Freesurfer October 2018

freesurfer@nmr.mgh.harvard.edu

113 participants
156 discussions

denoising and recon-all
by Lisa Crystal Krishnamurthy 11 Oct '18

11 Oct '18

External Email - Use Caution Hi, I have found that denoising the MPRAGE prior to FS recon-all seems to improve the segmentation (see attached pdf). However, it is not clear if the denoising algorithm may cause some signal intensity changes (especially in voxels with partial voluming at the edge of the brain) that violate assumptions of recon-all. Could you help me understand what the assumptions of your algorithm are, and what I need to do to make sure my images conform to those assumptions? Your help is greatly appreciated. Best, -Lisa

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Recon-all with/without T2 give the same stats
by Jianzhong Chen 11 Oct '18

11 Oct '18

External Email - Use Caution Dear All, I tried recon-all with/without T2 image using FS 5.3.0. Then I found that the aseg stats and aparc stats with/without T2 are exactly the same. When I check the pial surfaces, I can see that they are very similar but not the same. So is it reasonable to see exactly the same stats? An example of the pial surfaces with/without T2 is attached here. The red line is lh.pial with T2 and the yellow line is the lh.pial without T2 My command for recon-all with T2 is: recon-all -s ${subject} -i T1.nii -all -T2 T2.nii -T2pial -sd ${T2_dir} My command for recon-all without T2 is: recon-all -s ${subject} -i T1.nii -all -sd ${T1_dir} Thanks, Jianzhong

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Difference between 2 mgh files in surf dir (or: effects of 'mri_surf2surf --prune' without smoothing)
by ts+ml＠rcmd.org 11 Oct '18

11 Oct '18

External Email - Use Caution Dear FreeSurfer experts, what is the difference between the following 2 files found in a subject's surf/ directory: * file #1: lh.area.fsaverage.mgh * file #2: lh.area.fwhm0.fsaverage.mgh I see in the logs (<SUBJECT>/scripts/recon-all.log), that file #2 is generated from file #1 by running the following command: mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm0.fsaverage.mgh --cortex I know that if fwhm > 0, spatial smoothing will be applied. But what happens if fwhm is 0? From a quick comparison of the data in both files, they seem to be identical, but the hashes of the files differ. Is the difference only about the header? Thanks for your help, -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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masking cortical thickness
by N Saf 11 Oct '18

11 Oct '18

External Email - Use Caution Dear Freesurfer Experts, I wonder how can I show the cortical thickness surface on just one region of my interest in Freeview. assume that I want to see the thickness surface of one of the regions in DKTatlas. does it work if I make a binary mask of that specific region on aparcDKTatlas.annot and then multiply it to the ?h.thickness surface ?? any help will be appreciated. Best Regards, Nazanin

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Pet Surfer
by David.Mackarthy 10 Oct '18

10 Oct '18

External Email - Use Caution Dear Dr Greeve, I am following petsurfer pipeline to do surface based analysis of PET-FDG data and I have interest in doing partial volume correction. I would like to inquire about: 1) Can partial volume correction be applied on white mater, or just on gray matter? 2) Can partial volume correction be applied between gray matter and CSF? According to Muller-Gartner (MG) Method we segment the brain to gray/white and csf, then we apply partial volume correction only on gray matter. why not on the other parts. I apologies if my question is basics and I appreciate your input. Thanks for publishing this valuable manuscript https://www.ncbi.nlm.nih.gov/pubmed/26915497 With all respect! Dev

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Moving VOI to FreeSurfer Space
by Sarosh, Cyrus 10 Oct '18

10 Oct '18

External Email - Use Caution Hello FreeSurfer Experts, I'm trying to find the best method and command to move a hand drawn VOI in original MRI space to FreeSurfer space. These scans have already been ran through the entire FreeSurfer process and the hand drawn VOIs have already been converted to .mgz files. Thanks for your help Thanks, Cyrus Cyrus Sarosh [Description: Description: Description: Description: Description: Description: Description: cid:image002.png@01CC3BB7.F8D9A990] Research Area Specialist Associate Department of Radiology Functional Neuroimaging, Cognitive and Mobility Laboratory Domino's Farms Lobby B Suite 1200 24 Frank Lloyd Wright Dr PO BOX 362 Ann Arbor, MI 48106 t: 734-998-4790 f: 734-998-8403 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Re: [Freesurfer] error glm-fit-sim (message 11)
by Caroline Beelen 10 Oct '18

10 Oct '18

External Email - Use Caution Few clusters survive glm fit. No clusters seem to survive glm-fit-sim (when visualizing). However, I'm not sure if I should also see this in a text file. Opening cache.th40(or 30).abs.sig.cluster.summary it seems to have found no clusters. At least, under the line ClusterNo Max VtxMax Size MNIX MNIY etc. nothing is written. But does a lack of significant clusters also explain the weird messages of "colortable with 1 entries read (originally none)" (& "CTABisEntryValid: index -1 was OOB" & "Resource temporarily unavailable") that show up in the terminal? Thanks very much, 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: dinsdag 9 oktober 2018 18:00 Aan: freesurfer(a)nmr.mgh.harvard.edu Onderwerp: Freesurfer Digest, Vol 176, Issue 9 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. FW: RE: error glm-fit-sim (Caroline Beelen) 2. Re: output values of vertices on surface into a textfile (Sims, Sara A) 3. Re: output values of vertices on surface into a textfile (Bruce Fischl) 4. Re: output values of vertices on surface into a textfile (Sims, Sara A) 5. Re: Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab (Pradeep) 6. Re: Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab (Iglesias Gonzalez, Eugenio) 7. hippocampal subfields (Marcel Heers) 8. Re: hippocampal subfields (Iglesias Gonzalez, Eugenio) 9. Re: Difference between 6.0.1 and 6.0.0 (Dicamillo, Robert) 10. Talairach failed in monkey brain (Frehiwot Woldeyes) 11. Re: FW: RE: error glm-fit-sim (Greve, Douglas N.,Ph.D.) 12. Mri Convert Help (Justin Arnett) 13. Re: Mri Convert Help (Greve, Douglas N.,Ph.D.) 14. Re: Recon-all with/without T2 give the same stats (Greve, Douglas N.,Ph.D.) 15. Re: Recon-all with/without T2 give the same stats (Jianzhong Chen) 16. m.khalilian(a)sutech.ac.ir sent you files via WeTransfer (WeTransfer) 17. very bad result using "mris_ca_train" and "mris_ca_label" (Maedeh Khalilian) 18. Re: Talairach failed in monkey brain (Greve, Douglas N.,Ph.D.) 19. Re: Recon-all with/without T2 give the same stats (Greve, Douglas N.,Ph.D.) 20. Re: very bad result using "mris_ca_train" and "mris_ca_label" (Bruce Fischl) 21. Re: Extract individual vertex thickness values from cortical parcellations (Greve, Douglas N.,Ph.D.) 22. Re: nu_correct disk i/o issues (Greve, Douglas N.,Ph.D.) 23. Re: masking cortical thickness (Greve, Douglas N.,Ph.D.) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Oct 2018 16:12:06 +0000 From: Caroline Beelen <caroline.beelen(a)kuleuven.be> Subject: [Freesurfer] FW: RE: error glm-fit-sim To: "freesurfer-bounces(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu>, "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4051d561c94b40e0b641202b7bad7192(a)ICTS-S-EXMBX25.luna.kuleuven.be> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution The command: gop@gop-linux:~/freesurfer$ freeview -f $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot -viewport 3d The output: reading colortable from annotation file... colortable with 1 entries read (originally none) colortable with 1 entries read (originally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) The command with a bit less strict significance level: gop@gop-linux:~/freesurfer$ freeview -f $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=3,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot -viewport 3d The output: reading colortable from annotation file... colortable with 1 entries read (originally none) colortable with 1 entries read (originally none) (and then it says no more). Both commands visualize the data, but no clusters are found. Is this how it should be? Does it mean that there is a problem with reading colortables or not? Best, Caroline Message: 2 Date: Mon, 1 Oct 2018 17:10:28 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> Subject: Re: [Freesurfer] error glm-fit-sim 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>> Message-ID: <504d6069-399f-163d-39a9-dcc6c02d32f9(a)mgh.harvard.edu<mailto:504d6069-399f-163d-39a9-dcc6c02d32f9@mgh.harvard.edu>> Content-Type: text/plain; charset="Windows-1252" What says that? What command are you running? What is the other terminal output? On 10/01/2018 04:54 AM, Caroline Beelen wrote: > > ????????External Email - Use Caution > > Dear FS, > > I followed the group analysis page for glm analysis and it worked fine > until the final step. I?m using version 5.3. After performing > glm-fit-sim it says ?glm-fit done? (for all files), but when trying to > open these it says: > > ?Reading colortable from annotation file? > > Colortable with 1 entries read (originally none) > > Colortable with 1 entries read (originally none) > > CTABisentryvalid: index -1 was 00B > > Resource temporarily unavailable > > CTABisentryvalid: index -1 was 00B > > Resource temporarily unavailable > > Resource temporarily unavailable? > > (etc..) > > It opens, but nothing is visible and I have the feeling it cannot open > color files?? > > MRI glmfit gives positive clusters for some values. I therefore used > the abs sign for glm-fit-sim. > > What might be wrong? > > Thanks. Caroline

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Re: [Freesurfer] Disjointed thalamic nuclei segmentation
by Iglesias Gonzalez, Eugenio 10 Oct '18

10 Oct '18

External Email - Use Caution Thanks, Niels. It is definitely a matter of hyperintensity of voxels close to the lateral boundary, particularly in the anterior region (which has a fuzzy boundary with the white matter in first place). Whether these hyperintensities are due to MS pathology, that I do not know (I’m really not the person to tell…). These could be cleaned up with postprocessing (e.g., filling holes, or using a Markov Random Field), but the impact on the volumes would be negligible. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: Niels Bergsland <theniels(a)gmail.com> Date: Wednesday, 10 October 2018 at 15:42 To: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> Subject: Re: [Freesurfer] Disjointed thalamic nuclei segmentation Hi Eugenio, Thanks for the lightning fast response! :) I've attached them here. It looks like it might actually be the opposite in this case in that the voxels here are darker. Some of the cases are MS patients and so it's conceivable that they have thalamic lesions. Admittedly though, I have not really spent time in the past looking for thalamic lesions on T1-weighted images and this hasn't been an issue in the past since the thalamic segmentation in the aseg doesn't end up being affected by these voxels with lower intensities. If you would like to look at some other cases or need other outputs, just let me know and I'm happy to send them along! Thanks again, Niels On Wed, Oct 10, 2018 at 4:30 PM Iglesias Gonzalez, Eugenio <e.iglesias(a)ucl.ac.uk<mailto:e.iglesias@ucl.ac.uk>> wrote: External Email - Use Caution Thanks, Niels. I suspect the problem is that, for some reason, such voxels have much brighter intensity than their surroundings, and are classified as white matter / reticular nucleus. But that shouldn’t be happening that far from the lateral boundary of the thalamus… Can you please send us norm.mgz and the thalamic segmentation file, so I can take a look? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Niels Bergsland <theniels(a)gmail.com<mailto:theniels@gmail.com>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, 10 October 2018 at 15:22 To: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Disjointed thalamic nuclei segmentation External Email - Use Caution Hi Eugenio, Thank you again for the fantastic thalamic nuclei segmentation tool! I'm going through and QC'ing a batch of subjects that were processed through the pipeline. Data was originally processed with freesurfer-6.0.0 and then processed through the thalamic nuclei stream (dev-20180818-e30e6f9). I have found that for some cases, there are some isolated patches of voxels that are disconnected and seemingly in the wrong place. I've noticed it primarily for the MDm and my impression is that it tends to happen more in the right hemisphere. I've attached a sample image to show you what I mean. The red cross has been placed on a set of these voxels. It is not the case that they are connected in 3D. Any input is appreciated and thanks again! If it can be useful, I'm happy to upload the data -Niels _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Disjointed thalamic nuclei segmentation
by Niels Bergsland 10 Oct '18

10 Oct '18

External Email - Use Caution Hi Eugenio, Thank you again for the fantastic thalamic nuclei segmentation tool! I'm going through and QC'ing a batch of subjects that were processed through the pipeline. Data was originally processed with freesurfer-6.0.0 and then processed through the thalamic nuclei stream (dev-20180818-e30e6f9). I have found that for some cases, there are some isolated patches of voxels that are disconnected and seemingly in the wrong place. I've noticed it primarily for the MDm and my impression is that it tends to happen more in the right hemisphere. I've attached a sample image to show you what I mean. The red cross has been placed on a set of these voxels. It is not the case that they are connected in 3D. Any input is appreciated and thanks again! If it can be useful, I'm happy to upload the data -Niels

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Postdoctoral Fellowship Positions in Traumatic Stress Disorders
by Emma Brown 10 Oct '18

10 Oct '18

External Email - Use Caution POSTDOCTORAL FELLOWSHIPS IN TRAUMATIC STRESS DISORDERS Collaborating research groups at the VA Boston Healthcare System anticipate up to two NIMH-funded postdoctoral fellowships to begin by September 2, 2019. These two-year training positions are designed to prepare researchers for academically-oriented careers in the psychology and neurobiology of stress-related disorders. Previous fellows have launched successful careers in universities and academic medical settings. Candidates with backgrounds in neuroimaging and/or genetics are encouraged to apply. The fellowship program is affiliated with Boston University School of Medicine and is located primarily at the Jamaica Plain Campus of VA Boston. Affiliated centers include the Behavioral Science and Women's Health Sciences divisions of the National Center for PTSD, the Translational Research Center for TBI and Stress Disorders, the Neuroimaging Research for Veterans Center, the VA National Center for PTSD Brain Bank, and the Center for Healthcare Organization and Implementation Research. These programs offer outstanding resources including existing datasets, technical support personnel, well-equipped laboratories, advanced computing facilities, and a broad range of professional expertise. The anticipated salary and benefits package is competitive, and supplemental funds will be available to support further coursework and other educational opportunities, conference attendance, and travel. The program offers training in several core areas. Candidates may contact the following program leaders prior to application for more information about the specific cores:Clinical Neuroscience and Neuroimaging(David Salat salat(a)nmr.mgh.harvard.edu) Molecular Biomarkers and Genetics (Mark Miller: mark.miller5(a)va.gov) Assessment, Diagnosis, and Epidemiology (Brian Marx:brian.marx@va.gov), Treatment Development and Optimization (Denise Sloan:denise.sloan@va.gov), and Implementation and Dissemination (Terry Keane:terry.keane@va.gov). Fellows will have the opportunity to participate in ongoing research projects conducted by program faculty, initiate independent research projects, conduct secondary analyses on existing data sets, prepare grant applications to federal and other funding agencies, and learn about all aspects of laboratory management. Each fellow will have a senior faculty member assigned to serve as a primary mentor. For license-eligible clinical psychology fellows, arrangements are available outside the program to provide direct clinical services to patients under the guidance of a clinical supervisor. Materials will be reviewed and interviews arranged on a first-come basis. Preliminary applications should include a statement of interests and goals, a curriculum vita, and three professional references that should be sent directly by the recommendation writer. Applicants must be U.S. Citizens and have completed all requirements for their doctoral degree prior to starting the program. Minority candidates are strongly encouraged to apply. Applications should be submitted electronically no later than December 3, 2018 to Denise Sloan, Ph.D. (denise.sloan(a)va.gov) The VA Boston Healthcare System is an equal opportunity employer.

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Freesurfer October 2018