Re: [Freesurfer] error installing tensorflow

[Vishnu S]

External Email - Use Caution

Maybe you want to check your .NET core version?

https://secure-web.cisco.com/1yA0JP579_nnFgIsajBEG82WAZ8ZXFFAjhKmNhWALkdw3hWQHGEcHyIQn9f2Zja-3VCQLCFm9O0vC7xCZ_M4GHuJonItW4QLqSd4D3b7dVWPWb8b-NWodb-k9cpmqMdEGAH3pZnQ3hXuGkzltwOzrIGPZTkE_T-1ht-5GhHd-1bwYhz42vrq_kA885Iex-1TOugC-ktILkE7eYWn-UWDgTvloa6sK6PzcGTuCKH2N64-fOBxvnMYUo0COaP98cZrVV9ryDBJqEZBKm0-XQigEsA/https%3A%2F%2Fgithub.com%2Fdotnet%2Fcore%2Fissues%2F4005

On Sat, 17 Apr 2021, 09:33 AJ,  wrote:

> External Email - Use Caution
>
> sorry, but I get the same error after
> conda create -n myenv python=3.6
> conda activate myenv
>
> (myenv) MacBook-Pro-4:~ AJ$ fspython -m pip install tensorflow==1.13.1
> Collecting tensorflow==1.13.1
>   Using cached *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1PYyai9yVcs6NF9QTeYJQKKzhmJD1Cj2tfunF8HGhyEkgUANawCQLz3uvqJG-qLS2mDGgCrt7yo9aNIsu61w7z4ar8w2Onc5TQS3cu31qUwxhsisgXdgeb3ZYFTzEn4kJ-LjJCJX1pne1boKXnZkHi7u82Z6dOEvM44oY6515C8chf0zehkIIGNt2KYLB1Ly3-cM7-mhsS8nd8Eg9_QrSD_Xa9c_Tww_YbgYpbdMIKVIou9aF1OPOTiOHyaWEuhwuKiJFt_IDxfBxnoz7kQDBWQ/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Ff6%2F7b%2F5ab19bac13810661ff9e2485811553f1dea9a5d611ce846345aed4766bbe%2Ftensorflow-1.13.1-cp36-cp36m-macosx_10_11_x86_64.whl
> 
> Requirement already satisfied: numpy>=1.13.3 in
> /Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.13.1)
> (1.18.4)
> Collecting keras-preprocessing>=1.0.5 (from tensorflow==1.13.1)
>   Using cached *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1UKGwLWWcLjWqgPIi4HUQtMXzUmhQSVbbsL1UaZxcKSpUFFLwlBWqScAcZMqBYXbaKB_zo2lJfqkSVKKdbnX5mO1FTmtNa9iu6LSQQDNMn75q3uW8ABeXLOo9kO89YEgr6IRfO_EULfOF0-AgqqeoG16leMzSBL7It3qPFxrGr-dTtc7TQ63NMEJZCtTFa_3J7VvAhZvNWAu1MWUZotcKrGoDvblCaKGsNO9HRt_HLPyCcfzA1SMuwfurKwZSasKjeRQMnIC2sM6HAHcyDaNhbg/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F79%2F4c%2F7c3275a01e12ef9368a892926ab932b33bb13d55794881e3573482b378a7%2FKeras_Preprocessing-1.1.2-py2.py3-none-any.whl
> 
> Collecting keras-applications>=1.0.6 (from tensorflow==1.13.1)
>   Using cached *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1krAkzV_96c49iEc6Vasp1HZYQfLmJj8EjzdNj7xoyCBW2IGKxwG0lNIxZVJLp4S3kq8Y_M-unqGe0kll8TG6EjRgPE54nylUMbjxev8VBOeaX0MFnQ65L04JIYn-Np8DlhN4LKtj0cKLiKqRRdy4v6SsPmlaodCv1-ZfrB1qRkiLzR_MDhIxDnw7zLcRFaIgBtgvmNKaHMCR3h8HU0rKozt3D8l-sfrdwwPRS1-YLelbBlddI1gCcHX0bnEIz6U4_UEX9zm5gsvHyx1-JYIEww/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F71%2Fe3%2F19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f%2FKeras_Applications-1.0.8-py3-none-any.whl
> 
> Collecting tensorboard<1.14.0,>=1.13.0 (from tensorflow==1.13.1)
>   Using cached *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1l_e8k7JdJofF7vSCnPmk0y1cGD8hpWqfl6Fc-_LuBs0jZpDPX83PXhha6D0OtTbxjnyIpjFQ3gtZ7cMXz8_0H-51eLITvDfOFienCsImqbep6w7jALKjTi1090aQXjmtWDphBCUT3Wyu6GztxIplTri2IPiOkMBVkUtwsMu5sFpYaoPta0ebrbFQRXP-XbcSzyawPoilkmRewJm4Df4JXFu6sDs_y6tnOZl1M8YCH18lp5GUkbdBtpqIKf-KEJs-OKCeVDaXRKRQSeTpqD7_iw/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F0f%2F39%2Fbdd75b08a6fba41f098b6cb091b9e8c7a80e1b4d679a581a0ccd17b10373%2Ftensorboard-1.13.1-py3-none-any.whl
> 

Re: [Freesurfer] error installing tensorflow

[AJ]

External Email - Use Caution

sorry, but I get the same error after
conda create -n myenv python=3.6
conda activate myenv

(myenv) MacBook-Pro-4:~ AJ$ fspython -m pip install tensorflow==1.13.1
Collecting tensorflow==1.13.1
  Using cached
https://secure-web.cisco.com/1C5BUhTq5pnEX5z8UIP5qxXAPEwas1cAOBy4qpE4PlzpmVsAmga6sqAnBwspHDx5J-SE0_xc8QOQ-uZSeuGSYoRau4TkOHluhBWVTocfJOCXY75iUBxbcO9mu2Jbmp59C78Ec2dEeb9p2QukXaJlbbW3Ks_itTDaZ6944Av991ZgHaNaUB-zCeaxVO-gTN-V5Gx4G2oKuMLk5h4dqrqNrk-Lvz-k5r7uFcXXdWVYL0dDfCaWixyOJPmAOhc8U0u7fkIlolTEJj7PD8wjdzP2DIQ/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Ff6%2F7b%2F5ab19bac13810661ff9e2485811553f1dea9a5d611ce846345aed4766bbe%2Ftensorflow-1.13.1-cp36-cp36m-macosx_10_11_x86_64.whl
Requirement already satisfied: numpy>=1.13.3 in
/Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.13.1)
(1.18.4)
Collecting keras-preprocessing>=1.0.5 (from tensorflow==1.13.1)
  Using cached
https://secure-web.cisco.com/1RMFXu4xTNiyrlVHbqnFhCp06zcdACw-b85vgi-wBoMDkIycA4pXi8xb5Wd97atgVnp5x1tGG6PrqPcH-AtQi2iMfbdY1Hw2Sh4Z52sW5U1LhBKxPYiFJmB5wwdVjaU0Rx-TmaoQbeLMVz8tugeVp4e8dC8_kMIw50hrEk3rEpbLBo0TFyMSHe_Jn2n63vW6ywfiywtr0B0rzMLTHwI2e9NvDZRzP8YZtbnnN2N86u-WsnyGSK2flOryf3YPYw5tM4zQ3ADoIs_hoKasrRLCYmQ/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F79%2F4c%2F7c3275a01e12ef9368a892926ab932b33bb13d55794881e3573482b378a7%2FKeras_Preprocessing-1.1.2-py2.py3-none-any.whl
Collecting keras-applications>=1.0.6 (from tensorflow==1.13.1)
  Using cached
https://secure-web.cisco.com/1kRRYu1Ow6YxW0Khbw-X-FXQesqZx5RGeDuDDhnxlJZW2qDSltc0yDQeHeUNdpQb6xWEJmNcsc94e747p1zYGWBjD21VPp6A5JyBE472z3_9IsJSimgpwQsjJIr5FajJz0wtLKMvndRW6qIa2Vlr-e4OGId3NHIK-kauEd8DM6nvBGLFM8zKN0ofVgT4Y1PF6YR5ILpi3vobatS3Y5I6gOgTMpRE_M3dSQDQBVszLjLxGYtvREzN4DOmouqfpE3JEbicX7a4kNtNnhdVaSAwXnw/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F71%2Fe3%2F19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f%2FKeras_Applications-1.0.8-py3-none-any.whl
Collecting tensorboard<1.14.0,>=1.13.0 (from tensorflow==1.13.1)
  Using cached
https://secure-web.cisco.com/1DuHaJXQMeMGT1jSh18-c60sFQ1TmVw4VULDPbDgadCNTI47e26ZawLYtcu-ujZdAJteq-1pdGekw7OpGhmeWrQL-0VXiVGTtvJQcJeSIH8_mQTXOMC8ovqeq-O5wXFMPpkhKqoDxso56hVb98qERwI5BPROunenEYXJv8gr0dodc1kermpsWy3XfhSka0JBLgbXTFltKHWk7fQdx4FV1JFTnnYlLLG5f2liyk4SmlIOwFJTX8AY9lNQHKqQ-6o5GJbBE5dblg1v36BJayT5IUA/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F0f%2F39%2Fbdd75b08a6fba41f098b6cb091b9e8c7a80e1b4d679a581a0ccd17b10373%2Ftensorboard-1.13.1-py3-none-any.whl
Collecting tensorflow-estimator<1.14.0rc0,>=1.13.0 (from tensorflow==1.13.1)
  Using cached
https://secure-web.cisco.com/1XjPxKgC0iuP1Vhu3UzHno87XzlnjbF2pyl1vq5mOTETI9BrRUnazrEbHy7UK6TmPif8eyWtvGs1rzU6bI5rT6qgrv4yiNEHmZHlJY6QJkHRD0q7a7c91ysMOQCHJdrD6pn9J_1RQt_OG5JmzWa7IZ_Gn8GGO6lpS9BnycJzJdUo23nNk4VHSU4y5N_NxQA8M7ro8UNUseOABYxb5nEbYOQZZOIpR2xCQTxowIQcyBFgXG8KIkj94wp1tjh2N6NrZcJDUbHCBfN4cW82gWhMn7w/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Fbb%2F48%2F13f49fc3fa0fdf916aa1419013bb8f2ad09674c275b4046d5ee669a46873%2Ftensorflow_estimator-1.13.0-py2.py3-none-any.whl
Collecting gast>=0.2.0 (from tensorflow==1.13.1)
  Using cached
https://secure-web.cisco.com/1qzsjLCKgYcK_AJgUNXaXcKJa1CddJXYChdKQELykHZC-EUd2AJ0eoT0tAPCKXNaY_7kg4dlrEFxz5h8FUkO2aoTDKnW3snDEaCp85v58NltmX_KSMrheD50JQyF9QLFbVXdiy2Z7ExoTQSRvQ4hpG8LsWCha9I1Rn5FxTwG5Bo_-9_RB5lCUnaLuq5M1TvzOR-biLFWPHSfOTKtn7CNBBlxPIYJopCnztUgxRPAxTHQKgQaJeFBktK8_ywPY-ASFFwONEInvLk3zYIcilFsl9w/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Fb6%2F48%2F583c032b79ae5b3daa02225a675aeb673e58d2cb698e78510feceb11958c%2Fgast-0.4.0-py3-none-any.whl
Collecting absl-py>=0.1.6 (from tensorflow==1.13.1)
  Using cached
https://secure-web.cisco.com/1rpEEAxTMf8PfN_WvIbiyJFdfoA7Y7rn2ipzQcDVA6q4FmsVOQLwk1U6a2My_6yulIdyLy-ZUXDICgacq6s4qJzl-rDY8RU9dg0FYqrtZu5c_9o2QwD46IglNOB2TQveCkBsM1wfZ5cN7AZgKbovSM2gtSt8WCeWH-_2Lq7m1NKBE8YBNhOs0UgXVFcvYVeaaHV-cvclJPJVNEE8PjU6HlbUr5bcZnzBRknwLCfyYoUNBkAPoCDodOr-RtRZ6MjdiTd3nOfMgU0bVBZTYaSK_CA/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F92%2Fc9%2Fef0fae29182d7a867d203f0eff8296b60da92098cc41db33a434f4be84bf%2Fabsl_py-0.12.0-py3-none-any.whl
Requirement already satisfied: six>=1.10.0 in
/Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.13.1)
(1.14.0)
Collecting grpcio>=1.8.6 (from tensorflow==1.13.1)
  Using cached
https://secure-web.cisco.com/1fTUp4MeMKUXUrQ58sWKdjndW3CRI_jbpUzXVRRTOECaWHjErEoXBVwlkdlSmnYPwp9gvcNHegNgwFeSwqScx8tjFPxPIQDOpiiP-W03TSXPdZ2TvvTq8QIgUEWIyusohWXPWrkVMEwAYCpwVBvp_I9EziQdb91JuXf8V-Cbfau4oSXddDTd7-eEV3no4L0fkatSSJU3ALAWCdhPI1a1sEw4LWwhtmOmlYFQEkDD-1iyYuuomdTc7XtT67D2AQis_GHlb21gY9J5pdKfOSCwtYQ/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F0c%2F6f%2Fc5fcad9177ebf85e2adff2ad247de19718ac9710bff9574a65f2b8e3c5eb%2Fgrpcio-1.37.0-cp36-cp36m-macosx_10_10_x86_64.whl
Collecting wheel>=0.26 (from tensorflow==1.13.1)
  Using cached

Re: [Freesurfer] error installing tensorflow

[AJ]

External Email - Use Caution

thank you so much.  I just installed conda.
(base) MacBook-Pro-4:~ AJ$ conda -V
conda 4.9.2
Is myenv /Aplications/freesurfer/7.1.0
thank you.
aj

On Fri, Apr 16, 2021 at 10:22 PM Vishnu S  wrote:

> External Email - Use Caution
>
> 1. Make sure you have conda installed
> 2. In your terminal, then
>
> conda create -n myenv python=3.6
> conda activate myenv
>
> 3. Then you should be able to install TF 1.13
>
> On Sat, 17 Apr 2021, 08:46 AJ,  wrote:
>
>> External Email - Use Caution
>>
>> sorry for being non-tech, but how do I exactly do creating a conda venv
>> with Python 3.6.
>> many thanks
>> aj
>>
>> On Fri, Apr 16, 2021 at 9:56 PM Vishnu S  wrote:
>>
>>> External Email - Use Caution
>>>
>>> Hi AJ,
>>>
>>> So tensorflow 1.13.0 is looking for Python 3.6 as far as I know. Python
>>> >=3.7 only supports TF2. Can you try creating a conda venv with Python 3.6
>>> and try again?
>>>
>>> On Sat, 17 Apr 2021, 08:23 AJ,  wrote:
>>>
 External Email - Use Caution

 Thank you so much for your help.
 Here's the error:
 MacBook-Pro-4:~ AJ$ fspython -m pip install tensorflow==1.15
 Collecting tensorflow==1.15
   Using cached *MailScanner has detected a possible fraud attempt from
 "secure-web.cisco.com" claiming to be*
 https://secure-web.cisco.com/1yT5r5ADjPf-v2uZXvyrS2mEfKgjiqMH9Zoo8ycbzun2bFM9t_h0MYDjmeuXE0JIJL5iKrXkbdzD-gFTJQSl2UaK0o6CnwnVcTvr2FL1e7kftb9UBeMlUtVLJFfKo09QZ1MkOlVeQyX73c-cJR24f96QB0hduxXeSFJ1Ig1Xnpx8Bd3NjT9Sv1x4vFRougdk6wKUg9-mFrrQyvjQb3u3TR4p_5WqA18Oj2mbC2XgfDnNQPrgAVB5HsDexFrnXfaf3T7m6JkZ2uOxfVub_9JSXMQ/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Ffe%2F01%2F997a5d608162cf5371dae49e8cb68baaa5773b091a3e74576ea30dae51e6%2Ftensorflow-1.15.0-cp36-cp36m-macosx_10_11_x86_64.whl
 
 Requirement already satisfied: six>=1.10.0 in
 /Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.15)
 (1.14.0)
 Collecting keras-applications>=1.0.8 (from tensorflow==1.15)
   Using cached *MailScanner has detected a possible fraud attempt from
 "secure-web.cisco.com" claiming to be*
 https://secure-web.cisco.com/1IK-jpUzLR8GMNs7_gGITDXyHip-T6GYjQX9-WhaXkEJfUeqBXzRC2iya5NshWFT6FyWVSZTIZr3BfPWFVrEohsrEwnihoSw12d-quWyhvxW_2Rs0bwkHyInMr74_9pSl67i7CqedHyDRgB9mlsMEk_TZR6IcoqdyBvJ-weGvJkOCLWL6A6R7KyxBDPhcHgqm-8lUdmbSQg97WKQg7zf0tPubKmo1o4S1k2r-VvOmwU8B7oY9UXGi-SdoCikP5W06Z0g77wx0tF4xV_6Ia_03WQ/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F71%2Fe3%2F19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f%2FKeras_Applications-1.0.8-py3-none-any.whl
 
 Collecting tensorflow-estimator==1.15.1 (from tensorflow==1.15)
   Downloading *MailScanner has detected a possible fraud attempt from
 "secure-web.cisco.com" claiming to be*
 https://secure-web.cisco.com/1bRizO-QQIp1jF8QL6AQZKU7cTnHxGspJ9RUYEh5xNnU6tQoCFwXXTYdekZgZ6Pvdislfufiwamcx_3X-pAUwEGE9BmBJumaPZJiVgo3g8OE7HMlxFFT9MS6oCUSRrXfz_fcq8MHjxHfPPpD7dTaUfyvMPjzrefk8HEJJtoM9TJbpZeVzHan5Fk1FJ9xCZ5uke2DBTwcGQc-8Phbb8SK7WXDqxqc563FJC_GYDZaAOsfXsq3o_JRqVQS3MdEyeS3YYFtZ8znJS45vbz1i70Uvzg/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Fde%2F62%2F2ee9cd74c9fa2fa450877847ba560b260f5d0fb70ee0595203082dafcc9d%2Ftensorflow_estimator-1.15.1-py2.py3-none-any.whl
 
 (503kB)
 100% || 512kB 5.8MB/s
 Collecting opt-einsum>=2.3.2 (from tensorflow==1.15)
   Downloading *MailScanner has detected a possible fraud attempt from
 

Re: [Freesurfer] error installing tensorflow

[Vishnu S]

External Email - Use Caution

1. Make sure you have conda installed
2. In your terminal, then

conda create -n myenv python=3.6
conda activate myenv

3. Then you should be able to install TF 1.13

On Sat, 17 Apr 2021, 08:46 AJ,  wrote:

> External Email - Use Caution
>
> sorry for being non-tech, but how do I exactly do creating a conda venv
> with Python 3.6.
> many thanks
> aj
>
> On Fri, Apr 16, 2021 at 9:56 PM Vishnu S  wrote:
>
>> External Email - Use Caution
>>
>> Hi AJ,
>>
>> So tensorflow 1.13.0 is looking for Python 3.6 as far as I know. Python
>> >=3.7 only supports TF2. Can you try creating a conda venv with Python 3.6
>> and try again?
>>
>> On Sat, 17 Apr 2021, 08:23 AJ,  wrote:
>>
>>> External Email - Use Caution
>>>
>>> Thank you so much for your help.
>>> Here's the error:
>>> MacBook-Pro-4:~ AJ$ fspython -m pip install tensorflow==1.15
>>> Collecting tensorflow==1.15
>>>   Using cached *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1lC38JXl_XpQbS-qcHxSm4Q9jqwcOGiQIP56TrdWCNLmj6CjsX3p8DuPvqcUasXCmvsM8yYDvsbNV9xtQzCs5-caATMuh77fPWRIidpIM_x8f_BdUrHliQ0fg6DXMWCS_QMvYe98YGULmAjpgLp1-2GWhiQb31F2YUTTpNmeWCB5gxVkLJTHo51nX8qroB2QztHlqfM1V5Dwa1MTOyUkmaBDEv7ZyI8Am2PsSJMH-tFGP8LoOmOegIJ9NVGO6H-Sz5iWmJFMbwEPN6GUPQHwinA/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Ffe%2F01%2F997a5d608162cf5371dae49e8cb68baaa5773b091a3e74576ea30dae51e6%2Ftensorflow-1.15.0-cp36-cp36m-macosx_10_11_x86_64.whl
>>> 
>>> Requirement already satisfied: six>=1.10.0 in
>>> /Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.15)
>>> (1.14.0)
>>> Collecting keras-applications>=1.0.8 (from tensorflow==1.15)
>>>   Using cached *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/131b3FTDtlNu2NDQ70UpfLbsvILQUrtZ3dkGwJoyLFF_vlh5-6xllwhn8G36M3Vu7wu0JTUFhr5GlWzt9pskAcUUCAHK5eu-eqrmWC8r52oyvQi5D7QKJ-CH66-izrfyc3eItBUINCE85uSTyAdQ85N0sXUfqlHEVjrlKKx6611mnCjDHNxV4TxdZ9BCe7ftKj1hdhI6msRXmOwIyaFBj9HNvl0btWrz6Ba3zXGfS0Pbg6Ghx3mqH0zPv1f58w_xIt6OSWlPbnIVpxJvktCdQeA/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F71%2Fe3%2F19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f%2FKeras_Applications-1.0.8-py3-none-any.whl
>>> 
>>> Collecting tensorflow-estimator==1.15.1 (from tensorflow==1.15)
>>>   Downloading *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1B1qccajVpEsMmVW7UYufRRnfj5LKd8bnokNgScbjZ0LvYhsyolYLYjPq5NDW4YUiyaTCrVayW9StX5DyQqEGHCP1rldCdmv6lf-YWDSU8rD6rYj9GLPoqkKfSq6MD9JcqAVVjBvaxiVJq49AlDxJD5Jy_0Z7oAD1ZuhrS1I2cVE6ZeMsMaaxRHp-IfY1GvOPXNZDYglWJJQ7IaLAnsYw2_JTxkXN_tY0xteufr9nuxr1IRNPqFeZ7A4JIStxPPc4rO7L1HbV_thOMKlVRfKxEw/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Fde%2F62%2F2ee9cd74c9fa2fa450877847ba560b260f5d0fb70ee0595203082dafcc9d%2Ftensorflow_estimator-1.15.1-py2.py3-none-any.whl
>>> 
>>> (503kB)
>>> 100% || 512kB 5.8MB/s
>>> Collecting opt-einsum>=2.3.2 (from tensorflow==1.15)
>>>   Downloading *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> 

Re: [Freesurfer] error installing tensorflow

[AJ]

External Email - Use Caution

sorry for being non-tech, but how do I exactly do creating a conda venv
with Python 3.6.
many thanks
aj

On Fri, Apr 16, 2021 at 9:56 PM Vishnu S  wrote:

> External Email - Use Caution
>
> Hi AJ,
>
> So tensorflow 1.13.0 is looking for Python 3.6 as far as I know. Python
> >=3.7 only supports TF2. Can you try creating a conda venv with Python 3.6
> and try again?
>
> On Sat, 17 Apr 2021, 08:23 AJ,  wrote:
>
>> External Email - Use Caution
>>
>> Thank you so much for your help.
>> Here's the error:
>> MacBook-Pro-4:~ AJ$ fspython -m pip install tensorflow==1.15
>> Collecting tensorflow==1.15
>>   Using cached *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1wwPzWSmj33HqYdebXpB94Mxz97lpbSG6V3sftjLn84p_gJfo-gpEygXRaxgbMrLQHutp-C3BGFzuBaM3r5wjYvmbunvTt5vgvPv4Zc0xrHDo_e28a_raDs9oBGn_355zGt1AiRku4rQfALLzG6Bpen34Q_d5bLHr2TVP2BXZdAqnc1BzHvhNnGjMpl5fnzrSftpFazxQCeaM-kYNe_xQSMIPKUTdnFCD6IpZt8D67RJjY8Cv86LCdp2CUy8yWHaAg1-ctDKhUKnK5EdUTj-YJg/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Ffe%2F01%2F997a5d608162cf5371dae49e8cb68baaa5773b091a3e74576ea30dae51e6%2Ftensorflow-1.15.0-cp36-cp36m-macosx_10_11_x86_64.whl
>> 
>> Requirement already satisfied: six>=1.10.0 in
>> /Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.15)
>> (1.14.0)
>> Collecting keras-applications>=1.0.8 (from tensorflow==1.15)
>>   Using cached *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1KfwevaV6mhlNO7qYXMtzztspKXLtVDQcTPGVeZ0PqLeIX1_qes210XSlgOelvW6hVxiiNVeHM1NglT1UnjVBP2stZkw_g0uMGUP-dvvxzfR_09JgtpKTx0aqLiuCpHDkqxuNaEPavCPWyYhSFgl9QM3C7lzOaAbcb_BjSM7leg-Zvwmw3V6cbLDLK5DpEakg6nHjkf46SyKmDU32CPaI6m_Oq38J7xm6BjEjfnc40c9fGGRLP6mrfCe1JwgQ0Wc96nUgB1AOWtBAwIGAgne-Mw/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F71%2Fe3%2F19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f%2FKeras_Applications-1.0.8-py3-none-any.whl
>> 
>> Collecting tensorflow-estimator==1.15.1 (from tensorflow==1.15)
>>   Downloading *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1dudqbbYnYYhEjsbI-npCpFGMzpIKjZboKcIy94ECwqjzSdN_9Nxqh9eUsSLG_3xgBnY9K17WPIf2fxNezhlOb5E1LtxH6IoHX323YMKp8jGXPFYhVPxhYLFQqlBpDWj84pXgVwNlS37HkqC3UQmPTfXAIcPTbQIQt8-qoVBL78ScF0hvp-9lciHfr0BXQHu_WZcryK1XqOFl1-QzqbveX85DiMNSjCy_V_ZTSWNoGGOKSDIlRuR_p2WzEeUbIdutL1u6P02GMzTdIwoAVvCRrA/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Fde%2F62%2F2ee9cd74c9fa2fa450877847ba560b260f5d0fb70ee0595203082dafcc9d%2Ftensorflow_estimator-1.15.1-py2.py3-none-any.whl
>> 
>> (503kB)
>> 100% || 512kB 5.8MB/s
>> Collecting opt-einsum>=2.3.2 (from tensorflow==1.15)
>>   Downloading *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1QJna5xdu9S16-pWp_ZVTNPSQ5fgx4rXiJTcC0s89a1ipwkivhPbvTNt-j_CuAwu6VWw4jrLymeX7gm4B4dK_YZ9Ph1FiLYidEkkrc4LjZdC0yol378_DjWa6DcKYz1nTjd985UjN-5zSBygNRvUBrB1fFM41YWriFENMoANYgoJd95ruAMQz_ZRBlxJTTub2AJO1DH1b_Jgp3O-XDrvTA88WqN7MwezOuYIRPSVbtq3xTTxcLCTu9qlq5IiSl06nTmC3St7dg-JB7jSuZUcyqg/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Fbc%2F19%2F404708a7e54ad2798907210462fd950c3442ea51acc8790f3da48d2bee8b%2Fopt_einsum-3.3.0-py3-none-any.whl
>> 

Re: [Freesurfer] error installing tensorflow

[Vishnu S]

External Email - Use Caution

Hi AJ,

So tensorflow 1.13.0 is looking for Python 3.6 as far as I know. Python
>=3.7 only supports TF2. Can you try creating a conda venv with Python 3.6
and try again?

On Sat, 17 Apr 2021, 08:23 AJ,  wrote:

> External Email - Use Caution
>
> Thank you so much for your help.
> Here's the error:
> MacBook-Pro-4:~ AJ$ fspython -m pip install tensorflow==1.15
> Collecting tensorflow==1.15
>   Using cached *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1Xgk2gE4RIgC6_VOOURb5DzNEKxx0egN-mDv3JuslrSUFDX0yKKnt2EJPLWeNspWrR1zHgAh3xSlb7ADPaE6OEgggPxeMoR8iLddk9fBGHyKYX1eGnQ17wkLKHKsecXAXfPnFSyiWLNStoJkCCq3sv28KzVzcrHHmyvxOGMVMSW4pnGiUzB1fxhK0aJ78omJVRuOSMnTlNPWNcEhGXLA8xHiD73PV0f5_-S3H8ScbX8ZKzkZMMDeSwctkw1M2w5fiCzCOcXxTwZnG4cn3sQEH5A/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Ffe%2F01%2F997a5d608162cf5371dae49e8cb68baaa5773b091a3e74576ea30dae51e6%2Ftensorflow-1.15.0-cp36-cp36m-macosx_10_11_x86_64.whl
> 
> Requirement already satisfied: six>=1.10.0 in
> /Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.15)
> (1.14.0)
> Collecting keras-applications>=1.0.8 (from tensorflow==1.15)
>   Using cached *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1KtxtRjsrdq5RvnMxSAiekcBRdpEUWljfrKJkGjTvkYa7VpZ3LUQa8M6KOS_FgxfEHcnQA7iteg08Qyif59dTkb6oBJxQATLZ7YT8vpqwq0ZJdAeXlsPOje-Q0pkAouScaZhp5o6ZcZqNfqbNS5t7opemwhiHD3ZreWoUT9bkKlDhGcn-gzsSacVydDUi2hSSfvGhaKqbCe1SEiF5cVO3fDrfzUrEp3z7fvAX6GMTZUOQKJZ3bpQEgtj961ZBUIFybW1rlFGzWJzRAoYjLhaxaA/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F71%2Fe3%2F19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f%2FKeras_Applications-1.0.8-py3-none-any.whl
> 
> Collecting tensorflow-estimator==1.15.1 (from tensorflow==1.15)
>   Downloading *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1qyFwJVU1W6XXMgvFqvwFkzk2WcgtkNCd6_yBD6yqJFVqo9MNxZXX2jrwjSDz2XN1b68_PEovKmwa84Jwh4r6pN5qSuGoDzoDQwa7n8bGTpYhaFm1f7-Q61hhZRyugwOqWZO8Is0rczV_43eZ30LJs2nknoIphzQZ_-0tl2LF5G_DnMItzbVL_dgU-YyJGg3BXKc3ziBEmg5OVbLSopU2HFX2fjy4WT1K27iTW_jOThj0t2fl9CxjHt9ntNua9iT-fj53DRr_KJaRWeE1B8uPUQ/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Fde%2F62%2F2ee9cd74c9fa2fa450877847ba560b260f5d0fb70ee0595203082dafcc9d%2Ftensorflow_estimator-1.15.1-py2.py3-none-any.whl
> 
> (503kB)
> 100% || 512kB 5.8MB/s
> Collecting opt-einsum>=2.3.2 (from tensorflow==1.15)
>   Downloading *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1TSEIrJ_qTP3JeBMjv1Qhkq4Pl5cyIjZFJ5HJ96VahOwdtoi0V_iao0pm6tb0d1Bzaqtdc2OCrBR1w2kdzK5aWVb2eJtHWQcPN4IF_qgugSJmnbprbBFn9VLoJC9l-_xYq_o8IZFVKVASc2zsHtwbMWctVfIQsKt62x1xKpdcKwFuDQfje-O1JAu2rZiOJRXiKMRd-8gYysFC6d9JSjSjYqmsr7Lj2Y9jiyFpaOIdkTwF27TYFKfEFICU0bhXdqqk8vkjJxY7_dg1LP_sloLmLw/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Fbc%2F19%2F404708a7e54ad2798907210462fd950c3442ea51acc8790f3da48d2bee8b%2Fopt_einsum-3.3.0-py3-none-any.whl
> 

Re: [Freesurfer] error installing tensorflow

[AJ]

External Email - Use Caution

Thank you so much for your help.
Here's the error:
MacBook-Pro-4:~ AJ$ fspython -m pip install tensorflow==1.15
Collecting tensorflow==1.15
  Using cached
https://secure-web.cisco.com/1ZvNOAlnI2lRZHzC8bF1ZCoyoP8DTiHNr8j1wTUnCTH_6rls1cn1Sa-HIOOKz42STunfJWtpRhpfYWUR_hQKpwEzbay5arD5d6sIsm-zCHNqBRHOGhG_c912RuMdn7fm8LtWxtipJ4aSJAUpgiysGWS8w8AEB4PmmBA4FCvzgCS7HWOquoWaPvoIV-puUl877869Gu2Kfi-yt92oHjOOjIdJYq_6q-JZZeRmsqjXApUoKuxETrkMNlL5XP05DG2eIQ_15EXbsChlaMEZlEtVHSg/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Ffe%2F01%2F997a5d608162cf5371dae49e8cb68baaa5773b091a3e74576ea30dae51e6%2Ftensorflow-1.15.0-cp36-cp36m-macosx_10_11_x86_64.whl
Requirement already satisfied: six>=1.10.0 in
/Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.15)
(1.14.0)
Collecting keras-applications>=1.0.8 (from tensorflow==1.15)
  Using cached
https://secure-web.cisco.com/1DcmYmbuovnDyI2Z0h-owN-BxOcIjVXAXtKR-NCsfl6cFq6AWJWBS4YXYdKMpUZiuJxvlniImLirgDwxswqgvM7RTyJnU_e6xefrYlCx-R_Mvz_yuKLts2pFOaj0gKRVkXxqqzhrYMJaugGjLlGvG1yFT_Oo7CW-y6szD-arokgU94mcZ6UBN4BTSwTLCzAJd5tTgnbXX5P1VrksWcvF8jjgydRzemkQ9reAB8CdMD7b4TEMvNF2BRT9yxwX8LR6X1V1WbDOdmlqkiDpYttHssA/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F71%2Fe3%2F19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f%2FKeras_Applications-1.0.8-py3-none-any.whl
Collecting tensorflow-estimator==1.15.1 (from tensorflow==1.15)
  Downloading
https://secure-web.cisco.com/1N2EMaYVq0NsXllEiLWsAFPAXf5YA198UHng2nrMoKsayJ7gEzGjwCrkD4acaacg4AcPDtJVjS3IxlDL-NOzP6sbeQcRBgA2kg_FT1hcjidY_clABoclxq8WNcFmnDgt3wNeoI6xRYtCf0xHj2EnCiXgVLXSXGFFgX-I9d6BJjAmIiMg_vX3JyhUOWO77cAJ_OlTT7JV02fbfAvqijtkwFmLuWcNrc_MfEfNd0LSOmLRURrH6eXS94NBI6ZGznd7jNKH0PvdlWuNp6og69tcJrA/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Fde%2F62%2F2ee9cd74c9fa2fa450877847ba560b260f5d0fb70ee0595203082dafcc9d%2Ftensorflow_estimator-1.15.1-py2.py3-none-any.whl
(503kB)
100% || 512kB 5.8MB/s
Collecting opt-einsum>=2.3.2 (from tensorflow==1.15)
  Downloading
https://secure-web.cisco.com/1FpEwtMXkNi56QvaosjmSa66qprPWMnvB6zsh7VNx7cXMaxxI_bZ5JzInsqIWxxqatws5D-9aegnNMRCn3t2tGEa2rCiSAS9lCd1FciKhcsH3xSVdkU20hA8EyidzUzzhxtBr7Qy_-Amu7LMri1PneDYx-R7DP3GvWPnca6w_SiXsXu9ukJ5Y3QMYpbWL_YzM85_9K4wUlg1PHcBVJMhxGvQFVaJnMzJr6wZYiwBEpjI7CiKHGJSddtp8eOKuqfWfJSZXSVGtU7XUz9muUfYHdA/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2Fbc%2F19%2F404708a7e54ad2798907210462fd950c3442ea51acc8790f3da48d2bee8b%2Fopt_einsum-3.3.0-py3-none-any.whl
(65kB)
100% || 71kB 13.9MB/s
Requirement already satisfied: numpy<2.0,>=1.16.0 in
/Applications/freesurfer/7.1.0/python/packages (from tensorflow==1.15)
(1.18.4)
Collecting absl-py>=0.7.0 (from tensorflow==1.15)
  Using cached
https://secure-web.cisco.com/1CF6wIxhTxNhqjOHCO0n_o68HO5NQrPPCEHVucjzREKB9ieVQbhZP8MSkSBi-NAOcNglybTP9_CVVeV3VE8Vafk4P02rJyPpvdfcoWQ_PWqxlkozfnuKaLdAxGdiODrs4XUefw__9r0r3BQIHQgsuH6uJp7HVn2BehLwQermDhk0UUDd95FBiHkvf0JUG1_lzdsggkZLwxToi4KpEgD9JmP24z8QKWkW_1X6UfRH-q3pGNVFDG_atVYTFOcNVwiV-eZ9i8YZTJuoM6l-3EvHEuQ/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F92%2Fc9%2Fef0fae29182d7a867d203f0eff8296b60da92098cc41db33a434f4be84bf%2Fabsl_py-0.12.0-py3-none-any.whl
Collecting wrapt>=1.11.1 (from tensorflow==1.15)
  Using cached
https://secure-web.cisco.com/1VKtu9AcWmZQ4tg3wO1i429lGQp7kPtE0hXoQMMa0KR2z-hjOzWyCqWVpqFakWoVcoh6auhwH6aj7D46hnfK5nQbxckk9IhbIHNt0toB87Jt0z2H83vwrdUqJ1IhAmnbEXh81irpr638yRi80Iy2u36_nd5jfP7Ik3I0PKpR2Ldv34gVuZNGgbr1toe2yBmvkivaagOjctjw_-5HWD_Ycpf0owWYQRI5M1QNXpZlONuZmvsxV_Zz3djcqKrVGt-Ngnp57qfncblWSj_cPDyZEow/https%3A%2F%2Ffiles.pythonhosted.org%2Fpackages%2F82%2Ff7%2Fe43cefbe88c5fd371f4cf0cf5eb3feccd07515af9fd6cf7dbf1d1793a797%2Fwrapt-1.12.1.tar.gz
dyld: lazy symbol binding failed: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib

Abort trap: 6



On Fri, Apr 16, 2021 at 12:45 PM Hoopes, Andrew 
wrote:

> Hi AJ,
>
>
>
> Freesurfer ships its own python distribution, so it doesn’t matter what
> you have installed on your system. Can you let us know the specific version
> of macOS you are using and send the full error report from pip?
>
>
>
> Thanks
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of AJ <
> ajcns1...@gmail.com>
> *Date: *Friday, April 16, 2021 at 11:56 AM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] error installing tensorflow
>
> *External Email - Use Caution*
>
> Hi,
>
> I have python both versions of python installed:
>
> MacBook-Pro-4:~ AJ$ python3 --version
> Python 3.9.4
> MacBook-Pro-4:~ AJ$ python --version
> Python 2.7.10
>
>
>
> when installing  fspython -m pip install tensorflow==1.13.1, I get the

Re: [Freesurfer] Talairach Failed: Distorted T1

[Harkey, Thomas Jarrott]

External Email - Use Caution

Douglas,

Here is the advice you previously offered.
You can measure the volume of the brainstem and add it on. Eg,
mri_segstats --ctab-default --seg aseg.mgz --id 16 --sum brainstem.dat

My question is:
Is this value in the brainstem.dat file accurate or is it subject to the same 
limitation in that the value will depend on the field of view of volume 
acquisition?
In other words, is it valid to add this number to the brain to obtain total 
brain volume?

Thanks again for all your help.
Kindly,
Thomas Harkey
UAMS College of Medicine M3



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Wednesday, April 14, 2021 9:25 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

Sorry, what is the brainstem.dat file? Is that something we create?

On 4/6/2021 7:53 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution

Douglas,
Thanks again. Is this value in the brainstem.dat file accurate or is it subject 
to the same limitation in that the value will depend on the field of view of 
volume acquisition?
In other words, is it valid to add this number to the brain to obtain total 
brain volume?
Kind regards,
Thomas Harkey
UAMS College of Medicine M3

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Harkey, Thomas Jarrott 

Sent: Tuesday, March 30, 2021 6:03 PM
To: Freesurfer support list 

Subject: Re: [Freesurfer] Talairach Failed: Distorted T1


External Email - Use Caution

Douglas,
Thank you for your help. Another question. The FreeSurfer wiki states that for 
version 5.2 and later, the brainstem is not included in the global measures of 
volume because the amount of brainstem changes depending upon the field of view 
of the volume acquisition.
We are interested in the obtaining the volume of the entire brain using the 
BrainVolNotVent value. Does this mean that BrainVolNotVent does not include the 
brainstem and therefore underestimates total brain volume? Is there a way to 
correct for this?
Kind regards,
Thomas Harkey
UAMS College of Medicine M3


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, March 25, 2021 9:48 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

That is an axial scan that only covers 25mm of the brain inferior-superior. 
This is not whole brain coverage, which is causing the problem

On 3/25/2021 9:07 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution

Douglas,
Thank you for your help. I have pasted the result below.

Volume information for 2020-24axialScalarvolumeall/mri/orig/001.mgz
  type: MGH
dimensions: 384 x 384 x 25
   voxel sizes: 0.598958, 0.598958, 1.00
  type: SHORT (4)
   fov: 230.000
   dof: 1
xstart: -115.0, xend: 115.0
ystart: -115.0, yend: 115.0
zstart: -12.5, zend: 12.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -0.9841, y_r =  -0.0087, z_r =  -0.1777, c_r =15.3722
  : x_a =   0.0272, y_a =  -0.9944, z_a =  -0.1022, c_a =14.0701
  : x_s =  -0.1758, y_s =  -0.1054, z_s =   0.9788, c_s =   -75.3479

talairach xfm :
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
   -0.5894  -0.0052  -0.1777   131.7540
0.0163  -0.5956  -0.1022   126.5760
   -0.1053  -0.0631   0.9788   -55.2497
0.   0.   0. 1.

voxel-to-ras determinant 0.358751

ras to voxel transform:
   -1.6429   0.0454  -0.2935   194.5030
   -0.0144  -1.6602  -0.1759   202.3262
   -0.1777  -0.1022   0.978890.4171
0.   0.   0. 1.

Kindly,
Thomas Harkey
UAMS College of Medicine class of 2022

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, March 25, 2021 9:11 AM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

It looks like something is wrong with your 

Re: [Freesurfer] glmfit with aseg table: view surface overlay

[Griem, Julia]

External Email - Use Caution

Hi Doug,

Ok, that's fine. Is it possible to visualize subcortical volume differences in 
any way?

Thank you!
Julia

NIHR Maudsley Biomedical Research Centre PhD Student
Forensic & Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience
King's College London
16 De Crespigny Park, Camberwell
London, SE5 8AB

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: 16 April 2021 16:11
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] glmfit with aseg table: view surface overlay

Are you trying to correct the table? You can't do that with mri_gtlmfit-sim. 
That looks for clusters, which does not make sense when you are using table 
data. There are a couple of ways you can do it. One is with bonerfonni 
correction (ie, multiply the p-value by the number of ROIs) or with FDR.
On 4/15/2021 11:13 AM, Griem, Julia wrote:

External Email - Use Caution

External Email - Use Caution
Hi Doug,

Thank you. Makes sense. Is there any way to visualize significance overlays for 
the subcortical volumes?

I've also moved on to the correction for multiple comparisons in my subcortical 
volumes, using:

mri_glmfit-sim -- glmdir roi.binarygroup.glmdir --perm 1000 1.3 abs --cwp 0.05 
--2spaces --bg 1

This did not create any new files in the Contrast subdirectories, but the log 
file does say that it was run and finished. Can I find a table with corrected 
p-values anywhere? Or would it make more sense to move the aseg_table into a 
different stats package and calculate my GLM there, correcting for multiple 
comparisons post-hoc (manually)?

Thank you so much
Julia

NIHR Maudsley Biomedical Research Centre PhD Student
Forensic & Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience
King's College London
16 De Crespigny Park, Camberwell
London, SE5 8AB

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 On Behalf Of Douglas N. Greve
Sent: 15 April 2021 15:14
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] glmfit with aseg table: view surface overlay

The input is a table, so the output is a table (the sig.mgh file will just have 
the number of values that are in the table; this is not a "volume" you can look 
at in FV). Look in the sig.table.dat file for the sigs.
On 4/13/2021 8:41 AM, Griem, Julia wrote:

External Email - Use Caution

External Email - Use Caution
Dear Freesurfer team,

I am comparing subcortical volumes (aseg table) in 2 groups with no other 
variables. Based on the GLM lecture slides from the course I attended, I ran 
the following glmfit command:
mri_glmfit
--table aseg_table.txt
--fsgd FSGD/DemographicsSubcortBinaryGroup.fsgd
--C Contrasts/HC-ASPD.mtx
--C Contrasts/ASPD-HC.mtx
--glmdir roi.binarygroup.glmdir

It created all the correct output and subdirectories.

I then used
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=ASPD-HC/sig.mgh

but an error saying "failed to load surface overlay" comes up and the terminal 
error message is "number of vertices in overlay data does not match with 
surface". I assume this is because I am trying to load a 'whole-brain' sig.mgh 
onto a lh surface? Do I have to change the glmfit command to specify 
hemispheres, and if so, how do I do that since I do not want to look at 
cortical but subcortical data? Or alternatively, can I load both hemispheres 
into freeview so the overlay sig.mgh fits?

Thank you so much,
Julia




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[Freesurfer] problem running last step longitudinal analysis

[Zeng, Qi]

External Email - Use Caution

Hi Experts,

I am running the last step (-long) for a longitudinal analysis, However,
encountering an error message saying: "error: ERROR: number of asegs and
norm volumes do not match" for all the subjects I run this time. A similar
problem has been reported before as the following link. The answer to the
question is 'Freesufer version too old'. I have been following the exact
same steps two months ago for my last cohort and it was fine. However, this
time all the subjects reporting error messages (attaching error.log).
Re: [Freesurfer] mri_fuse_segmentations error in longitudinal stream
(mail-archive.com)

My system: x86_64 GNU/Linux
Freesufer version: freesurfer/6.0.0
attached the error.log

Best,
Qi


30452536.stdout
Description: Binary data
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Re: [Freesurfer] Autorecon1 failure

[Abdollahi, Shervin (NIH/NINDS) [C]]

External Email - Use Caution

So yes running it from scratch would work. But I was trying to implement 
fmriprep approach in which they have chosen the optimal approaches for 
skull-stripping or intensity normalization via other applications like ANTs or 
FSL and they imported those to be used in Freesurfer instead of internally 
calculated skull-strip brain mask (brainmask.mgz).  The last step of 
autorecon-1 is where the skull stripping needs to be off and that’s where it 
fails, cause its waiting for that brainmask.mgz and cant find it. Has there 
been any collaboration between freesurfer and fmriprep people on this matter?

Thanks
Shervin

From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 
Date: Friday, April 16, 2021 at 11:08 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Autorecon1 failure

If you run it from scratch (recon-all -s subject -all), does it work? If you 
are going to pick and chose which options to apply, then there is a high risk 
of missing steps
On 4/14/2021 2:23 PM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

External Email - Use Caution
Hi Douglas, Sure, here is the copy of recon-all.log

From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 

Date: Wednesday, April 14, 2021 at 10:32 AM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Autorecon1 failure

Sorry, can you resend the recon-all.log file?
On 4/7/2021 8:45 AM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

External Email - Use Caution


From: "Abdollahi, Shervin (NIH/NINDS) [C]" 

Date: Thursday, March 18, 2021 at 12:42 PM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Autorecon1 failure

Hello Freesurfer Developers,

am trying to use run freesurfer that is configured inside 
smriprep.workflow.anatomical.py under init_anat_preproc_wf pipeline. this 
workflow, does the following:


  1.  T1w reference: realigning and then averaging T1w images
  2.  Brain Extraction and INU (bias field) correction (antsBrainExtraction.sh)
  3.  Brian tissue segmentation (@fsl_fast)
  4.  Spatial normalization to standard space (antsRegistration)
  5.  Surface reconstruction with Freesurfer

When it gets to step 5, it takes skull-stripped t1, ants_segm, and 
bias_corrected image to use in freesurfer recon-all command. In the surface 
reconstruction section, it starts by running the following command:

recon-all -autorecon1
-i /path-to /sub-03_ses-20140624_T1w.nii
-T2 /path-to/sub-03_ses-20140624_T2w.nii
-noskullstrip
-hires
-openmp 1
-subjid sub-03
-sd /Users/abdollahis2/Desktop/fcd_nipype/derivatives/freesurfer
-expert 
/Users/abdollahis2/Desktop/fcd_nipype/single_subject_03/anat_preproc_wf/surface_recon_wf/_subject_id_03/autorecon1/expert.opts

And surely soon, it gives me an error that it can not read mgh file 
(brainmask.mgz). looking into freesurfer/sub-03/mri directory I can see that 
brainmask.mgz is not created and I am not sure if this is because the option 
-noskullstrip was used? I have attached the recon-all.log file. I would 
appreciate any suggestion on how to debug this problem.


  1.  Freesurfer version: 7.1.1 (freesurfer-darwin-macOS-7.1.1-20200811-8b40551)
  2.  Platform: macOS Catalina, Version 10.15.7
  3.  uname -a: Darwin ndsd-eeg-cedar 19.6.0 Darwin Kernel Version 19.6.0: Tue 
Jan 12 22:13:05 PST 2021; root:xnu-6153.141.16~1/RELEASE_X86_64 x86_64
  4.  Recon-all.log: see attached






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Re: [Freesurfer] docker pull freesurfer: manifest error

[Hoopes, Andrew]

Hi Christina,

You’ll need to specify the version tag. You can try:

docker pull freesurfer/freesurfer:7.1.1

best,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Chr. Roßmanith 

Date: Friday, April 16, 2021 at 8:41 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] docker pull freesurfer: manifest error
External Email - Use Caution

Hi,

I'd like to use FS 7 in a docker container. When pulling freesurfer I
get the following error message:

docker pull freesurfer/freesurfer
Using default tag: latest
Error response from daemon: manifest for freesurfer/freesurfer:latest
not found: manifest unknown: manifest unknown

Any hint what I'm doing wrong?

Regards,
Christina Roßmanith


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Re: [Freesurfer] error installing tensorflow

[Hoopes, Andrew]

Hi AJ,

Freesurfer ships its own python distribution, so it doesn’t matter what you 
have installed on your system. Can you let us know the specific version of 
macOS you are using and send the full error report from pip?

Thanks
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of AJ 
Date: Friday, April 16, 2021 at 11:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] error installing tensorflow

External Email - Use Caution
Hi,
I have python both versions of python installed:
MacBook-Pro-4:~ AJ$ python3 --version
Python 3.9.4
MacBook-Pro-4:~ AJ$ python --version
Python 2.7.10

when installing  fspython -m pip install tensorflow==1.13.1, I get the error:
dyld: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib
Abort trap: 6

Is the issue that freesurfer is looking for python3?  I am not sure how to get 
past this installation of tensorflow?
Thank you for your help.
AJ


On Fri, Apr 16, 2021 at 12:58 AM Vishnu S 
mailto:vishnudab...@gmail.com>> wrote:

External Email - Use Caution
Can you try downgrading to python 3.6 in a conda env? Python 3.7 support only 
TF 2.0 and higher.

On Fri, 16 Apr 2021, 11:24 AJ, 
mailto:ajcns1...@gmail.com>> wrote:

External Email - Use Caution
Hi,

I am having trouble installing:  fspython -m pip install tensorflow==1.13.1
Not sure what the issue is.  Any help would be greatly appreciated.
best
AJ
Error message while installing:

dyld: lazy symbol binding failed: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib


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Re: [Freesurfer] Running recon-all with FLAIR

[Edina Szabó]

External Email - Use Caution

Hi Douglas,

Thank you for your response! I really appreciate it.

I ran the command – it works if I replace  --i with --mov.

How can I use the new FLAIRraw.lta to create a new FLAIR-based pial
surface? For example, should I run recon-all -autorecon2 or some later step?

Also, we were assuming that registration of the FLAIR to the T1 was the
problem (underestimated pial surface), since the FLAIR.mgz produced by
Freesurfer was not well registered to the T1.mgz. So, if that's the case,
and I have another well-registered FLAIR (using FSL or SPM), is there a way
to skip the Freesurfer registration and use that FLAIR to create the FLAIR
pial surface?

Thank you for your help in advance!

All the best,
Edina Szabo

__
Edina Szabo, PhD
Research Fellow
Department of Anesthesiology, Critical Care and Pain Medicine
Boston Children's Hospital | Harvard Medical School

-

Try this
cd subject/mri
mri_coreg --i orig/T2raw.mgz --targ orig.mgz --reg transforms/T2raw.lta
You can run with multiple threads by adding --threads N
where N is the number of threads

On 3/29/2021 5:18 PM, Edina Szabó wrote:


External Email - Use Caution

Dear All,


We are running recon-all on the latest version of FreeSurfer (v7.1.1). We
are using both T1 and FLAIR images to better define the pial surfaces, but
when we run the recommended command line (recon-all -subject subjectname -i
/path/to/input_volume -FLAIR /path/to/FLAIR_volume -FLAIRpial -all) the
pial surface is very underestimated (?.pial.FLAIR – and the aseg volume is
based on these surfaces), and we get better results without the FLAIR. It
seems that FreeSurfer mis-registers the FLAIR to the T1 during the process.
Is there a separate step we should do to register FLAIR to T1?

Thank you,
Edina

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Re: [Freesurfer] error installing tensorflow

[AJ]

External Email - Use Caution

Hi,
I have python both versions of python installed:
MacBook-Pro-4:~ AJ$ python3 --version
Python 3.9.4
MacBook-Pro-4:~ AJ$ python --version
Python 2.7.10

when installing  fspython -m pip install tensorflow==1.13.1, I get the
error:
dyld: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib
Abort trap: 6

Is the issue that freesurfer is looking for python3?  I am not sure how to
get past this installation of tensorflow?
Thank you for your help.
AJ


On Fri, Apr 16, 2021 at 12:58 AM Vishnu S  wrote:

> External Email - Use Caution
>
> Can you try downgrading to python 3.6 in a conda env? Python 3.7 support
> only TF 2.0 and higher.
>
> On Fri, 16 Apr 2021, 11:24 AJ,  wrote:
>
>> External Email - Use Caution
>>
>> Hi,
>>
>> I am having trouble installing:  fspython -m pip install
>> tensorflow==1.13.1
>> Not sure what the issue is.  Any help would be greatly appreciated.
>> best
>> AJ
>> Error message while installing:
>>
>> dyld: lazy symbol binding failed: Symbol not found: _utimensat
>>   Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
>>   Expected in: /usr/lib/libSystem.B.dylib
>>
>> dyld: Symbol not found: _utimensat
>>   Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
>>   Expected in: /usr/lib/libSystem.B.dylib
>>
>>
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Re: [Freesurfer] Curvature Stats func. error among step by step in recon-all process

[Douglas N. Greve]

Yes, this is a known error that will be fixed in 7.2, thanks for 
pointing it out


On 4/9/2021 2:51 AM, Yoonho Hwang wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compute cortical thickness and to analyze it between 
groups.
So I perform "recon-all", but rather than using recon-all -all, some 
problems arise while performing each of the steps in it. These 
problems are as follwing.


*1.  By perform "Curvature Stats" of recon-all in parallel, This 
process is required for ?h.curv file. This file is created after 
-white or -whitesurf process, but looking at recon-all file in 
/usr/local/freesurfer/bin/, -whitesurf is running after this process, 
so I think so, Is it correct to move position of curvature stats after 
the pialsurf to fix the error?*

*
*
*2. Looking at *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable 
 
and recon-all file, because order of autorecon -all is different 
between two reference, I am confused. Can you please tell me which one 
to refer to?*


1) FreeSurfer version: 
freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551

2) Platform: Ubuntu release 18.04.1
3) uname -a: Linux LABPC 5.4.0-70-generic #78~18.04.1-Ubuntu SMP Sat 
Mar 20 14:10:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

4) recon-all.log: see attached

Thank you very much.

Sincerely,
Yoonho


--
*Hwang, Yoonho*
*Medical Image Processing Laboratory (MIPL),*
*Department of Biomedical Engineering, Yonsei University.*
*
*
*#218 Sanhak-Kwan, 1, Yeonsedae-gil, Heungeop-myeon, Wonju,*
*Gangwon-do, 26493, Republic of Korea.*
*
*
*Office: +82-33-760-2499*
*Email: ken.lmsta...@gmail.com *

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Re: [Freesurfer] glmfit with aseg table: view surface overlay

[Douglas N. Greve]

Are you trying to correct the table? You can't do that with 
mri_gtlmfit-sim. That looks for clusters, which does not make sense when 
you are using table data. There are a couple of ways you can do it. One 
is with bonerfonni correction (ie, multiply the p-value by the number of 
ROIs) or with FDR.


On 4/15/2021 11:13 AM, Griem, Julia wrote:


External Email - Use Caution

External Email - Use Caution

Hi Doug,

Thank you. Makes sense. Is there any way to visualize significance 
overlays for the subcortical volumes?


I’ve also moved on to the correction for multiple comparisons in my 
subcortical volumes, using:


mri_glmfit-sim -- glmdir roi.binarygroup.glmdir --perm 1000 1.3 abs 
--cwp 0.05 --2spaces --bg 1


This did not create any new files in the Contrast subdirectories, but 
the log file does say that it was run and finished. Can I find a table 
with corrected p-values anywhere? Or would it make more sense to move 
the aseg_table into a different stats package and calculate my GLM 
there, correcting for multiple comparisons post-hoc (manually)?


Thank you so much

Julia

/NIHR Maudsley Biomedical Research Centre PhD Student/

/Forensic & Neurodevelopmental Sciences/

/Institute of Psychiatry, Psychology & Neuroscience/

/King’s College London/

/16 De Crespigny Park, Camberwell/

/London, SE5 8AB/

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* 15 April 2021 15:14
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] glmfit with aseg table: view surface overlay

The input is a table, so the output is a table (the sig.mgh file will 
just have the number of values that are in the table; this is not a 
"volume" you can look at in FV). Look in the sig.table.dat file for 
the sigs.


On 4/13/2021 8:41 AM, Griem, Julia wrote:

*External Email - Use Caution *

*External Email - Use Caution *

Dear Freesurfer team,

I am comparing subcortical volumes (aseg table) in 2 groups with
no other variables. Based on the GLM lecture slides from the
course I attended, I ran the following glmfit command:

mri_glmfit

--table aseg_table.txt

--fsgd FSGD/DemographicsSubcortBinaryGroup.fsgd

--C Contrasts/HC-ASPD.mtx

--C Contrasts/ASPD-HC.mtx

--glmdir roi.binarygroup.glmdir

It created all the correct output and subdirectories.

I then used

freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=ASPD-HC/sig.mgh

but an error saying "failed to load surface overlay" comes up and
the terminal error message is "number of vertices in overlay data
does not match with surface". I assume this is because I am trying
to load a 'whole-brain' sig.mgh onto a lh surface? Do I have to
change the glmfit command to specify hemispheres, and if so, how
do I do that since I do not want to look at cortical but
subcortical data? Or alternatively, can I load both hemispheres
into freeview so the overlay sig.mgh fits?

Thank you so much,
Julia



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Re: [Freesurfer] Autorecon1 failure

[Douglas N. Greve]

If you run it from scratch (recon-all -s subject -all), does it work? If 
you are going to pick and chose which options to apply, then there is a 
high risk of missing steps


On 4/14/2021 2:23 PM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:


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Hi Douglas, Sure, here is the copy of recon-all.log

*From: *"Douglas N. Greve" 
*Reply-To: *Freesurfer support list 
*Date: *Wednesday, April 14, 2021 at 10:32 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Autorecon1 failure

Sorry, can you resend the recon-all.log file?

On 4/7/2021 8:45 AM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

*External Email - Use Caution *

*From: *"Abdollahi, Shervin (NIH/NINDS) [C]"
 
*Date: *Thursday, March 18, 2021 at 12:42 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"



*Subject: *Autorecon1 failure

Hello Freesurfer Developers,

am trying to use run freesurfer that is configured inside
smriprep.workflow.anatomical.py under init_anat_preproc_wf
pipeline. this workflow, does the following:

 1. T1w reference: realigning and then averaging T1w images
 2. Brain Extraction and INU (bias field) correction
(antsBrainExtraction.sh)
 3. Brian tissue segmentation (@fsl_fast)
 4. Spatial normalization to standard space (antsRegistration)
 5. Surface reconstruction with Freesurfer

When it gets to step 5, it takes skull-stripped t1, ants_segm, and
bias_corrected image to use in freesurfer recon-all command. In
the surface reconstruction section, it starts by running the
following command:

recon-all -autorecon1

-i /path-to /sub-03_ses-20140624_T1w.nii

-T2 /path-to/sub-03_ses-20140624_T2w.nii

-noskullstrip

-hires

-openmp 1

-subjid sub-03

-sd /Users/abdollahis2/Desktop/fcd_nipype/derivatives/freesurfer

-expert

/Users/abdollahis2/Desktop/fcd_nipype/single_subject_03/anat_preproc_wf/surface_recon_wf/_subject_id_03/autorecon1/expert.opts

And surely soon, it gives me an error that it can not read mgh
file (brainmask.mgz). looking into freesurfer/sub-03/mri directory
I can see that brainmask.mgz is not created and I am not sure if
this is because the option -noskullstrip was used? I have attached
the recon-all.log file. I would appreciate any suggestion on how
to debug this problem.

 1. Freesurfer version: 7.1.1
(freesurfer-darwin-macOS-7.1.1-20200811-8b40551)
 2. Platform: macOS Catalina, Version 10.15.7
 3. uname -a: Darwin ndsd-eeg-cedar 19.6.0 Darwin Kernel Version
19.6.0: Tue Jan 12 22:13:05 PST 2021;
root:xnu-6153.141.16~1/RELEASE_X86_64 x86_64
 4. Recon-all.log: see attached



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Re: [Freesurfer] selxavg3 Input to SVD must not contain NaN or Inf

[Douglas N. Greve]

It looks like you have only a single 64 sec polar/eccen cycle to your 
acquisition. Is that right? It is pretty slow.


On 4/16/2021 9:44 AM, Michaël Vanhoyland wrote:


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Dear Freesurfer team,


I'm new to fMRI analysis and want to analyse Retinotopy data. I was 
following a retinotopy analysis tutorial 
(sites.psych.ualberta.ca/kylemathewson/retinotopy-in-freesurfercnl-protocol/#FUNC) 
when I encountered a problem while running selx3avg-sess. I found that 
some other people had similar issues on the mailing list, but most 
often the reason was that there were only positive polar or eccen 
runs. In this case, I'm analyzing all 4 conditions ( eccen/pos; 
eccen/neg; polar/pos; polar/neg) in 4 separate runs. The TR is 2 
seconds and there are 32 acquisitions per run.



I'm running the following freesurfer version:

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c


These are the first steps of the analysis, which ran without an error:

1. preproc-sess -s T1_EarlyVisualLesion -surface self lhrh -fsd 
Retinotopy -mni305 -fwhm 5 -per-run


2. mkanalysis-sess -a Retinotopy.T1_EarlyVisualLesion.lh -surface self 
lh -TR 2 -retinotopy 64 -paradigm rtopy.par -fsd Retinotopy -fwhm 5 
-per-run



When running the following:

selxavg3-sess -a Retinotopy.T1_EarlyVisualLesion.lh -s 
T1_EarlyVisualLesion



the following error appers:


% /data/local/Software/freesurfer/subjects
%  Retinotopy.T1_EarlyVisualLesion.lh
which fast_selxavg3
which fast_ldanaflac
which MRIread


fast_selxavg3b('/data/local/Software/freesurfer/subjects/T1_EarlyVisualLesion/Retinotopy/Retinotopy.T1_EarlyVisualLesion.lh/sxa3.config.txt')
if(~fast_fileexists('/tmp/selxavg3-sess-9836.ok')); quit; end
%


quit;
--
--
--- matlab output 
MATLAB is selecting SOFTWARE OPENGL rendering.

    < M A T L A B (R) >
  Copyright 1984-2019 The MathWorks, Inc.
  R2019a (9.6.0.1072779) 64-bit (glnxa64)
   March 8, 2019


To get started, type doc.
For product information, visit www.mathworks.com.

>> >> >> >> /data/local/Software/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> /data/local/Software/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>> /data/local/Software/freesurfer/matlab/MRIread.m
>> >> >> starting fast_selxavg3b


#@# T1_EarlyVisualLesion ###
/data/local/Software/freesurfer/subjects/T1_EarlyVisualLesion
-
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /data/local/Software/freesurfer/subjects
Extension format = nii.gz
INFO: key nSliceGroups unrecognized, line 11, skipping
nruns = 4
autostimdur =


outanadir = 
/data/local/Software/freesurfer/subjects/T1_EarlyVisualLesion/Retinotopy/Retinotopy.T1_EarlyVisualLesion.lh

Found 44756/124286 (36.0) voxels in mask 1
Creating Design Matrix
 ... creation time =  0.005 sec
DoMCFit = 1
ntptot = 128, nX = 36, DOF = 92
Saving X matrix to 
/data/local/Software/freesurfer/subjects/T1_EarlyVisualLesion/Retinotopy/Retinotopy.T1_EarlyVisualLesion.lh/Xtmp.mat

Error using svd
Input to SVD must not contain NaN or Inf.

Error in cond (line 35)
    s = svd(A);

Error in fast_selxavg3b (line 394)
  XCond = cond(XtX);

>> --
ERROR: fast_selxavg3() failed\n



I attached the xmap file and noticed that there are 4 rows/columns 
that are all 'Nan'  ( 5,6, 17 and 18).


I'm not sure why nX is 36: because freesurfer found 44756/124286 
(36.0) voxels or because it should be the amount of TR's during the 
run (32 conditions of 2 seconds each)?


The size of each run (.nii) is (112 by 112 by 54 by 32). So if nX 
should contain the amount of TR's per run, I'm not sure why it's 
adding 4 columns/rows to nX.



Any help and advice to fix this problem is very much appreciated.

Thanks in advance,

Michael Vanhoyland

Department of Neurophysiology

KULeuven, Belgium



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Re: [Freesurfer] Running qcache on recon-all output

[Douglas N. Greve]

You can just run recon-all -s subject -qcache
this will only run the qcache

On 4/16/2021 1:57 AM, Vishnu S wrote:


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Hello,

I downloaded some FreeSurfer recon-all analyses from the ADNI dataset, 
but these analyses have been run without the qcache flag.

Is there any way for me to re-analyse this with only the qcache flag?
If so, how would I do this and how long would it take?

Thanks for your help,
Vishnu




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Re: [Freesurfer] The cvs_avg35

[Zollei, Lilla,Ph.D.]

Hi Mudathir,

The two templates were created by using the same 40 subjects as a training data 
set as is used by Freesurfer.  The volumes were registered to a common space by 
an iterative framework in which you create a mean, register individuals to it 
and then re-create the mean. We then reconned the final mean. The MNI 
equivalent was created by moving the mean to the MNI152 space before running 
recon.

The above explains why those 40 subjects were used for the template.

Best, Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of バキット・ムダシル 

Sent: Wednesday, April 14, 2021 6:55 AM
To: Freesurfer support list 
Subject: [Freesurfer] The cvs_avg35

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Hi,
I was looking for any document describes how the cvs_avg35 and 
cvs_avg35_inMNI152 were made? Can you please send me a link or give me a brief 
about it please? I searched in the freesurfer wiki and here in the freesurfer 
folder but no success.
Also, I found from literature that the fsaverage was made from a data of 40 
subjects that includes 10 cases of Alzheimer disease. Can I ask what was the 
reason to include those 10 cases to create this template?

Thanks

Mudathir





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Re: [Freesurfer] Surface registration problem

[Manenti, Giorgio]

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Dear Greve, 

Thank you very much for your reply, 
yes indeed i found the problem which was connected to the deletion of 1 slice 
of the functional data in order to run the FSL "topup"  b02b0.cnf flag.
I solved it by changing this step, using the  b02b0_2.cnf for odd number of 
slices.



Many thanks again

Best 
Giorgio

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[Freesurfer] selxavg3 Input to SVD must not contain NaN or Inf

[Michaël Vanhoyland]

External Email - Use Caution

Dear Freesurfer team,


I'm new to fMRI analysis and want to analyse Retinotopy data. I was following a 
retinotopy analysis tutorial 
(sites.psych.ualberta.ca/kylemathewson/retinotopy-in-freesurfercnl-protocol/#FUNC)
 when I encountered a problem while running selx3avg-sess. I found that some 
other people had similar issues on the mailing list, but most often the reason 
was that there were only positive polar or eccen runs. In this case, I'm 
analyzing all 4 conditions ( eccen/pos; eccen/neg; polar/pos; polar/neg) in 4 
separate runs. The TR is 2 seconds and there are 32 acquisitions per run.


I'm running the following freesurfer version:

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c


These are the first steps of the analysis, which ran without an error:

1. preproc-sess -s T1_EarlyVisualLesion -surface self lhrh -fsd Retinotopy 
-mni305 -fwhm 5 -per-run

2. mkanalysis-sess -a Retinotopy.T1_EarlyVisualLesion.lh -surface self lh -TR 2 
-retinotopy 64 -paradigm rtopy.par -fsd Retinotopy -fwhm 5 -per-run


When running the following:

selxavg3-sess -a Retinotopy.T1_EarlyVisualLesion.lh -s T1_EarlyVisualLesion


the following error appers:

% /data/local/Software/freesurfer/subjects
%  Retinotopy.T1_EarlyVisualLesion.lh
which fast_selxavg3
which fast_ldanaflac
which MRIread


fast_selxavg3b('/data/local/Software/freesurfer/subjects/T1_EarlyVisualLesion/Retinotopy/Retinotopy.T1_EarlyVisualLesion.lh/sxa3.config.txt')
if(~fast_fileexists('/tmp/selxavg3-sess-9836.ok')); quit; end
%


quit;
--
--
--- matlab output 
MATLAB is selecting SOFTWARE OPENGL rendering.

< M A T L A B (R) >
  Copyright 1984-2019 The MathWorks, Inc.
  R2019a (9.6.0.1072779) 64-bit (glnxa64)
   March 8, 2019


To get started, type doc.
For product information, visit 
http://secure-web.cisco.com/1vaPLvSV7ygYtI5_OZ6fwnXZPrdpCQWbuMTl3qMCoMm4YYMnGcCb6Nfuh4HA92xXGYMTq1-3Cku0d41CtFPaPfes1skYbD_89DOOleKjHQYkHb3hzqfB8Y3uTHLrvfbiW7QwVe63tDlKsTCNtsoRB_aGdsisuvy3Lv0jRcGd62tGe_ze4btABZAYsXrtWMZ2nBcJnOVXzlRlvPtA4sH2EHTCo0TqqiK13o0oxKMgVT6QLC2MDUUuojjchLlcsSZAVBNraatVB8YZiGi5UCmKDiA/http%3A%2F%2Fwww.mathworks.com.

>> >> >> >> /data/local/Software/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> /data/local/Software/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>> /data/local/Software/freesurfer/matlab/MRIread.m
>> >> >> starting fast_selxavg3b


#@# T1_EarlyVisualLesion ###
/data/local/Software/freesurfer/subjects/T1_EarlyVisualLesion
-
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /data/local/Software/freesurfer/subjects
Extension format = nii.gz
INFO: key nSliceGroups unrecognized, line 11, skipping
nruns = 4
autostimdur =


outanadir = 
/data/local/Software/freesurfer/subjects/T1_EarlyVisualLesion/Retinotopy/Retinotopy.T1_EarlyVisualLesion.lh
Found 44756/124286 (36.0) voxels in mask 1
Creating Design Matrix
 ... creation time =  0.005 sec
DoMCFit = 1
ntptot = 128, nX = 36, DOF = 92
Saving X matrix to 
/data/local/Software/freesurfer/subjects/T1_EarlyVisualLesion/Retinotopy/Retinotopy.T1_EarlyVisualLesion.lh/Xtmp.mat
Error using svd
Input to SVD must not contain NaN or Inf.

Error in cond (line 35)
s = svd(A);

Error in fast_selxavg3b (line 394)
  XCond = cond(XtX);

>> --
ERROR: fast_selxavg3() failed\n



I attached the xmap file and noticed that there are 4 rows/columns that are all 
'Nan'  ( 5,6, 17 and 18).

I'm not sure why nX is 36: because freesurfer found 44756/124286 (36.0) voxels 
or because it should be the amount of TR's during the run (32 conditions of 2 
seconds each)?

The size of each run (.nii) is (112 by 112 by 54 by 32). So if nX should 
contain the amount of TR's per run, I'm not sure why it's adding 4 columns/rows 
to nX.


Any help and advice to fix this problem is very much appreciated.

Thanks in advance,

Michael Vanhoyland

Department of Neurophysiology

KULeuven, Belgium



Xtmp.mat
Description: Xtmp.mat
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[Freesurfer] docker pull freesurfer: manifest error

[Chr . Roßmanith]

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Hi,

I'd like to use FS 7 in a docker container. When pulling freesurfer I 
get the following error message:

docker pull freesurfer/freesurfer
Using default tag: latest
Error response from daemon: manifest for freesurfer/freesurfer:latest 
not found: manifest unknown: manifest unknown

Any hint what I'm doing wrong?

Regards,
Christina Roßmanith


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Re: [Freesurfer] Tract endpoint density map surface overlay

[バキット・ムダシル]

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Hi, Anastasia. Thanks a lot. Sure I will try your suggestions.

Mudathir

> On Mar 31, 2021, at 13:00, Yendiki, Anastasia  
> wrote:
> 
> Hi Mudathir - There are several ways to configure the projection from the 
> volume to the surface, so you might want to look at the options of 
> mri_vol2surf to make sure that it's doing exactly what you want. There are 
> ways to control how deep you go from the surface (projfrac/projdist) and ways 
> to control what quantity you extract from the volume voxels along that depth 
> (avg/max). It also gives you the option to smooth the points in the volume 
> before projecting or on the surface after projecting. You can play with these 
> things to change the appearance of the end result.
> 
> Anastasia.
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  
>  > on behalf of バキット・ムダシル 
> mailto:m-bak...@fmu.ac.jp>>
> Sent: Tuesday, March 30, 2021 11:02 PM
> To: Freesurfer support list  >
> Subject: [Freesurfer] Tract endpoint density map surface overlay
>  
> External Email - Use Caution
> Hi everyone,
> 
> I need to confirm if the steps below are correct, so I would like to ask 
> freesurfer experts help. By using the Left-Cerebral-White-Matter mask 
> imported from freesurfer as a seed I created a tract end points density image 
> of the arcuate fasciculus in a NIFTI format (first figure). I want to display 
> the image on the same subject’s white matter surface. So, I wrote the command 
> as follows 
> 
> 
> mri_vol2surf --src DensityMAP.nii.gz --out filename.mgh --hemi lh --surf 
> white --out_type mgh --regheader subject_id
> 
> The output as seen in the second figure. 
> 
> Thanks 
> 
> Mudathir
> 
> 
> 
> 
> 
> 
> 
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> 
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