Re: [Freesurfer] Mac OS M2 M3 computers

2024-02-04 Thread fsbuild 
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 The current 7.4.1 (Intel binary) release from June 2023 should run on 
Silicon Macs and I believe was tested with MacOS (13.X) Ventura.  We did 
not have MacOS (14.X) Sonoma available at that time for testing.  The 
Freeview image viewing application requires graphics/X-Windows and for that you 
need X-Quartz installed on your Mac.  We have a native Silicon Mac 
development build available but it is currently unstable.
The graphics card spec assumed the graphics card has its own dedicated memory. 
 That spec is somewhat obsolete now w.r.t Silicon Macs since their unified 
memory design means the CPU’s and GPU’s share the same memory.  The spec 
to look for on Silicon Macs is how large is “unified memory”.

Commands that are python scripts (and not Intel or arm64 binaries) using 
modules like tensorflow may not work on Silicon Macs when trying to utilize the 
GPU’s.
If you have not already done so, download and install Xquartz,
https://secure-web.cisco.com/1m9nMZoww5EBHuzCVnK1bRHfdp34oRBsReQGIi-7nF_TereiKLeFE0wV4a4heu4IG4aeHTF9KbcxR24tjHn5fIxKqu4LxSEgeQ8wmm8Q4xbnMFHYwYTY0UHlIENTkDMLYo3DlkhFLMAJZlTu1ccE2K1eh3bvTZ-BkbC_tkl75_agj_kbF0KP5y5mHFYc7xQ90ySlgwcCg6IxgC2KaW4OLOMa901CPYe7bgKc-5NLbXuiMNAnf1vaEneXx-ScWAKTyGvJMmrMqc3PZ63Q0MH6U7ctsM465JxdY4JDmrLuiw_fYKbwEs5j8SKmg_4OFKIOugXUUbkp4dpWCQFQXYurT1Q/https%3A%2F%2Fwww.xquartz.org
The 7.4.1 installer package can be downloaded from,
https://secure-web.cisco.com/1sijobmA3UkgB0Ha5oTzDO0KSCYb2unjOllCiEFgnLqS_Tx2LDrErGMRSS2lvZUAYzU2QZ1ZTncLzfdGcfuepyVFU3QiOnQAOTCWeUaRJ1_tKS4Rte9Ip5fLBZKhbmlE0tznV3WiY2-QKfEKo2T9KPiLpeHSMHVTvZzLeYaEJVWbOk9ABy_rNH35nm3v86C9_eSRlboHzCS_Fjnz9veMWwRi5vCt0T8FtGn94DuzeQQdrq7nDOO96TLwCG2HCkk3TnYzKii68VhahsXqUmxMeF0b9KTHkPngM5SNUX1lC9jHaETzq6i8oLShzbV-OGdZMCjWlRSxqCQgURNIy1wpDFw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
RIGHT CLICK on the installer package and under “install with” select the 
default installer.app.  This should bypass having to open system 
preferences to make a security exemption.
- R.

On Feb 4, 2024, at 00:49, Fatima Karim  
wrote:External Email - Use 
CautionI have been using free 
surfer for a year nowon Mac m2 max and it's working fine. On Sat, Feb 3, 
2024, 23:42 Charles Leger  wrote:  
      External Email - Use Caution      
  There seems to be some contention if FreeSurfer will support Mac 
OSsilicon (M2, M3) computers. In the technical requirements section, itis 
clearly specified that a " 3D graphics card with its own graphicsmemory & 
accelerated OpenGL drivers" is required. But in the emailarchive (caution 
suggested) it is noted that "binaries should run oncurrent Macs with M1, M2, M3 
arm64".Currently. Apple has not indicated plans to support eGPUs, which, 
onpaper, makes all newer non-intel Mac computers not compatible 
withFreeSurfer.Any suggestions would be greatly 
appreciated.-- *Dr. Charles 
Stevens LegerPhD Psychology, Neuroscience diplomaDepartment of 
PsychologyConcordia University7141 Sherbrooke Street W.Montreal, Quebec, 
CanadaH4B 1R6___Freesurfer mailing 
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Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

2024-02-04 Thread Sven Kühn 
   External Email - Use Caution


Hi Dr. Greve, hi all

I have tried your code. I copied it from the website into a text file
and replaced mri_glmfit-sim in the freesurfer/bin folder. The file is
executable but aborts after a few lines with no indication of a cause.
The following output is generated:


/xx@xxx:~/Schreibtisch/WMH_DCS$ mri_glmfit-sim --glmdir
rh.volume.DCS.10.glmdir --cache 2.3 abs --cwp 0.05 --2spaces --spatial-sum//
//cmdline mri_glmfit.bin --y rh.volume.DCS.10.mgh --fsgd
FSGD/DCSstudy.fsgd --C Contrasts/DCS-DCSK.mtx --C Contrasts/DCSK-DCS.mtx
--surf fsaverage rh --cortex --glmdir rh.volume.DCS.10.glmdir//
//SURFACE: fsaverage rh//
//Unmatched `./


Even if I run --help, only some of the lines appear:

/mri_glmfit-sim --help//
//
// --glmdir glmdir//
// --cwp cwthresh : cluster-wise p-value threshold (.05)//
//
//Use pre-computed z-based monte-carlo simulations (see mri_mcsim)//
// --mczsim vwthreshold sign//
//If you have run your own simulations (mri_mcsim), then specify //
//   --mczsim-dir dir : default is FREESURFER_HOME/average/mult-comp-cor//
//   --mczsim-label label : default is cortex//
//
//Use permutation simulation//
// --perm nsim CFT sign : permutation simulation with nsim iterations//
//Unmatched ".//
/


Do you have any idea why this might be?
Like Xiaoxu before me, I have already tried to convert the file with
dos2unix. However, without the desired effect.

I am using Linux Ubuntu 16.04 and Freesurfer Vers. 6.0.

I would be very grateful for any tips.

Best regards


sven

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Re: [Freesurfer] Mac OS M2 M3 computers

2024-02-04 Thread Charles Leger 
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Thank you!

On Sun, Feb 4, 2024 at 12:50 AM Fatima Karim  wrote:
>
> External Email - Use Caution
>
> I have been using free surfer for a year nowon Mac m2 max and it's working 
> fine.
>
> On Sat, Feb 3, 2024, 23:42 Charles Leger  
> wrote:
>>
>> External Email - Use Caution
>>
>> There seems to be some contention if FreeSurfer will support Mac OS
>> silicon (M2, M3) computers. In the technical requirements section, it
>> is clearly specified that a " 3D graphics card with its own graphics
>> memory & accelerated OpenGL drivers" is required. But in the email
>> archive (caution suggested) it is noted that "binaries should run on
>> current Macs with M1, M2, M3 arm64".
>>
>> Currently. Apple has not indicated plans to support eGPUs, which, on
>> paper, makes all newer non-intel Mac computers not compatible with
>> FreeSurfer.
>>
>> Any suggestions would be greatly appreciated.
>> --
>> *
>> Dr. Charles Stevens Leger
>> PhD Psychology, Neuroscience diploma
>> Department of Psychology
>> Concordia University
>> 7141 Sherbrooke Street W.
>> Montreal, Quebec, Canada
>> H4B 1R6
>>
>> ___
>> Freesurfer mailing list
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>>  .
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>  
> 
>  .

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