Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30071 discussions

Postdoctoral or experienced research position in a Neuroscience/Resilience/Twin Research Program
by Yann Quidé 28 Aug '18

28 Aug '18

External Email - Use Caution Posted on behalf of Dr Justine Gatt. Dear Colleagues Our team is currently advertising a postdoc / experienced research assistant position in a neuroscience research program focusing on wellbeing and resilience in twins. Applications close 28th September. https://www.seek.com.au/job/37080366?_ga=2.13993015.160255953.1535437739-80… <https://www.seek.com.au/job/37080366?_ga=2.13993015.160255953.1535437739-80…> I would appreciate if you could please circulate to your peers and colleagues. Many thanks Justine Dr Justine M Gatt Group Leader and Senior Research Scientist Gatt Resilience Group Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia T +61 2 9399 1812 M PO Box 1165 Randwick Sydney NSW 2031 Australia neura.edu.au <https://www.neura.edu.au/staff/dr-justine-m-gatt/> School of Psychology University of New South Wales Randwick NSW 2052 Australia psy.unsw.edu.au <http://www.psy.unsw.edu.au/contacts-people/research-staff/dr-justine-gatt> research.unsw.edu.au <https://research.unsw.edu.au/people/dr-justine-megan-gatt>

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TRACUAL eddy_correct Usage
by Timothy Hendrickson 28 Aug '18

28 Aug '18

External Email - Use Caution Hello, I notice that within TRACULA 6.0 that eddy_correct is used for the eddy current correction. This is an older tool as compared to eddy, is there a reason that eddy_correct is still used? Have you done cross comparisons between eddy_correct and eddy? If so did you find much difference in eddy current corrections? Thanks! -Tim

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Re: [Freesurfer] questions about Tracula and doeddy=1 or 0
by Yendiki, Anastasia 28 Aug '18

28 Aug '18

This is not entirely surprising. You have a b-value that’s quite high (b=3000) and eddy_correct will not work well with such high b-values, because is tries to register the b=3000 images to a b=0 image, and the b=3000 images do not have enough anatomical detail to be registered correctly. You can “set doeddy = 0" in your config file and first use another preprocessing tool that’s better suited for high-b images like eddy, then run TRACULA on the corrected images. The command that extracts motion measures (dmri_motion) will work with the output of either eddy_correct or eddy (run dmri_motion without arguments for more info). From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Daumail, Loic Jean" <LDAUMAIL(a)mgh.harvard.edu<mailto:LDAUMAIL@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, July 26, 2018 at 1:58 PM 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] questions about Tracula and doeddy=1 or 0 Dear FreeSurfer experts, I had sent several times this email since the last few months, and never obtained any reply. Would anyone be able to provide me little bit of insight please? I am analyzing a dataset (Q-Ball) of subjects with TRACULA on FreeSurfer 6.0. b1=0, b2=3000 s/mm2 and diff directions = 90. Surprisingly the trac-all reconstruction with doeddy =1 was not as good as with doeddy = 0 on average on all the subjects, as in our dataset there were more tracts missing with doeddy=1 among all the subjects, which is a very curious result, shouldn't we get the reverse? ==> should I rely more on the doeddy=0 result then? ==> or should I modify the configuration parameters, such as adding more control points , ... and maybe others? Secondly, we are using the head motion parameters (computed with doeddy=1) to exclude subjects who moved too much. Is that appropriate? In other words, can we trust the motion parameters and exclude subjects on that basis? Thank you for your time and consideration, Sincerely, Loïc Daumail Graduate Intern at Athinoula A. Martinos Center for Biomedical Imaging MGH/HST ________________________________ From: Daumail, Loic Jean Sent: Thursday, July 12, 2018 4:50 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: gdesbord(a)nmr.mgh.harvard.edu<mailto:gdesbord@nmr.mgh.harvard.edu> Subject: questions about Tracula and doeddy=1 or 0 Dear FreeSurfer experts, I am analyzing a dataset (Q-Ball) of subjects with TRACULA on FreeSurfer 6.0. b1=0, b2=3000 s/mm2 and diff directions = 90. Surprisingly the trac-all reconstruction with doeddy =1 was not as good as with doeddy = 0 on average on all the subjects, as in our dataset there were more tracts missing with doeddy=1 among all the subjects, which is a very curious result, shouldn't we get the reverse? ==> should I rely more on the doeddy=0 result then? ==> or should I modify the configuration parameters, such as adding more control points , ... and maybe others? Secondly, we are using the head motion parameters (computed with doeddy=1) to exclude subjects who moved too much. Is that appropriate? In other words, can we trust the motion parameters and exclude subjects on that basis? Thank you for your time and consideration, Sincerely, Loic

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Re: [Freesurfer] Question about Freeview, 20% threshold
by Yendiki, Anastasia 28 Aug '18

28 Aug '18

The output of TRACULA is a probability distribution that tells you how likely each voxel is to be part of the tract that you’re looking at. Voxels with low probability values are not very likely to be part of the tract. Setting the threshold in freeview to 20% means that you only want to display the voxels that have probability values greater than 20% of the voxel with the greatest probability to be part of this tract. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Daumail, Loic Jean" <LDAUMAIL(a)mgh.harvard.edu<mailto:LDAUMAIL@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, July 20, 2018 at 10:13 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: [Freesurfer] Question about Freeview, 20% threshold Dear FreeSurfer experts, I am currently using TRACULA( from freeSurfer 6.0), and on the freeview visualization of merged files of the probability distributions of the tracts, I don't understand the thing about the "20% threshold". Indeed, on the tracula tutorial, it is written that the tracts are displayed in a way that they are at 20% of their maximum threshold. However, what does this mean? Is it the 20% of the most probable paths for each tracts? The adjustment bar on the side of the screen permits to vary this threshold, but when we reduce the level of the threshold, the size of the tracts increase, which seems in contradiction with the previous statements... I then suppose that my guess must be wrong? Thank you for your time and consideration! Sincerely, Loïc

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[TRACULA] eddy_correct /affine registration matrices / motion/ eddy currents
by Daumail, Loic Jean 28 Aug '18

28 Aug '18

Dear FreeSurfer experts, I would like to understand better the principle of eddy_correct: -in which way the eddy currents caused by motion are set apart from the eddy currents caused by fast switching diffusion-encoding gradients? -and then, how are the affine registration matrices reflecting motion computed by eddy_correct considering the previous issues? -does eddy_correct even computes these affine registration matrices(dwi.ecclog)? or is it another tool of dmri_motion? Thanks, Loïc Daumail Graduate intern at Athinoula A. Martinos Center for Biomedical Imaging MGH/HST

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error opening file dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz
by Montserrat Domingo Ayllón 28 Aug '18

28 Aug '18

External Email - Use Caution Hi everybody! I have an error in one of my subjects preprocessing error opening file dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz In the dlabel folder of this subject, the mni folder has the half of the items that the rest of subjects have (2036 vs 4568). It is a subject with severe atrophy, therefore, I don't know if the trac-preproc has exited with errors due to this atrophy or because of other facts that I'm not able to detect. Thank you in advance, Montse

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Parcellation labels error
by Ali,Mohamed Tarek Mohamed 27 Aug '18

27 Aug '18

External Email - Use Caution Hello FreeSurfer Developers, While I am using [vec,labels,cnames] = read_annotation('lh.aparc.annot'), I am getting values in labels which are not found in cnames.table(:,5). These values are 0. I assigned the values to the unknown area. However, when I looked at the number of vertices per brain regions I found that corpuscallosum has no vertices in the DK atlas. This is my first week using a neuroimaging software and Freesurfer is my first software to work on, so I just don't know if that's ok or if there is something wrong. I am attaching the output of a python code I wrote to count the number of vertices per brain region in the left hemisphere of a structural MRI image from our dataset. Thanks in advance, Mohamed T. Ali Ph.D. student, Bioengineering, University of Louisville.

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correlation between blood biomarkers and longitudinal decrease in cortical thickness
by Foad Taghdiri 27 Aug '18

27 Aug '18

External Email - Use Caution Hello, I have done freesurfer (v6) longitudinal preprocessing for 20 subjects (baseline and 2-year follow-up). We also have levels of some blood biomarkers (e.g. tau, neurofilament light) for these subjects at the baseline. I am interested to figure out if the level of blood biomarkers at the baseline is related to the amount of cortical thinning over time, and if so, which brain regions’ cortical thinning are significantly correlated with the blood biomarker. I was wondering if you could please guide me through this analysis and let me know how I can do it. Thanks Best, Foad

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recon-all with mri_ca_normalize (longitudinal)
by miracle ozzoude 27 Aug '18

27 Aug '18

External Email - Use Caution Hello FreeSurfer team, In order to create the longitudinal base after norm.mgz, Is the command below the right way to end recon-all after creating norm.mgz? recon-all -s subjectID -autorecon1 -autorecon2 -i T1image -canorm. Thank you. Best, Paul

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Follow-Up: Longitudinal Processing - Retaining Manual Edits
by KALEY E ELLIS 27 Aug '18

27 Aug '18

External Email - Use Caution Dear FreeSurfer Developers, I posted this question last week, but did not receive a response. Please let me know if I can provide any additional information. We are using your longitudinal processing pipeline (version 6.0) for our study (n=140, 3 timepoints). Our scanner was upgraded a year ago and the a filter was used on the raw images to adjust for hyperintensities in the images due to using a multi-channel coil. At this point, our bases have already been processed and consist of three timepoints with a mix of filters: T1 no filter, T2 no filter, T3 with filter. Since we have invested many resources into the manual editing process, we want to try to retain all the manual edits that have been done to the base. We still have the original scan and the filtered scan for each subject. We have some ideas on how we might be able to retain the edits, but would you be able to provide input regarding whether this seems reasonable? Your feedback is greatly appreciated! Plan A: 1) Create a new T3 cross-sectional with the correct nifti 2) Run recon-all on the existing base Q: Will this retain the previous manual edits AND incorporate the new cross-sectional image? Plan B: 1) Create a new T3 cross-sectional with the correct nifti 2) Create a new base Q: Is it possible to transfer data from old manual edits to a new base? If so, how? Thank you! Kaley Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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