Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30081 discussions

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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

2 1

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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Re: [Freesurfer] Questions about geting a license file
by fsbuild 31 May '21

31 May '21

External Email - Use Caution Hello Nana, Your browser should display a “CAPTCHA” box at the bottom of the freesurfer license page just above the button where you click “I AGREE”. If you do not see the CAPTCHA box in your browser then it is probably blocking some javascript that would allow it to be displayed.  Make sure you have javascript enabled in your browser.  You could try a different browser that does not block javascript (or cookies). You should check the “I’m not a robot” box and pick out the images it asks you for.  Then it should display a green checkmark.  Then click on the “I AGREE” button below. - R.On May 31, 2021, at 10:19, fengnana <fengnana_y(a)163.com> wrote:<微信图片_20210531221632.png>

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Re: [Freesurfer] about the root password of virtual box ubuntu 710 clone
by fsbuild 31 May '21

31 May '21

External Email - Use Caution Hello Wu, Sending the info to your posted email. - R.. On May 31, 2021, at 03:49, HuiNing Wu <huining.wu.psy(a)gmail.com> wrote:        External Email - Use Caution        Dear all,I'm using freesurfer virtual box ubuntu 710 clone.However, I didn't find the root password to enter sudo mode...Would you please let me know what it is or where it is?With best regards,Wu_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard..eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Questions about geting a license file
by fengnana 31 May '21

31 May '21

External Email - Use Caution Dear Sir: I met registration error when I provided all the personal information to register the copy of FreeSurfer and obtain the license.txt key file, is there any way for me to get the license file? The error figure is attached and thank you for your kindness! Yours sincerely Nana Feng

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