Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

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

1 0

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

1 0

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>

1 0

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!

1 0

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…>

1 0

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

15 Dec '21

1 0

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…>.

1 0

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…

2 1

mri_label2label: one-to-one for subjectNo --> ico
by Krieger, Donald N. 14 Dec '21

14 Dec '21

External Email - Use Caution Dear Bruce, Doug, and everyone, 1. I am projecting labels from a subject's labels onto the icosahedron and note that the mapping is not one-to-one. Because of this, I cannot tell which subject vertex maps to which icosahedron vertex which I need to able to do. What am I missing here? 2. Just double-checking something simple - The center of the icosahedron is as the origin, i.e. 0,0,0, yes? Thanks - Don

2 3

Re: [Freesurfer] Questions about contrasts
by Laura Willers de Souza 14 Dec '21

14 Dec '21

External Email - Use Caution Dear Douglas, Thank you so much for your answer! Sorry, but I don't think I explained myself correctly in the previous email. I want to analyze the difference in cortical thickness between two groups (CU and CI), adjusting for a covariate (cortisol CSF) and the interaction between them. So my model would be: cortical thickness ~ diagnosis + CSF cortisol + diagnosis*CSF cortisol Using the GLM DODS, the contrasts, according to the wiki example (https://secure-web.cisco.com/1PUyQNFnXt6UhBGwXfB_vPfCTd6uW7Jf3dH3GiO0aIPFHh…) would be: * To verify if only the diagnosis regression coefficient is significant (diagnosis changes cortical thickness regardless of cortisol): * 1 -1 0 0 * * To verify if the regression coefficient of the interaction between diagnosis and cortisol is significant (the two change cortical thickness dependently): * 0 0 1 -1 * * To verify if only the cortisol regression coefficient is significant (cortisol changes cortical thickness regardless of diagnosis): * 0 0 0.5 0.5 Are these contrasts corret to represent the model we designed? Thank you so much again! Best regards, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

2 3

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer