Re: [Freesurfer] Recon-all Freezes on Parallel

2022-05-10 Thread falk.luesebr...@med.ovgu.de 
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Hi Joanna,


if I remember correctly, you won't see any screen output until the process is 
finished using parallel. So, I suppose it doesn't freeze. Have you kept the 
process running for some time?


Also you state that you want to use only 2 jobs at a time. However, in the 
command line you specify 3 jobs.


Best,

Falk




...

[http://secure-web.cisco.com/1Xg2HcdvF9dRzTa2ZFIhf3Kl-wpULX1tKJmpGmfMvcbKrMbdfqPxQLXGI3SEiMfs71F3UZU3EuqqMhA0oIo1WB9bky3inuOGAkia2rEVe1p9i8J5iaE9ltDdQ-pprMR55f-eqheOd1qYmeIH4Y6sWyuCBV5i24RVsog0Hm3hG-vf2J7pDXBLccGZM4cuTrozS-tcHZ_c4BCAuZgyBbV3syYOHXmB7l_9zfYrJ7x_fTouneytuqEbDPfONopAUwdnP14DDVwmfLtRO0zqoMpAwidr6MNYJbSqEtmVirfuScODi4lOLs4uomfZ-rqFGGZVSje4b6IoNcJRGi7xJVp2dGQ/http%3A%2F%2Fwww.med.ovgu.de%2Funimagdeburg_mm%2Fummd_focus.gif]
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39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de>
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Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Joanna L Eckhardt 

Gesendet: Montag, 9. Mai 2022 23:27:02
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Recon-all Freezes on Parallel


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Dear FreeSurfer Team,

I have been trying to use the parallel command (following FreeSurfer tutorial) 
to run multiple subjects (Windows os running Ubuntu VM).

I only have 2 cores, so I have it set to 2 jobs instead of 8 as in the 
tutorial. When I use the code from the tutorial, there is an error with the 
.nii, and I assume it is because my files are .nii.gz.

developer@developer-VirtualBox:~/FreeSurfer/Cannabis_Reduced$ ls *.nii | 
parallel --jobs 3 recon-all -s {.} -i {} -all -qcache
ls: cannot access '*.nii': No such file or directory


So I changed the code to .gz with everything else the same, and FreeSurfer does 
nothing (it stalls/freezes). Is this just because my computer cannot handle the 
job? Is there anything else I can do to run parallel? If not, I can always just 
run 1 subject at a time, but I want to check and see if there is another way to 
get this to work.

Thank you for your time!
Joanna


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Re: [Freesurfer] Reversing mri_convert

2022-05-05 Thread falk.luesebr...@med.ovgu.de 
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Hi Victor,


in case you used mri_convert like this only, there is no change in orientation 
or spacing between orig.mgz and T1.nii. So, whatever you registered to the 
T1.nii should also be in space of the orig.mgz.


Best,

Falk


...

[http://secure-web.cisco.com/1bMxxPB2IQvUkA27JpoN6uYF_qZIvBhG7A1lEk_pEPVLjceSNqAuh2ELQrVXqmNwDxO-gqw8L1AEdbpyg24KUrplVS1nVMpzDvZMnLlMlxDizz858uiYsVJw3j_eJAy3F8ROeMbQQGdCNQdGmudIjjmSP-DmuF6zEpoivRhwTB0E-WM34a9y1lhuAPv-VfV01N0gdTr1Xu0mAeJ3pD89NxapxypjmT7CmixQuxq7DTT7jBhVsiWkIKPyDpRhTYXFDyhcmx2miIgf8JZXKyLUXTZiFip_eG0Rh9fS0KS7VC72MB4ubvSdGrS9rptNnBeE85QA02JCM-cayZ2SoocYUMw/http%3A%2F%2Fwww.med.ovgu.de%2Funimagdeburg_mm%2Fummd_focus.gif]
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Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de>
http://secure-web.cisco.com/1Ot95tcBSI8NwAu9j3-MCi-WNazHI1x3J_Wd7KLcLqqDxbYOgUclzwlyOXOLYHH412QcBGDnXDUOxzgguWCcQel8L9ZaACvmWHS4zTEdK8m4QYnGS7xdkGY5RGp0vFAppqrzydZAf5JmpYcPyBnyWZKvGyEXVs4m-zIc-l0qYdee1xdYpnuNye9cAN_EA7WpEICaRtzUMDWnXay-IFvAa1sx-CEhdTWl_sspDuOZKqHB0SYGJ-szyMlAYGZFOOg42NNc91WEMisk0SlaKG7_cgfvjHUrowbBBNtrdR_lL3mwsJ8-Tq9I_Xgwp-2hdoPYS4GVMivfLvRmcMR4Gt4lZkA/http%3A%2F%2Fwww.kneu.ovgu.de%2Fkneu.html

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Zeng, Victor (BIDMC - 
Keshavan - Psychiatry) 
Gesendet: Donnerstag, 5. Mai 2022 10:09:26
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Reversing mri_convert


External Email - Use Caution

Hi,

I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii

I now have something registered to the T1.nii and would like to move it back to 
Freesurfer space. How would you go about doing that? I am assuming I would do 
the inverse of the mri_convert, but I can't seem to find the option to write 
the matrix.

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--


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Re: [Freesurfer] parallel make_average_subject

2022-04-12 Thread falk.luesebr...@med.ovgu.de 
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Hi Marina,


whenever I want to parallelize something which doesn't have a built in 
function, I'm using GNU parallel. Just google for it. The documentation is 
quite good.


Best,

Falk


...

[http://secure-web.cisco.com/1ZOQLXeEUYkEe-uLh_AhkGhdRee6u0HM4FgGRlgF7MqTQ2qnbOHrqhOwmAHjbzNqknHgOQ3ikU_MokLPD2LGdD2xgMxp6devAWGOLfKWxhGvZYnj5jQx3TKLNdCuhN_ZeEKms_Lla_yvkdQrf4FsJnVyAAbza9n6nx6VZoLe7tsiye--TJTLgZye5WkuPA8zp7CfnsfwjC93ZvXasDk-IIz5wDknm4AQlXXC_a93P9uOhe8EQOOrfGk5_OG01Zna1rKjcSLKqr4YJ_UMCr1veLOpEuEx6gHH58wMQPWNtmH9m9_8Vn3t-sHBByWOIFliA/http%3A%2F%2Fwww.med.ovgu.de%2Funimagdeburg_mm%2Fummd_focus.gif]
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Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Marina Fernández 

Gesendet: Montag, 11. April 2022 15:54:13
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] parallel make_average_subject


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Dear experts,

I would like to create an average subject from a very large population. I am 
going to compute it on a computer with a lot of threads and I would like to 
know if it is possible to parallelize the make_average_subject function to try 
to shorten the computation time. I have tried to add the -openmp flag but I get 
the error that the flag is unrecognized.
How can I solve this?

Thank you in advance.

Best regards,
Marina






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Re: [Freesurfer] mri_normalize error MP2RAGE

2022-01-31 Thread falk.luesebr...@med.ovgu.de 
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Hi Cornelius,


this doesn't address your issue directly and I may have simply been lucky, 
however, I haven't had any difficulties to process (7T) MP2RAGE data after 
background removal suggested by Marques et al. 
(https://secure-web.cisco.com/1fEVC_xpeM5msAvRKs8URofSZUL1vh4MEY9PS93M8WS4k2A4rZboiiUGNSE87l_4ab4OAR1phVaejWMtcI1vxv7PYJXeFmjk1eyCGBX74RlOteFVYZqC2IKRu03jybbRKeQtoRvSclItC46SeaLnfZexquwuoxUsN7wwabbqVtjDDmPIgw3Iwl_owCJzjlZ9GqCqtARqvgsgo4x5Bs5bAWSgRM8vUe3c8gamk7M76_O84gNGASjAAAJYk4XocpvkgzcSVHcCOArfhUgu4OgoOA0oTK3l6mmXyiuuNzLDdz1jcdT-l5HB_YppiCqYFAdx8Oogg2ICGu8juK-0EkdfhKg/https%3A%2F%2Fgithub.com%2FJosePMarques%2FMP2RAGE-related-scripts
 I'd omit the skullstripping, too.


Maybe this helps.


Best,

Falk


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Dr. Cornelius Kronlage 

Gesendet: Montag, 31. Januar 2022 10:14:22
An: 'freesurfer@nmr.mgh.harvard.edu'
Betreff: [Freesurfer] mri_normalize error MP2RAGE

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Dear freesurfer experts,

when running recon-all (FS version 7.2.0) on skullstripped 3T MP2RAGE 
sequences, about 10-20% of scans from one scanner fail because of this:

mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz

 [...]

Iterating 2 times
-
3d normalization pass 1 of 2
error: No such file or directory
error: MRInormFindControlPoints: could not find enough control points
error: No such file or directory
error: MRInormFindControlPoints failed
Command exited with non-zero status 253


nu.mgz as the input to mri_normalize looks good to me. I am of course happy to 
provide full logs and some example data - please let me know.

The exact same problem (also MP2RAGE data) has been described twice before, but 
I couldn't find a solution:
https://secure-web.cisco.com/1r3_UfItk0odyQTEjL22mLAxycj89_vXfN--AkpFwUzred-OQT3ckmk1p9JLbc29ymXguFMzz6rV70r7A9LeDMz_kYEm1cy8e9ibgxgnRwgtJLUfjnfuY7OkKyKDITcG13L9huWbQSuMS4eo6ea1DFHfrbfd9b_1msdUkWpfAFMV_UBe8nf3eVw5dmY-zapW2LYz0tifCErjKgm631dwA8U8RH3BRPmSdKNv6NT8vQmby7TV0Kd5S490MWVKNPO_Ve7SGS1clbqmTblxJRiNt2m0AUFzGrZcY8EQLNhMWPz1sfmDFgZFw999W7vwhhAa5YQXJ8pZbUYMGXMaJJ3dyig/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66557.html
https://secure-web.cisco.com/1_dIFX4W-YMl78kLd-J9E7AGEkpzUy7zCtCTsFt-L6nLdAv_ixABY3RDMvbdmBUDMJNZ-4u1RxJGsBMdpoUXKZMDoxX7orbApLXZgx30JCvhLAp31DqNIdIJHJF-OsxyycEnct0FCwOQJric_qQLQ_noGjYTi2qa7coQda6l04uWLmjnF5LIOjIJ7s2L95fZdSdTNaiLBUo1XQjQWPwr7dXmXIDk_ly61SRk8r9EyMv-7Bv5URoFumrNXPLHoWhcyDOgq2i2x7f3gdfB3pTN36GbygyujShpYQdRwE24fPj5sUN9VqAfIvJ1y5JqSahF9u5u07COsUHW5POQQHTK06Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg70463.html

Thanks you in advance and
best wishes

Cornelius



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Re: [Freesurfer] Using SPM segmentations in FreeSurfer

2022-01-27 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Glad to hear it worked out in the end.


Best,

Falk


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Nathan Kindred (PGR) 

Gesendet: Donnerstag, 27. Januar 2022 12:20:52
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer


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Hi both,

Thank you so much to both of you for the help. I have now managed to get it to 
work using Falk’s command. I’ve made a note of your suggestion too, Douglas, 
just in case I have any errors with other subjects.

Best,
Nathan

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

Date: Wednesday, 26 January 2022 at 21:52
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
I think that should work.
One other issue is that the wm.seg.mgz might need to be uchar (a relic
of when computers did not have so much memory). If it does not work with
falk's command, you can try
mri_convert -odt uchar --no_scale 1 wm.seg.mgz wm.seg.mgz


On 1/24/2022 2:47 AM, falk.luesebr...@med.ovgu.de wrote:
>  External Email - Use Caution
>
> Oh, sorry... Following the steps from the previous mail you should run this 
> command:
>
>
> mri_mask brain.mgz new_segmentation.mgz wm.seg.mgz
>
>
> Best,
>
> Falk
>
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  im Auftrag von 
> falk.luesebr...@med.ovgu.de 
> Gesendet: Montag, 24. Januar 2022 08:41:15
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
>
>  External Email - Use Caution
>
> Hi Nathan,
>
>
> well, once again, I can't be much of help with regards to your error message. 
> Have you had a look at the data and does it looks reasonable up to that 
> point? Which FreeSurfer version are you running?
>
>
> FreeSurfer needs to have the data in a very specific form. In case of the 
> white matter segmentation the resulting volume should have a value of 110 
> where white matter is located. The SPM segmentation has values of 0 to 1. 
> Therefore, if you would simply try to use that, it wouldn't work. The given 
> command should do that while using the SPM segmentation to mask the 
> brain.mgz. Afterwards, the ventricles and subcortical structures will be 
> filled based on the aseg.presurf.mgz and set to values of 250. The other 
> commands changes the WM segmentation so that the neighbors of all voxels 
> labeled as WM have a face in common - no edges or corners allowed.
>
>
> Best,
>
> Falk
>
>
>  "secure-web.cisco.com" claiming to be 
> https://secure-web.cisco.com/14nwA-wqvm5kUO9O0CsIsE56npxQFbhl00lDoBBn2Lt0jPyQd2MOLdD6qyI7YDiLjFj2iBWdyjbc3GFnQRYrJbJEGplbV7Yi75yeodKQxt6wQXGAJJFATFWE7Cup4jEtDmDUaIXp2MFMQm9jbSWGlNTCdHAYSaU60VTRi3UToEmalYfSvSd3LkEPhCRvXlCfOqGDCkBbs-KXI7dRab7n15-VsUqDVncyW5pIk-OBdL7twQx1TD-FOf8cRs6UROEuM5RpQFZgc-vR_hyQHMLpbvPJDiNN7DqErbTiXKnVg6P7fkHfVJnFA3rzcFdOe3yMAFl9AUZ9ndlL-2kWb1T1wPQ/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsecure-web.cisco.com%252F1mIUaa7F-i8b4cYwNnbztpMSGC1LS0vhF8ATfmhtgiZxT6lh0vSh_fcPYFd0tYgHhhlC0czxOdn69ctn9ZyRSKCYMcXsmmkriPcmLaomDWhtmJ5W4il1ZwhsIARbrSX2L7lwOY4WpeD17uvDPZEr9lJH-8xglQ5ObufKxfy2D3vtvwE2N-M8VOR-hEb0TVWvq5U9gQ4kxRHAcpk8alzRctnBGXIBmyM_-d1Aj1RjAD6VdhMQjTTWweZbJ9MvFjIDFEoeAmvs02ErbmlqFjhY8W97SzZV2Z2hoWaCtKNzqWxvGDQld_eKtmrykF9fMby4w%252Fhttp%25253A%25252F%25252Fwww.kneu.ovgu.de%25252Fkneu.html%26data%3D04%257C01%257Cn.kindred1%2540newcastle.ac.uk%257Ce41576f561da483306eb08d9e116165f%257C9c5012c9b61644c2a91766814fbe3e87%257C1%257C0%257C637788307247196211%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3D0ejbAPnogyKL0%252FkmGEBUrBLIWh9a%252F%252Bd%252FGtlAzVEfKJY%253D%26reserved%3D0<https://secure-web.cisco.com/1WQvlhU2N1HmOz5_ibma0MtD5I0xYtIOayQE8FNVw0DYO7dJz7qy7NLAuW107y-Nq4wF7UPyjS8N_fJ9tbMWvGXbrsSyCnxfuTsKV5ElLRfhNYiQ03_QUOEk187_hAIHkeuA3a0-1HAnEFkks1taNmFYyfxTA5WOG3yYinApiYVPHiF2F2X1lrS5Q084zUjLvmFA1OLaP0vPUFgSkUJGDl_VKmIaeQV40QT3GQG8CddYUz7hprutgTBzCS7wnA1PHYp4ssleEp2CTRtcCnQAbOwCZYPsriLYCKGfgwm4vfPyjtEK94Ar3K39sf88TiHzSq_8E83dHPR4AeZdqgeAmp8SCmj53cvvRzZTTaYyw6Nw/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsecure-web.cisco.com%252F1mIUaa7F-i8b4cYwNnbztpMSGC1LS0vhF8ATfmhtgiZxT6lh0vSh_fcPYFd0tYgHhhlC0czxOdn69ctn9ZyRSKCYMcXsmmkriPcmLaomDWhtmJ5W4il1ZwhsIARbrSX2L7lwOY4WpeD17uvDPZEr9lJH-8xglQ5ObufKxfy2D3vtvwE2N-M8VOR-hEb0TVWvq5U9gQ4kxRHAcpk8alzRctnBGXIBmyM_-d
1Aj1RjAD6VdhMQjTTWweZbJ9MvFjIDFEoeAmvs02ErbmlqFjhY8W97SzZV2Z2hoWaCtKNzqWxvGDQld_eKtmrykF9fMby4w%252Fhttp%25253A%25252F%25252Fwww.kneu.ovgu.de%25252Fkneu.html%26amp%3Bdata%3D04%25

Re: [Freesurfer] Using SPM segmentations in FreeSurfer

2022-01-23 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Oh, sorry... Following the steps from the previous mail you should run this 
command:


mri_mask brain.mgz new_segmentation.mgz wm.seg.mgz


Best,

Falk


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von 
falk.luesebr...@med.ovgu.de 
Gesendet: Montag, 24. Januar 2022 08:41:15
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer

External Email - Use Caution

Hi Nathan,


well, once again, I can't be much of help with regards to your error message. 
Have you had a look at the data and does it looks reasonable up to that point? 
Which FreeSurfer version are you running?


FreeSurfer needs to have the data in a very specific form. In case of the white 
matter segmentation the resulting volume should have a value of 110 where white 
matter is located. The SPM segmentation has values of 0 to 1. Therefore, if you 
would simply try to use that, it wouldn't work. The given command should do 
that while using the SPM segmentation to mask the brain.mgz. Afterwards, the 
ventricles and subcortical structures will be filled based on the 
aseg.presurf.mgz and set to values of 250. The other commands changes the WM 
segmentation so that the neighbors of all voxels labeled as WM have a face in 
common - no edges or corners allowed.


Best,

Falk


<http://secure-web.cisco.com/1mIUaa7F-i8b4cYwNnbztpMSGC1LS0vhF8ATfmhtgiZxT6lh0vSh_fcPYFd0tYgHhhlC0czxOdn69ctn9ZyRSKCYMcXsmmkriPcmLaomDWhtmJ5W4il1ZwhsIARbrSX2L7lwOY4WpeD17uvDPZEr9lJH-8xglQ5ObufKxfy2D3vtvwE2N-M8VOR-hEb0TVWvq5U9gQ4kxRHAcpk8alzRctnBGXIBmyM_-d1Aj1RjAD6VdhMQjTTWweZbJ9MvFjIDFEoeAmvs02ErbmlqFjhY8W97SzZV2Z2hoWaCtKNzqWxvGDQld_eKtmrykF9fMby4w/http%3A%2F%2Fwww.kneu.ovgu.de%2Fkneu.html>

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Nathan Kindred (PGR) 

Gesendet: Freitag, 21. Januar 2022 18:18:14
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer


External Email - Use Caution
Hi Falk,

Thank you, I appreciate your help. By using the convert and mask steps you used 
I can get through to the -pial stage of autorecon3 before hitting an error 
(command terminated by signal 11).
I was wondering about the mri_edit_wm_with_aseg and mri_pretess steps you take 
though as won’t these essentially overwrite the wm.mgz file so that the SPM 
segmentation is no longer incorporated? Apologies if I am miss understanding, 
that is just what appears to happen when I try to replicate those steps (with 
those included I hit no errors but the outputs are unchanged from before I 
incorporated the SPM file).

Best,
Nathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
falk.luesebr...@med.ovgu.de 
Date: Thursday, 20 January 2022 at 07:57
To: Freesurfer support list 
Subject: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
External Email - Use Caution

Hi Nathan,


well, I never encountered that error. Therefore, I probably can't be of much 
help. Anyways, if you provide more details, e.g. which FreeSurfer version you 
are using, the recon-all.log, and what commands you are running exactly to 
incorporate the SPM segmentation someone else probably can help.


When I was using different WM segmentations in v6, I did the following:


  *   Convert the segmentation (e.g. mri_convert -rl wm.mgz 
new_segmentation.nii new_segmentation.mgz)
  *   Mask brain.mgz using the segmentation (e.g. mri_mask brain.mgz 
new_segmentation.mgz wm.mgz)
  *   Then continuing with the remaining steps of the segmentation stage 
accoring to the recon-all table (MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1RWkD9q9eCja6mIMMwKBpTWWFQ5PbuMZrYDBZdgbIW7YokGy5Exo0_Nsm-5KB_GfDGzkBwa_SPOhmq0TVt31PdKDL6fupuYoQHt-kO8ScTxIuxQJ8E43OdjHwAGJdoce49VkwLWy0deL3hzHqIPI0gFG3Qc36od_lUIhcUeIgWw00gw6MdjwCl_vlPqsXF1nXLxUB1CUqSJ1WLJstV86xkYhuK-3vWcOzeakMkmgysdB35QKyPJNUVueFXaIojXSloCaHh8hLJCk9wuq4Cd0RTb59cXEKOjmrj5klgvvesDeLfbOyTgtUTBkUgH7vwBjW/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F14Ybbj5o3PlY7rPb2i6Je_DtLBE_kvAlsgXuobTS7kuy-VQ4H0H0u_O6ON675Adm7LBJkPN_vbKMesdE-BPOlb6c9cWE6diVILr-eiEfuVnxEsFGJ_BDbWV5Vvhp8DXYvq0pbAMZpoReB6ERBzfAEp6u_T9joWGQX5b3F0vTAEGUh6bY3vcO8F70NmZCAhvzqxSzA6oJmHKlXuqoe4p1MDlDt20A8EyV3oESStmEgvCMc8O2DPvuiRBqjOM9d5JZSZ2ZakNr6H_llRM8aJh8XDUJmv1aFfE3T0a2UMJ2bz43xy_jEZSLjJo8a6MwlIgeVGD0UsPQhYLCsK4ff9qaZ6Q%252Fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Ffswiki%25252FReconAllTableStableV6.0%26data%3D04%257C01%257CN.Kindred1%2540newcastle.ac.uk%257C162fbeaa1c654f80909008d9dbea65b5%257C9c5012c9b61644c2a91766814fbe3e87%257C1%257C0%257C637782622499068823%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C2000%26sdata%3DdzLH8xPfzoOZHO5Gmlew9NBRmGfH3nDb

Re: [Freesurfer] Using SPM segmentations in FreeSurfer

2022-01-23 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Hi Nathan,


well, once again, I can't be much of help with regards to your error message. 
Have you had a look at the data and does it looks reasonable up to that point? 
Which FreeSurfer version are you running?


FreeSurfer needs to have the data in a very specific form. In case of the white 
matter segmentation the resulting volume should have a value of 110 where white 
matter is located. The SPM segmentation has values of 0 to 1. Therefore, if you 
would simply try to use that, it wouldn't work. The given command should do 
that while using the SPM segmentation to mask the brain.mgz. Afterwards, the 
ventricles and subcortical structures will be filled based on the 
aseg.presurf.mgz and set to values of 250. The other commands changes the WM 
segmentation so that the neighbors of all voxels labeled as WM have a face in 
common - no edges or corners allowed.


Best,

Falk


<http://secure-web.cisco.com/1mIUaa7F-i8b4cYwNnbztpMSGC1LS0vhF8ATfmhtgiZxT6lh0vSh_fcPYFd0tYgHhhlC0czxOdn69ctn9ZyRSKCYMcXsmmkriPcmLaomDWhtmJ5W4il1ZwhsIARbrSX2L7lwOY4WpeD17uvDPZEr9lJH-8xglQ5ObufKxfy2D3vtvwE2N-M8VOR-hEb0TVWvq5U9gQ4kxRHAcpk8alzRctnBGXIBmyM_-d1Aj1RjAD6VdhMQjTTWweZbJ9MvFjIDFEoeAmvs02ErbmlqFjhY8W97SzZV2Z2hoWaCtKNzqWxvGDQld_eKtmrykF9fMby4w/http%3A%2F%2Fwww.kneu.ovgu.de%2Fkneu.html>

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Nathan Kindred (PGR) 

Gesendet: Freitag, 21. Januar 2022 18:18:14
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer


External Email - Use Caution
Hi Falk,

Thank you, I appreciate your help. By using the convert and mask steps you used 
I can get through to the -pial stage of autorecon3 before hitting an error 
(command terminated by signal 11).
I was wondering about the mri_edit_wm_with_aseg and mri_pretess steps you take 
though as won’t these essentially overwrite the wm.mgz file so that the SPM 
segmentation is no longer incorporated? Apologies if I am miss understanding, 
that is just what appears to happen when I try to replicate those steps (with 
those included I hit no errors but the outputs are unchanged from before I 
incorporated the SPM file).

Best,
Nathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
falk.luesebr...@med.ovgu.de 
Date: Thursday, 20 January 2022 at 07:57
To: Freesurfer support list 
Subject: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
External Email - Use Caution

Hi Nathan,


well, I never encountered that error. Therefore, I probably can't be of much 
help. Anyways, if you provide more details, e.g. which FreeSurfer version you 
are using, the recon-all.log, and what commands you are running exactly to 
incorporate the SPM segmentation someone else probably can help.


When I was using different WM segmentations in v6, I did the following:


  *   Convert the segmentation (e.g. mri_convert -rl wm.mgz 
new_segmentation.nii new_segmentation.mgz)
  *   Mask brain.mgz using the segmentation (e.g. mri_mask brain.mgz 
new_segmentation.mgz wm.mgz)
  *   Then continuing with the remaining steps of the segmentation stage 
accoring to the recon-all table (MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1RWkD9q9eCja6mIMMwKBpTWWFQ5PbuMZrYDBZdgbIW7YokGy5Exo0_Nsm-5KB_GfDGzkBwa_SPOhmq0TVt31PdKDL6fupuYoQHt-kO8ScTxIuxQJ8E43OdjHwAGJdoce49VkwLWy0deL3hzHqIPI0gFG3Qc36od_lUIhcUeIgWw00gw6MdjwCl_vlPqsXF1nXLxUB1CUqSJ1WLJstV86xkYhuK-3vWcOzeakMkmgysdB35QKyPJNUVueFXaIojXSloCaHh8hLJCk9wuq4Cd0RTb59cXEKOjmrj5klgvvesDeLfbOyTgtUTBkUgH7vwBjW/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F14Ybbj5o3PlY7rPb2i6Je_DtLBE_kvAlsgXuobTS7kuy-VQ4H0H0u_O6ON675Adm7LBJkPN_vbKMesdE-BPOlb6c9cWE6diVILr-eiEfuVnxEsFGJ_BDbWV5Vvhp8DXYvq0pbAMZpoReB6ERBzfAEp6u_T9joWGQX5b3F0vTAEGUh6bY3vcO8F70NmZCAhvzqxSzA6oJmHKlXuqoe4p1MDlDt20A8EyV3oESStmEgvCMc8O2DPvuiRBqjOM9d5JZSZ2ZakNr6H_llRM8aJh8XDUJmv1aFfE3T0a2UMJ2bz43xy_jEZSLjJo8a6MwlIgeVGD0UsPQhYLCsK4ff9qaZ6Q%252Fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Ffswiki%25252FReconAllTableStableV6.0%26data%3D04%257C01%257CN.Kindred1%2540newcastle.ac.uk%257C162fbeaa1c654f80909008d9dbea65b5%257C9c5012c9b61644c2a91766814fbe3e87%257C1%257C0%257C637782622499068823%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C2000%26sdata%3DdzLH8xPfzoOZHO5Gmlew9NBRmGfH3nDb6AfWcqoKS70%253D%26reserved%3D0<https://secure-web.cisco.com/1reDdF1_RCvW1SGMg5MMY-wNwDhAcqYlMuRhT7puZZazh6cHAAmF7lnsn7jJqJ8wdHakIuCBcXvymW_lA7nXBXILZ7ZVPyQBmriS9NCkHdcVv_jTnlnMsHJ8xa8eHSlj_wYaBzYgbIOyBxY6UxPpeSOkLtg0_YxULA89rZbvMzFh1bPqw8Yxn1BmFFx8DUltD_WnPVfriQHVaX0LzOsi59Uc5a41oYI5lCTdcCjc_oFeekPKD4ouKHauD412lhBAlFKNKrRNIH0l14i1bPx-sbT9-YaQgW5gq5pnUybQOIYEmdf9GJ-f5T-y2mHUpU15sE7nRKGxBk55DZY5_mjNw8c9Z3kqmhaworwVuXo9HNTI/

Re: [Freesurfer] Using SPM segmentations in FreeSurfer

2022-01-19 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Hi Nathan,


well, I never encountered that error. Therefore, I probably can't be of much 
help. Anyways, if you provide more details, e.g. which FreeSurfer version you 
are using, the recon-all.log, and what commands you are running exactly to 
incorporate the SPM segmentation someone else probably can help.


When I was using different WM segmentations in v6, I did the following:


  *   Convert the segmentation (e.g. mri_convert -rl wm.mgz 
new_segmentation.nii new_segmentation.mgz)
  *   Mask brain.mgz using the segmentation (e.g. mri_mask brain.mgz 
new_segmentation.mgz wm.mgz)
  *   Then continuing with the remaining steps of the segmentation stage 
accoring to the recon-all table 
(https://secure-web.cisco.com/14Ybbj5o3PlY7rPb2i6Je_DtLBE_kvAlsgXuobTS7kuy-VQ4H0H0u_O6ON675Adm7LBJkPN_vbKMesdE-BPOlb6c9cWE6diVILr-eiEfuVnxEsFGJ_BDbWV5Vvhp8DXYvq0pbAMZpoReB6ERBzfAEp6u_T9joWGQX5b3F0vTAEGUh6bY3vcO8F70NmZCAhvzqxSzA6oJmHKlXuqoe4p1MDlDt20A8EyV3oESStmEgvCMc8O2DPvuiRBqjOM9d5JZSZ2ZakNr6H_llRM8aJh8XDUJmv1aFfE3T0a2UMJ2bz43xy_jEZSLjJo8a6MwlIgeVGD0UsPQhYLCsK4ff9qaZ6Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllTableStableV6.0)
 by running
 *   mri_edit_wm_with_aseg wm.seg.mgz brain.mgz aseg.presurf.mgz 
wm.asegedit.mgz
 *   mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
  *   Then continuing with the remaining stages of autorecon2 of recon-all by 
running
 *   recon-all -s  -fill -tessellate -smooth1 -inflate1 -qsphere 
-fix -white -smooth2 -inflate2 -curvHK -curvstats -autorecon3

This will work for FreeSurfer v6. For v7 the stages of recon-all have changed 
and you might miss something. However, there is no such table like for v6 and I 
haven't been using v7 much, so I can't provide a guide like above for v7.


Best,

Falk


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Nathan Kindred (PGR) 

Gesendet: Mittwoch, 19. Januar 2022 14:00:23
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer


External Email - Use Caution
Hi Falk,

Thank you for the response!
I have given your suggestion a try and I am still getting the following error:

free(): double free detected in tcache 2
Command terminated by signal 6

Best,
Nathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
falk.luesebr...@med.ovgu.de 
Date: Wednesday, 19 January 2022 at 12:52
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.

External Email - Use Caution

Hi Nathan,


are you sure that the SPM segmentation and the wm.mgz share the same space? You 
could try e.g. mri_convert -rl wm.mgz your_spm_segmentation.nii spm_wm.mgz


Best,

Falk


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Nathan Kindred (PGR) 

Gesendet: Mittwoch, 19. Januar 2022 13:29:46
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Using SPM segmentations in FreeSurfer


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


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1sf6L0NHJmhkr10Cj74JcEIEEcoND2pR2q0X9Pm9lMkMR5LyldwoXLMPs1mD3hBeEqQ3hcHfXesZFKgFzz5Enia-82_2rxoJMrsi6NeZxJSOsfbVnI2wxtB8IHFALA6nKvi4tL98vRHEEghhEJJA4_DdcLEvH9Ix_Zfv0czIF9TJualfnQ0kgRhpdtO26eeI3mStgLO35_hhmO5AV9U_2vIt9P1jSaByTKh1d85ojjCtv-Y_9Fx9werVTVjKwm0zT_8IT22pB8-HoYVRVbhbiNYCziFpw8NLXBOlEvoN8U2hBp_g2oo1gl9TvoJH1oWKzJFtYOga9PdRes7w9xdMWlA/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Cn.kindred1%2540newcastle.ac.uk%257Cf53b338b194a4f634fa408d9db4a8342%257C9c5012c9b61644c2a91766814fbe3e87%257C1%257C0%257C637781935340044379%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C2000%26sdata%3DQoKAAdwJTjthPD0gPZPmt0owIasgazNfdz6hI9CYRK0%253D%26reserved%3D0<https://secure-web.cisco.com/1qP4Jy-ZkJCg8fJaNq7BoJiZKPJyBcdrMGJqMXQVE40fMwCpTZchKdAfKRVcRq8abnakPJRCfynb4Qri0idb3vh95cJmW

Re: [Freesurfer] Using SPM segmentations in FreeSurfer

2022-01-19 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Hi Nathan,


are you sure that the SPM segmentation and the wm.mgz share the same space? You 
could try e.g. mri_convert -rl wm.mgz your_spm_segmentation.nii spm_wm.mgz


Best,

Falk


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Nathan Kindred (PGR) 

Gesendet: Mittwoch, 19. Januar 2022 13:29:46
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Using SPM segmentations in FreeSurfer


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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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Re: [Freesurfer] data sharing of freesurfer processed data

2021-02-03 Thread falk.luesebr...@med.ovgu.de 
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Hi Stacey,

aren't participant IDs already anonymized or at least pseudonymized? In any 
case, if that ID is part of the file name, you should delete or change the 
recon-all.cmd, recon-all.done, recon-all.log files as the input file name is 
written in it.

Besides, you should remove any image files that were created before 
brainmask.mgz was produced. In case of v7, these should be: all files in 
./mri/orig/, rawavg.mgz, orig.mgz, orig_nu.mgz, nu.mgz, and T1.mgz

Best,
Falk



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von STACEY M SCHAEFER 

Gesendet: Donnerstag, 28. Januar 2021 16:46:56
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] data sharing of freesurfer processed data


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Does the freesurfer group have any recommendations or procedures for public 
sharing data that has been processed with freesurfer? In particular, procedures 
to automatically swap out participant IDs to anonymize the data?


Stacey M. Schaefer, Ph.D.
Center for Healthy Minds

University of Wisconsin-Madison

625 W Washington Ave

Madison WI 53703




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Re: [Freesurfer] recon-all for 0.85 isotropic images error (bump)

2020-11-17 Thread falk.luesebr...@med.ovgu.de 
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Dear Kristine,


I haven't had any issues processing high resolution data with version 6 or 7 
using either the -cm or -hires flag. However, I never used the -cw 256 flag as 
my FoV was never greater than 256.


Could you post the size of the created files? Especially orig.mgz with and 
without using the cw256 flag? Have you tried to not include the T2 volume? Just 
an educated guess, but maybe cropping of the FoV is done on the T1 only and, 
therefore, results in the error you are facing due to the additional contrasts.


Best,

Falk




Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Lee Subin Kristine 

Gesendet: Montag, 16. November 2020 18:56:55
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] recon-all for 0.85 isotropic images error (bump)


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-Bumping this question up because still could not find a solution 

-Any contributions or ideas would be greatly appreciated -



I am still having problems with running the high resolution recon-all (on v.6.0 
stable).

I have tried multiple flags (-hires, -cm, with and without cw256), but they all 
lead to the same error message, basically saying that the orig.mgz  FOV is more 
than 256 (even when I try to conform the image to 256).

(ERROR! FOV=272.000 > 256)/



When I try recon-all.v6.hires, the rawavg.mgz is not able to be created.



I have tried on both Ubuntu 14.04 and 16.04, but still get the same results.



Has anyone had any success in using the hires option of recon-all?

Any input would be appreciated.



Best Regards,

Kristine





Windows 10용 
메일에서
 보냄



보낸 사람: Lee Subin Kristine
보낸 날짜: Friday, October 30, 2020 9:40 PM
받는 사람: freesurfer@nmr.mgh.harvard.edu
제목: recon-all for 0.85 isotropic images error



Hello FreeSurfer Developers,



I'm trying to run recon-all (v.6) on T1- and T2-weighted images that have 
0.85mm^3 isotropic voxels



I have entered the command as below,

with the T2, T2pial, cm, cw256 flags.



recon-all -i $T1_DIR/"oT1_"$subj.nii -T2 $T2_DIR/"oT2_"$subj.nii -T2pial -cm 
-cw256 -subject $subj"_test" -all



However, I keep getting the error as follows.



ERROR! FOV=272.000 > 256

Include the flag -cw256 with recon-all!

Inspect orig.mgz to ensure the head is fully visible.

I'm guessing that conforming to the small voxel size results in a FOV that is 
out of limit?

However, when I check the orig.mgz file it looks fine.

(It has an image dimension of 320 x 320 x 320).

Even when I include the flag -cw256 as the error message says, I still get the 
same error message.

(Also, I cannot find any documentation about the -cw256flag on the help page).



I have pasted the full log below.



Thank you for your help.



Best regards,

Kristine



-

subin@ubuntu:/mnt/hgfs/subindata/MYELIN-QSM/SCRIPT$ ./run_fs_1

INFO: all volumes are conformed to the min voxel size

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW

Actual FREESURFER_HOME /usr/local/freesurfer

Linux ubuntu 4.15.0-112-generic #113~16.04.1-Ubuntu SMP Fri Jul 10 04:37:08 UTC 
2020 x86_64 x86_64 x86_64 GNU/Linux

'/usr/local/freesurfer/bin/recon-all' -> 
'/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/scripts/recon-all.local-copy'

-cw256 option is now persistent (remove with -clean-cw256)

/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test



 mri_convert /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii 
/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz



mri_convert.bin /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii 
/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii...

TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (0.8, -0.00515189, -0.00357438)

j_ras = (0.00515192, 0.87, 0)

k_ras = (0.00357433, -1.83865e-05, 0.94)

writing to 
/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz...

#

#@# T2/FLAIR Input Fri Oct 30 05:19:16 PDT 2020

/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test



 mri_convert --no_scale 1

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

2020-09-09 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Hi Jim,

The -hires will conform the data to the highest resolution of your input data, 
instead of 1mm^3. In case it was an isotropic resolution, it will stay at 
native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled 
to 0.3mm^3 - which is not really recommended. The segmentation and surface 
placement will take place at that resolution.

The -conf2hires flag will conform your input data to 1mm^3. Segmentation and 
initial surface placement will be handled at conformed (1mm) resolution. Then 
the initial surface placement is used at native resolution to refine the 
surface placement.

With -hires the number of vertices per hemisphere depends on your input 
resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. With -conf2hires 
the number of vertices will be around 140k per hemisphere and, therefore, 
processing (especially the topologic correction) will be much faster compared 
to -hires. The principle behind -conf2hires was used in the processing pipeline 
of the HCP (https://doi.org/10.1016/j.neuroimage.2013.04.127) and has been 
shown to improve the segmentation in highly myelinated areas, e.g. around the 
visual cortex or central sulcus.

Natalia Zaretskaya and Jon Polimeni 
(https://doi.org/10.1016/j.neuroimage.2017.09.060) and I 
(https://doi.org/10.1016/j.neuroimage.2012.12.016) could show that the 
principles behind the -hires flag yield different results than downsampling 
high resolution input data or using 1mm data to being with. It is hypothesized 
that using high resolution data with the -hires flag leads to better surface 
placement and, therefore, more accurate cortical thickness measures. However, 
missing ground truth always makes it complicated to proof.

To answer your question which is recommended: In the release notes of 
FreeSurfer it is written with regards to conf2hires "This was originally 
programmed for the HCP. The now-standard hi-res stream should work just as 
well, but we kept conf2hires for backwards compatibility."

I don't think someone published a comparison between -hires and -conf2hires, 
yet. However, I would use the -hires flag instead of -conf2hires. I assume the 
surface placement to be equally good, with potential benefits towards -hires 
due to the higher number of vertices. The drawbacks of -hires (e.g. longer 
processing time) should be compensated to some extent by the new denoising 
feature prior to the intial surface placement. Personally, I haven't had much 
time to test v7 intensively, though.

Hope this helps.

Best,
Falk


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Alexopoulos, Dimitrios
Gesendet: Mittwoch, 9. September 2020 05:27
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] -hires vs -conf2hires in 7.1.1.


External Email - Use Caution
Does the hires flag still generate segs at the native hi resolution and place 
surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but 
places surfaces on the hires images?

Which option is recommended and why?

Jim


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Re: [Freesurfer] use of ANTs Denoising in FS 7.1

2020-08-26 Thread falk.luesebr...@med.ovgu.de 
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Dear Jim,

I had been looking at the effect of denoising the data to improve processing 
speed in case of noisy data in an ISMRM abstract couple of years ago. However, 
I haven't had the time to follow up on this. Glad to see something similar now 
being implemented in recon-all.

As Doug and Matt pointed out, denoising the input data will bias your results 
potentially which is why it is not recommend to do at all. However, denoising 
the data just for the initialization will reduce defects and errors of the 
initial white matter surface, reducing processing time from many to a few hours 
in case of noisy data. As the actual surface is fitted using the unfiltered 
data this should not impair surface placement.

Best,
Falk


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Alexopoulos, Dimitrios
Gesendet: Mittwoch, 26. August 2020 06:04
An: Freesurfer support list 
Betreff: Re: [Freesurfer] use of ANTs Denoising in FS 7.1


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Thanks for clarifying.

Some initial results on a cohort of 1-2 yo subjects we have run through both 
the infant FS and 7.1.1 pipelines,  seem to benefit from using a denoised T1 
image as input. Specifically, denoising in images with motion generates better 
WM segmentations in complexly folded regions (i.e. occipital/calcarine). We are 
still evaluating.

Jim


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From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>
Sent: Tuesday, August 25, 2020 10:17:43 PM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] use of ANTs Denoising in FS 7.1


* External Email - Caution *

brain.mgz is denoised to create antsdn.brain.mgz. This volume is then used to 
create the initial surface. The final surfaces are created from the unfiltered 
brain.mgz but using the orig surface created with the denoised brain.mgz. So 
the denoising helps to create the orig surface which is then used to initialize 
the final surfaces.
On 8/25/2020 5:37 PM, Alexopoulos, Dimitrios wrote:

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I'm looking through the pipeline table , looking to see where the orig surfaces 
are created, which appear to be in autorecon2 /tessellation step . What 
advantage is gained by denoising the image (which image is actually denosed?) 
at this stage if id does not contribute the final surfaces?



Sorry for asking for more detail, just want to make sure I understand the 
application of the utility. Many groups are now denoising their input images 
into many pipelines.



Jim



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

 On Behalf Of Douglas N. Greve
Sent: Tuesday, August 25, 2020 4:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] use of ANTs Denoising in FS 7.1



* External Email - Caution *


It is only used to create the orig surface. It is not used in the volume 
segmentation or the final placement of the surfaces. Volume smoothing of any 
kind has the potential to bias the surface placement so we recommend against 
denoising the input.

On 8/25/2020 4:56 PM, Alexopoulos, Dimitrios wrote:

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Hi all,



In previous datasets, and prior to FS 7, we independently ran ANTs denosing on 
the input T1s prior to running recon-all,

However, FS 7.1 now appears to use the  denosing utility in parts of the 
pipeline.



"ANTS denoise is used when creating the orig surface (but not thefinal 
surfaces)"



Does this mean the denoised image is only used in the segmentation part of the 
pipeline (to generated the aseg.mgz) and does not propagate through to final 
surfaces?  Why not use  denoised T1 through the surface-generation phase of the 
pipeline.



Can you provide some further clarification.

Thx.

Jim











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Re: [Freesurfer] bias correction on 7T MEMPRAGE

2020-02-20 Thread falk.luesebr...@med.ovgu.de 
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Dear Vale,

using the GUI of SPM you cannot get a FWHM of lower than 30. You have to save 
the batch to disk, load it in MATLAB and change the parameters to your liking. 
In case this sounds too complicated, you can use part of a reconstruction 
pipeline I have put together on Github. Just get the files from this folder: 
https://github.com/fluese/reconstructionPipeline/tree/master/processingPipeline/biasCorrection

To use it: SPM12 needs to be properly set up (e.g. added to MATLAB path), 
change the variables to your liking (either by creating a settings variable 
with the given structure or just hardcode it in the m-file), the variable 
filename should contain the path as well if the script is run from a different 
folder than the data is located at.

I haven't worked with MEMPRAGE data myself, so somebody else may chime in on 
that. However, the echoes should simply be combined by RMS 
(https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Isitrecommendedthatpeopleusememprage.3FHowaretheyanalyzed.3FJustsqrtsumsqroftheechoes.3FOristheresomethingmoreelaborate.3F)
 and can for example be done using mri_concat 
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_concat?highlight=%28memprage%29).
 Although I remember vaguely, that the combination of echoes was implemented 
somewhere else as well.

In case you have further questions, just let me know.

Best,
Falk


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Barletta, Valeria
Gesendet: Mittwoch, 19. Februar 2020 17:19
An: Freesurfer support list 
Betreff: [Freesurfer] bias correction on 7T MEMPRAGE

Dear Freesurfers,
I am trying to apply the bias correction on the 7T MEMPRAGE through the unified 
segmentation algorithm on SPM12, as a primary step to do the submillimetric 
recon on Freesurfer, as you suggested here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HighFieldRecon

For some reason, I cannot set the Bias FWHM to 18 on the SPM12 interface. Also, 
not sure how to use the 5D image that I obtain from the process.

Have you ever done this before? Any tips?

Thanks a lot,
Vale
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Re: [Freesurfer] Freesurfer 7T MPRAGE

2020-01-06 Thread falk.luesebr...@med.ovgu.de 
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Dear Manoj,


in case you want to rely on tools provided with FreeSurfer only, N3 can produce 
good results even for 7T data. However, in my experience, you need to supply a 
brainmask to N3 to achieve very similar results compared to SPM. Otherwise, 
especially around the temporal lobes the inhomogeneity will not be corrected 
sufficiently.


Tweaking recon-all for this is possible, but is slightly more complicated than 
changing the parameters of mri_nu_correct only. Furthermore, the procedure may 
change in case you use higher resolution 7T data.


Apart from that SPM, N3 as well as N4 of ANTs (also using a brainmask) will all 
produce similar results. I mostly use SPM for pre-processing my 7T data as it 
is the easiest to use in my processing pipeline.


Best,

Falk


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Manoj Saranathan 

Gesendet: Montag, 6. Januar 2020 23:51:23
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Freesurfer 7T MPRAGE


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Hi,


I am trying to process 7T MPRAGE data (not MP2RAGE) using recon-all. In 
previous threads, a few people have suggested using SPM to correct for bias 
first and then running recon-all. Alternatively I saw a thread which suggests 
modifying the mri_nu_correct command

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61913.html



Can I edit the recon-all to run this alternative command and simply run 
recon-all?  The threads are all really old and SPM is now SPM12 which 
integrates things. Is this modified bias correction inside FS as good as SPM ? 
I am mainly interested in thalamic segmentation.


Are there others with the same issue?


Thanks


manoj


Manoj Saranathan
Associate Professor, Dept. of Medical Imaging
University of Arizona
Ph: 520-626-6531



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Re: [Freesurfer] How to fasten recon-all execution time without using CUDA

2019-09-18 Thread falk.luesebr...@med.ovgu.de 
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Hi Vasudev,

in case you use v6, you can use the -parallel flag to process the hemispheres 
(and a few other things if I remember correctly) in parallel. Note that doing 
so will parse the -openmp flag to all instances. E.g.

recon-all -all -openmp 4 -parallel -s subjID -i inputFile

Also the reduction in processing time using openmp is limited – I don’t recall 
exactly if it was bound to the number of physical cores your CPU has or if it 
was an upper limit to due the way the parallelization works (I have something 
like in mind like not much of an increase beyond openmp 8).

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Dev vasu
Gesendet: Mittwoch, 18. September 2019 15:08
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] How to fasten recon-all execution time without using CUDA


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Dear all,

I am using - openmp 30 to run recon-all, i see now change in the execution time 
period.

Could you please highlight me a method to reduce the execution time for 
recon-all, if possible some parallel script to do that same.


Thanks
Vasudev
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Re: [Freesurfer] recon_all hires

2019-08-21 Thread falk.luesebr...@med.ovgu.de 
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Hi Mona,

Potentially you have a bad skull strip resulting in a huge defect which will 
take a long time to correct. Simply fix your skull strip and you should be fine.

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Nasiriavanaki, Zahra
Gesendet: Dienstag, 20. August 2019 16:19
An: Freesurfer support list 
Betreff: [Freesurfer] recon_all hires


Dear Freesurfer experts



I am doing recon-all on one of my subjects and it seems that it's stuck for 
days and not going through. I even re-run it and it's still stuck at the same 
spot as before.

I attached the log file and here is my command:

recon-all -all -s $subj -i /$subj/anat/$run/mT1v2.nii -expert 
expertopts/expert.opts -hires -mail zn025 -parallel

I appreciate any help.



Thanks

Mona





Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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Re: [Freesurfer] Change image orientation

2019-07-05 Thread falk.luesebr...@med.ovgu.de 
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Hi Miguel,

this should work with mri_convert --in_orientation RAI t1.nii t1_RAI.nii.

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Miguel Ángel Rivas 
Fernández
Gesendet: Freitag, 5. Juli 2019 11:00
An: Freesurfer support list 
Betreff: [Freesurfer] Change image orientation


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Dear Freesurfer devs,

Is possible to change the image orientation of the t1.nii images? In that case, 
what command should be used?. I would like to change them from a LPI 
orientation to a RAI orientation.

Best regards,

--
Miguel Ángel Rivas Fernández
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Re: [Freesurfer] FreeSurfer High Resolution vs. Low Resolution Volume Discrepancy

2019-05-22 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Dear Gaurav Verma,

this should fix your issue: 
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Verma, Gaurav
Gesendet: Dienstag, 21. Mai 2019 17:34
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] FreeSurfer High Resolution vs. Low Resolution Volume 
Discrepancy


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Dear FreeSurfer Community,

In processing high-resolution (0.7 mm^3 isotropic) and low resolution (1.0 mm^3 
isotropic) versions of the same data we have received conflicting volume data 
in our aseg.stats file. Below is the relevant excerpt from those files.

High-resolution (0.7 mm^3 isotropic)

# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 3264609.00, mm^3
# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume 
Without Ventricles, 3192286.00, mm^3
# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation 
Volume Without Ventricles from Surf, 1330806.023066, mm^3
# Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and 
choroid plexus, 60940.00, mm^3
# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 
230160.306401, mm^3
# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 
228696.462181, mm^3
# Measure Cortex, CortexVol, Total cortical gray matter volume, 458856.768582, 
mm^3
# Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere 
cerebral white matter volume, 158718.858711, mm^3
# Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere 
cerebral white matter volume, 161112.395773, mm^3
# Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white 
matter volume, 319831.254484, mm^3
# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 
149905.00, mm^3
# Measure TotalGray, TotalGrayVol, Total gray matter volume, 941078.768582, mm^3
# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 
970862.023066, mm^3
# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial 
volume, 909922.023066, mm^3
# Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial 
volume voxel count, 2790169.00, mm^3
# Measure Mask, MaskVol, Mask Volume, 4652001.00, mm^3
# Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to 
eTIV, 2.065785, unitless
# Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 2.943701, 
unitless
# Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces 
prior to fixing, 46, unitless
# Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces 
prior to fixing, 70, unitless
# Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces 
prior to fixing, 116, unitless
# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial 
Volume, 1580323.941985, mm^3

Low resolution (1.0 mm^3 isotropic)

# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1132377.00, mm^3
# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume 
Without Ventricles, 1107596.00, mm^3
# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation 
Volume Without Ventricles from Surf, 1106786.650039, mm^3
# Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and 
choroid plexus, 21069.00, mm^3
# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 
226998.297110, mm^3
# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 
225122.819041, mm^3
# Measure Cortex, CortexVol, Total cortical gray matter volume, 452121.116151, 
mm^3
# Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere 
cerebral white matter volume, 228780.783147, mm^3
# Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere 
cerebral white matter volume, 235221.750741, mm^3
# Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white 
matter volume, 464002.533888, mm^3
# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 
51537.00, mm^3
# Measure TotalGray, TotalGrayVol, Total gray matter volume, 619358.116151, mm^3
# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 
990616.650039, mm^3
# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial 
volume, 969547.650039, mm^3
# Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial 
volume voxel count, 968494.00, mm^3
# Measure Mask, MaskVol, Mask Volume, 1574410.00, mm^3
# Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to 
eTIV, 0.714626, unitless
# Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 0.993586, 
unitless
# Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces 
prior to fixing, 30, unitless
# Measure

Re: [Freesurfer] Longitudinal processing

2019-05-13 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Hi Martin,

thanks for your quick reply and the clarification regarding the output.

I have processed the 1 and 0.8 mm separately, so one base for each subject and 
resolution - no mixing has been conducted! :)

Actually, I want to look into changes due to hydration and other biological 
effects, e.g. due to hormone status. However, this is just a preliminary 
assessment of the variance in general (and getting to know the processing 
pipeline) as no meta data was acquired to correlate the measures against. 

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Martin Reuter
Gesendet: Montag, 13. Mai 2019 12:56
An: Freesurfer support list 
Betreff: Re: [Freesurfer] Longitudinal processing

Hi Falk, 

yes, the output of long_mris_slopes and long_stats_slopes is in percent
(100 * rate / value_of_fit_at_mid_time). 

Also running 1mm data is different (as you know :-) from .8 so maybe you would 
analyze both separately, e.g. creating one base on 1mm time points and another 
on the .8mm ? 

If you re-scan in short time interals (and if these are young and healthy, then 
even for mid to long intervals), you would not expect anatomical aging effects. 
Then the variance is probably mainly acquisition noise (e.g. induced by motion 
etc, see eg
https://www.ncbi.nlm.nih.gov/pubmed/25498430) plus some processing noise 
(different surface placement etc). Maybe there are also hydration effects (see 
https://www.ncbi.nlm.nih.gov/pubmed/26381562 ). 

Best, Martin


On Thu, 2019-05-09 at 09:51 +, falk.luesebr...@med.ovgu.de wrote:
> External Email - Use Caution
> Dear all,
>  
> I’m a beginner in using the longitudinal processing pipeline (as well 
> as statistical analysis) and it would be great to get some insights or 
> hints to analyze my data.
>  
> I have a dataset consisting of 11 subjects each acquired at 7 
> different time points with an isotropic resolution of 1 and 0.8 mm at 
> 3T using a 64-channel head coil. Using that dataset I want to 
> investigate short term differences in e.g. cortical thickness with the 
> goal to assess the degree of biological variance during that time 
> period.
>  
> I have plotted the mean cortical thickness of each time point of every 
> subject (using lme_timePlot and lme_lowessPlot) showing a somewhat 
> random distribution across time and from my perspective fairly high 
> standard deviation. I wanted to have a look at the individual percent 
> change by overlaying the symmetric percent change on fsaverage, but 
> wasn’t quite sure of the scale. Is it in percent?
> So in case I set the scale bar between 1 and 5, the color relates to
> 1 to 5 percent?
>  
> What other ways would make sense to have a look at? I definitely 
> cannot compare groups, as there is just one. The days and time of 
> acquistion are rather randomly choosen, so I potentially cannot use 
> either as a covariate.
>  
> Best,
> Falk
>  
> ...
>  
> 
> University Clinic for Neurology
>  
> Otto-von-Guericke-university Magdeburg Medical faculty Leipziger Str. 
> 44
> 39120 Magdeburg
>  
> Phone +49-391-6117-512
> 
> falk.luesebr...@med.ovgu.de
> http://www.kneu.ovgu.de/kneu.html
>  
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Primary slice direction and image origin?

2019-05-10 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Exellent! Thank you!

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Greve, Douglas N.,Ph.D.
Gesendet: Donnerstag, 9. Mai 2019 22:19
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Primary slice direction and image origin?

It looks at the RAS of the direction cosines for the direction going from one 
slice to the next. If the absolute value of the R component is the max of the 
three, then it is assigned to be sagittal. If the A component is max, then it's 
coronal. If S, then axial

On 5/9/19 5:52 AM, falk.luesebr...@med.ovgu.de wrote:
>  External Email - Use Caution
>
> Thanks Doug, I think I may have resolved my orientation / transformation 
> issue.
>
> Do you happen to know how the primary slice direction is determined?
>
> Best,
> Falk
>
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  Im Auftrag von Greve, Douglas 
> N.,Ph.D.
> Gesendet: Freitag, 3. Mai 2019 17:31
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] Primary slice direction and image origin?
>
> You can get the image position from tag 20 32. It might not match what you 
> see in mri_info because we use RAS and dicom uses something else (LPS maybe), 
> so the "first voxel" might not be the same.
>
>
> On 5/3/2019 3:01 AM, falk.luesebr...@med.ovgu.de wrote:
>>   External Email - Use Caution
>>
>> Hi Doug,
>>
>> thanks for your answer. I know how to print the slice direction, however, as 
>> there is no DICOM tag directly related to it, it has to be determined from 
>> some information of the DICOM header. I was wondering which these are.
>>
>> Same for the image origin or the voxel to ras transform in general:
>> voxel to ras transform:
>>   0.9367   0.0327   0.0240  -111.2289
>>  -0.0206   0.8545  -0.4108   -82.6730
>>  -0.0339   0.3843   0.9114  -121.5813
>>   0.   0.   0. 1.
>>
>> In that transform the last column indicates the image's origin. However, I 
>> was unable to find the relation between the information available in the 
>> DICOM header and this transform.
>>
>> Best,
>> Falk
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  Im Auftrag von Greve, Douglas 
>> N.,Ph.D.
>> Gesendet: Donnerstag, 2. Mai 2019 17:33
>> An: freesurfer@nmr.mgh.harvard.edu
>> Betreff: Re: [Freesurfer] Primary slice direction and image origin?
>>
>> You can use --slicedirection to get the slice direction (it will also get 
>> printed out by just running mri_info on a file). What do you mean by the 
>> image origin?
>>
>> On 5/2/19 7:16 AM, falk.luesebr...@med.ovgu.de wrote:
>>>   External Email - Use Caution
>>>
>>> Dear all,
>>>
>>> This is not directly related to FreeSurfer, however, can anyone tell 
>>> me how the primary slice direction and image origin is determined 
>>> from the DICOM header as displayed for example using mri_info?
>>>
>>> Best,
>>>
>>> Falk
>>>
>>> ...
>>>
>>> klinikum_logo_schmal_e-mail_blau
>>>
>>> *Universitätsklinik für Neurologie*
>>>
>>>
>>> Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät 
>>> Leipziger Str. 44
>>> 39120 Magdeburg
>>>
>>> *Telefon: *+49-391-6117-512
>>>
>>> *falk.luesebr...@med.ovgu.de <mailto:falk.luesebr...@med.ovgu.de>*
>>> *http://www.kneu.ovgu.de/kneu.html*
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Primary slice direction and image origin?

2019-05-09 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Thanks Doug, I think I may have resolved my orientation / transformation issue.

Do you happen to know how the primary slice direction is determined?

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Greve, Douglas N.,Ph.D.
Gesendet: Freitag, 3. Mai 2019 17:31
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Primary slice direction and image origin?

You can get the image position from tag 20 32. It might not match what you see 
in mri_info because we use RAS and dicom uses something else (LPS maybe), so 
the "first voxel" might not be the same.


On 5/3/2019 3:01 AM, falk.luesebr...@med.ovgu.de wrote:
>  External Email - Use Caution
>
> Hi Doug,
>
> thanks for your answer. I know how to print the slice direction, however, as 
> there is no DICOM tag directly related to it, it has to be determined from 
> some information of the DICOM header. I was wondering which these are.
>
> Same for the image origin or the voxel to ras transform in general:
> voxel to ras transform:
>  0.9367   0.0327   0.0240  -111.2289
> -0.0206   0.8545  -0.4108   -82.6730
> -0.0339   0.3843   0.9114  -121.5813
>  0.   0.   0. 1.
>
> In that transform the last column indicates the image's origin. However, I 
> was unable to find the relation between the information available in the 
> DICOM header and this transform.
>
> Best,
> Falk
>
>
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  Im Auftrag von Greve, Douglas 
> N.,Ph.D.
> Gesendet: Donnerstag, 2. Mai 2019 17:33
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] Primary slice direction and image origin?
>
> You can use --slicedirection to get the slice direction (it will also get 
> printed out by just running mri_info on a file). What do you mean by the 
> image origin?
>
> On 5/2/19 7:16 AM, falk.luesebr...@med.ovgu.de wrote:
>>  External Email - Use Caution
>>
>> Dear all,
>>
>> This is not directly related to FreeSurfer, however, can anyone tell 
>> me how the primary slice direction and image origin is determined 
>> from the DICOM header as displayed for example using mri_info?
>>
>> Best,
>>
>> Falk
>>
>> ...
>>
>> klinikum_logo_schmal_e-mail_blau
>>
>> *Universitätsklinik für Neurologie*
>>
>>
>> Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät 
>> Leipziger Str. 44
>> 39120 Magdeburg
>>
>> *Telefon: *+49-391-6117-512
>>
>> *falk.luesebr...@med.ovgu.de <mailto:falk.luesebr...@med.ovgu.de>*
>> *http://www.kneu.ovgu.de/kneu.html*
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] Longitudinal processing

2019-05-09 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Dear all,

I'm a beginner in using the longitudinal processing pipeline (as well as 
statistical analysis) and it would be great to get some insights or hints to 
analyze my data.

I have a dataset consisting of 11 subjects each acquired at 7 different time 
points with an isotropic resolution of 1 and 0.8 mm at 3T using a 64-channel 
head coil. Using that dataset I want to investigate short term differences in 
e.g. cortical thickness with the goal to assess the degree of biological 
variance during that time period.

I have plotted the mean cortical thickness of each time point of every subject 
(using lme_timePlot and lme_lowessPlot) showing a somewhat random distribution 
across time and from my perspective fairly high standard deviation. I wanted to 
have a look at the individual percent change by overlaying the symmetric 
percent change on fsaverage, but wasn't quite sure of the scale. Is it in 
percent? So in case I set the scale bar between 1 and 5, the color relates to 1 
to 5 percent?

What other ways would make sense to have a look at? I definitely cannot compare 
groups, as there is just one. The days and time of acquistion are rather 
randomly choosen, so I potentially cannot use either as a covariate.

Best,
Falk

...

[klinikum_logo_schmal_e-mail_blau]
University Clinic for Neurology

Otto-von-Guericke-university Magdeburg
Medical faculty
Leipziger Str. 44
39120 Magdeburg

Phone +49-391-6117-512

falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de>
http://www.kneu.ovgu.de/kneu.html

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Re: [Freesurfer] Primary slice direction and image origin?

2019-05-03 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Hi Doug,

thanks for your answer. I know how to print the slice direction, however, as 
there is no DICOM tag directly related to it, it has to be determined from some 
information of the DICOM header. I was wondering which these are.

Same for the image origin or the voxel to ras transform in general:
voxel to ras transform:
0.9367   0.0327   0.0240  -111.2289
   -0.0206   0.8545  -0.4108   -82.6730
   -0.0339   0.3843   0.9114  -121.5813
0.   0.   0. 1.

In that transform the last column indicates the image's origin. However, I was 
unable to find the relation between the information available in the DICOM 
header and this transform.

Best,
Falk


-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Greve, Douglas N.,Ph.D.
Gesendet: Donnerstag, 2. Mai 2019 17:33
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Primary slice direction and image origin?

You can use --slicedirection to get the slice direction (it will also get 
printed out by just running mri_info on a file). What do you mean by the image 
origin?

On 5/2/19 7:16 AM, falk.luesebr...@med.ovgu.de wrote:
>
> External Email - Use Caution
>
> Dear all,
>
> This is not directly related to FreeSurfer, however, can anyone tell 
> me how the primary slice direction and image origin is determined from 
> the DICOM header as displayed for example using mri_info?
>
> Best,
>
> Falk
>
> ...
>
> klinikum_logo_schmal_e-mail_blau
>
> *Universitätsklinik für Neurologie*
>
>
> Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät 
> Leipziger Str. 44
> 39120 Magdeburg
>
> *Telefon: *+49-391-6117-512
>
> *falk.luesebr...@med.ovgu.de <mailto:falk.luesebr...@med.ovgu.de>*
> *http://www.kneu.ovgu.de/kneu.html*
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] Primary slice direction and image origin?

2019-05-02 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Dear all,

This is not directly related to FreeSurfer, however, can anyone tell me how the 
primary slice direction and image origin is determined from the DICOM header as 
displayed for example using mri_info?

Best,
Falk



...

[klinikum_logo_schmal_e-mail_blau]
Universitätsklinik für Neurologie


Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de>
http://www.kneu.ovgu.de/kneu.html

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Re: [Freesurfer] recon from 7T data

2019-03-26 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Hi Valeria,

you can account for the inhomogeneities Bruce was talking about by either using 
SPMs or FreeSurfers inhomogeneity correction. Personally, I prefer SPM over 
FreeSurfer, but if you supply a brainmask to the FreeSurfer tool, it gives 
reasonable results around the temporal lobes, too. 

I haven't used an MEMPRAGE sequence, however, using an MPRAGE you can use a 
FWHM of 30 and a regularization of 0.001 in SPMs segmentation tool, setting the 
sample distance to 2 improves the correction further. Using the N3 implemented 
in FreeSurfer you could run (from the subject's directory) mri_nu_correct.mni 
--n 2 --uchar transforms/talairach.xfm --mask brainmask.mgz --stop 0.0001 
--distance 15 --fwhm 0.15 --shrink 2 --proto-iters 1 --i orig.mgz --o 
nu.mgz. Then proceed with the normalization of autorecon1. Both correction 
methods take quite some time.

In case of MP2RAGE or if the MPRAGE was divided by a GRE manually you will need 
to adjust these settings accordingly. The N4 algorithm of ANTs works fine also 
if a brainmask is supplied. In case someone wants to have some parameters to 
run an inhomogeneity with that tool or on MP2RAGE/Division data, let me know.

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Bruce Fischl
Gesendet: Montag, 25. März 2019 20:27
An: Freesurfer support list 
Cc: freesurfer-boun...@nmr.mgh.harvard.edu; Andre van der Kouwe 
; Jonathan Polimeni 
Betreff: Re: [Freesurfer] recon from 7T data

Hi Valeria

Jon Polimeni and Andre van der Kouwe put together a specific acquisition and 
set of preprocessing steps for 7T (mp2rage I believe). You need to account for 
the transmit inhomogeneities, which are what is causing you to lose the 
temporal lobes.

cheers
Bruce


On Mon, 25 Mar 2019, Barletta, Valeria wrote:

> 
> 
>  
> 
> Dear Freesurfers,
> 
> I am trying to perform the FreeSurfer cortical reconstruction process 
> from my 7 Tesla MEMPRAGE, but am getting very bad results (see first 
> attachment) compared to what I had using the 3 Tesla images (second 
> attachment).
> 
> Before launching the "recon-all ... -all" command, I applied the 
> FreeSurfer Gradient non-linearity correction.
> 
> 
> What can have been the problem?
> 
> 
> Thank you very much for your help,
> 
> Valeria
> 
> 
>


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Re: [Freesurfer] Problem with freeview in linux subsystem for windows

2019-02-20 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Hi Brady,

do you run a X server on windows? I run Xming and included in the .bashrc 
"export DISPLAY=localhost:0.0".

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Williamson, Brady
Gesendet: Dienstag, 19. Februar 2019 21:51
An: Freesurfer support list 
Betreff: [Freesurfer] Problem with freeview in linux subsystem for windows


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Hi,

I am trying to run freeview in the linux subsystem (Ubuntu 18.04) for windows 
10 but keep getting the following error:

failed to get the current screen resources
QXcbConnection: XCB error: 170 (Unknown), sequence: 170, resource id: 90, major 
code: 146 (Unknown), minor code: 20
QXcbConnection: XCB error: 170 (Unknown), sequence: 170, resource id: 90, major 
code: 146 (Unknown), minor code: 20


Freeview opens but there is no image. Is there a fix for this issue?

Thanks,
Brady
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Re: [Freesurfer] Freesurfer Recon-all error

2019-02-01 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Hi Kevin,

just an educated guess, but did you copy the line "recon-all -all -i 758251.dcm 
-s Subj14" from somewhere (e.g. word)? Because it seems the dash in front of 
each flag is an emphasized dash, probably resulting in the error. Try the 
following: "recon-all -all -i 758251.dcm -s Subj14"

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Jones, Kevin
Gesendet: Freitag, 1. Februar 2019 13:00
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Freesurfer Recon-all error


External Email - Use Caution
Dear Freesurfer team

Thanks for you help. I am new to freesurfer, using a mac and getting an error 
with recon all when using my MRI data.

I ran your tutorial recon all and the tutorial data worked fine. My burned CD 
T1 MRI files did not have the .dcm added so after renaming all the files with 
.dcm,  the recon function still gives an error message as below.


Last login: Fri Feb  1 06:51:44 on ttys000

Kevins-MacBook-Pro:~ kevin$ export FREESURFER_HOME=/Applications/freesurfer

Kevins-MacBook-Pro:~ kevin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer

FSFAST_HOME   /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR  /Applications/freesurfer/subjects

MNI_DIR   /Applications/freesurfer/mni

Kevins-MacBook-Pro:~ kevin$ export Case14=Applications/freesurfer/Case14

Kevins-MacBook-Pro:~ kevin$ export SUBJECTS_DIR=$Case14/7581/7583

Kevins-MacBook-Pro:~ kevin$ cd $Subjects_DIR

Kevins-MacBook-Pro:~ kevin$ echo $SUBJECTS_DIR

Applications/freesurfer/Case14/7581/7583

Kevins-MacBook-Pro:~ kevin$

Kevins-MacBook-Pro:~ kevin$ recon-all -all -i 758251.dcm -s Subj14

ERROR: Flag all unrecognized.

all i 758251.dcm s Subj14

Darwin Kevins-MacBook-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 12 
20:24:46 PST 2018; root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64



recon-all -s  exited with ERRORS at Fri Feb  1 06:55:38 EST 2019



For more details, see the log file

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



Kevins-MacBook-Pro:~ kevin$

Your suggestions are most appreciated.

Thanks Kevin
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Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

2019-01-25 Thread falk.luesebr...@med.ovgu.de 
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I was able to circumvent the error by switching from python3 to python2.

In python3 print was changed to a function making it necessary to put the 
arguments in brackets.

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von 
falk.luesebr...@med.ovgu.de
Gesendet: Freitag, 25. Januar 2019 10:42
An: Freesurfer Mailinglist 
Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for 
linux (WSL) using ubuntu 18.04.1 LTS


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Dear Juergen,

Thanks for your quick reply! Actually the spelling error is in the error 
message. Taken from http://martinos.org/~mreuter/long/long_mris_slopes

# extensive error checks
#if options.fsgd is None and
if options.qdec is None:
#print 'ERROR: Specify --fsgd or --qedc'
parser.print_help()
print '\nERROR: Specify --qedc (and other required arguments)\n'
sys.exit(1)

#if options.fsgd is not None and options.qdec is not None:
#print 'ERROR: Specify either --fsgd or --qedc, not both'
#sys.exit(1)

At least Martin is consistent with his typo. :D

Best,
Falk

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 Im Auftrag von Juergen Haenggi
Gesendet: Freitag, 25. Januar 2019 10:35
An: Freesurfer Mailinglist 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for 
linux (WSL) using ubuntu 18.04.1 LTS


External Email - Use Caution
Dear Falk

I have no idea, but recognised that the error refers to --qedc and not to 
--qdec.
maybe there is a spelling error somewhere that is related to your problem.

HTH
Cheers
Jürgen
-
University of Zurich
Dr. Jürgen Hänggi, Ph.D.
Department of Psychology
Division Neuropsychology
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland

0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)

j.haen...@psychologie.uzh.ch<mailto:j.haen...@psychologie.uzh.ch> (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

This email (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
email in error) please notify the sender immediately and destroy this
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On 25 Jan 2019, at 10:26, 
falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de> wrote:

External Email - Use Caution

Dear all,

Has anyone run the longitudinal pipeline successfully using the WSL? I’m 
running it with Ubuntu 18.04.1 LTS and 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.

I’m trying to process my first longitudinal data set following the instructions 
of the tutorial as close as possible. The data has been processed without 
issues and now I want to do the statistical analysis. When I run:
long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh 
--do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years 
--qcache fsaverage --sd $SUBJECTS_DIR

I get the following error:
File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448
print '\nERROR: Specify --qedc (and other required arguments)\n'
   ^
SyntaxError: invalid syntax

I get comparable errors for any other long_* command I try to run, e.g. 
long_qdec_table with or without any arguments gives:
File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119
   print '\nERROR: Specify --qedc'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean 
print('\nERROR: Specify --qedc')?

Does anyone have a clue where this error originates from using either WSL or 
Ubuntu 18.04?

Best,
Falk
...


Universitätsklinik für Neurologie


Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de>
http://www.kneu.ovgu.de/kneu.html

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Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

2019-01-25 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Dear Juergen,

Thanks for your quick reply! Actually the spelling error is in the error 
message. Taken from http://martinos.org/~mreuter/long/long_mris_slopes

# extensive error checks
#if options.fsgd is None and
if options.qdec is None:
#print 'ERROR: Specify --fsgd or --qedc'
parser.print_help()
print '\nERROR: Specify --qedc (and other required arguments)\n'
sys.exit(1)

#if options.fsgd is not None and options.qdec is not None:
#print 'ERROR: Specify either --fsgd or --qedc, not both'
#sys.exit(1)

At least Martin is consistent with his typo. :D

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Juergen Haenggi
Gesendet: Freitag, 25. Januar 2019 10:35
An: Freesurfer Mailinglist 
Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for 
linux (WSL) using ubuntu 18.04.1 LTS


External Email - Use Caution
Dear Falk

I have no idea, but recognised that the error refers to --qedc and not to 
--qdec.
maybe there is a spelling error somewhere that is related to your problem.

HTH
Cheers
Jürgen
-
University of Zurich
Dr. Jürgen Hänggi, Ph.D.
Department of Psychology
Division Neuropsychology
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland

0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)

j.haen...@psychologie.uzh.ch<mailto:j.haen...@psychologie.uzh.ch> (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

This email (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
email in error) please notify the sender immediately and destroy this
email. Any unauthorised copying, disclosure or distribution of the
material in this email is strictly forbidden.
-




On 25 Jan 2019, at 10:26, 
falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de> wrote:

External Email - Use Caution

Dear all,

Has anyone run the longitudinal pipeline successfully using the WSL? I’m 
running it with Ubuntu 18.04.1 LTS and 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.

I’m trying to process my first longitudinal data set following the instructions 
of the tutorial as close as possible. The data has been processed without 
issues and now I want to do the statistical analysis. When I run:
long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh 
--do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years 
--qcache fsaverage --sd $SUBJECTS_DIR

I get the following error:
File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448
print '\nERROR: Specify --qedc (and other required arguments)\n'
   ^
SyntaxError: invalid syntax

I get comparable errors for any other long_* command I try to run, e.g. 
long_qdec_table with or without any arguments gives:
File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119
   print '\nERROR: Specify --qedc'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean 
print('\nERROR: Specify --qedc')?

Does anyone have a clue where this error originates from using either WSL or 
Ubuntu 18.04?

Best,
Falk
...


Universitätsklinik für Neurologie



Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de>
http://www.kneu.ovgu.de/kneu.html

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[Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

2019-01-25 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Dear all,

Has anyone run the longitudinal pipeline successfully using the WSL? I'm 
running it with Ubuntu 18.04.1 LTS and 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.

I'm trying to process my first longitudinal data set following the instructions 
of the tutorial as close as possible. The data has been processed without 
issues and now I want to do the statistical analysis. When I run:
long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh 
--do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years 
--qcache fsaverage --sd $SUBJECTS_DIR

I get the following error:
File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448
print '\nERROR: Specify --qedc (and other required arguments)\n'
   ^
SyntaxError: invalid syntax

I get comparable errors for any other long_* command I try to run, e.g. 
long_qdec_table with or without any arguments gives:
File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119
   print '\nERROR: Specify --qedc'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean 
print('\nERROR: Specify --qedc')?

Does anyone have a clue where this error originates from using either WSL or 
Ubuntu 18.04?

Best,
Falk
...

[klinikum_logo_schmal_e-mail_blau]
Universitätsklinik für Neurologie


Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de>
http://www.kneu.ovgu.de/kneu.html

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