Freesurfer May 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
109 discussions

FreeSurfer VM Password
by Tan Yee Fan 02 May '23

02 May '23

External Email - Use Caution Dear, Hi, Can I have the pass code to open the image FS_7_2_0_Ubuntu_18_04_06.ova.7z <https://secure-web.cisco.com/1IoqYUGwHuzQdlOE0rLMBtJZpyQRVU2rJ9Y81ZPBraGbu8…> ? Thank you Regards, Yee Fan

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FreeSurfer VM Password
by Tan Yee Fan 02 May '23

02 May '23

External Email - Use Caution Dear, Hi, Can I have the pass code to open the image FS_7_2_0_Ubuntu_18_04_06.ova.7z <https://secure-web.cisco.com/1z_NdmMAkddAHx73QOczb8xyZL78hDIbFMngL422AWR3pI…> ? Thank you Regards, Yee Fan

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Re: [Freesurfer] dcmunpack behavior with scouts
by Douglas N. Greve 02 May '23

02 May '23

External Email - Use Caution I've attached a new version of dcmunpack. Try running this with -keep-scouts and without -keep-scouts Let me know if this runs successfully in both situations (I'm using you as my tester:) On 4/18/2023 10:51 AM, Proulx, Jean Sebastien wrote: > > Sorry for the late follow-up. > > Yes, that is what I’m doing. With dcmunpack -auto-runseq I convert > everything, then use the log/series-info.dat to do further renaming to > BIDS—at least that is what I am trying to, but this is another topic. > > Thanks for the help and > > Have a very good day! > > Sébastien >

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Error Sourcing Freesurfer
by Turco, Isabella 02 May '23

02 May '23

External Email - Use Caution Hello, When trying to source Freesurfer version 7.1.1 using the command below, I'm getting the error "No such file or directory." source /usr/local/freesurfer/fs-stable711-env-autoselect Any guidance on potential solutions would be much appreciated! Thanks, Isabella Isabella Turco, B.S. Senior Clinical Research Coordinator Massachusetts General Hospital Department of Anesthesia, Critical Care and Pain Medicine 617-643-2896 iturco(a)mgh.harvard.edu<mailto:iturco@mgh.harvard.edu>

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Re: [Freesurfer] mri_normalize error MP2RAGE
by Douglas N. Greve 02 May '23

02 May '23

External Email - Use Caution The current versions of FS require an intensity normalization step be run on 7T data prior to running it through FS. I have used SPM VBM for this, but I think samseg should work too, eg, samseg --i t1.mgz --o samseg Then use samseg/mode01_bias_corrected.mgz as input to FS. On 5/2/2023 10:28 AM, Jastrzebowska, Maya Anna wrote: > > External Email - Use Caution > > Dear Doug, > > I'm having the same issue as numerous others have described: a failure > to run the Intensity Normalization step of recon-all on a single > subject's skull-stripped T1-MP2RAGE 7T data, with the following error > displayed in the log file: > > mri_normalize -g 1 -seed 1234 -mprage -noconform nu.mgz T1.mgz > > [...] > > 3d normalization pass 1 of 2 > > error: MRInormFindControlPoints: could not find enough control points > > error: MRInormFindControlPoints failed > > I am attaching the log file here. > > I am able to run recon-all without errors for other subjects with the > same sequence and preprocessing steps (removing MP2RAGE background > noise as suggested by Marques et al., bias correction and > skull-stripping). > > Please let me know if a solution has been found for this issue. Thank > you in advance for your help! > > Best, > > Maya Jastrzebowska > > >

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mri_synthseg problem with CT... freesurver v 7.3.2
by Gonzalo Rojas Costa 02 May '23

02 May '23

External Email - Use Caution Hi: I downloaded some CT from OASIS 4 database... I tried to segment it using mri_synthseg (freesurfer v 7.3.2)... But I got bad results... Only I got the segmentation of one region of the brain... Also, I do the crop of the image, and the threshold from 0-80 hounsfield units... Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785

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QDEC Alternative
by Lauren Stephens 02 May '23

02 May '23

External Email - Use Caution Dear Freesurfers, We are looking to do a voxel-wise analysis on cross sectional and longitudinal data. We wanted to use QDEC but see that it is no longer maintained and has been removed in version 7.3.2 which we are using. Is there going to be a GUI replacement released in the near future? Are there alternatives for QDEC besides the command-line analysis, or potential third-party alternatives that are compatible with freesurfer? Thank you, Lauren

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covariates in 2nd level anaysis
by Maria Czarnecka 01 May '23

01 May '23

External Email - Use Caution Dear Sisters and Brothers in neuroscience I am analyzing functional data in FSfast in Freesurfer. I define my conditions in an osgm file, then I create contrasts. On the second level, I would like to add two covariates (scanning facility and handedness). I don't need contrasts, I just need the model to account for the variance. Can I define both osgm and fsgd files? How do I construct the fsgd? I will be grateful for your suggestions. Best, Maria Czarnecka

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VirtualBox VM
by Aqeel Mohamed 01 May '23

01 May '23

External Email - Use Caution Hi, I have recently downloaded Freesurfer and am planning on using VirtualBox VM. I was wondering if I could please have the password to open the .7z file of the Freesurfer image? Many thanks! Aqeel

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Freesurfer May 2023