sender. > > > > > > > > > > > > _______________________________________________ > > > > 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 > > > gr...(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 > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > <file://localhost/transfer/outgoing/flat/greve> > > > > > > > > > > > > The information in this e-mail may be privileged and confidential, > > > intended only for the use of the addressee(s) above. Any unauthorized > > > use or disclosure of this information is prohibited. If you have > > > received this e-mail by mistake, please delete it and immediately > > > contact the sender. > > > > > > > > > _______________________________________________ > > > 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 > > gr...(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. > > > > > > Joseph Aloi > > Graduate Student, MD/PhD Scholars Program > > Department of Pharmacology and Experimental Neuroscience > > University of Nebraska Medical Center > > > > Neurobehavioral Research Assistant, Center For Neurobehavioral Research > > Boys Town National Research Hospital > > > > > > > > The information in this e-mail may be privileged and confidential, > > intended only for the use of the addressee(s) above. Any unauthorized > > use or disclosure of this information is prohibited. If you have > > received this e-mail by mistake, please delete it and immediately > > contact the sender. > > > > > > _______________________________________________ > > 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 > gr...(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 > > > Joseph Aloi > Graduate Student, MD/PhD Scholars Program > Department of Pharmacology and Experimental Neuroscience > University of Nebraska Medical Center > > Neurobehavioral Research Assistant, Center For Neurobehavioral Research > Boys Town National Research Hospital > > > > The information in this e-mail may be privileged and confidential, > intended only for the use of the addressee(s) above. Any unauthorized > use or disclosure of this information is prohibited. If you have > received this e-mail by mistake, please delete it and immediately > contact the sender. > > > _______________________________________________ > 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 gr...(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 may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Fwd: bug report
by siya sherif 07 Jun '16

07 Jun '16

FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: jessie/sid Kernel info: Linux 4.2.0-36-generic x86_64 --------------------------------------------------------------------- Please include the following additional information in your report: 1) subject name bret4 2) the entire command-line executed setenv SUBJECTS_DIR /media/brain/C60E9D2E0E9D188F/testFreesurfur recon-all -i ICBM_MNI_0101_MRI_T1-FFE_br_20050118145643139_S6730_I2233.nii -subject bert3 -all 3) the error message generated #-------------------------------------------- #@# Talairach Fri Jun 3 14:54:45 IST 2016 /media/brain/C60E9D2E0E9D188F/testFreesurfur/bert5/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux IBT-MS-7971 4.2.0-36-generic #42~14.04.1-Ubuntu SMP Fri May 13 17:27:22 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert5 exited with ERRORS at Fri Jun 3 14:55:29 IST 2016 For more details, see the log file /media/brain/C60E9D2E0E9D188F/testFreesurfur/bert5/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 4) optionally include the subject's /script/recon-all.log -- Dr. Siya Sherif Ph.D Senior R & D Engineer Neuroimaging & Neurospectroscopy Lab National Brain Research Centre NH-8, Manesar, Gurgaon Haryana-122 051 India email : siya.physics(a)gmail.com , siya.sherif(a)imdea.org Tel (mob) : +91- 9447753634

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errors in wm and pial boundaries
by Corinna Bauer 07 Jun '16

07 Jun '16

Hello all, We are analyzing data from our collaborators and are running into some difficulties with the accuracy of the pial and wm boundaries. The wm.mgz appears to follow the actual WM, independent of the wm surface boundary. Attached is an example showing two types of problems. 1. the WM surface is inaccurate regardless of the number of control points used. 2. The pial surface is inaccurate, missing a bunch of the sulcal and gyral patterns of the left parietal lobe (see area around cursor). For completeness, I have also included the wm.mgz at the same slice. I should mention that these problems has been occurring in multiple subjects. Any suggestions?? Thanks Corinna

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Save REG in tkregister2
by Hao wen 07 Jun '16

07 Jun '16

Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI

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converting Tracula outputs to Wavefront OBJ files
by David Allan Ziegler 06 Jun '16

06 Jun '16

Dear Freesurfer/Tracula team, I would like to convert some of the outputs from Tracula into wavefront objects in order to render them in Unity. Does anyone have any advice on how to do so? Based on previous threads and looking into Brainder.org's aseg2surf, I assume I need to use a combination of mri_pretess and mri_tess to generate tesselated surfaces that can then be converted into ascii files and then into .obj files using Brainder's surf2obj. My problem is in figuring out how to generate the surface meshes from the Tracula outputs. If anyone can point me to documentation on how to do this or provide any advice, I'd appreciate it. Cheers, David

1 0

CORRECTING DEFECT
by maryam koochaki 06 Jun '16

06 Jun '16

Hi Bruce,I am wondering if you saw my last email, about uploading my subject in your ftp server.I uploaded the subject "test_emc_039.tar.gz".I appreciate any help. Thank you, Maryam

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Freesurfer June 2016