Freesurfer June 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
140 discussions

Re: [Freesurfer] PVC to calculate myelin maps
by Marina Fernández 01 Jun '21

01 Jun '21

External Email - Use Caution Thank you very much for your response Doug. What PVC method is most recommended to use to calculate the T1 / T2 ratio (RBV or MG)? And what value of PSF should we specify to calculate this ratio? To my knowledge, this is an acquisition related parameter and if I set it to 0 I will turn off PVC. Best wishes, Marina. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Douglas N. Greve <https://secure-web.cisco.com/1y-OD2P8BWHc0h287Xl8Diwwr6Ds9fMYa9s6RyGJbPbpYx…> Mon, 31 May 2021 17:39:23 -0700 <https://secure-web.cisco.com/1cF0PzjgERhEsaW2ZJdBauXH4XR9YM93MndhHQk1vpHHyU…> Yes, you can use PETsurfer. I would apply it to the ratio On 5/28/2021 10:25 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I want to calculate myelin maps using the ratio of T1w and T2w MRI images. I saw that the correction of partial volume effects can be used to create the maps (Shafee, Buckner & Fischl, 2015)*. Can I use the PVC functions of PetSurfer for this purpose? And in case I can: Should I apply PVC only on T1? Or also in T2? Which T1 should I use? The original T1 or the T1 with corrections (for example, the nu.mgz file that is corrected for variations in intensity)? Any other advice for calculating myelin maps would be welcome. Thank you in advance, Marina *Link: *MailScanner has detected a possible fraud attempt from " secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1QZOfvqmKfuLQOn-6qhxRHDDmKDXv8lZm-TGv73nobyUAH… < https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsO… >

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mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)
by Diógenes Bispo 01 Jun '21

01 Jun '21

External Email - Use Caution Hi Freesurfer team. I made the following command: #!/bin/tcsh setenv study $argv[1] foreach hemi (lh rh) foreach smoothing (10) foreach meas (volume) mris_preproc --fsgd FSGD/{$study}.fsgd \ --cache-in {$meas}.fwhm{$smoothing}.fsaverage \ --target fsaverage \ --hemi {$hemi} \ --out {$hemi}.{$meas}.{$study}.{$smoothing}.mgh end end end ---- #!/bin/tcsh set study = $argv[1] foreach hemi (lh rh) foreach smoothness (10) foreach meas (volume) mri_glmfit \ --y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \ --fsgd FSGD/{$study}.fsgd dods \ --C Contrasts/Contrast-1_group.diff.mtx \ --C Contrasts/Contrast-2_group-x-age.mtx \ --C Contrasts/Contrast-3_group-x-icv.mtx \ --C Contrasts/Contrast-4_group-x-age-x-icv.mtx \ --C Contrasts/Contrast-5_GCCV.intercept.mtx \ --C Contrasts/Contrast-6_GCCV.age.mtx \ --surf fsaverage {$hemi} \ --cortex \ --glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir \ --eres-save end end end ---- #!/bin/tcsh setenv study $argv[1] foreach meas (volume) foreach hemi (lh rh) foreach smoothness (10) foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir) mri_glmfit-sim \ --glmdir {$dir} \ --grf 2.0 neg \ --cwp 0.05 \ --2spaces \ end end end end I have the following error: ... mri_surfcluster --in rh.volume.covid.10.glmdir/Contrast-1_group.diff/sig.mgh --mask rh.volume.covid.10.glmdir/mask.mgh --cwsig rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.mgh --sum rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.summary --ocn rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.masked.mgh --no-fixmni --csd-out rh.volume.covid.10.glmdir/csd/all.grf.th2.0.neg-Contrast-1_group.diff.csd --fwhm 13.965488 --hemi rh --subject fsaverage --thmin 2.0 --sign neg --oannot rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.annot --bonferroni 2 --surf white ERROR: need --csd with --csd-out How should I proceed to solve this problem? Thanks Diógenes Bispo diogenesdiego(a)gmail.com

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OHBM Brainhack 2021
by tibor.auer＠gmail.com 01 Jun '21

01 Jun '21

External Email - Use Caution Dear all, We are happy to announce the upcoming Organization for Human Brain Mapping (OHBM) Brainhack 2021 happening June 16-18 around the clock around the world! Join the party by registering here <https://secure-web.cisco.com/1u2I1GuBsfMI2DztYAaydXDkB0RNxUncy__lFbm-SDdTWm… tings&action=startRegistration&conferenceID=136&reginit=1&pageID=4073> ($25 fee, or optional fee waiver; check out some project proposals here <https://secure-web.cisco.com/1UFXLRFeTjTUKpaCUe2A5OoP6MkJNr_s4w0USA_K3ZpLEM…> ). We are also looking for volunteers to help spread the word and facilitate Brainhack activities. We'd like to recruit around 100 volunteers-so any contribution is more than welcome, no prerequisites needed! Volunteer by filling out this form <https://secure-web.cisco.com/1fj3giytjty06ouXa4eieRxeQrKqnaUTei05izNvGIf01X…> (more information about volunteer roles here <https://secure-web.cisco.com/114kTuwVJBTKR8p5Z7O5ECuQ0yNJyNNG7W9ImirtCxFrNF… 2LG8/edit> ). About Brainhack: Brainhacks <https://secure-web.cisco.com/1OFqeoe3DhJ2HFRk731XAuL_ZhIr3mkQLrs1klsF23uuCs…> (including OHBM Brainhack <https://secure-web.cisco.com/1KlYvRlwLlb7R-u7A-iVfMxqZxByTv1jlTSvCNbGksHAxN…> ) are events promoting interdisciplinary neuroscience research; they bring researchers together from a variety of subfields (e.g., neurobiology, psychology, computer science, etc.) and research backgrounds (e.g., medical student, industry professional, RA, etc.) to collaborate on projects and ideas and teach open science-oriented technical skills. The focus on intensive community- and skill-building opens doors to a number of professional opportunities (learn more about these benefits here <https://secure-web.cisco.com/1ek4KT5yiBQGfsE5TvK-ZoFBZ7UwbmOkcRm2cDDK0U-v5B…> ). Brainhacks are not your typical hackathon-they are actively inclusive rather than competitive. To that end, even if you have never attended a hackathon before or written a line of code, you are welcome! No need to work with neuroimaging methods or be part of OHBM to attend. All you need is to come along and share your ideas, expertise, contributions with whatever pace and form you can make it happen while having a chance to collaborate and meet with many other researchers all around the world! We particularly welcome the contributions of groups traditionally underrepresented in neuroscience, including women, BIPOC, LGBTQ+, individuals with disabilities, and more. Brainhacks are safe spaces, with a policy of zero tolerance for harassment. OHBM Brainhack 2021 is intended for everyone to feel safe, learn from each other and share knowledge. Our event would be enriched by your involvement and contributions. To support our mission, please share this widely-we'd especially love your help translating and sharing this message in your local language to reach as many people around the world as we can! Events will take place across two main time slots to support as many time zones as possible. About us: We are the Open Science Special Interest Group (OSSIG) within the Organization for Human Brain Mapping (OHBM) society, which hosts a yearly conference on mapping the brain with neuroimaging. The OSSIG is dedicated to promoting Open Science in this community and neuroscience more broadly. Please contact ohbmopenscience(a)gmail.com <mailto:ohbmopenscience@gmail.com> if you have any questions. Thank you! All the best, Matteo and Tibor On the behalf of the OHBM Open Science SIG

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(no subject)
by Francisca Ferreira 01 Jun '21

01 Jun '21

External Email - Use Caution Dear Experts, I have extracted subcortical vols corrected for intracranial vols using asegstats2table and I ran mri_glmfit using the following command mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C groupdiff.mtx \--glmdir aseg.glmdir this seems to have worked. I am now trying to visualise my results adapting the recommended wiki command freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5 -viewport 3d Freeview crashes and I'm getting the following error Number of vertices in overlay data (64 or 64) does not match with surface (163842). Number of vertices in overlay data (64 or 64) does not match with surface (163842). Is there something wrong with the commands priot to this step?

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Acquisition/pipeline question
by Massieh Moayedi 31 May '21

31 May '21

External Email - Use Caution Hi, We’re collecting multiecho T1s. We have individual T1 images with different echoes, and the RMS files. I’ve run freesurfer using both the RMS files, and the multiple echo files (labelled as 001, 002…). I get slightly different results in the parcellation outcomes with the two different methods. Why would that be? What do you recommend for input — the RMS file, or the individual echo files? Thanks, massieh ______________________ Massieh Moayedi, PhD Assistant Professor and UTCSP Pain Scientist, Faculty of Dentistry Co-Director, Centre for Multimodal Sensorimotor and Pain Research University of Toronto http://secure-web.cisco.com/1K6w7Y_uJDRfNwqfL6uDO6MJy1eSSJ1WkHHxHgSG36WhM_v…<http://secure-web.cisco.com/1LEvYjhl0pitHhLUTNoJ9RpfqXnN1s5qlijKej9VsxU6jIk…> pronouns: he/him/his

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extract % signal change in FSFAST analysis
by Star Xi 31 May '21

31 May '21

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FW: mri_convert changing orientation but lose last coronal slice
by Melissa Marie Rundle 31 May '21

31 May '21

External Email - Use Caution Hi, I am using mri_convert to change the orientation of an image in its native space from LPS to PSR. Ex. Mri_convert -out_orientation PSR input_file output_file Sometime when I do this, I lose the last coronal slice(s) of the occipital lobe when the image is converted to PSR. Is there some way to ensure that when I change the orientation, I get the whole brain back? Thanks, Melissa

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PVC to calculate myelin maps
by Marina Fernández 31 May '21

31 May '21

External Email - Use Caution Dear experts, I want to calculate myelin maps using the ratio of T1w and T2w MRI images. I saw that the correction of partial volume effects can be used to create the maps (Shafee, Buckner & Fischl, 2015)*. Can I use the PVC functions of PetSurfer for this purpose? And in case I can: Should I apply PVC only on T1? Or also in T2? Which T1 should I use? The original T1 or the T1 with corrections (for example, the nu.mgz file that is corrected for variations in intensity)? Any other advice for calculating myelin maps would be welcome. Thank you in advance, Marina *Link: https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsO…

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Choosing projfrac/projdist and checking mri_vol2surf output
by M Pope 31 May '21

31 May '21

External Email - Use Caution Hi all, I have a question regarding checking the output of mri_vol2surf. I am converting a manually segmented volume ROI into a surface label in order to gain information such as cortical thickness. What is the best practice for quality control and checking the surface rendering of the ROI? Are there any protocols or suggestions? As slight changes in projfrac change the output by a large degree, it's difficult to assess what is the closest to the original volume ROI. The suggestions also vary (others say projfrac 0.5, others to use projfrac-max or projdist). The main output statistic I'm interested in cortical thickness of the region (if this influences the options). How do you choose and establish what is the best option? Thanks Marianna

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tkregister2 problem on its GUI
by 张威 31 May '21

31 May '21

External Email - Use Caution Hello Freesurfer developers, I am attempting to manually register a cerebral blood flow images to a T1 weighted images via the command tkregister2; I have successfully done the recon-all and bbregister followed the guide and got the report that "recon-all finished without error". I also got no problem to run the tkregister2 and the GUI display. In terse words, the problem is that GUI is clickable on several bottons but cannot make any changes within the bar of GUI. These are details: I cannot make any changes (coronal, sagittal, horizontal, brain slice, and translate brain) through the bar of the GUI, while I can click the botton (target, moveable, and COMPARE). I can try to close the GUI; a new window comes up and asks me if I want to save the changes, but all the botton (save, don't save, close and cancel) do not clickable. This new window can be closed but tkregister2 is still now working. I have done the similar work on Mac last year and I did not meet such a problem. I have searched the list and no similar errors have been reported. Does anyone have any thoughts on how to make it work? Also, I have attached the recon-all.log and register_perfusion.log (bbregister) in case it's of any use. 1) Freesurfer version: freesurfer-Linux-Centos6-x86-64-7.1.1-20200723-8b40551 2) Platform: Ubuntu 18.04.5 LTS Thank you for your kind help, I hope you have a great day! Best, Wei

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Freesurfer June 2021