Freesurfer August 2018

freesurfer@nmr.mgh.harvard.edu

104 participants
167 discussions

smoothing only on cortex when using mris_preproc
by Alon Baram 29 Aug '18

29 Aug '18

External Email - Use Caution Hello, When smoothing with mri_surf2surf, it's possible to use the --cortex flag to constrain the smoothing only to cortex (exclude the medial wall and zero it out). Is there a way to tell mris_preproc to do the same (i.e to pass the --cortex flag when it calls mri_surf2surf? thanks!

2 1

create surface mesh from arbitrary volume?
by Russell Butler 29 Aug '18

29 Aug '18

External Email - Use Caution hello, i would like to create a mesh, such as the one in surf/lh.pial, using an arbitrary binary volume. i'm aware that freesurfer can convert the subcortical volume ROIs to surfaces, does anyone know if this can be applied to an arbitrary binary volume? i would like to replicate the script by Anderson Winkler (see below) but instead of on subcortical aseg, on an arbitrary volume that i supply. is this possible? thanks, # Pre-tessellate echo "==> Pre-tessellating: ${s}, ${lab0}" ${FREESURFER_HOME}/bin/mri_pretess \ ${SUBJECTS_DIR}/${s}/mri/aseg.mgz ${lab} \ ${SUBJECTS_DIR}/${s}/mri/norm.mgz \ ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz # Tessellate echo "==> Tessellating: ${s}, ${lab0}" ${FREESURFER_HOME}/bin/mri_tessellate \ ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz \ ${lab} ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth # Smooth echo "==> Smoothing: ${s}, ${lab0}" ${FREESURFER_HOME}/bin/mris_smooth -nw \ ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth \ ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0} # Convert to ASCII echo "==> Converting to ASCII: ${s}, ${lab0}" ${FREESURFER_HOME}/bin/mris_convert \ ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0} \ ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc mv ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc \ ${SUBJECTS_DIR}/${s}/ascii/aseg_${lab0}.srf

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LME Univariate pvalue inconsistent
by Wang, Xiaoyu 29 Aug '18

29 Aug '18

External Email - Use Caution Hello Freesurfer Developers, I'm attempting to use Univariate LME analysis to compare the symptomatic and asymptomatic hemispheres of early stage Parkinson's disease patients. I re-organized the data so that the symptomatic hemisphere is the left hemisphere and the Asymptomatic is the right (by flipping the orig.mgz before recon-all). I followed the LME model tutorial for univariate on the freesurfer wiki and created my qdec.tabel.dat to have the same layout as in the example with group 1 as left hemisphere and group 2 as right hemisphere. I have a design matrix to do a simple linear model containing a group by time interaction with the contrast of [0 0 0 1 0 0] After running the F-test however, I noticed that the p-value was really inconsistent across atlases. I used multiple atlases and noticed that the p-value can be as low as 1.00E-30 for many structures. This is too good to be true especially since after sending the thickness value to a statistician she came back with values greatly different from mine. However, the Bhat values were similar. Can someone give me a hint as to what is going on? Xiaoyu

2 1

fsaverage for a Left vs Right hemisphere Longitudinal Comparison
by Wang, Xiaoyu 29 Aug '18

29 Aug '18

External Email - Use Caution Hello Freesurfer Experts, I am trying to compare the left and right hemisphere of a group of PD patients with Mass-Univarate LME. >From what I can see in the wiki tutorial, the mris_preproc only assembles data from one hemisphere at a time, which is not very usefull if I am doing a hemisphere comparison where each hemisphere is a different group. I am thinking of getting around this issue by flipping each subject time point so that the right hemisphere is on the left and adding it as a new timepoint. For example: S01_1 s01_base S01_1f s01_base S01_2 s01_base S01_2f s01_base However, Can I still create the base file the same way using this? recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all also for the fsaverage, would make_average_subject still work? Xiaoyu

2 1

Manually editing location of surface
by Elena Nicole Dominguez 29 Aug '18

29 Aug '18

External Email - Use Caution Hello FreeSurfer Developers, On the tutorial it states that it is not possible to directly edit the location of a surface. However, on the corresponding video posted onto the website the gentleman mentions being able to accomplish this. I have been trying to locate the literature on how to do this and have not been successful. I am using 'freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c' I would kindly appreciate some help on locating any tutorials or information available. Thank you for your help.

3 5

Seeing Parcels as volumes
by Maedeh Khalilian 29 Aug '18

29 Aug '18

External Email - Use Caution Dear Douglas Greve; Thank you for your great help.I did what you said successfully.Now I have another question. I have used "mri_divide_parcellation" to have more parcels.this command gives me a ".annot" file.How can i change this file into a format such as .nii so i can see the volumes in Mricro? Cheers Maedeh,

2 1

Saving the Results into the Original Space
by Maedeh Khalilian 29 Aug '18

29 Aug '18

External Email - Use Caution Dear FreeSurfer experts, How can I save the result of parcellation and segmentation into the original space? I would appreciate any help. Best regards, Maedeh

1 0

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>

1 0

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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Freesurfer August 2018