Freesurfer July 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
160 discussions

Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli 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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Postdoctoral position: Neuroimaging, PCAN lab, University of Calgary, Canada, 2 years
by Alexandru Hanganu 16 Jun '21

16 Jun '21

External Email - Use Caution Dear All, The PCAN lab: http://pcanlab.ca has a two-year funded postdoctoral research fellow position under the supervision of Dr. Oury Monchi starting immediately to work on the following project: *Neuroimaging and other predictors of cognitive and neuropsychiatric evolution in Parkinson’s disease using multi-modal MRI imaging techniques and machine learning.* The project is funded by the Canadian Institutes of Health Research (CIHR) . It involves longitudinal analyses of cortical thickness, tractography and BOLD resting-state fMRI analyses and will benefit from collaborations with Dr. Alexandru Hanganu at the Department of Psychology of the University of Montreal. Other collaborators include Dr. Nils Forkert head of the Medical Imaging Processing and Machine Learning laboratory. A special focus will be given to the neural origins and predictors of Mild Behavior Impairment (MBI) in Parkinson’s disease in collaboration with Dr. Zahinoor Ismail who has led the development of the MBI-checklist. The project will make use of an existing longitudinal study containing structural, diffusion weighted imaging and functional MRI, neuropsychological and behavioural assessment, and genotyping at three time points. The PCAN lab has been a pioneer in using different neuroimaging techniques to study the origins and evolution of cognitive more recently neuropsychiatric deficits in Parkinson’s disease with the ultimate goal of early prediction of dementia in the disease. Other interests include the function and application of neuromodulation techniques such as transcranial magnetic stimulation, Transcranial direct stimulation and low intensity focused ultrasound. The PCAN Lab is located in the Healthy Brain Aging labs of the Hotchkiss Brain Institute part the Foothills Campus of the University of Calgary. The Foothills campus is home to the Seaman Family MR Research Centre which host a General Electric 3T research dedicated MRI scanner. Requirements of the position include a PhD in Neuroscience, biomedical engineering, biomedical sciences, or Psychology with experience in the analysis of one or multiple MRI neuroimaging techniques such as cortical thickness/volumetry (e.g. *Freesurfer, FSL*), functional connectivity (e.g. *PPI, ICA, graph theory*), diffusion weighted imaging (e.g. *Dipy, MRTrix, FSL*). Some fluency in computer programming (e.g. *Linux, Unix, MATLAB, or Python)* is also required as well as the ability to write scientific peer-reviewed manuscripts. Please send applications (Cover letter, CV, and the name of 2 references including current supervisor) to Oury Monchi: oury.monchi(a)ucalgary.ca

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Job ad: MRI physicist
by Keith Schneider 07 May '21

07 May '21

External Email - Use Caution The Center for Biomedical and Brain Imaging (CBBI) is a core imaging facility at the University of Delaware dedicated to scientific research. It is equipped with a Siemens Prisma 3T MRI scanner, Bruker 9.4T small bore MRI scanner, TMS, and MRI-compatible EEG. It supports a wide range of scientific investigations through imaging of humans, animals and materials. Under general direction of the CBBI Manager, the MRI Physicist is responsible for supporting the operations of the Siemens and Bruker MRI scanners. The MRI Physicist is expected to contribute to both research and training efforts that will include pulse sequence programming, parameter and image quality optimization, protocol design, scanner operation, technical support and user training. The candidate will be expected to maintain a broad knowledge of state-of-the-art MRI technology and equipment. The incumbent must have excellent communication and organizational skills, the ability to positively interact with a diverse group of MRI users, and a strong motivation to learn new MRI techniques. MAJOR RESPONSIBILITIES: • Pulse sequence programming on Bruker 9.4T and Siemens 3T MRI scanners • Assist users on appropriate choice and use of coils • Technical liaison for obtaining sequences or protocols for non-standard imaging (e.g. cardiac, musculoskeletal) from Siemens and other sites • File reports as needed for WIP sequences and Siemens MRA • Ensure data quality from the viewpoint of machine fundamentals • Technical support 9.4T and 3T scanners • Protocol design and testing for 9.4T scanner, including imaging of live animals and awake animals; as-needed for 3T • Routine quality assurance for 9.4T and 3T MRI scanners • Train users, including students, on use of 9.4T and 3T MRI scanners • Help users optimize pulse sequence parameters to maximize SNR and avoid imaging artifacts • Consult on image analysis, as needed • Review journals and abstracts to keep abreast of new developments • Collaborate with ongoing research as needed; may have independent research projects if desired • Consult users about imaging details for manuscript preparation and grant applications, as needed • Perform miscellaneous job-related duties as assigned QUALIFICATIONS: • PhD in MR physics or MS with equivalent experience • expert understanding of MR physics, image acquisition, signal processing, imaging processing and image reconstruction • MR pulse sequence programming • Experience with Bruker and Siemens MRI scanners • MRI scanning experience with both humans and animals—willing to handle animals • Ability to design experiments, optimize MRI protocols, troubleshoot image artifacts, analyze data, and interpret results • Knowledge of functional MRI, DTI, MRS, T1/T2 relaxation and perfusion • Siemens IDEA and ICE certification (or ability to obtain) http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office <http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office> For further information, contact me. keith ----- Keith Schneider Director, Center for Biomedical and Brain Imaging Associate Professor Department of Psychological and Brain Sciences University of Delaware

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Parcellation Error Pre-Post Central Gyrus R but not L Hemisphere
by Fraser Smith 26 Apr '21

26 Apr '21

External Email - Use Caution Hi there I have a clear parcellation error with one participant who does look to have an atypical structure around the right post-central gyrus (looks split in two). Both the pre and post central gyri are shifted significantly backwards – but only for the right not the left hemisphere. I see this has been mentioned before in the archives – but I have been unable to find a fix for this. Could you provide any tips on what to try? I am using v6.0.0. Best wishes Fraser Smith

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label to surface
by Sam W 02 Feb '21

02 Feb '21

External Email - Use Caution Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam

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Correct for sulcuses & ventricles size
by John Anderson 13 Dec '20

13 Dec '20

External Email - Use Caution Dear Freesurfer experts, I have two groups of subjects (healthy and patients). The patients have different degrees of atrophy. Looking into the individual scans, the subjects are largely different in the space between the sulcuses and the size of ventricles. My questions are: 1. Is there any way to correct for these differences in the surface based analysis? 2. Including eTIV covariate does it help in this case? 3. Does the resampling to "fsaverage" overcome the challenge of these differences between the subjects? I appreciate any advice, John

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peak MNI coordinates within a masked sig.mgh
by Fred Sampedro 18 Sep '20

18 Sep '20

External Email - Use Caution Dear FS experts, I have a rather simple question: I would like to obtain the MNI coordinates of the most significant vertex in a sig.mgh map but within a specific ROI (for instance the left supramarginal region). Here is my attempt but with practical gaps in terms of command parameters: 1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG? --o roimask.mgh 2) fslmaths sig.mgh mult roimask.mgh -o maskedsig.mgh 3) which command could I use to obtain the MNI coordinates of the peak value in maskedsig.mgh? Thanks a lot in advance!

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Visualizing significant clusters, monte-carlo and permutation
by Avi Gharehgazlou 27 Aug '20

27 Aug '20

External Email - Use Caution Hi experts, I am a bit confused with visualizing my significant clusters after having corrected my results for multiple comparisons. after running mri_glmfit, I corrected with monte carlo and permutation as explained below, will you please confirm my understanding below is correct ? 1. I ran monte carlo simulation (1.3 sig level). My understanding is that "cache.th13.abs.sig.cluster.summary" shows the clusters that are significant after correction for multiple comparisons. I have 1 cluster listed in this file. Thus, I am interpreting this as having 1 significant cluster after correction at p<0.05, is this correct? When I want to visualize my corrected results I use the command line below. I am assuming this command line displays only the significant clusters that survived multiple comparison correction because only the cluster that is listed in my "cache.th13.abs.sig.cluster.summary" file appears on the brain here, and because I have put " cache.th13.abs.sig.cluster.mgh" and as overlay " cache.th13.abs.sig.ocn.annot" and set the threshold to 1.3 in my command line. Is it correct that the cluster that appears when running the below command line is my significant cluster surviving multiple comparisons correction at p<0.05? vglrun freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated :overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.cluster.mgh:overlay_ threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.ocn.annot -viewport 3d also, how can I get the clusters to look their appropriate colours when I am vieweing them with the command line above? all my clusters appear gray (regardless of whether they have positive or negative max values, in which case they should be yellow and blue, respectively) 2. I then ran permutation testing. My "perm.th13.abs.sig.cluster.summary" file is blank. I interpret this as no clusters having survived multiple comparison correction with permutation testing. Am I correct? When I use the below command line to visualize my result I see a blank brain (with no clusters coloured). Which makes sense to me because my "perm.th13.abs.sig.cluster.summary" also showed no significant clusters. is this interpretation and the command line I am using below correct? vglrun freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/perm.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/perm.th13.abs.sig.ocn.annot -viewport 3d -layout 1 I think my understanding is correct, but I am confused because the FreeSurfer instructions state that the above command lines will display "all clusters, regardless of significance"... but using the above command lines seems to only display my significant clusters. I am assuming this is because I set my threshold to 1.3 (the same threshold I used to correct for multiple comparisons in 1 and 2 above). But wanted to make sure I am correct before proceeding. Thank you so much for your support, Avi

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ROI-wide cortical thickness for each network !
by Martin Juneja 22 Aug '20

22 Aug '20

External Email - Use Caution Hi experts, I extracted network-wise cortical measures (i.e., 7 cortical thickness values for 7 networks for Yeo atlas). I was wondering if there is a way to get the cortical thickness of each ROI within each of these networks e.g., cortical thickness values of all the ROIs which constitute default-mode network of Yeo's 7 network parcellation, and then cortical thickness values of all the ROIs which constitute limbic network of Yeo's 7 network parcellation, and so on. I know Desikan atlas can be used to get morphometry measures of 34 ROIs per hemisphere. But the problem is that e.g., default-mode ROIs from Desikan atlas do not completely overlap with the DMN of 7-network parcellation from Yeo atlas. In other words, superior frontal cortex from default-mode network of Yeo 7 network parcellation is a big chunk compared to several small ROIs (some partial and some full) in Desikan atlas, so I do not see any way how to find ROIs which just match with that superior frontal cortex of default-mode of Yeo's 7 network. Any help would be much appreciated !

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Re: [Freesurfer] Recon-all Soft Errors
by Elana Sarabin 17 Aug '20

17 Aug '20

External Email - Use Caution Here is the recon-all.log file. Thanks, Elana -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: July 30, 2020 10:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 197, Issue 59 [△EXTERNAL] 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. FS 7.1.0 - Editing intensity values for WM (Nils B?er) 2. Re: FS 7.1.0 - Editing intensity values for WM (Fischl, Bruce) 3. Creating .annot file for a mri_decimate downsampeld version of pial surface (Donelson Berger) 4. GONE: -make to recon-all (Johnson, Hans J) 5. Re: fsgd file - glmfit error (Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience) 6. Re: Recon-all Soft Errors (Zollei, Lilla,Ph.D.) 7. bad interpreter: No such file or directory error (Hengameh Marzbani) 8. Re: overlapping/ superimposing regions of one analysis over another (Douglas N. Greve) 9. Re: Creating .annot file for a mri_decimate downsampeld version of pial surface (Douglas N. Greve) 10. Re: Recon-all Soft Errors (Douglas N. Greve) 11. Re: Coregistration to MNI (Douglas N. Greve) 12. mri_aparc2aseg: how to remove redundant output labels? (Ellen Ji) 13. Re: bad interpreter: No such file or directory error (fsbuild) ---------------------------------------------------------------------- Message: 1 Date: Wed, 29 Jul 2020 21:27:03 +0200 From: Nils B?er <nils.tobias94(a)gmail.com> Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CALZW1G2=-OvWkL81sZxTBiMCKBwiOn6EwSfd2xP0NzEWQYBSTw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello everyone, I just have a short question, because I can't find anything helpful in the tutorials. In my MRI scans freesurfer includes areas to the white matter, even though visual inspection concludes that the area should be grey matter. Is there a possibility to change the value at which freesurfer includes areas to the WM, which i can just change? For example freesurfer includes areas to the WM with intensity values below 85 and i want to change that. I'd be thankful for any feedback/links to guides. Best regards, Nils -- Nils B?er Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401 Email: nils.tobias94(a)gmail.com / nboeer(a)mail.uni-paderborn.de <nils.tobias94(a)gmail.com> Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ https://sug.uni-paderborn.de/department/it/ <https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virenfrei. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/4… ------------------------------ Message: 2 Date: Wed, 29 Jul 2020 20:32:34 +0000 From: "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FS 7.1.0 - Editing intensity values for WM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BL0PR04MB660985EC505DEECB596362ADEF700(a)BL0PR04MB6609.namprd04.prod.outlook.com> Content-Type: text/plain; charset="utf-8" Hi Nils There are expert options for this. You can specify things like -min_white 90 to some of the programs like mri_segment and the surface placement stuff Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Nils B?er Sent: Wednesday, July 29, 2020 3:27 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM External Email - Use Caution Hello everyone, I just have a short question, because I can't find anything helpful in the tutorials. In my MRI scans freesurfer includes areas to the white matter, even though visual inspection concludes that the area should be grey matter. Is there a possibility to change the value at which freesurfer includes areas to the WM, which i can just change? For example freesurfer includes areas to the WM with intensity values below 85 and i want to change that. I'd be thankful for any feedback/links to guides. Best regards, Nils -- Nils B?er Research Assistant with Bachelor Degree (WHB) Psychology and Movement University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401 Email: nils.tobias94(a)gmail.com / nboeer(a)mail.uni-paderborn.de<mailto:nils.tobias94@gmail.com> Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ https://sug.uni-paderborn.de/department/it/<https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/> [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-anima…]<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virenfrei. www.avast.com<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/a… ------------------------------ Message: 3 Date: Wed, 29 Jul 2020 15:51:03 -0500 From: Donelson Berger <donelsongrahamberger(a)gmail.com> Subject: [Freesurfer] Creating .annot file for a mri_decimate downsampeld version of pial surface To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAAKWbtXL5vQOPXEoO6TUeRM_dHowghOYVX=ptXWPE8+GkAMENA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello FreeSurfer Expert, I've run into a problem that I just can't seem to solve. After downsampling teh ?.pial surfaces using mri_decimate to 20,000 surfaces and 10,002 points, I don't know how to create .annot files for the new surfaces I created. I want to be able to tell which ROI each vertex is in for my new surface based off a parcellation. I've been trying to use mri_ca_label, mri_ca_train, and mris_sample_parc, but I can't seem to get anything to work. Do you have any suggestions? Thanks for your help, Donelson Graham Berger -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/d… ------------------------------ Message: 4 Date: Wed, 29 Jul 2020 22:22:47 +0000 From: "Johnson, Hans J" <hans-johnson(a)uiowa.edu> Subject: [Freesurfer] GONE: -make to recon-all To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <9DB20083-D647-47E0-9396-C24308B503B9(a)uiowa.edu> Content-Type: text/plain; charset="utf-8" External Email - Use Caution The release notes for 7.0.0 claim that the -make option is "Gone" from recon-all. This option, however, is still available and does not seem to fail. I am running several thousand data sets on a cluster through Freesurfer 7.1.0, and periodically the process fails for some subjects. In the past the "recon-all -make all" feature was a very convenient way to complete freesurfer runs that were terminated early for some unknown reason Q1) should "recon-all -make all" be avoided for FreeSurfer 7.1.0? Q2) is there an alternate way to "continue form the point where results are missing" in the pipeline? Thanks, Hans -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/f… ------------------------------ Message: 5 Date: Wed, 29 Jul 2020 15:49:44 -0700 From: "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" <ladn(a)email.gwu.edu> Subject: Re: [Freesurfer] fsgd file - glmfit error To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CACE7MB+VaV5UyPsnRSfnyDA8XT0_dDhe1sxd2-rumCf3z0_PDA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Thank you Douglas! On Tue, Jul 28, 2020 at 9:34 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote: > Try putting 1 after GroupDescriptorFile, ie, > > GroupDescriptorFile 1 > > On 7/28/2020 12:21 PM, Lab of Autism and Developmental Neuroscience, > Lab of Autism and Developmental Neuroscience wrote: > > External Email - Use Caution > Here is my fsgd file. > Thank you! > > > On Mon, Jul 27, 2020 at 8:44 PM Douglas N. Greve > <dgreve(a)mgh.harvard.edu> > wrote: > >> Please send the fsgd file >> >> On 7/27/2020 11:34 PM, Lab of Autism and Developmental Neuroscience, >> Lab of Autism and Developmental Neuroscience wrote: >> >> External Email - Use Caution >> Dear Freesurfer experts, >> >> Hope this email finds you well. I am having some trouble with the >> fsgd file for glmfit and I'm confused why. This is the error I'm >> getting when running glmfit: >> >> iMac-Pro:BAP_complete ajobsaid$ mri_glmfit --y >> mrip.rh_volume_F7_BNB.00.mgh --fsgd fsgd_8.fsgd --C Cor_2.mtx --surf >> fsaverage rh --cortex --glmdir contrast2.rh_volume_BNB.glmdir >> gdfRead(): reading fsgd_8.fsgd >> ERROR: FSGDF version 0 unsupported (fsgd_8.fsgd) >> iMac-Pro:BAP_complete ajobsaid$ >> >> If needed, I can send you my fsgd file, but I have triple checked the >> design and format of the file (it is saved as .fsgd), and I'm still >> getting this error message. >> >> Thank you, >> Alex >> >> _______________________________________________ >> Freesurfer mailing >> listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/ma >> ilman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing > listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mai > lman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/2… ------------------------------ Message: 6 Date: Thu, 30 Jul 2020 09:34:12 +0000 From: "Zollei, Lilla,Ph.D." <LZOLLEI(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all Soft Errors To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <DM6PR04MB44127C2DB157BB07AB669F41E3710(a)DM6PR04MB4412.namprd04.prod.outlook.com> Content-Type: text/plain; charset="windows-1252" Hi Elena, What is the age range of your subjects? Best, Lilla ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Elana Sarabin <elana.sarabin1(a)ucalgary.ca> Sent: Wednesday, July 29, 2020 11:02 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Recon-all Soft Errors External Email - Use Caution Hi Freesurfer experts, I am a first time user of FreeSurfer and I haven?t been able to find any threads for how to fix some of my problems. I have a very large dataset and as I am editing on freeview I am noticing that ? or more of my participants have a large area missing in the brainmask.mgz file but the region is visible from the T1.file. In some participant scans the areas missing arent too big however other scans (the photo I attached) have a very large portion of the brain missing. I have tried quite a few things to fix this including re running recon-all, adding control points, and adjusting the wsthresh value, however, none have worked. Wondering if there is a way to fix this kind of error and if there is a way to prevent this from happening as I run recon-all on future participants. In addition, I have been duplicating my files before editing in order to always have the original files as a backup. With some participants when I duplicate the files their T1.mgz file ends up completely white (image attached). I have yet to see this in a none duplicated file however with some participants I can duplicate the files and have no issue. I have attached photos of both of my problems. Any suggestions for fixes would be greatly appreciated. Thanks, Elana -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/d… ------------------------------ Message: 7 Date: Thu, 30 Jul 2020 17:49:49 +0430 From: Hengameh Marzbani <marzbani91(a)gmail.com> Subject: [Freesurfer] bad interpreter: No such file or directory error To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAFn2Bowe=LPArymmLwu=K_3WgEZC0GnG9OkV5qAeBPdZuGV8zw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Freesurfer developers, I have installed FreeSurfer v7 on 2 machines running Ubuntu and made sure that the setting are fine. Also, freeview works by simply typing the freeview command. However,I have tried to run recon-all. but, I have got the following error message on all PCs: *bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory* also The build-stamps.txt file contents: *freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b* Thank you in advance, Best regards, Hengameh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/4… ------------------------------ Message: 8 Date: Thu, 30 Jul 2020 10:20:07 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] overlapping/ superimposing regions of one analysis over another To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <c4e336e0-b3b8-89eb-e59b-1894fdf856b8(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" To obtain the common regions, first binarize the clusterwise significance maps with something like mri_binarize --min 2.0 --i clustersigmap1.mgh --o bin.clustersigmap1.mgh Same for the other groups Then take the intersection fscalc clustersigmap1.mgh and clustersigmap2.mgh -o intersection.mgh On 7/27/2020 2:17 PM, Sunil Khokhar wrote: > > ????????External Email - Use Caution > > To operate the visualization and obtain the common regions of my > between-group difference results and the correlation results in one > image. In other?words, overlapping/ superimposing?my correlation > results on the between-group results (to obtain the common regions > from the two separate analysis). > > Thanks > _______________ > Sunil K Khokhar > PhD Scholar, > Department of Neuroimaging & Interventional Radiology, NIMHANS, > Bengaluru, INDIA. > khokharsunil1(a)gmail.com <mailto:khokharsunil1@gmail.com> > +91-9413101839 > > > On Mon, Jul 27, 2020 at 8:21 PM Douglas N. Greve > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: > > are you asking how to create positive and negative regions or are > you asking how to operate the visualization? > > On 7/25/2020 9:40 AM, Sunil Khokhar wrote: >> >> ????????External Email - Use Caution >> >> Dear Experts, >> >> I have done a between group (2 groups) difference in whole brain >> voxel based cortical thickness using QDEC, which showed >> significant regional differences in certain clusters >> bilaterally?in the brain. I also did a correlation between >> cortical thickness and behavioral scores separately?in these two >> groups. Now, I want to superimpose regions (clusters) which >> showed positive and negative correlation on the?results/ >> regions?I obtained in my between group analysis. How can I do this? >> >> Thanks in advance! >> Sunil. >> _______________ >> Sunil K Khokhar >> PhD Scholar, >> Department of Neuroimaging & Interventional Radiology, >> NIMHANS, Bengaluru, INDIA. >> khokharsunil1(a)gmail.com <mailto:khokharsunil1@gmail.com> >> +91-9413101839 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/7… ------------------------------ Message: 9 Date: Thu, 30 Jul 2020 10:21:14 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Creating .annot file for a mri_decimate downsampeld version of pial surface To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <ec2eef74-6cd8-0c36-dbeb-983240090223(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Use mris_apply_reg --sval-annot lh.your.annot --streg lh.pial lh.pial.decimated --o lh.your.decimated.annot On 7/29/2020 4:51 PM, Donelson Berger wrote: > > ????????External Email - Use Caution > > Hello FreeSurfer Expert, > > I've run into a problem that I just can't seem to solve. After > downsampling teh ?.pial surfaces using mri_decimate to 20,000 surfaces > and 10,002 points, I don't know how to create .annot files for the new > surfaces I created. I want to be able to tell which ROI each vertex is > in for my new surface based off a parcellation. > > I've been trying to use mri_ca_label, mri_ca_train, and > mris_sample_parc, but I can't seem to get anything to work. > > Do you have any suggestions? > > Thanks for your help, > Donelson Graham Berger > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/e… ------------------------------ Message: 10 Date: Thu, 30 Jul 2020 10:26:22 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all Soft Errors To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <78c6cfdd-63ba-9ed1-1c26-fcbc76472ac8(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" for the first error, can you send the recon-all.log file? For the second error, you need to adjust the intensity ranges. For some reason they are coming up as 0s. On 7/29/2020 11:02 AM, Elana Sarabin wrote: > > ????????External Email - Use Caution > > Hi Freesurfer experts, > > I am a first time user of FreeSurfer and I haven?t been able to find > any threads for how to fix some of my problems. I have a very large > dataset and as I am editing on freeview I am noticing that ? or more > of my participants have a large area missing in the brainmask.mgz file > but the region is visible from the T1.file. In some participant scans > the areas missing arent too big however other scans (the photo I > attached) have a very large portion of the brain missing. I have tried > quite a few things to fix this including re running recon-all, adding > control points, and adjusting the wsthresh value, however, none have > worked. Wondering if there is a way to fix this kind of error and if > there is a way to prevent this from happening as I run recon-all on > future participants. In addition, I have been duplicating my files > before editing in order to always have the original files as a backup. > With some participants when I duplicate the files their T1.mgz file > ends up completely white (image attached). I have yet to see this in a > none duplicated file however with some participants I can duplicate > the files and have no issue. I have attached photos of both of my > problems. Any suggestions for fixes would be greatly appreciated. > > > Thanks, > > Elana > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/5… ------------------------------ Message: 11 Date: Thu, 30 Jul 2020 11:31:47 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Coregistration to MNI To: "Camargo, Aldo" <ACamargo(a)som.umaryland.edu>, Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <9af8c73e-46a8-e9b6-4b84-ce507589efed(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" It looks like cvs failed. Can you send the log? Also, please remember to post to the list and not us personally. On 7/30/2020 11:13 AM, Camargo, Aldo wrote: > > ????????External Email - Use Caution > > Hi Douglas, > > > I was able to run the script to create the cvs folder and its files > but still I can not run the script that does the coregistration of the > Pet image to the MNI space. > > I am getting the following error: > > (base) > acamargo@acamargo-System-Product-Name:~/PET/MPRAGE/2006-09-27_14_15_46 > .0/S19445/subj1/mri$ > mri_vol2vol --gcam > /home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/me > anPET.nii.gz > register.dof6.lta > $SUBJECS_DIR/subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z > $FREESURFER_HOME/subject/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 > pet.cvs.2mm.sm00.ni.gz Loading mov > /home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/me > anPET.nii.gz > Loading source LTA register.dof6.lta > Loading GCAM /subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z > ERROR: cannot find or read > /subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z > > > > ---------------------------------------------------------------------- > -- > *From:* Douglas N. Greve <dgreve(a)mgh.harvard.edu> > *Sent:* Wednesday, July 29, 2020 10:39 AM > *To:* Camargo, Aldo <ACamargo(a)som.umaryland.edu>; Freesurfer support > list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] Coregistration to MNI Here is the command > mri_cvs_register --mov $subject --mni --openmp N > > This command can take a very long time to run. The --openmp N > indicates the number of processors to use if you have a multiprocessor > system. Even with N=3, it can take 18 hours. > > > > > On 7/29/2020 12:35 AM, Camargo, Aldo wrote: >> >> ????????External Email - Use Caution >> >> Hi Douglas, >> >> I don't have the folder cvs and I don't have the files bellow: >> >> cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z >> $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta >> >> How can I get these files, >> >> Aldo >> >> --------------------------------------------------------------------- >> --- >> *From:* Camargo, Aldo <ACamargo(a)som.umaryland.edu> >> <mailto:ACamargo@som.umaryland.edu> >> *Sent:* Monday, July 27, 2020 11:46 PM >> *To:* Douglas N. Greve <dgreve(a)mgh.harvard.edu> >> <mailto:dgreve@mgh.harvard.edu> >> *Subject:* Re: [Freesurfer] Coregistration to MNI Thanks a lot >> Douglas for your great input, >> >> Aldo >> --------------------------------------------------------------------- >> --- >> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >> <freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas >> N. Greve <dgreve(a)mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> >> *Sent:* Monday, July 27, 2020 10:46 AM >> *To:* freesurfer(a)nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject:* Re: [Freesurfer] Coregistration to MNI This command will >> allow you to have a registration file and sample into MNI152 2mm >> space >> >> mri_vol2vol --gcam pet.nii.gz register.dof6.lta >> $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z >> $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 >> pet.cvs.2mm.sm00.nii.gz >> >> you can get the registration file with mri_coreg --mov pet.nii.gz --s >> $subject --reg register.dof6.lta >> >> >> >> On 7/26/2020 9:19 AM, Zollei, Lilla,Ph.D. wrote: >>> Hi Aldo, >>> If you have a recon-ned structural MRI corresponding to your PET >>> scan then the answer is yes. >>> Lilla >>> -------------------------------------------------------------------- >>> ---- >>> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu >>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>> <freesurfer-bounces(a)nmr.mgh.harvard.edu> >>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of >>> Camargo, Aldo <ACamargo(a)som.umaryland.edu> >>> <mailto:ACamargo@som.umaryland.edu> >>> *Sent:* Saturday, July 25, 2020 12:19 AM >>> *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> *Subject:* [Freesurfer] Coregistration to MNI >>> >>> ????????External Email - Use Caution >>> >>> Hi Freesurfer experts, >>> >>> I want to coregister a PET image to the MNI space, can I use >>> mri_cvs_register ? >>> >>> Thanks a lot, >>> >>> Aldo Camargo >>> >>> _______________________________________________ >>> 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. > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/d… ------------------------------ Message: 12 Date: Thu, 30 Jul 2020 17:39:06 +0200 From: Ellen Ji <ellen.ji(a)bli.uzh.ch> Subject: [Freesurfer] mri_aparc2aseg: how to remove redundant output labels? To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <24cc8874-81ee-1e68-85ad-b8fe662c4fc3(a)bli.uzh.ch> Content-Type: text/plain; charset="utf-8"; format="flowed" External Email - Use Caution Dear experts, I am running mri_aparc2aseg using two annotations as input (one for each hemisphere), each with 159 labels, and wish to end up with a single output segmentation of 318 labels. However, when I run the below, this is not the case: mri_aparc2aseg \ ??????????????? --s subject1 \ ??????????????? --annot 500_sym.aparc \ ??????????????? --wmparc-dmax 2 \ ??????????????? --labelwm \ ??????????????? --hypo-as-wm? \ ??????????????? --o subject1/mri/parcellation.nii.gz In fact, the output has 680 labels rather than 318 labels. A few questions. - How can I see what exactly the 680 label names are (how to extract from the .nii.gz output file)? Currently, I have just quantified it to be 680 by doing this in matlab: gunzip('parcellation.nii.gz') ???? a = MRIread('parcellation.nii'); ???? u = unique(a.vol(:)); ???? length(u) % total number of labels - I believe the extra labels are from the Freesurfer LUT. How can I make sure they are not added when running mri_aparc2aseg? (such that only my annotation labels are included in the output) Thank you very much, Ellen ***** Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Z?rich ellen.ji(a)bli.uzh.ch homanlab.github.io/ellen/ ------------------------------ Message: 13 Date: Thu, 30 Jul 2020 17:48:25 +0200 From: fsbuild <fsbuild(a)contbay.com> Subject: Re: [Freesurfer] bad interpreter: No such file or directory error To: freesurfer(a)nmr.mgh.harvard.edu Cc: marzbani91(a)gmail.com Message-ID: <1596124105.5f22ebc98f04a(a)trashmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Hengameh, You probably need to install tcsh (and or csh). I would try, $ sudo apt-get install csh tcsh - R.. On Jul 30, 2020, at 09:19, Hengameh Marzbani <marzbani91(a)gmail.com> wrote:        External Email - Use Caution        Hello Freesurfer developers,I have installed FreeSurfer v7 on 2 machines running Ubuntu and made sure that the setting are fine. Also, freeview works by simply typing the freeview command.However,I have tried to run recon-all. but, I have got the following error message on all PCs:bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directoryalso The build-stamps.txt file contents:freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297bThank you in advance, Best regards, Hengameh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/8… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 197, Issue 59 *******************************************

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Freesurfer July 2020