[Freesurfer] An estimated date for FreeSurfer 7.3 release

2022-05-06 Thread King-Wai Chu 
External Email - Use Caution

Hello,

I saw in 
https://secure-web.cisco.com/15xzpk6DF2_1DXEdVnlyo_B20R76xyd06ashqKEsp8aYWp1b4lzwZu3iSa3wCz-HT8smnvRB-Je3Lpyvr_mPj1hZVI5wZosUHkwC-eDAVSm4SIHtt5XgBNVYRbGotE4Y6StaP6FHmnJ0pRWfnGnnYj4kfUF4Ewi6ArPw3o3xkiZxEz4WiBHELvpaZjJirbA5JiNzft8olDLvpW8AGLIgLVRrSfD_IDrY-vCfw1l9X_w1l4tsslZCuyS8nvPMvQxWMgUNg-qI-J-aWNIhktite0EIfckDAmLxs9IwlnpeCUNzHbo9dwQzG5szYTxlUtX0HK1G2JioEQS4eqr9KHIsyug/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTracula
 that TRACULA in
FreeSurfer 7.3 is upcoming.
Do you have an estimated date of when that will happen?

We want to update our version 7.1.1 to the latest release.
If 7.3 is coming out in a couple of months, we can wait for it.
Or should we install 7.2 instead?

Thanks,

King-Wai
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Re: [Freesurfer] TRACULA -bedp parallel processing

2022-07-18 Thread King-Wai Chu 
External Email - Use Caution

Hi Ela,

I ran into the exact same problem.  Here is how I fix it.

1) edit pre.Parallel.docx
bedpostx_preproc.sh takes 2 arguments. Add a 2nd argument 0 at the end

bedpostx_preproc.sh /home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri 0
bedpostx_preproc.sh /home2/am2359/fs6_data/TRACULA/subjects_dir/58/dmri 0

2) create nodif_brain_mask.nii.gz link in dmri
cd /home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri
ln -s ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz nodif_brain_mask.nii.gz

3) create dirs
dmri.bedpostX/diff_slices
dmri.bedpostX/logs/monitor
dmri.bedpostX/xfms
in /home2/am2359/fs6_data/TRACULA/subjects_dir/57

same for 58

now you can run Parallel.docx

Hope I didn't miss anything.

Best,

King-Wai Chu

On Tue, Jun 14, 2022 at 8:55 PM Salar Dini, Elaheh <
elaheh.salard...@yale.edu> wrote:

> External Email - Use Caution
>
> I tried to troubleshoot this, but I couldn't. I just want to follow-up and
> make sure no other solutions come to your mind. If not, we will run it out
> of cluster which seems to work just fine.
>
> Thanks and all the best,
> Ela
> --
> *From:* Salar Dini, Elaheh 
> *Sent:* Wednesday, June 8, 2022 3:32 PM
> *To:* Yendiki, Anastasia ; Freesurfer support
> list 
> *Subject:* Re: TRACULA -bedp parallel processing
>
>
> Thanks Paul.
>
> bedpostx_preproc.sh is the first job that is I submit to my cluster. My input 
> file is attached to this email.
>
>
> Thanks,
>
> Ela
>
>
>
> *From: *Wighton, Paul
> <https://secure-web.cisco.com/1NvethJ2okwtBXYYV_EyxsXJx5qGOow2E5QtYJaKI1BCp3t8jVc7IQ9rNW9tMpRV7L5vP3mrgesq1jcnJKE5f_4HVbjGFYV70G8S40lFftxXK7lxGCnq56Ox0Mu9_i7WwuRnk-7bEGf-7R5dadwyxjWvyMgzXEvQhgfKan92fgm9AL_h7CtjK-_N5jWdO_f-cmdqFGeCspKHVODcFE4-d20kekjIkZbYia8GoJDcu27_d-Srd8pTig-g2Hi5NunkLAfpIgE4Io3ruNC0zu8Zvn6VCWVq-hy4a2HZ9ZIw7dodjmDWPVKcHcEqYkVV6sxGCB2gOlbzBrL_eeK8QHBJI7gRy-z5aUx-9dp2Io1Ww55g/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Wighton%252C%2BPaul%2522>
> *Sent: *Wed, 08 Jun 2022 10:06:21 -0700
> <https://secure-web.cisco.com/15JpdRjHpUwrjYyCfG0RWTJDoX413v5LN2Sed5H1OslWtt5j0CeOmss-WcOppPt0oWLSB3h1PXVS_mcB3lalLOjHb6zPQlqIN5vKRfohF0Mj1EXgkfg0eUNX1yvy0h7osnt39YaN4kHZT7dfh8b7lz5n4RFrfT49bz3uqGnbqEs88Gh1DFJfa0LBN6nlNlEKYcoVvEErAAZFcteu_-Fs__cSYKIWeATxNwCnCosyRS6peTz-ZPAzsA-i_ouJNkB4PDeJ7ZZm-i4vAbOAQGsBIU2404dp98DCAambIEO3SOkLgFcCG2V6DbgqudzsWc-oSIdI2OS0Pz_xJc4IFm7JoPovTTYe4NOyIusf9MhmMMAY/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220608>
>
> *Subject:*Re: TRACULA -bedp parallel processing
>
>
> Hi Ela,
>
> It looks to me like line 79 of bedpostx_preproc.sh is:
>
> if [ ${gflag} -eq 1 ]; then
>
> Which is consistent with the error:
>
> -eq: unary operator expected
>
> What this error is saying is that the variable `gflag` has not been set, so 
> the
> script does not know how to perform the comparison.
>
> `gflag` is set a few lines above to the second parameter passed when executing
> `bedpostx_preproc.sh`.  I would investigate how `bedpostx_preproc.sh` is being
> invoked to chase down the cause of this error.
>
> -Paul
>
>
> --
> *From:* Salar Dini, Elaheh 
> *Sent:* Wednesday, June 8, 2022 12:32 PM
> *To:* Yendiki, Anastasia ; Freesurfer support
> list 
> *Subject:* Re: TRACULA -bedp parallel processing
>
> That actually helps but not solving all the problems. So, what happens is
> that if I create dmri.bedpostX folder, the first error goes away, a.k.a. (cp:
> target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is
> not a directory). However, the second error still exists: a.k.a.
> (home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator
> expected". line 79 is "${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask).
> And when I try to run Parallel lines, I still get the error 
> (dmri.bedpostX/logs/log:
> No such file or directory). So, my guess is, it still doesn't copy the
> whole needed package for some reason. So, what we end up having in 
> dmri.bedpostX
> folder is a)bvals, b)bvecs, c) nodif_brain_mask.nii.gz.
>
> I can always manually copy all needed file from fsl folder to our subjects
> folder, but I am curious why we get the error and why everything is not
> copied automatically. I also don't know what files we need to manually
> copy.
>
> Thanks again,
> Ela
> --
> *From:* Yendiki, Anastasia 
> *Sent:* Tuesday, June 7, 2022 2:46 PM
> *To:* Salar Dini, Elaheh ; Freesurfer support
> list 
> *Subject:* Re: TRACULA -bedp parallel processing
>
> What if yo

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

2022-07-31 Thread King-Wai Chu 
FSvoxelSpace.mgz
>
>
>
> trac-all finished w/o problem.
>
>
>
> trac-all -version
>
> trac-all 7.3.0
>
>
>
> I seems trac-all in v7.3 forgets to update the fact that
> segmentThalamicNuclei.sh output v13 of the file.
>
> Or it is looking for v12 for a reason?
>
>
>
> Is my fix correct?
>
>
>
> Thanks,
>
>
>
> King-Wai
>
>
>
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-- 
King-Wai Chu, Ph.D.
Program Analyst
Mental Illness Research, Education and Clinical Center (MIRECC, VISN3)
James J. Peters Dept. of Veterans Administration Medical Center (OOMH)
130 W. Kingsbridge Road
Bronx, NY 10468
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Re: [Freesurfer] Tracula Config file.

2022-08-05 Thread King-Wai Chu 
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>
>
> --
> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>
>
>
> *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
> Neuroscience*
> *University of Texas, School of Medicine*
>
> *Rio Grande Valley*
>
> *Texas.*
>
>
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>  .
>


-- 
King-Wai Chu, Ph.D.
Program Analyst
Mental Illness Research, Education and Clinical Center (MIRECC, VISN3)
James J. Peters Dept. of Veterans Administration Medical Center (OOMH)
130 W. Kingsbridge Road
Bronx, NY 10468
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Re: [Freesurfer] Tracula Config file.

2022-08-05 Thread King-Wai Chu 
External Email - Use Caution

Hi Alan,

They still don't match.
See attached excel file.

Best,

King-Wai

On Fri, Aug 5, 2022 at 2:35 PM Alan Francis 
wrote:

> External Email - Use Caution
>
> Hello King-Wai -
>
> I made the change to the ncpts. But still an error message persists.
>
> ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm
> cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af
> <http://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af>
> rh.af
> <http://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af>
> lh.ar
> <http://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar>
> rh.ar
> <http://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar>
> lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc
> lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1
> rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID
> list
> ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0
> 0 0 10 49 0 0 0 0 0 0 0 0) do not match
>
>
>
> I have attached the RC file. Could you please shed some light on this?
>
> Thank you
>
> Alan
>
> On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu 
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Alan,
>>
>> Your pathlist and "Number of path control points"(ncpts) don't match.
>> You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
>>
>> Best,
>>
>> King-Wai
>>
>>
>>
>>
>> On Fri, Aug 5, 2022 at 10:53 AM Alan Francis 
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> Good morning Anastasia -
>>>
>>> I made the changes you suggested and removed "extraneous" commands. But
>>> the error message still persists. Could you please shed some light on this?
>>> Attached - latest RC file.
>>>
>>> The error message is : unmatched ' " '
>>>
>>> Thank you
>>>
>>> Alan
>>>
>>> On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia <
>>> ayend...@mgh.harvard.edu> wrote:
>>>
>>>> Hi Alan - dcmroot is the root directory under which the dicom files are
>>>> saved. It's actually optional. In your case, either of the following will
>>>> have the same, correct effect:
>>>>
>>>> set dcmroot = /home/afrancis/Imaging
>>>> set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>>
>>>> OR
>>>>
>>>> set dcmlist =
>>>> (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>>
>>>> In addition, there are *a lot *of things that you left in there from
>>>> the example RC file. You should delete them entirely, unless you
>>>> specifically want to set one of those things to something other than the
>>>> default. These are examples that may not give you the default behavior.
>>>> Also the field mapping files - delete those lines because you're just using
>>>> the example names and they're not going to work. You want your RC file to
>>>> have the minimum necessary for your analysis.
>>>>
>>>> Best,
>>>> Anastasia.
>>>>
>>>>
>>>> --

Re: [Freesurfer] Tracula Config file.

2022-08-05 Thread King-Wai Chu 
External Email - Use Caution

Hi Alan,

In your pathlist, the 1st path is acomm.  You have "ac" in your file.
Change ac to acomm and you should be good to go.

Best,

King-Wai

On Fri, Aug 5, 2022 at 4:23 PM Alan Francis 
wrote:

> External Email - Use Caution
>
> Hi King-Wai -
>
> First of all, thank you so much for taking the time to investigate my RC
> file. I made the changes that you suggested, but the error keeps coming up.
>
> I have attached the file.
>
> Thanks again,
>
> Alan
>
> On Fri, Aug 5, 2022 at 2:03 PM King-Wai Chu  wrote:
>
>> External Email - Use Caution
>>
>> Hi Alan,
>>
>> They still don't match.
>> See attached excel file.
>>
>> Best,
>>
>> King-Wai
>>
>> On Fri, Aug 5, 2022 at 2:35 PM Alan Francis 
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> Hello King-Wai -
>>>
>>> I made the change to the ncpts. But still an error message persists.
>>>
>>> ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm
>>> cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af
>>> <http://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af>
>>> rh.af
>>> <http://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af>
>>> lh.ar
>>> <http://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar>
>>> rh.ar
>>> <http://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar>
>>> lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc
>>> lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1
>>> rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID
>>> list
>>> ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0
>>> 0 0 0 10 49 0 0 0 0 0 0 0 0) do not match
>>>
>>>
>>>
>>> I have attached the RC file. Could you please shed some light on this?
>>>
>>> Thank you
>>>
>>> Alan
>>>
>>> On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu 
>>> wrote:
>>>
>>>> External Email - Use Caution
>>>>
>>>> Hi Alan,
>>>>
>>>> Your pathlist and "Number of path control points"(ncpts) don't match.
>>>> You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
>>>>
>>>> Best,
>>>>
>>>> King-Wai
>>>>
>>>>
>>>>
>>>>
>>>> On Fri, Aug 5, 2022 at 10:53 AM Alan Francis 
>>>> wrote:
>>>>
>>>>> External Email - Use Caution
>>>>>
>>>>> Good morning Anastasia -
>>>>>
>>>>> I made the changes you suggested and removed "extraneous" commands.
>>>>> But the error message still persists. Could you please shed some light on
>>>>> this? Attached - latest RC file.
>>>>>
>>>>> The error message is : unmatched ' " '
>>>>>
>>>>> Thank you
>>>>>
>>>>> Alan
>>>>>
>>>>> On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia <
>>>>> ayend...@mgh.harvard.edu> wrote:
>>>>>
>>>>>> Hi Alan - dcmro

Re: [Freesurfer] Tracula - Preproc

2022-08-12 Thread King-Wai Chu 
VpjBIMpH9Nml3JUBod6IgJGY-r-FiApP-1Qjq7IEcSiTDziBfRZ64RiYYgPhYh5mnBAPiA39QyviDts0LFEwFMad48dZN_wbbt-XzotWZl-fXA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>> <https://secure-web.cisco.com/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzCMAD3ZeH7i0TMQH5Zhg4QbeZG7s_QdP_E5obZXlgHiw-nadkn11dbv3lBRemXneow/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> <*MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1q5No534S3eCaYMPbpL73aDavRve-q80-4p88Pn9BopRGlLQI1tU_C1Z7nerNEfGNQG7jtovxmvHvXxNMPROSRiAKNw2aZ-q3aq1WmtcmpOoXvRwiwdnnjRKwChdCmOnfIT8wofo0PX29IeXcb94DlmzuNYshWxDX5mgBposqt4Tys2fjDnSQ4D3zTn54qHmF3wWW4XON5ejopaNPdibMgayrdMIHwFKy3VnpiyiJVpjBIMpH9Nml3JUBod6IgJGY-r-FiApP-1Qjq7IEcSiTDziBfRZ64RiYYgPhYh5mnBAPiA39QyviDts0LFEwFMad48dZN_wbbt-XzotWZl-fXA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>> <https://secure-web.cisco.com/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzCMAD3ZeH7i0TMQH5Zhg4QbeZG7s_QdP_E5obZXlgHiw-nadkn11dbv3lBRemXneow/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>>
>> .
>>
>
>
> --
> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>
>
>
> *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
> Neuroscience*
> *University of Texas, School of Medicine*
>
> *Rio Grande Valley*
>
> *Texas.*
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1ya6JvGMaiTaLdV_RFI9p755zjyL9Xf7XygbVoLWjVcp1aMfCW54Ve6BXwyVTgw-sXgRlCbmWpM_HbJqT31X3b13LFy66hGznBK01PvWGqUimueqP9QVQYDFwMKYAt-U07t8W-9hFs5dcHM0tuz8fwSxvrgoEdY77mF3-sRfq_zNd6fLw9A_2iJlecVDkDmPNVs8t6YO5uEV2HK1MIO2GjjVBCgqOOAOroVb6ZNL5Y2hJus5WrH8CVwLBN5mijz1uxDoKZENg4ESJj8LMFh9_AYnIRkIenN3xWRP1hhC9yuBAAL732Uw4iEB7CAATwQSGjvqdGG1W_Opkjw8eqCL96A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> The information in this e-mail is intended only for the person to whom it
> is addressed.  If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> https://secure-web.cisco.com/1q5No534S3eCaYMPbpL73aDavRve-q80-4p88Pn9BopRGlLQI1tU_C1Z7nerNEfGNQG7jtovxmvHvXxNMPROSRiAKNw2aZ-q3aq1WmtcmpOoXvRwiwdnnjRKwChdCmOnfIT8wofo0PX29IeXcb94DlmzuNYshWxDX5mgBposqt4Tys2fjDnSQ4D3zTn54qHmF3wWW4XON5ejopaNPdibMgayrdMIHwFKy3VnpiyiJVpjBIMpH9Nml3JUBod6IgJGY-r-FiApP-1Qjq7IEcSiTDziBfRZ64RiYYgPhYh5mnBAPiA39QyviDts0LFEwFMad48dZN_wbbt-XzotWZl-fXA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/1q5No534S3eCaYMPbpL73aDavRve-q80-4p88Pn9BopRGlLQI1tU_C1Z7nerNEfGNQG7jtovxmvHvXxNMPROSRiAKNw2aZ-q3aq1WmtcmpOoXvRwiwdnnjRKwChdCmOnfIT8wofo0PX29IeXcb94DlmzuNYshWxDX5mgBposqt4Tys2fjDnSQ4D3zTn54qHmF3wWW4XON5ejopaNPdibMgayrdMIHwFKy3VnpiyiJVpjBIMpH9Nml3JUBod6IgJGY-r-FiApP-1Qjq7IEcSiTDziBfRZ64RiYYgPhYh5mnBAPiA39QyviDts0LFEwFMad48dZN_wbbt-XzotWZl-fXA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>


-- 
King-Wai Chu, Ph.D.
Program Analyst
Mental Illness Research, Education and Clinical Center (MIRECC, VISN3)
James J. Peters Dept. of Veterans Administration Medical Center (OOMH)
130 W. Kingsbridge Road
Bronx, NY 10468
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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] Tracula - Preproc

2022-08-12 Thread King-Wai Chu 
External Email - Use Caution

Hi Alan,

You need to install Advanced Normalization Tools(ANTS)
https://secure-web.cisco.com/1xl8ADqLGMhYjn7TbMOsRonEy_R5C4feN8mMJ-Q7bddD3E_kk_PzT6LUVVJPXi70pbS8fDlYVtT5FZrovy4oO8F6esYTNDGGmBMZIcnfJjKjqysycppupQwOtlATRsVGkxuOe_hdaI5TbjfjkBv6w3Sy0DIhpR6yfl6YYGbceEbrDPEyiri7niCivYdPtWY7roMFW1urF87IjvtXzJTpdRjnKuM_GCbZ1A7MarsQB-elnw6ZSy-uE4Jo5QALYd1tAMpAVAb1JVbjj2DImfV5v3vsL5T0Ftffq2F7_UmQy8JDepEGdgvtyOH5Zt0aM_Yo9ZBBOdUfHr-ZPBJfino6Xgg/https%3A%2F%2Fsourceforge.net%2Fprojects%2Fadvants%2F

You can compile from source or get the binaries.

Best,

King-Wai

On Fri, Aug 12, 2022 at 4:37 PM Alan Francis 
wrote:

> External Email - Use Caution
>
> Hi Anastasia and King_Wei :
>
> Thank you for your suggestions. I have fixed the bet issue by reinstalling
> FSL. But I have one more error:
>
> ERROR: must set ANTSPATH environment variable to use ANTs
>
> I tried setting
>
> set ANTSPATH = 0 but that did not work.
>
> I looked up the web to see if there were any default values I could use
> for ANTs but did not come up with any.
>
> Thanks again for your help,
>
> Alan
>
> On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu 
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Alan,
>>
>> If you really have FSL installed inside Freesurfer, it is not the way to
>> do it.
>> If you type
>> echo $FSLDIR
>> does it return anything?
>> If FSL is installed the way you said it is, echo $FSLDIR should give
>> something like
>> /usr/local/freesurfer/7.2.0-1/FSL
>> in your system
>>
>> Also, if you type
>> which bet
>> It should return something like
>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>> or type
>> ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>> Does it say "No such file or directory" or return
>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>
>> If you don't get all these, your FSL is not installed correctly.
>>
>> Best,
>>
>> King-Wai
>>
>> On Fri, Aug 12, 2022 at 12:34 PM Alan Francis 
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> Hi Anastasia and King wei -
>>>
>>> I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL
>>> is part of that installation. Do you recommend a second installation of FSL
>>> separately?
>>>
>>> Thanks so much for your help and comments!
>>>
>>> Alan
>>>
>>> On Thu, Aug 11, 2022 at 2:50 PM  wrote:
>>>
>>>> External Email - Use Caution
>>>>
>>>> Hi Alan,
>>>>
>>>>
>>>>
>>>> As Anastasia said, bet is part of FSL.
>>>>
>>>> If you don’t have it installed already, you need to install FSL.
>>>>
>>>>
>>>>
>>>> Best,
>>>>
>>>>
>>>>
>>>> King-Wai
>>>>
>>>>
>>>>
>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki,
>>>> Anastasia
>>>> *Sent:* Thursday, August 11, 2022 3:42 PM
>>>> *To:* Freesurfer support list 
>>>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>>>
>>>>
>>>>
>>>> Yes that's from FSL. It's needs to be in $FSLDIR.
>>>> --
>>>>
>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>>> alandarkene...@gmail.com>
>>>> *Sent:* Thursday, August 11, 2022 3:30 PM
>>>> *To:* Freesurfer 
>>>> *Subject:* [Freesurfer] Tracula - Preproc
>>>>
>>>>
>>>>
>>>> *External Email - Use Caution*
>>>>
>>>> Hi Anastasia, King Wei:
>>>>
>>>>
>>>>
>>>> I did as you suggested with the config file and the preprocessing ran
>>>> for a bit but then an error occurred. I have attached the run script. It
>>>> says BET not found. Is this the Brain Extraction tool?
>>>>
>>>>
>>>>
>>>> Could you please shed some light on this?
>>>>
>>>>
>>>>
>>>> thanks so much,
>>>>
>>>>
>>>>
>>>> Alan
>>>>
>>>>
>>>> --
>>>>
>>>> *|~|~

Re: [Freesurfer] Tracula - Preproc

2022-08-12 Thread King-Wai Chu 
External Email - Use Caution

For bash shell
ANTSPATH=/home/afrancis/Imaging/ANTs

For tcsh
setenv ANTSPATH /home/afrancis/Imaging/ANTs

On Fri, Aug 12, 2022 at 5:54 PM Alan Francis 
wrote:

> External Email - Use Caution
>
> Hi Anastasia :
>
> I installed ANTS and tried this
>
> set ANTSPATH = /home/afrancis/Imaging/ANTs
>
> but it did not work. Is there a different set path?
>
> Thanks,
>
> Alan
>
> On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> If you want to use ANTs for registration, you have to have ANTs installed
>> and set ANTSPATH to its location.
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>> alandarkene...@gmail.com>
>> *Sent:* Friday, August 12, 2022 4:35 PM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>
>>
>> External Email - Use Caution
>>
>> Hi Anastasia and King_Wei :
>>
>> Thank you for your suggestions. I have fixed the bet issue by
>> reinstalling FSL. But I have one more error:
>>
>> ERROR: must set ANTSPATH environment variable to use ANTs
>>
>> I tried setting
>>
>> set ANTSPATH = 0 but that did not work.
>>
>> I looked up the web to see if there were any default values I could use
>> for ANTs but did not come up with any.
>>
>> Thanks again for your help,
>>
>> Alan
>>
>> On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu 
>> wrote:
>>
>> External Email - Use Caution
>>
>> Hi Alan,
>>
>> If you really have FSL installed inside Freesurfer, it is not the way to
>> do it.
>> If you type
>> echo $FSLDIR
>> does it return anything?
>> If FSL is installed the way you said it is, echo $FSLDIR should give
>> something like
>> /usr/local/freesurfer/7.2.0-1/FSL
>> in your system
>>
>> Also, if you type
>> which bet
>> It should return something like
>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>> or type
>> ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>> Does it say "No such file or directory" or return
>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>
>> If you don't get all these, your FSL is not installed correctly.
>>
>> Best,
>>
>> King-Wai
>>
>> On Fri, Aug 12, 2022 at 12:34 PM Alan Francis 
>> wrote:
>>
>> External Email - Use Caution
>>
>> Hi Anastasia and King wei -
>>
>> I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL
>> is part of that installation. Do you recommend a second installation of FSL
>> separately?
>>
>> Thanks so much for your help and comments!
>>
>> Alan
>>
>> On Thu, Aug 11, 2022 at 2:50 PM  wrote:
>>
>> External Email - Use Caution
>>
>> Hi Alan,
>>
>>
>>
>> As Anastasia said, bet is part of FSL.
>>
>> If you don’t have it installed already, you need to install FSL.
>>
>>
>>
>> Best,
>>
>>
>>
>> King-Wai
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia
>> *Sent:* Thursday, August 11, 2022 3:42 PM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>
>>
>>
>> Yes that's from FSL. It's needs to be in $FSLDIR.
>> --
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>> alandarkene...@gmail.com>
>> *Sent:* Thursday, August 11, 2022 3:30 PM
>> *To:* Freesurfer 
>> *Subject:* [Freesurfer] Tracula - Preproc
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi Anastasia, King Wei:
>>
>>
>>
>> I did as you suggested with the config file and the preprocessing ran for
>> a bit but then an error occurred. I have attached the run script. It says
>> BET not found. Is this the Brain Extraction tool?
>>
>>
>>
>> Could you please shed some light on this?
>>
>>
>>
>> thanks so much,
>>
>>
>>
>> Alan
>>
>>
>> --
>>
>> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~

Re: [Freesurfer] Tracula - Preproc

2022-08-15 Thread King-Wai Chu 
External Email - Use Caution

Hi Alan,

Do you have the latest version of ANTs?
It should be 2.1.0
Older version don't have all the binaries and scripts required by trac-all.

Best,

King-Wai

On Mon, Aug 15, 2022 at 11:49 AM Alan Francis 
wrote:

> External Email - Use Caution
>
> Hello King Wai -
>
> I used the C shell pathway just as you specified. But I got this error
> message right at the end of the processing:
>
> #@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022
> /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d 3 -m
> /home/afrancis/Imaging/111312-2/dmri/dtifit_FA.nii.gz -f
> /usr/local/freesurfer/7.2.0-1/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o
> /home/afrancis/Imaging/111312-2/dmri/xfms/diff2syn
> /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh: Command not found.
> Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT
> 2022 x86_64 x86_64 x86_64 GNU/Linux
>
> trac-preproc exited with ERRORS at Mon Aug 15 10:32:25 CDT 2022
>
> In the installed ANTs folder I could not find the
> *antsRegistrationSyNQuick.sh* script. Should I create this script?
>
> Thanks ever so much!
>
> Alan
>
> On Mon, Aug 15, 2022 at 10:13 AM Alan Francis 
> wrote:
>
>> Thank you so much King Wai,
>>
>> On Fri, Aug 12, 2022 at 5:12 PM King-Wai Chu 
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> For bash shell
>>> ANTSPATH=/home/afrancis/Imaging/ANTs
>>>
>>> For tcsh
>>> setenv ANTSPATH /home/afrancis/Imaging/ANTs
>>>
>>> On Fri, Aug 12, 2022 at 5:54 PM Alan Francis 
>>> wrote:
>>>
>>>> External Email - Use Caution
>>>>
>>>> Hi Anastasia :
>>>>
>>>> I installed ANTS and tried this
>>>>
>>>> set ANTSPATH = /home/afrancis/Imaging/ANTs
>>>>
>>>> but it did not work. Is there a different set path?
>>>>
>>>> Thanks,
>>>>
>>>> Alan
>>>>
>>>> On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <
>>>> ayend...@mgh.harvard.edu> wrote:
>>>>
>>>>> If you want to use ANTs for registration, you have to have ANTs
>>>>> installed and set ANTSPATH to its location.
>>>>> --
>>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>>>> alandarkene...@gmail.com>
>>>>> *Sent:* Friday, August 12, 2022 4:35 PM
>>>>> *To:* Freesurfer support list 
>>>>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>>>>
>>>>>
>>>>> External Email - Use Caution
>>>>>
>>>>> Hi Anastasia and King_Wei :
>>>>>
>>>>> Thank you for your suggestions. I have fixed the bet issue by
>>>>> reinstalling FSL. But I have one more error:
>>>>>
>>>>> ERROR: must set ANTSPATH environment variable to use ANTs
>>>>>
>>>>> I tried setting
>>>>>
>>>>> set ANTSPATH = 0 but that did not work.
>>>>>
>>>>> I looked up the web to see if there were any default values I could
>>>>> use for ANTs but did not come up with any.
>>>>>
>>>>> Thanks again for your help,
>>>>>
>>>>> Alan
>>>>>
>>>>> On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu 
>>>>> wrote:
>>>>>
>>>>> External Email - Use Caution
>>>>>
>>>>> Hi Alan,
>>>>>
>>>>> If you really have FSL installed inside Freesurfer, it is not the way
>>>>> to do it.
>>>>> If you type
>>>>> echo $FSLDIR
>>>>> does it return anything?
>>>>> If FSL is installed the way you said it is, echo $FSLDIR should give
>>>>> something like
>>>>> /usr/local/freesurfer/7.2.0-1/FSL
>>>>> in your system
>>>>>
>>>>> Also, if you type
>>>>> which bet
>>>>> It should return something like
>>>>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>>>> or type
>>>>> ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>>>> Does it say "No such file or directory" or return
>>>>> /usr/local/fr

Re: [Freesurfer] Tracula - Preproc

2022-08-15 Thread King-Wai Chu 
External Email - Use Caution

Hi Alan,

First find out the version of ANTs you have by running the command below
antsRegistration --version

If it is below 2.1.0
download the 2.1.0 binaries here, it works for me.
https://secure-web.cisco.com/1NMd_rcPaYSvhGkOTDq6LZhGGFrvJPOKYz-pvH2Y8mi4GpUZhsdzgMiDYBrwA13AACNGNmIhkqZqQoEIs5fSIgISExrttLBYgDTATDAQ5lxNqC2J_SgADNsbw4OyIDVabLhAWxR0PqOIHYjqGICgWOpQSNH1KD1ng_fPfLqRfhcavePNTbCgLbM4n3fXSDbP6PkHxNn-F5ty6DhoULggX1RmZNaLXy5ad4UjX_cUhC3H6numGQgfYK7nFTnaFrdDP9WDUJluOnkqsLIJNcn3L2REEr0O3ZIwDrPHmuuMMo7mlcUTrG86Jmy5muPEYeTBs/https%3A%2F%2Fgithub.com%2FANTsX%2FANTs%2Freleases%2Ftag%2Fv2.1.0

If you want to use your script, edit the yellow lines to remove "#"
# If you want to build a particular release, do so here
# cd ANTs
# git checkout v2.3.1
# cd -

# If you want to build a particular release, do so here
cd ANTs
git checkout v2.3.1
cd -

you can also try v2.3.5 or v2.4.0.

I don't know if it will work or not because I don't write this script.

Best,

King-Wai

On Mon, Aug 15, 2022 at 1:15 PM Alan Francis 
wrote:

> External Email - Use Caution
>
> Hi King Wai -
>
> I used a script (enclosed) to install ANTs. Is there anyway this script
> could be modified to install the latest version?
>
> Thank you so much,
>
> Alan
>
> On Mon, Aug 15, 2022 at 11:40 AM King-Wai Chu 
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Alan,
>>
>> Do you have the latest version of ANTs?
>> It should be 2.1.0
>> Older version don't have all the binaries and scripts required by
>> trac-all.
>>
>> Best,
>>
>> King-Wai
>>
>> On Mon, Aug 15, 2022 at 11:49 AM Alan Francis 
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> Hello King Wai -
>>>
>>> I used the C shell pathway just as you specified. But I got this error
>>> message right at the end of the processing:
>>>
>>> #@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022
>>> /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d 3 -m
>>> /home/afrancis/Imaging/111312-2/dmri/dtifit_FA.nii.gz -f
>>> /usr/local/freesurfer/7.2.0-1/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o
>>> /home/afrancis/Imaging/111312-2/dmri/xfms/diff2syn
>>> /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh: Command not
>>> found.
>>> Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT
>>> 2022 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> trac-preproc exited with ERRORS at Mon Aug 15 10:32:25 CDT 2022
>>>
>>> In the installed ANTs folder I could not find the
>>> *antsRegistrationSyNQuick.sh* script. Should I create this script?
>>>
>>> Thanks ever so much!
>>>
>>> Alan
>>>
>>> On Mon, Aug 15, 2022 at 10:13 AM Alan Francis 
>>> wrote:
>>>
>>>> Thank you so much King Wai,
>>>>
>>>> On Fri, Aug 12, 2022 at 5:12 PM King-Wai Chu 
>>>> wrote:
>>>>
>>>>> External Email - Use Caution
>>>>>
>>>>> For bash shell
>>>>> ANTSPATH=/home/afrancis/Imaging/ANTs
>>>>>
>>>>> For tcsh
>>>>> setenv ANTSPATH /home/afrancis/Imaging/ANTs
>>>>>
>>>>> On Fri, Aug 12, 2022 at 5:54 PM Alan Francis 
>>>>> wrote:
>>>>>
>>>>>> External Email - Use Caution
>>>>>>
>>>>>> Hi Anastasia :
>>>>>>
>>>>>> I installed ANTS and tried this
>>>>>>
>>>>>> set ANTSPATH = /home/afrancis/Imaging/ANTs
>>>>>>
>>>>>> but it did not work. Is there a different set path?
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Alan
>>>>>>
>>>>>> On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <
>>>>>> ayend...@mgh.harvard.edu> wrote:
>>>>>>
>>>>>>> If you want to use ANTs for registration, you have to have ANTs
>>>>>>> installed and set ANTSPATH to its location.
>>>>>>> --
>>>>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>>>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>>>>>> alandarkene...@gmail.com>
>>>>>>> *Sent:* Friday, August 12, 2022 4:35 PM
>>>>>>> *To:* Freesur

[Freesurfer] Tracula statistics outputs

2022-09-26 Thread King-Wai Chu 
External Email - Use Caution

Hi,

I have 3 questions on tracula statistics outputs.

1) There are duplicate points in pathstats.byvoxel.txt, is it normal?
I didn't try it on all 42 tractcs.  For the few I've looked at, they all
have duplicate points.
I used the default setting in the config file to run trac-all.

2) When I do along-tract statistical analysis, sig.mgh and z.mgh are 1D
files.
When embed the sig.mgh and z.mgh statistical maps from the analysis into
the template .trk
(*.display.trk, which is 3D), it seems to me that sig.mgh and z.mgh don't
have enough information to give *.display.trk the voxel values for the
*.overlay.trk.  There is no one-to-one voxel corresponding between sig.mgh
and *.display.trk.  What am I missing?  Or what's the embedding process do?

3) When I convert .trk(*.overlay.trk, for example) to nii.gz or ascii using
dmri_trk2trk or
mri_convert the voxel values of the .trk file don't get converted into the
.nii.gz or ascii file,
only the x,y,z coordinates are converted.  Is there a way to get the voxels
values of the .trk file
when converting to .nii.gz or ascii format?

Thanks,

King-Wai

-- 
King-Wai Chu, Ph.D.
Program Analyst
Mental Illness Research, Education and Clinical Center (MIRECC, VISN3)
James J. Peters Dept. of Veterans Administration Medical Center (OOMH)
130 W. Kingsbridge Road
Bronx, NY 10468
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[Freesurfer] Tracula statistics outputs for version 7.2

2022-10-04 Thread King-Wai Chu 
External Email - Use Caution

Hi,

Upon further examination of pathstats.byvoxel.txt and pathstats.overall.txt,
I have 2 more questions.
Since my previous 3 questions still have not been answered, I'm including
them here
so that they are all in one place.  The 2 new questions are 4) and 5), my
previous 3
questions are appended after.

4) I have noticed that the averages of AD, RD, MD and FA in
pathstats.byvoxel.txt
are exactly the same as the *_Avg_Center in pathstats.overall.txt.
According to the tutorial, *_Avg_Center in pathstats.overall.txt is
the "average over highest-probability path only" and the
AD, RD, MD and FA in pathstats.byvoxel.txt is the value at the
"position on the maximum a posteriori path".
Does it mean that "highest-probability path only" and "position on the
maximum a posteriori path" are the same or one of them should be changed to
the other one?

5) Are the averages of AD_Avg, RD_Avg, MD_Avg and FA_Avg in
pathstats.byvoxel.txt
suppose to match *_Avg(average over the entire support of the path
distribution)
in pathstats.overall.txt?
When I removed the duplicate points in pathstats.byvoxel.txt, the averages
of
AD_Avg, RD_Avg, MD_Avg and FA_Avg come very close to the value of *_Avg in
pathstats.overall.txt

I don't think I can calculate the averages by including the duplicate
points in 4)
but removing them in 5).  Either including them in both or not at all.

Questions from my previous email.

1) There are duplicate points in pathstats.byvoxel.txt, is it normal?
I didn't try it on all 42 tractcs.  For the few I've looked at, they all
have duplicate points.
I used the default setting in the config file to run trac-all.

2) When I do along-tract statistical analysis, sig.mgh and z.mgh are 1D
files.
When embed the sig.mgh and z.mgh statistical maps from the analysis into
the template .trk
(*.display.trk, which is 3D), it seems to me that sig.mgh and z.mgh don't
have enough information to give *.display.trk the voxel values for the
*.overlay.trk.  There is no one-to-one voxel corresponding between sig.mgh
and *.display.trk.  What am I missing?  Or what's the embedding process do?

3) When I convert .trk(*.overlay.trk, for example) to nii.gz or ascii using
dmri_trk2trk or
mri_convert the voxel values of the .trk file don't get converted into the
.nii.gz or ascii file,
only the x,y,z coordinates are converted.  Is there a way to get the voxels
values of the .trk file
when converting to .nii.gz or ascii format?

Thanks,

King-Wai

-- 
King-Wai Chu, Ph.D.
Program Analyst
Mental Illness Research, Education and Clinical Center (MIRECC, VISN3)
James J. Peters Dept. of Veterans Administration Medical Center (OOMH)
130 W. Kingsbridge Road
Bronx, NY 10468
___
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.