Freesurfer December 2021

freesurfer@nmr.mgh.harvard.edu

56 participants
87 discussions

Re: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter
by Kang, Jee Won 22 Dec '21

22 Dec '21

External Email - Use Caution Hi Bruce, Again, so sorry if this message has been spammed to the mailing list; I kept getting messages that the body of the message was too big whenever I tried to send it with the attachments, so I'm instead sending along a dropbox link to the requested files from a subject with the described problem: https://secure-web.cisco.com/1bc6MB5a_uvCZt5sOF35dk1a-glsFH3pnjNrc9AoxTGiIk… Thank you for your insight and assistance with this! Sincerely, Jee Won ________________________________________ Message: 2 Date: Tue, 21 Dec 2021 15:31:42 +0000 From: "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BY5PR04MB6614B1B44ADDBBB00C9E7109EF7C9(a)BY5PR04MB6614.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Hi Jee Won Can you send us the recon-all.log file? And ideally an example orig.mgz that we can try things on Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Kang, Jee Won Sent: Tuesday, December 21, 2021 9:19 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter External Email - Use Caution Hello all, I found a very common error in our data while I was correcting recons. The lateral ventricles (usually the horns) are being misclassified as white matter in aseg.mgz. This happened in around 1/3 of our 108 subjects. We were able to fix this issue by manually filling in the ventricles in aseg.presurf.mgz and re-running Freesurfer with the command autorecon2-noaseg -autorecon3, but this is obviously quite a labor-intensive fix for a substantial portion of our data. This was also the only way to fix the segmentation - filling in the mislabeled areas as 255 in the wm.mgz did not fix the problem. I'm not sure why Freesurfer is having issues here, as the areas it is mislabeling have very distinct intensity boundaries - the T1 intensity is usually between 20 and 45 in the areas that are being mislabeled. I've attached a screenshot of a subject's aseg.presurf.mgz who had this ventricle segmentation issue, and you can see that a large portion of the right ventricle has just not been segmented properly; the intensity of the area in the aseg.presurf.mgz and wm.mgz volumes is just 0, and it was 41 (R cerebral white matter) in aseg.mgz. Would you be able to provide some insight into why this might have been happening, and what we could do in the future to prevent such extensive manual editing in the future? I can also say that this data was processed with a T2 image as well, and supplying that flag didn't help with the segmentation issue. Thank you, Jee Won

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Postdoctoral Research Fellow position in Neuroimaging
by Aganj, Iman 20 Dec '21

20 Dec '21

The Laboratories for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging invites applications for a Postdoctoral Research Fellow position at the Massachusetts General Hospital and Harvard Medical School. The project will consist of human brain connectivity analysis, brain image segmentation, and/or multimodal MRI data harmonization, with application in studying Alzheimer's disease. The appointment is for two years with the possibility of a third year based on performance and the availability of funding. The project involves analyzing structural and functional brain networks through diffusion-weighted and functional MRI as well as brain structure segmentation, and examining the relationship of brain connections with different stages of dementia. The Research Fellow will be supervised by Dr. Iman Aganj, in close collaboration with Dr. Bruce Fischl. The candidate is required to have: * a Ph.D. in engineering, neuroscience, or a related field by the start date, * strong programming skills in MATLAB, Python, or a similar environment, and * a medical image analysis background. Familiarity and experience with any of the following will be a plus: neuroimaging, connectomics, medical image segmentation, diffusion-weighted MRI, functional MRI, MRI data harmonization, machine/deep learning, graph theory, dementia studies, mathematical modeling. Interested applicants are invited to send a cover letter describing research interests and experience, an up-to-date CV, and names and contact information of three references to: iaganj(a)mgh.harvard.edu<mailto:iaganj@mgh.harvard.edu> https://partners.taleo.net/careersection/ghc/jobdetail.ftl?job=3180937 Iman Aganj Assistant Professor of Radiology Harvard Medical School Associate Investigator Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital

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MRI Artifact
by Marilena Wilding 20 Dec '21

20 Dec '21

External Email - Use Caution Dear Freesurfers, while acquiring our fMRI data we stumbled upon an artifact in our structural data none of us has ever seen before. I wanted to ask, if maybe you have seen something like this and have an idea about its origin? We followed your suggesed morphometry protocol (without multiecho, based on a standard MRAGE siemens protocol --> https://secure-web.cisco.com/10ieaIo5lzXeZK3jmi_ma4CitDtsCtqHlLkGJmLgjS_Ihl… ). Our structural acquisition parameters were: 192 slices, voxel size = 1 x 1 x 1 mm, TR = 1600 ms, TE = 2360 ms, TI = 1200 ms, flip angle = 9 °, FOV = 256 mm, bandwidth = 250 Hz/ Px, echo spacing = 6.78 ms. We were using a 3 Tesla Magnetom Vida scanner with a 64-channel head coil. There's a picture of the artifact attached. Thanks a lot, we'd be really curious to know, whether you've seen somehting like this before! Best, Marilena Wilding MORPHOMETRY PROTOCOLS (January 2009) MPRAGE<https://secure-web.cisco.com/10ieaIo5lzXeZK3jmi_ma4CitDtsCtqHlLkGJmLgjS_Ihl…> Acquisition time: 8:28 Voxel size: 1.0 x 1.0 x 1.0 mm3 Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, phase encoding anterior-posterior (readout superior-inferior) (3D encoding) Timing: TR 20 ms, TE 1.85+n2.0 ms (n = 0,..,7), bandwidth 651 Hz/px for all echoes (bipolar readout trajectory) RF: non-selective excitation at 30° and 5° (then 20°, then 3°) surfer.nmr.mgh.harvard.edu

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Re: [Freesurfer] Freeview Transform Volume tool - output nifti keeps rotations but loses translations
by fsbuild 17 Dec '21

17 Dec '21

External Email - Use Caution Hello Chris, The XCB error could mean X forwarding is not setup correctly with however you connect to the machine.  It might help to know how you connect to the machine, what version of Ubuntu Linux you are running and if Ubuntu is native or running in a VM or some virtualized/container environment like WSL on Windows. - R. On Dec 17, 2021, at 11:41, Christopher Panks <cpanks(a)uw.edu> wrote:        External Email - Use Caution        Hi Ruopeng, I can send the niftis to an individual, but I cannot post them to a listserv. Version info:freesurfer-linux-ubuntu18_x86_64-dev-20211028-42af00dFreeView Version 3.0 Build Oct 28 2021 08:53:38 I get this warning when I start FreeView:X server does not support XInput 2failed to get the current screen resourcesQXcbConnection: XCB error: 1 (BadRequest), sequence: 165, resource id: 90, major code: 130 (Unknown), minor code: 47QXcbConnection: XCB error: 170 (Unknown), sequence: 178, resource id: 90, major code: 146 (Unknown), minor code: 20QXcbConnection: XCB error: 170 (Unknown), sequence: 178, resource id: 90, major code: 146 (Unknown), minor code: 20 Thank you so much for your help! Chris Panks  From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Wang, RuopengSent: Tuesday, December 14, 2021 6:12 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] Freeview Transform Volume tool - output nifti keeps rotations but loses translations What version of Freesurfer are you using? Would it be possible to send us the volume files before and after the rotation?  Best,RuopengOn Dec 14, 2021, at 6:10 PM, Christopher Panks <cpanks(a)uw.edu> wrote:         External Email - Use Caution         I’m trying to get images of post-mortem brains, some from cadavers, some excised, into standard space. I’m new to Freeview, so I’m not sure if I’m doing something wrong, or my expectations are wrong. I find the Transform Volume tool easy to use to get an image that is correctly rotated, and shifted so that the image is centered in the frame. The image looks great in the Freeview panes. Upon saving and then opening  the output nifti, I find the rotational changes have stuck, but the image is as off-center as the original, with the coronal and axial off towards one side, and the sagittal not at the midbrain. When saving the image, I click on ‘Save Volume as…’, leave the boxes unchecked (‘do not resample’’, and ‘crop to’ ), I modify the file name, then click OK.  I don’t click on ‘Move Center…’, I don’t check ‘Apply to all…’. My expectation is that the image would not only be correctly rotated, but that it would also be centered. Is that the expected behavior here? I’ve tried the ‘Move Center to Current Cursor Location’, and the Apply to all visible volumes, and see no difference. The off-centeredness is visible in multiple viewers, FSLEyes, MRIcroGL, and ROIEditor. The directions seem so simple and clear, I’m just baffled. Thank you!_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] 6187 Illegal instruction Error
by fsbuild 16 Dec '21

16 Dec '21

External Email - Use Caution The ${FSLDIR}/bin/bet script is calling the ${FSLDIR}/bin/bet2 binary which is failing/core dumping, but I don’t see from the output what that exact command is other than "${FSLDIR}/bin/bet2 $IN $OUT $bet2opts”. Your FSLDIR environment variable is apparently set to the latest fsl version,/autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit/6.0.4 But the “current” link there under /autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit  points to revision 5.0.7.  So I’m wondering if FSLDIR is set correctly given it’s not what current points to and that 6.0.4 binary does not appear to work. - R. On Dec 16, 2021, at 15:59, Kaplan, Elizabeth <elizabeth_kaplan(a)brown.edu> wrote:<trac-all.log>

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6187 Illegal instruction Error
by Kaplan, Elizabeth 16 Dec '21

16 Dec '21

External Email - Use Caution I am working on processing diffusion data with Tracula however I am running into an error that reads " line 399: 6187 Illegal instruction". I have not been able to find any guidance in the mailing list archives. My Trac-all.log and configuration file are attached below. Any suggestions? Thank you!

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Re: [Freesurfer] Longitudinal BASE, missing data and potential time skew?
by Jacob Levenstein 15 Dec '21

15 Dec '21

External Email - Use Caution Good evening Martin, Thank you for the quick reply and for the considerations. Much appreciated, Jacob ________________________________ Message: 9 Date: Wed, 15 Dec 2021 06:55:48 +0000 From: "Reuter, Martin,Ph.D." <MREUTER(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal BASE, missing data and potential time skew? To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <8A86E65D-345B-4CBC-BBFB-C948D0ED4CB7(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Jacob, whenever there is is systematic difference, there is also potential for a bias. In your specific situation no one knows how large this bias could be. I would think it will not really be measurable, as the base is only used for initialisation and within such a small time frame, the methods should be flexible enough to fine-tune to the final time points, independent of where the initialisation starts. So I would not be worried too much. I also don?t know the numbers of your situation. E.g. if the majority of subjects has 4 time points and only some are missing one in the middle, I would be worried even less. The only concern would be when lots of subjects miss one of the middle time points and when there is a strong bias across your variable of interest (e.g. disease group). For example, most healthy are missing time point 3 and most disease are missing time point 2. That setting could be problematic (and as I said above, even that setting probably is not problematic). The weighting you describe does not really work. To increase robustness we are using a voxel-wise intensity median to create the base image. If you are really concerned (e.g. because of a strong bias across groups), you could create the base from the first and last time point only, then add the two or one additional middle time points to that base later. That way all are processed in a similar way. I once created an -add-tp option for adding time points later without re-processing base and all longs. Best, Martin On 14. Dec 2021, at 04:24, Jacob Levenstein <jacob.levenstein(a)ndcn.ox.ac.uk<mailto:jacob.levenstein@ndcn.ox.ac.uk>> wrote: Dear Freesurfer friends, It seems that prior messages* on longitudinal recon with missing timepoints have suggested that it is okay for a subset of participants to include different numbers of timepoints into the longitudinal pipeline, so long as there is not a systematic bias (e.g., one group consistently contains more scans than another group, etc.). Assuming that is still true, I am working with an adolescent dataset from 11 year-olds scanned every 3 months for a year (4 scans total). For participants missing a scan at either timepoint 2 or timepoint 3, I was wondering if creating the BASE/subject-specific template from only three sessions might introduce a temporal bias toward either timepoint 1 (i.e., formed from timepoints 1, 2 & 4), or bias toward timepoint 4 (i.e., formed from timepoint 1, 3 & 4). With consideration to the developmental changes we anticipant measuring over the year, would you be concerned with the potential early vs late skew in the BASE for these missing data cases? If so, for the missing timepoint participants, I was wondering if I should then avoid generating their subject-specific templates in a way that imposes an even weighting across the three timepoints (i.e., .33 each), and instead adjust the weighting of each timepoint relative to time acquired over the year (e.g., temporal based average), such that timepoint 1 is weighted at .25 and timepoint 2 and 4 are weighted at .375. If this is not a sensible approach, could you please let me know what you think best? Thank you for your insight! Much appreciated, Jacob * MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1HAQOcN7NCopD74rm5eEY_F21rM1W3QVvMKlsVL_Htsl8x…<https://secure-web.cisco.com/13XDoOLfZ54QTh8NENJtaYSGUInOnTixvVUeeTP66Z4AcO…> * MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1lMiThDqj19ucfm-HrTiY08cVplcdglC_y-c7X04d17nQk…<https://secure-web.cisco.com/1ivSG2acZebGirLVnyV8qW29ZHDaGha1z3dT3TsM9w986h…>

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Please remember to cite FreeSurfer in your OHBM abstract. Thanks!
by Douglas N. Greve 15 Dec '21

15 Dec '21

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Using several scanners as covariates in Qdec
by Nilab Nasrullah 15 Dec '21

15 Dec '21

External Email - Use Caution Hello, I am sending you this email again since it has not been posted and I haven't got a response from you. I am doing a cortical thickness analysis for a research project in Qdec. Since we have gathered the MRI-scans from different sites and used different scanners, I want to use 6 different scanners as covariates in the analysis. I have tried with making 6 columns and entered 1 for the subjects that used a specific scanner and entered zeros in all the other spaces. This has not worked but it works to to have three differetent scanners as covariates. Do you have a suggestion on what I can do? Thanks in advance, Nilab När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://secure-web.cisco.com/1xPxeRGBEaxLlTyN7VSDHFHB5fWEy5UrAK6QuJDXKufO37…>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://secure-web.cisco.com/1kBKH1iJP86S39drFgoihHyRdAU2RCkw19J7AILhGtsEyu…>.

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Longitudinal BASE, missing data and potential time skew?
by Jacob Levenstein 15 Dec '21

15 Dec '21

External Email - Use Caution Dear Freesurfer friends, It seems that prior messages* on longitudinal recon with missing timepoints have suggested that it is okay for a subset of participants to include different numbers of timepoints into the longitudinal pipeline, so long as there is not a systematic bias (e.g., one group consistently contains more scans than another group, etc.). Assuming that is still true, I am working with an adolescent dataset from 11 year-olds scanned every 3 months for a year (4 scans total). For participants missing a scan at either timepoint 2 or timepoint 3, I was wondering if creating the BASE/subject-specific template from only three sessions might introduce a temporal bias toward either timepoint 1 (i.e., formed from timepoints 1, 2 & 4), or bias toward timepoint 4 (i.e., formed from timepoint 1, 3 & 4). With consideration to the developmental changes we anticipant measuring over the year, would you be concerned with the potential early vs late skew in the BASE for these missing data cases? If so, for the missing timepoint participants, I was wondering if I should then avoid generating their subject-specific templates in a way that imposes an even weighting across the three timepoints (i.e., .33 each), and instead adjust the weighting of each timepoint relative to time acquired over the year (e.g., temporal based average), such that timepoint 1 is weighted at .25 and timepoint 2 and 4 are weighted at .375. If this is not a sensible approach, could you please let me know what you think best? Thank you for your insight! Much appreciated, Jacob * https://secure-web.cisco.com/13XDoOLfZ54QTh8NENJtaYSGUInOnTixvVUeeTP66Z4AcO… * https://secure-web.cisco.com/1ivSG2acZebGirLVnyV8qW29ZHDaGha1z3dT3TsM9w986h…

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Freesurfer December 2021