Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

surface based group analysis
by David 24 Jan '22

24 Jan '22

External Email - Use Caution Hello FreeSurfer Developers, Hello, I would like to ask if there are other correction methods besides multiple comparison correction when surface based group analysis.

1 0

Reading files from an external hard drive
by krystaly 24 Jan '22

24 Jan '22

External Email - Use Caution Hi FreeSurfer experts, I’m trying to open nifty/ DICOM files, which are stored in a hard drive (SEAGATE - Backup Plus Hub; Model: SRD0PV1). However, the files cannot be found in any of the folders on Freesurfer 7.1.0 of which operates on Visual Machine on Window 10. May I know whether I should: 1. Import those folders to Freesurfer for viewing at Freeview; or 2. Set anything for opening the files directly from the hard drive? Please kindly advise. Thanks a lot. Best regards, Krystal

2 1

Using SPM segmentations in FreeSurfer
by Nathan Kindred (PGR) 24 Jan '22

24 Jan '22

External Email - Use Caution Hi, I have been trying to incorporate segmentation files from SPM into FreeSurfer to improve the surfaces, but I am not sure if I am going about it in the right way. I have been replacing the wm.mgz file with a file from SPM and then running ‘recon-all -s ${subject} -autorecon2-wm -autorecon3’, but I keep getting errors. I have tried using both conform and conform_min as part of mri_convert when replacing the wm.mgz file with an SPM file but in both cases I still get errors. Are there other steps I should be taking or a different line of code I should run to get this to work? Thanks, Nathan

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Tracula -prep error: cannot stat dwi_orig_las.1.bvecs
by John Pap 23 Jan '22

23 Jan '22

External Email - Use Caution Hello to everyone! I'm trying to run the preprocessing step of tracula to my subject and I keep getting the following error: mv: cannot stat '/home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.bvecs': No such file or directory As a matter of fact this file was never created during the process. My files are in nifti format and I try to reconstruct the corticospinal tracts. I attach my configuration file and the log file. Thanks in advance for your help! Ioannis P.

2 4

VM password
by REEM ABU BAKR BAHATHIQ 23 Jan '22

23 Jan '22

External Email - Use Caution ---------- Forwarded message --------- From: REEM ABU BAKR BAHATHIQ <rbahathiq0001(a)stu.kau.edu.sa> Date: Wed, Jan 19, 2022, 3:11 PM Subject: VM password To: <freesurfer(a)nmr.mgh.harvard.edu> Dear Freesurfer mailing list, I have just downloaded the virtual machine + ubuntu package, as outlined on the website when running a VM in windows. However, ubuntu is asking for a developer password to open within the VM. I see on the help page (on the website) that the log in ID could be in the README doc, but I can't actually get the VM open to get there. Does anyone know the password so I can set up the VM and get started with freesurfer? Thanks so much in advance!

1 0

Re: [Freesurfer] VM password
by fsbuild 21 Jan '22

21 Jan '22

External Email - Use Caution Sending the password to your email shortly …. On Jan 21, 2022, at 15:35, REEM ABU BAKR BAHATHIQ <rbahathiq0001(a)stu.kau.edu.sa> wrote:        External Email - Use Caution        Dear Freesurfer mailing list,I have just downloaded the virtual machine + ubuntu package, as outlined on the website when running a VM in windows. However, ubuntu is asking for a developer password to open within the VM. I see on the help page (on the website) that the log in ID could be in the README doc, but I can't actually get the VM open to get there.Does anyone know the password so I can set up the VM and get started with freesurfer? Thanks so much in advance!_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Fwd: VM password
by REEM ABU BAKR BAHATHIQ 21 Jan '22

21 Jan '22

External Email - Use Caution Dear Freesurfer mailing list, I have just downloaded the virtual machine + ubuntu package, as outlined on the website when running a VM in windows. However, ubuntu is asking for a developer password to open within the VM. I see on the help page (on the website) that the log in ID could be in the README doc, but I can't actually get the VM open to get there. Does anyone know the password so I can set up the VM and get started with freesurfer? Thanks so much in advance!

1 0

-hires recon-all error w MP2RAGE
by Fred Dick 21 Jan '22

21 Jan '22

External Email - Use Caution Hi all I'm following up on a previous report from May of 2021 that seemed to have the same issue. When running an MP2RAGE (7T, 0.65mm isotropic, pTx), I got the following error using recon-all -all -hires that seemed line one that Corinna did: ##### 3d normalization pass 1 of 2 error: MRInormFindControlPoints: could not find enough control points error: MRInormFindControlPoints failed Darwin Unknown-a0:78:17:6c:fe:8f 20.6.0 Darwin Kernel Version 20.6.0: Wed Nov 10 22:23:05 PST 2021; root:xnu-7195.141.14~1/RELEASE_ARM64_T8101 arm64 ###### [Note this is on an M1 chip mac] The same volume works when it's conformed to 1mm. Happy to supply said volume if helpful, and also try on different architecture. cheers Fred

1 0

mri_glmfit-sim error: Flag --1d unrecognized
by Tarumi Takashi 20 Jan '22

20 Jan '22

External Email - Use Caution Dear FreeSurfer Developers: I am attempting to perform cluster-wise correction for the along-tract measures, as described on the Tract statistics tutorial ( https://secure-web.cisco.com/1k_UHTgDkMyztiBV5VO6PazEUkIHIp4tFCos8o1vMfT5Xa… But, when I run the command below, the flag --1d is not recognized. Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05 --perm 1000 1.3 pos Error: Flag --1d unrecognized. I could not find similar errors reported. Does anyone have any thoughts on how to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an M1 Mac machine with macOS 12.1. Thank you so much for your help. Sincerely, Taka

2 4

In the Desikan-Killiani parcellatino scheme, which parcellations contain the extrastriate cortex?
by Knut J Bjuland 20 Jan '22

20 Jan '22

External Email - Use Caution Dear freesurfer experts In the Desikan-Killiani parcellatino scheme, which parcellations contain the extrastriate cortex? Knut Jørgen Bjuland

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