Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

Re: [Freesurfer] medial wall metric file
by Alexopoulos, Dimitrios 28 Jan '20

28 Jan '20

External Email - Use Caution Yes, a label or roi metric file of 0 and 1s (preferably 0s for the medial wall vertices) for that can be converted to workbench format. Jim On Jan 28, 2020 5:42 PM, "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> wrote: Attention: This email originated from outside the university. Do you mean you want a binary mask of the medial wall? You can create a mask of the cortical label (?h.cortex.label) with mri_label2label You can then invert that with something like fscalc lh.cortex.mask.mgz not -o lh.medialwall.mask.mgz On 1/28/2020 6:31 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Is there a freesurfer file that contains metric info that delineates the medial wall in the native surface output for an individual? It appears to be associated with the ?lh.aparc.annot file (below). I’d like to be able to export the medial wall metric into Worbench. Thanks. Jim [cid:part1.330140F5.A370F13A@mgh.harvard.edu] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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medial wall metric file
by Alexopoulos, Dimitrios 28 Jan '20

28 Jan '20

External Email - Use Caution Is there a freesurfer file that contains metric info that delineates the medial wall in the native surface output for an individual? It appears to be associated with the ?lh.aparc.annot file (below). I'd like to be able to export the medial wall metric into Worbench. Thanks. Jim [cid:image001.jpg@01D5D600.D5100A80] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] help: fs-fast group level analysis per run
by Rami Hamati 28 Jan '20

28 Jan '20

External Email - Use Caution Thanks Dr. Greve. We've made our script available on github for anyone who may be interested! https://github.com/MolecularImagingLab/fMRI_scripts -- Rami Hamati, MSc. Royal's Institute of Mental Health Research Molecular Imaging Laboratory (MIL) 1145 Carling Ave, Ottawa, ON K1Z 7K4 Rami.Hamati(a)theroyal.ca rhama036(a)uottawa.ca

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what is the argument for arguments for symmetric Geometric Transfer Matrix and two-compartment model (Meltzer Method) in the PETsurfer ?
by Kate Marvel 28 Jan '20

28 Jan '20

External Email - Use Caution Hi Freesurfer community, I would like to know the arguments to use for symmetric Geometric Transfer Matrix and two-compartment model (Meltzer Method) in the petsurfer command "mri_gtmpvc". Thank you, -- kate

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Re: [Freesurfer] Flag for recon-all to output aparc2005 labels (freesurfer 6.0)
by Greve, Douglas N.,Ph.D. 28 Jan '20

28 Jan '20

Not sure, we have not been using that flag in a while. When you look at the volume in freeview, you can see what the code is by clicking on a voxel. You can change the offset by including --base-offset XXX to mri_aparc2aseg, On 1/24/2020 2:40 PM, Grodin, Erica wrote: External Email - Use Caution Hi Doug, Thanks for your reply. I ran the mris_ca_label command manually using the lh.atlas2005_simple.gcs and rh atlas. I then ran the mri_aparc2aseg with the --a2005s flag, which gives me an aparc.a2005s image. However, when I try to extract the VOIs that I need from that image I end up with an empty file and when I look at the aparc.a2005s image, the intensities only seem to go up to the 2000's instead of the 9000's which is what I need for the VOIs. I'm wondering if I am using the wrong .gcs file, but the simple 2005 one is the only one that seems appropriate. Thanks for your help! Erica ---------------------- Erica Grodin, Ph.D. Postdoctoral Fellow University of California, Dept. of Psychology and Psychiatry ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu><mailto:DGREVE@mgh.harvard.edu> Sent: Thursday, January 16, 2020 3:40 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] Flag for recon-all to output aparc2005 labels (freesurfer 6.0) I don't think so, but you can run mris_ca_label by hand. Look in the recon-all.log file for the command, then use the 2005 tif instead of the 2009 tif. I think it should work. On 1/16/2020 3:31 PM, Grodin, Erica wrote: External Email - Use Caution Hello, I am running recon-all on my data using freesurfer 6.0 which is working correctly. However, I need to create some VOIs which labels are only outputted from the aparc2005 set and do not appear in the aparc2009 set; specifically: 9001, 9501 ctx-lh-primary-motor, ctx-rh-primary-motor 9005, 9505 ctx-lh-prim-sec-somatosensory, ctx-rh- prim-sec-somatosensory 9002, 9502 ctx-lh-premotor, ctx-rh-premotor 9004, 9504 ctx-lh-posterior-parietal, ctx-rh-posterior-parietal Is there a flag or some other option to output the 2005 set in addition to the 2009? Thank you for your help, Erica Grodin ---------------------- Erica Grodin, Ph.D. Postdoctoral Fellow University of California, Dept. of Psychology and Psychiatry _______________________________________________ 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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recon exited with errors
by Desel, Tenzin 28 Jan '20

28 Jan '20

Hello FreeSurfer Developers, I'm attempting to run recon-all after unpacking data. It is exiting with errors - mri_cc: no WM voxels found with norm > 40 -- check skull stripping I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb 2) Platform: centos7_x86_64 3) uname -a: Linux lemmiwinks.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you!

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Reconstruction editing
by Jane Tseng 28 Jan '20

28 Jan '20

External Email - Use Caution Dear Freesurfer experts, I would like to ask for some advice about reconstruction editing. We have a subject that doesn't have great image quality, but we would like to try our best to make the data usable. One issue that we have is the pial surface is not capturing all of the gray matter (i.e. some gyri get cut out). I have tried adding control points and it improved in some regions but not all. Below are some examples, the light blue contour is the original pial surface and the red contour is the edited pial surface, the yellow contour is the edited white matter surface. Are there any suggestions on what else can be done? Just wanted to make sure that we've looked into all the options. Thank you!! Best wishes,Jane

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Recommendation for CFT and CWT FreeSurfer analysis
by Martin Juneja 28 Jan '20

28 Jan '20

External Email - Use Caution Hi, I am using Monte-Carlo simulations (for cortical thickness and volume - behavioral analysis) for clusterwise correction for multiple comparisons. My results are either significant at (i) CFT < 0.001 and CWT < 0.1 (i.e., CWT = 0.07) (smoothing 12 mm) for cortical thickness-behavior analysis - with maxima at -4.3 (CFT) or (ii) CFT < 0.05 and CWT < 0.001 (i.e., CWT = 0.0002) (smoothing 10 mm) for cortical volume-behavior - with maxima at -4.53 (CFT) Both the clusters in (i) (lateral orbital frontal) and (ii) (rostral middle) are within the frontal cortex, but not overlapping ! Also, although maxima is at (i) -4.3 and (ii) -4.53, still the clusters do not survive recommended thresholds suggested in https://www.ncbi.nlm.nih.gov/pubmed/29288131 And the FPR in this paper at strong CWT (i..e, 0.001) and liberal CFT (i..e, 0.05) is not calculated. So I was wondering if there is any recommendation from the experts regarding these results, or none of these make sense because I never get CFT < 0.001 and CWT < 0.05 (at-least). Any help would be really appreciated.

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dwi to native transformation
by Sam W 27 Jan '20

27 Jan '20

External Email - Use Caution Hello! I'm trying to create an fsl reg file that maps a dwi image to native anatomical space. 1. I used bbregister to create a reg file that maps the transformation from nodif to freesurfer's conformed space: bbregister --s sub001 --mov nodif.nii.gz --reg nodif2orig.dat --dti --init-fsl --fslmat nodif2orig.mat 2. then I aligned my dwi images to orig.mgz using the reg file from step 1 mri_vol2vol --fstarg --reg nodif2orig.dat --mov dwidata.nii --o dwi-in-freesurfer.nii 3. finally I mapped dwi-in-freesurfer image to native anatomical space mri_vol2vol --target mri/rawavg.mgz --regheader --mov dwi-in-freesurfer.nii --o dwi-in-rawavg.nii However I only get the registration file nodif2orig.mat, which only maps the nodif to freesurfer space? How can I get an fsl.mat for the transformation from freesurfer to native space? mri_vol2vol has no flag to output an fsl-type registration file. Best regards, Sam

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Calculate thickness in a ROI volume
by Larrabee, Matthew 27 Jan '20

27 Jan '20

Hi Karel, These are the commands we would run to calculate thickness in an ROI volume: mri_vol2surf mri_vol2label (please ignore misleading name, will also work on surfaces) mris_anatomicalstats The wiki has documentation on all of these programs, but if you would like further details feel free to reach out! https://surfer.nmr.mgh.harvard.edu/fswiki -Matt

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Freesurfer January 2020