Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

Brainmask edit error
by Sabrina Yu 09 Jun '16

09 Jun '16

Hello, I'm having problems with regenerating the surfaces for stroke cases after editing the brainmask.mgz file. In the aseg.mgz file, the brain matter around lesion area is correctly classified as brain matter. In the pial surface, this brain matter is not included. I've tried to edit the brainmask.mgz file to include this region, but when I run: recon-all -subjid <SUBJECT> -autorecon2-pial, the surfaces generated are not changed at all. I have attached some images to this email. I'm new to Freesurfer, so any help would be greatly appreciated. Thank you.

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Older Freesurfer Version with Freesurfer v. 6 HSF & Brainstem Modules
by Douglas Merkitch 08 Jun '16

08 Jun '16

Hello Freesurfer experts, I have two questions regarding the use of old (version 5.1) processed Freesurfer data with the new hippocampal subfields (HSF) and brainstem modules in Freesurfer version 6: 1) Is it possible to use data processed in Freesurfer v. 5.1 and run it directly though the new v. 6 HSF and brainstem modules? 2) Our data was acquired using a 1.5 T scanner (~1mm isotropic). Would this be an issue for either the new v. 6 HSF or brainstem modules? Any answers and/or comments as to your thought process behind your response would be appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu>

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FS volume estimates
by Otília 08 Jun '16

08 Jun '16

Greetings, I have two questions regarding FS volume measurements. I intend to use the volume information of .stats files but I got some doubts regarding the methods used. 1) I read that eTIV estimation is based on the TAL transformation, but what about the volumes of cortical and subcortical areas? Is it a simple voxel count? 2) In some studies the authors normalize the volumes to eTIV. In others the authors don't do any normalization. Some of them use it as co-variate. What's your opinion regarding this matter? Thank you in advance! Best regards,

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latest freeview
by Jason Tourville 08 Jun '16

08 Jun '16

Hi there, Looking over the freeview development page, it looks like there are some (relatively) new features that would come in handy. Could I get a link to download the latest freeview beta? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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cespct in FS 5.3
by S.V.Shepherd [work] 08 Jun '16

08 Jun '16

Hi all, I ran an analysis on data after dividing each voxel mean across the run, and then multiplying by 100. (My intuition was that the percent signal change should be more consistent across varying SNR that the non-normalized betas). I had naively expected ces.nii and cespct.nii to be equivalent in this case, but in fact, cespct.nii is steeply larger and only imperfectly correlated with ces.nii. What am I missing? stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699

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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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