Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

About volumetry results by Freesurfer
by fahimeh palizban 12 Dec '20

12 Dec '20

External Email - Use Caution Hello, I am a Bioinformatician using Freesurfer for Brain volumetry analysis particularly for clinical usage. I encountered an issue when using Freesurfer for a patient having MRI data at two different time points; The volumes related to some brain sites have been increased when comparing with the previous MRI data and it is kind of impossible biologically. It would be kind of you to inform me of the mentioned problem and its reason. Thanks for your time and consideration Best regards Fahimeh

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Re: [Freesurfer] Computing thickness from woT2.pial surfaces {Disarmed}
by Antonín Škoch 11 Dec '20

11 Dec '20

External Email - Use Caution Hi, Bruce, I did not find any mris_thickness command line option for masking medial wall during thickness computation. The masking of ?h.thickness file ex post would not probably help, since it is not equivalent. I tested this by running mris_anatomical_stats (which I suppose by principle takes medial wall into account) and obtained still slightly different results. So I finally retreated to rerunning recon-all -pial and recon-all -T2pial and stored ?h.thickness of both processes. Regards, Antonin You probably want to mask the medial wall Bruce On Dec 9, 2020, at 11:31 PM, Antonín Škoch <a...(a)ikem.cz> wrote: External Email - Use Caution Hi, Bruce, in the meantime, I found the old thread https://secure-web.cisco.com/1aNvaY2F2Wzk88I3TCWDZ8sNnAxHgbRgs7ryiKYBIUsjQE… which suggests to set -N 20 parameter to mris_thickness to make thickness computation consistent to mris_make_surfaces. Indeed, the values are now consistent, with exception of several thousands of vertices mainly around medial wall. Is here any other option missing, which makes mris_thickness computed values of thickness fully consistent to mris_make_surfaces? Thank you in advance, Antonin Hi, Bruce, thank you for the instructions! I ran mris_thickness on one example subject to test the procedure. However, inspecting the values of created thickness file, I encountered problem. In many locations, the values of thickness file differ from the values of thickness file created in recon-all -T2pial. Even when the input files used for thickness measurement are (should) be the same. (I double-checked my input surfaces, when I use woT2.pial surface, the thickness values are different everywhere). Attached see the binarized difference of these thickness files with the cursor, where difference is zero (red spots) and where is non-zero (transparent). Could you please clarify, where could be the problem? Does not the thickness computation in mris_make_surfaces use different options? Could it be the reason, that I am operating with data processed by longitudinal stream? (I don't think so...). This inconsistence makes me puzzled. Regards, Antonin Hi Antonín You can specify what surfaces to use in mris_thickness: mris_thickness -pial <path to pial surface> -white <path to white surface> … cheers Bruce From: freesurfer-boun...(a)nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...(a)nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Antonín Škoch Sent: Wednesday, December 9, 2020 6:16 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Computing thickness from woT2.pial surfaces External Email - Use Caution Dear experts, I have processed my data with -T2pial option. I would like now to also compute thickness from woT2.pial surfaces (i.e. surfaces created by T1 only). Is here a comannd which does the trick, without running recon-all -pial (which rewrites current .pial and .thickness files generatedy by -T2pial? I am using freeSurfer version 6.0. Thank you in advance, Antonin Skoch

2 1

Error: must specify as many DWI dicoms as subjects
by Shanika Jayakody 10 Dec '20

10 Dec '20

External Email - Use Caution Dear FreeSurfer team I have been trying to run trac-all & keep get the error " too many ('s must specify as many DWI dicoms as subjects" There is no mismatch between my subjects list (the number and IDs) and dcmlist. I have tried changing spaces after "\" too Any suggestion is appreciated- I have attached here my configurationfile Many thanks Oshad

1 0

Re: [Freesurfer] FreeSufer v7.1.1 dev table {Disarmed}
by Jaiashre Sridhar 10 Dec '20

10 Dec '20

External Email - Use Caution No, I am looking for an updated version of this: https://secure-web.cisco.com/1DIb6cINWVCZCYBQY2omVxYlmCbafLA4lkD7T69Oedes1X… ReconAllTableStableV6.0 - Free Surfer Wiki<https://secure-web.cisco.com/1DIb6cINWVCZCYBQY2omVxYlmCbafLA4lkD7T69Oedes1X…> This table shows the recon-all steps for the stable, publicly released, version 6.0 of FreeSurfer (available here).. See also the OtherUsefulFlags for other recon-all options. surfer.nmr.mgh.harvard.edu Thanks! Jaiashre

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userid login as "developer" - VM_67_win {Disarmed}
by Amice Maries 10 Dec '20

10 Dec '20

External Email - Use Caution Dear all, I am trying to install Freesurfer on my Windows10 with a VM following these instructions: https://secure-web.cisco.com/1q0U-_mEzDjDxzeEdksNy6TWmfK6OyrdBwiQEuhnVHPLVU… After the creation of the VM with the cloned VM *Ubuntu_710_clone_2.7z,* I am stuck at the login window where I should login with a password for 'developer'. What is this password? The instructions quoted below, refer to a README file, but I cannot get into the desktop of the ubuntu because it I don't have a password. "*This VM contains both the freesurfer 6.0.0 release, the 7.0.0 beta 1 release, and a copy of the tutorial data used in the freesurfer courses from 2019. Please **see the README* files for more details in the home directory for the userid login as "developer". However, it does not contain a license.txt** file needed to run some commands*. " kind regards, Amice Maries

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Re: [Freesurfer] Computing thickness from woT2.pial surfaces
by Antonín Škoch 10 Dec '20

10 Dec '20

External Email - Use Caution Hi, Bruce, in the meantime, I found the old thread https://secure-web.cisco.com/10LHEZSoeNL-wnQ2e6UBEnyfB6PA04qM13lFZXbRypPzlX… which suggests to set -N 20 parameter to mris_thickness to make thickness computation consistent to mris_make_surfaces. Indeed, the values are now consistent, with exception of several thousands of vertices mainly around medial wall. Is here any other option missing, which makes mris_thickness computed values of thickness fully consistent to mris_make_surfaces? Thank you in advance, Antonin Hi, Bruce, thank you for the instructions! I ran mris_thickness on one example subject to test the procedure. However, inspecting the values of created thickness file, I encountered problem. In many locations, the values of thickness file differ from the values of thickness file created in recon-all -T2pial. Even when the input files used for thickness measurement are (should) be the same. (I double-checked my input surfaces, when I use woT2.pial surface, the thickness values are different everywhere). Attached see the binarized difference of these thickness files with the cursor, where difference is zero (red spots) and where is non-zero (transparent). Could you please clarify, where could be the problem? Does not the thickness computation in mris_make_surfaces use different options? Could it be the reason, that I am operating with data processed by longitudinal stream? (I don't think so...). This inconsistence makes me puzzled. Regards, Antonin Hi Antonín You can specify what surfaces to use in mris_thickness:mris_thickness -pial <path to pial surface> -white <path to white surface> … cheers Bruce From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> On Behalf Of Antonín Škoch Sent: Wednesday, December 9, 2020 6:16 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Computing thickness from woT2.pial surfaces External Email - Use Caution Dear experts, I have processed my data with -T2pial option. I would like now to also compute thickness from woT2.pial surfaces (i.e. surfaces created by T1 only). Is here a comannd which does the trick, without running recon-all -pial (which rewrites current .pial and .thickness files generatedy by -T2pial? I am using freeSurfer version 6.0. Thank you in advance, Antonin Skoch

2 1

Re: [Freesurfer] Computing thickness from woT2.pial surfaces
by Antonín Škoch 09 Dec '20

09 Dec '20

External Email - Use Caution Hi, Bruce, thank you for the instructions! I ran mris_thickness on one example subject to test the procedure. However, inspecting the values of created thickness file, I encountered problem. In many locations, the values of thickness file differ from the values of thickness file created in recon-all -T2pial. Even when the input files used for thickness measurement are (should) be the same. (I double-checked my input surfaces, when I use woT2.pial surface, the thickness values are different everywhere). Attached see the binarized difference of these thickness files with the cursor, where difference is zero (red spots) and where is non-zero (transparent). Could you please clarify, where could be the problem? Does not the thickness computation in mris_make_surfaces use different options? Could it be the reason, that I am operating with data processed by longitudinal stream? (I don't think so...). This inconsistence makes me puzzled. Regards, Antonin Hi Antonín You can specify what surfaces to use in mris_thickness:mris_thickness -pial <path to pial surface> -white <path to white surface> … cheers Bruce From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> On Behalf Of Antonín Škoch Sent: Wednesday, December 9, 2020 6:16 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Computing thickness from woT2.pial surfaces External Email - Use Caution Dear experts, I have processed my data with -T2pial option. I would like now to also compute thickness from woT2.pial surfaces (i.e. surfaces created by T1 only). Is here a comannd which does the trick, without running recon-all -pial (which rewrites current .pial and .thickness files generatedy by -T2pial? I am using freeSurfer version 6.0. Thank you in advance, Antonin Skoch

1 0

Re: [Freesurfer] FreeSufer v7.1.1 dev table
by fsbuild 09 Dec '20

09 Dec '20

External Email - Use Caution Hello Jaiashre, If you mean a table/list of files you can download, there is one here, https://secure-web.cisco.com/1CkjOUuN9hNVVgSuWP7wNpfK9nrS_Jawc0Plb_PFZyQu36… - R. > On Dec 9, 2020, at 17:00, Jaiashre Sridhar <jaiashre.sridhar(a)northwestern.edu> wrote: > >         External Email - Use Caution         > Hello, > > I see that the dev table for FreeSurfer version 7.1.1 is not available yet. Will it be available anytime soon? > > Thanks! > > Jaiashre > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1qlqgOwLej9LJfdwglKsliEcLwMDc2VM0uVsO2w9_A8XHU…

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FreeSufer v7.1.1 dev table
by Jaiashre Sridhar 09 Dec '20

09 Dec '20

External Email - Use Caution Hello, I see that the dev table for FreeSurfer version 7.1.1 is not available yet. Will it be available anytime soon? Thanks! Jaiashre

1 0

MP2RAGE pial surface error
by Elisa Rehbein 09 Dec '20

09 Dec '20

External Email - Use Caution Dear Freesurfer experts, we are currently running recon-all for our MP2RAGE images, using Freesurfer 7. However, when trying to edit pial surface errors and re-running (recon-all -autorecon-pial -subjid) it does not adjust the surface for some participants. For denoising the salt and pepper noise in the background we used the script provided by (Marcques et al. 2010). We are very confused as to why this may be happening for some subjects, as the background noise seems to be removed equally for all subjects. Do you maybe have suggestions for us how to solve this problem? Many thanks in advance! Kind regards, Elisa

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