External Email - Use Caution
Hi Doug,
Sorry for the late reply, and thanks for all your help. Attached is the text file of the output. This was testing autorecon-pial, but the bug is the same no matter if it's autorecon2-wm, autorecon3, or any place it hits the "if ( $ud" statement.
Best,
Kody
Run it with -debug as the first option, capture the output, and send it
to us.
On 4/1/2021 8:29 PM, zalewk wrote:
>
> ????????External Email - Use Caution
>
> Hi Freesurfer team,
>
> My lab recently switched over from FS6 to FS7 and I think I've
> encountered a bug with recon-all.
> I'm running subjects stepwise and editing them, running recon-all with
> the -autorecon2 and -autorecon3 flags initially are no problem, they
> run fine.? Trying to re-run them or use the -autorecon2-wm,
> -autorecon-pial etc. flags lead to crashing at certain parts of the
> program. The error message I get is "if: expression syntax". Digging
> into the code, it seems to crash when it hits a line of code "if($ud
> || $ForceUpdate)". The syntax superficially looks right (I don't know
> tcsh), checking the variables it seems like $ForceUpdate is never set,
> but removing it from recon-all doesn't fix the problem.
> It seems the $ud variable is for checking if updates are needed for a
> set of volumes passed to the program. I don't know why that would be a
> problematic argument, removing that part seems to fix it, but this
> also seems like an important variable and I don't know enough about
> tcsh to understand why it works after removing it. Can one of the
> folks who wrote the recon-all script help me out? I'm running the
> commands step-wise as a work-around, but that is much less convenient.
>
> Best,
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu>
Sent: Tuesday, April 6, 2021 6:41 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Freesurfer Digest, Vol 206, Issue 6Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit
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You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Freesurfer Website Ports (Swearingen, Hannah)
2. mris_average_surface fails (?????????)
3. Re: 2mm thick image for hippocampal segmentation. (Ramesh Babu)
4. Re: fMRIPrep BOLD Output (Douglas N. Greve)
5. Re: mri_glmfit error (Douglas N. Greve)
6. Re: Regarding recon all (Douglas N. Greve)
7. Re: retaining label ids (Douglas N. Greve)
8. Re: recon-all bug (Douglas N. Greve)
9. Re: mris_label2annot - make all command exiting with errors
(Douglas N. Greve)
10. Re: recon-all bug (Douglas N. Greve)
11. Re: Dicom Tag Problem Reconall (Douglas N. Greve)
12. unsubscribe (Coleman, Katherine)
13. Re: mri_gtmpvc error Checking tissue type ERROR:
CheckSegTissueType() tissue type for seg (Douglas N. Greve)
14. Re: Problem with freesurfer measures (Douglas N. Greve)
15. Re: Freesurfer Website Ports (Douglas N. Greve)
16. Re: mris_average_surface fails (Douglas N. Greve)
17. Re: 2mm thick image for hippocampal segmentation.
(Douglas N. Greve)
18. Freesurfer Versions - Zeros in the Cortex (Daniel Gutstein)
19. Re: mri_gtmpvc error Checking tissue type ERROR:
CheckSegTissueType() tissue type for seg (Bahar Hazal Yal??nkaya)
----------------------------------------------------------------------
Message: 1
Date: Mon, 5 Apr 2021 15:20:31 -0400
From: "Swearingen, Hannah" <hannah_swearingen1@brown.edu>
Subject: [Freesurfer] Freesurfer Website Ports
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAG+grQp1wJ8ywX0StrT4VJO38JYtwfxivTNvdH3KwQrhtwiRGw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi,
I am setting up an Access Control List for an isolated VLAN in which my
center's neuroimaging computing workstations will be connected to our
hospital's network for data back-up.
We want to be able to connect to Freesurfer's website while connected to
the VLAN, and we need to supply which ports the website accesses. I used
nmap to scan and see which ports are open, and I found this:
PORT STATE SERVICE
21/tcp open ftp
80/tcp open http
443/tcp open https
Our hospital's IT is unsure if the FTP port can be opened without a
security breach, and they are wondering if we will still be able to access
the website without the 21/FTP port opened?
Can anyone provide me with that information?
Thanks,
Hannah
--
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------------------------------
Message: 2
Date: Tue, 6 Apr 2021 19:39:40 +0900
From: ????????? <m-bakhit@fmu.ac.jp>
Subject: [Freesurfer] mris_average_surface fails
To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>
Message-ID: <D78D558F-CE86-441D-B824-2D90D22E1749@fmu.ac.jp>
Content-Type: text/plain; charset="us-ascii"
External Email - Use Caution
Hi,
I am trying to make an average subject but when the process reaches mris_average_surface it fails as seen below.
My command was as follow:
make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
Can you please guide me to solve this issue.
Thanks
Mudathir
###########################################
#@# Making average lh.white surface ---------------------
Tue Apr 6 19:23:39 JST 2021
/Applications/freesurfer/subjects/avgsubject
mris_make_average_surface -i 7 -o white -sdir-out /Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
reading vertex positions from white...
---------------------------------------------------
hemi = lh
avg_surf_name = white
canon_surf_name = sphere.reg
out_sname = avgsubject
xform = talairach.xfm
---------------------------------------------------
Is a directory
Is a directory
ERROR: creating directory /
ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surf
mris_average_surface failed
ERROR: make_average_surface
#################################################
------------------------------
Message: 3
Date: Tue, 6 Apr 2021 17:40:29 +0530
From: Ramesh Babu <mgrameshbabu2013@gmail.com>
Subject: Re: [Freesurfer] 2mm thick image for hippocampal
segmentation.
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAHRhR0BLJv7Du65i1x0DKkUe1Nm_jxcJauUpkBXQ-JrSQ4ybqg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear Eugenio and Philipp,
Thank you very much for your suggestions. Could you please give more input
on "acquire the T1WI double and average it after coregistration, this
increases the SNR".
Should aquire twise the same sequence with 1x1x2 voxel dimension?
Thanks
Ramesh
On Fri, 2 Apr, 2021, 9:00 PM Iglesias Gonzalez, Juan E., <
JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
> That all sounds right, thanks a lot Philipp!
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://secure-web.cisco.com/1yAlNRge1To1jCEouu9JnBYJFnIJRo-86GCJ4EIWmAyj8pkkdBifGwyirgDc1KI-N6H7_dg4rBnLgE3CaKBeQuxL7GotNy9SzxKSD4OusIQrdGgcD_E0ObeWLPWYbYhFPgBDLEjcGPr-D8PT-k8bLD71quTve1q2fA_-MJY73fb-zPWX2QNDMT39_ceuRLWK8XGl18IGjSIXm6QeDK2erHCdQTO-rww0uRlSIph9mtjeVoEggFnM0sluSy0XceT-MPg9TJwCFg8RuNNq4J20pSw/http%3A%2F%2Fwww.jeiglesias.com
>
>
>
>
>
>
>
> *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Saemann,
> Philipp" <saemann@psych.mpg.de>
> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Date: *Friday, April 2, 2021 at 03:51
> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, Umesh
> Rurdrapatna <umeshrs@gmail.com>
> *Subject: *Re: [Freesurfer] 2mm thick image for hippocampal segmentation.
>
>
>
> * External Email - Use Caution *
>
> Hi,
>
>
>
> I try to answer but Eugenio may also add comments. Several points that are
> important:
>
> - 1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm can
> manage.
>
> - Post-aquisition reslicing to a higher resolution does not really
> increase the information content. Internally the algorithm works at a much
> higher resolution, anyway.
>
> - If possible, switch to 3 Tesla.
>
> - If possible and this is a prospective study, add a coronal T2 image and
> use the bi-channel option. See papers of Iglesias et al. on this.
>
> - What you could also do on a 1.5 T is acquire the T1WI double and average
> it after coregistration, this increases the SNR.
>
> - Generally, isometric resolutions are good due to the symmetry, of course.
>
> - Also on 1.5 T, you may go bit below 1 mm with good head immobilization,
> and a longer scanning time. BRAVO in general is a good T1 option.
>
>
>
> Best,
>
> Philipp
>
>
> ------------------------------
>
> *Von:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Ramesh Babu <
> mgrameshbabu2013@gmail.com>
> *Gesendet:* Freitag, 2. April 2021 09:29
> *An:* Freesurfer support list; Umesh Rurdrapatna
> *Betreff:* Re: [Freesurfer] 2mm thick image for hippocampal segmentation.
>
>
>
> * External Email - Use Caution *
>
> Dear experts,
>
> Sorry for reposting. I am expecting some response from experts, so that I
> can proceed with confidence.
>
> For our project work, we are looking for hippocampal and its
> subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with
> 1x1x1 resolution, 256x256x160 dimension with 8* flip angle which produced
> images with a lot of noise. Then we tried the same sequence with 1x1x2
> resolution, and 256x256x80 FOV, which produced a clean image without noise.
> When we reformatted the images, it produces 0.5x0.5x1 resolution with
> 512x512x172 dimension.
>
>
>
> Is this sequence good for hippocampal volume estimation and subfield
> segmentation (also for whole-brain VBM analysis)?
>
> Could you please suggest to me a correct sequence, if need to be changed?
>
>
>
> Regards
>
> Ramesh
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1IXus-BXNwSxxsWt0Hl4GNJkM1JdHvv3SmnEoV0r7QyM62LQaQ7GOor7RtRN0aQzfhFM7lc_9Uu5fcLfv9rDBmaLelquFxD0i5EeJz7dRB1fSkcrH9OXh7CcxyQUdtB4YnGDLHG1bIPRqDN88-MQD4DLOCFxhRwE-yMzpgybXDc7HTRizMdSWlMKBuA-Ut2s6ZjmZ1o1v6hOcCdFt73IOXO-n12alCMDKQF2h4U1gnWzOiaxIt45LuwnOsHIljxgM20xQqjqxBim8X_oH_yng5Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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------------------------------
Message: 4
Date: Tue, 6 Apr 2021 09:11:52 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] fMRIPrep BOLD Output
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <0b7e2dda-5e83-a588-7aef-1d029775f75c@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
Did you check that the bold is really in register with the anat? You can
do this with
tkregisterfv --mov bold_preproc.nii.gz? --s sub-01--reg deleteme.lta --surfs
On 3/31/2021 10:49 AM, Karan Desai wrote:
>
> ????????External Email - Use Caution
>
> Hi FS Forum,
>
> I am following up on this post because after using mri_vol2surf to
> downsample my scans to fsaverage4, I ended up with empty files when
> viewed in Freeview. This is the command that I ran generally:
>
> mri_vol2surf--srcbold_preproc.nii.gz?--outlh.imagename.nii.gz--regheadersub-01--trgsubject
> fsaverage4 -hemilh
>
> I am assuming there are some tags that I may be missing which are
> leading me to output with empty nii.gz files. The input bold
> preprocessed files are viewed normally in Freeview, but the output is
> empty.
>
> Thank you in advance.
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
> <dgreve@mgh.harvard.edu>
> *Sent:* Thursday, March 18, 2021 9:43 PM
> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] fMRIPrep BOLD Output
> sounds like you need mri_vol2surf (use --projfrac 0.5)
>
> On 3/18/2021 11:38 AM, Karan Desai wrote:
>>
>> ????????External Email - Use Caution
>>
>> Hi Freesurfer List,
>>
>> I am running fMRIPrep and getting the first two FS output files (aseg
>> and aparcaseg seen above in the screenshot), but not the actual file
>> I need which is the one where it is resampled to the mesh. I have run
>> fMRIPrep and have those two files except the actual BOLD series
>> resampled to the surface mesh. Is there?a FS command that can be used
>> to do that one step?
>>
>> Best,
>> Karan
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> *MailScanner has detected a possible fraud attempt from
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>> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1QIaXg-8LQBS_EXFAPAJlIGB2KdZVTHRQGggikNFrtrkeccmXeeGTs_Qp9vAS4BIaEjvw6BgDglDxSE14qp3qStxfFCyxXsz_fjTbQqK0n8dTs7GGi6Gu6iB4TLP3THW-KMSxIFzb0HOyAxGwP-Gb-ksJin-tL-WpJ8RogAeT7p4m-UHGd2cP4AtVHeocCKbVKwIsTPSOuJBAWZNrR8iyaO5UO0rmegxjIp6leP8SclNlHzUr0AcWsRKaXYvLy4h__7OoYuTFWKBMYRfjVUHM_A/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21OToaGQ%21-h4MWw396gD3z49jo6LdVAWrLGBKXoxjPwhDzfywh0a74lR7yGse_sfcp4Vw4TwnyQ%24>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------
Message: 5
Date: Tue, 6 Apr 2021 09:14:36 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_glmfit error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <0f19df0b-fbd4-19ea-3903-28775075232b@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
The format is not correct. It should be
Input SubjectID Class
You have SubjectID in there twice
On 4/1/2021 1:15 AM, Ishi Tandon AIB, Jaipur wrote:
>
> ????????External Email - Use Caution
>
> Hello FS experts,
>
> I attempted to execute? mri_glmfit on my structural?data through the
> following command -
>
> mri_glmfit --y final.lh.mTBI.volume.10.mgh --fsgd FSGD/mild.tbi.fsgd
> dods -C contrats/HC-mTBI.mtx --surf fsaverage --cortex --glmdir
> lh.volume.glmdir
>
> But it gives me an error (attached below) indicating?a formatting
> problem in my FSGD file (attached).
> I have been trying to figure that out for a while. But I am unable to
> debug it.
>
> Could someone please help me resolve it?
> Thanks for your time.
>
> /Regards,/
> /Ishi Tandon/
> /B.Tech + M.Tech - Cognitive Neuroscience/
> /Amity University, Rajasthan/
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------
Message: 6
Date: Tue, 6 Apr 2021 09:15:04 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Regarding recon all
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <0b627188-d0c3-e1ce-1955-d078f696ba1f@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Include the flag -cw256 with recon-all!
On 4/1/2021 1:52 AM, Amar Shukla wrote:
>
> ????????External Email - Use Caution
>
> Dear Team,
>
> Actually I am trying to test my own data in recon all , but i have
> taken only one subject for recon. It shows me this error.
>
> ERROR! FOV=408.000 > 256
> Include the flag -cw256 with recon-all!
> Inspect orig.mgz to ensure the head is fully visible.
> ****************************************
>
> Linux amar-GV62VR-7RF 5.8.0-48-generic #54~20.04.1-Ubuntu SMP Sat Mar
> 20 13:40:25 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
>
> --
> With Regards,
> Amar Shukla
> Assistant Professor,
> M tech AI ANN(2014-2016),
> Centre Of Information Technology,
> UPES
> Contact :+91 897 977 8016
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------
Message: 7
Date: Tue, 6 Apr 2021 09:15:56 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] retaining label ids
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <1acc0845-8087-77ec-c427-ffe427378093@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
I don't understand, please elaborate
On 4/1/2021 2:00 PM, miracle ozzoude wrote:
>
> ????????External Email - Use Caution
>
> Hello Experts,
>
> I did like to extract wm whilst retaining the label ids. I tried
> mri_extract_labels but it didn't work.
>
> Any help?would be appreciated.
>
> Many?thanks,
> Paul
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------
Message: 8
Date: Tue, 6 Apr 2021 09:17:12 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all bug
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <ccd97428-0587-d4cc-88fa-e54f632ea16d@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
Run it with -debug as the first option, capture the output, and send it
to us.
On 4/1/2021 8:29 PM, zalewk wrote:
>
> ????????External Email - Use Caution
>
> Hi Freesurfer team,
>
> My lab recently switched over from FS6 to FS7 and I think I've
> encountered a bug with recon-all.
> I'm running subjects stepwise and editing them, running recon-all with
> the -autorecon2 and -autorecon3 flags initially are no problem, they
> run fine.? Trying to re-run them or use the -autorecon2-wm,
> -autorecon-pial etc. flags lead to crashing at certain parts of the
> program. The error message I get is "if: expression syntax". Digging
> into the code, it seems to crash when it hits a line of code "if($ud
> || $ForceUpdate)". The syntax superficially looks right (I don't know
> tcsh), checking the variables it seems like $ForceUpdate is never set,
> but removing it from recon-all doesn't fix the problem.
> It seems the $ud variable is for checking if updates are needed for a
> set of volumes passed to the program. I don't know why that would be a
> problematic argument, removing that part seems to fix it, but this
> also seems like an important variable and I don't know enough about
> tcsh to understand why it works after removing it. Can one of the
> folks who wrote the recon-all script help me out? I'm running the
> commands step-wise as a work-around, but that is much less convenient.
>
> Best,
> Kody Zalewski
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------
Message: 9
Date: Tue, 6 Apr 2021 09:18:35 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_label2annot - make all command exiting
with errors
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <0a8872e7-1d93-c58a-4973-d8e161500d05@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
The "-make" functionality does not work in V7. We should have disabled
that flag
On 4/2/2021 3:41 AM, Marion DURTESTE wrote:
>
> ????????External Email - Use Caution
>
> Dear?FreeSurfer developers,
>
> When running*recon-all -make all *after correcting a few errors from
> the recon-all output, it exits with an error.?This occurs when the
> mris_label2annot command is called.
>>
>> Loading
>> /Users/mariondurteste/Documents/PhD/FreeSurfer/ReconstructedAfterQC/ToDo/ALA076_1/surf/lh.orig
>> 1 1376057 FG1
>> 2 16711935 FG2
>> ERROR: lh.FG2.mpm.vpnl.label, n=580, vertex 119494 out of range
>>
> If we rerun the -make all command a second time it then finishes
> without errors.?Do you know why this is ?
>
> * FREESURFER version:?freesurfer-darwin-macOS-7.1.1-20200811-8b40551
> * Platform: macOS BigSur 11.2.2
>
> Thanks for your help !
> Marion D
>
>
> _______________________________________________
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Message: 10
Date: Tue, 6 Apr 2021 09:19:41 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all bug
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <8ac90e23-495c-4067-424d-f7632644fae1@mgh.harvard.edu>
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So the problem is that there are spaces in the path? That will probably
cause a lot of FS to fail
On 4/2/2021 11:30 PM, zalewk wrote:
>
> ????????External Email - Use Caution
>
> Hi freesurfer team,
>
> I've tried running recon-all as mentioned before with the -xf flag
> under different conditions.
> As far as I can tell, any line using the UpdateNeeded function. e.g.:
> "set ud = `UpdateNeeded $thickness $pial $white`" fails with the
> following if statement because the variable $ud includes paths as
> strings in it instead of a 0/1 integer. Setting it to a 1 or 0
> beforehand also seems to solve the problem. The function UpdateNeeded
> only seems to return an integer as an exit status, so I'm not sure why
> there are path strings in it causing it to fail.
> If I print out the $ud variable before it fails and the result is:
> "/subjectDirectory/subjectID_FREESURFER/mri mri mri_FREESURFER
> /subjectDirectory/subjectID_FREESURFER/mri/mri_FREESURFER/stats 1"
> It returns the exit status of 1 preceded by the path of the subject's
> mri directory, just "mri", "mri_FREESURFER" and the subject's stats
> directory (all subjects in this particular study have the suffix
> "_FREESURFER"). It prints this out these strings no matter the
> variables as .mgz file names, or number of variables passed to the
> UpdateNeeded function. I still don't have a clue what would cause this
> behavior. The UpdateNeeded function seems to work fine and as intended
> as far as I can tell, so I still don't know why these paths/strings
> are being added and causing it to crash.
>
> Best,
> Kody Zalewski
>
> Message: 3
> Date: Fri, 02 Apr 2021 03:49:02 +0200
> From: fsbuild <fsbuild@contbay.com>
> Subject: Re: [Freesurfer] recon-all bug
> To: freesurfer@nmr.mgh.harvard.edu
> Cc: cmacd@neurosurgery.washington.edu
> Message-ID: <1617328142.6066780ef2824@trashmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> ??????? External Email - Use Caution
>
> Hello Kody,
> One thing you could try to get more information printed about what
> is going on is to edit the very first line in the recon-all script
> to be:
> #! /bin/tcsh -xf
> ? instead of
> #! /bin/tcsh -f
> Adding the x option will echo each line in the script as it?s run
> with the variable values expanded, and seeing that output could
> help with debugging.
>
> - R.
>
> On Apr 1, 2021, at 20:29, zalewk <zalewk@uw.edu>
> wrote: External
> Email - Use
> Caution Hi
> Freesurfer team, My lab recently switched over from FS6 to
> FS7 and I think I've encountered a bug with recon-all.. I'm
> running subjects stepwise and editing them, running recon-all with
> the -autorecon2 and -autorecon3 flags initially are no problem,
> they run fine. Trying to re-run them or use the
> -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at
> certain parts of the program. The error message I get is "if:
> expression syntax". Digging into the code, it seems to crash when
> it hits a line of code "if($ud || $ForceUpdate)". The syntax
> superficially looks right (I don't know tcsh), checking the
> variables it seems like $ForceUpdate is never set, but removing it
> from recon-all doesn't fix the problem. It seems the
> $ud variable is for checking if updates are !
> ?needed fo
> ?r a set of volumes passed to the program. I don't know why that
> would be a problematic argument, removing that part seems to fix
> it, but this also seems like an important variable and I don't
> know enough about tcsh to understand why it works after removing
> it. Can one of the folks who wrote the recon-all script help me
> out? I'm running the commands step-wise as a work-around, but that
> is much less convenient. Best, Kody
> Zalewski_______________________________________________Freesurfer
> mailing
> listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer?
>
>
> _______________________________________________
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------------------------------
Message: 11
Date: Tue, 6 Apr 2021 09:22:33 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Dicom Tag Problem Reconall
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <bcd0a4ad-aa63-ba67-79a1-45f74cd4faf0@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Can you send /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out ?
If that is not there any more, run it again and send the newly created file
On 4/4/2021 3:57 PM, Banu Femir wrote:
>
> ????????External Email - Use Caution
>
> Dear Freesurfer Developers,
>
> I'm trying to analyze a set of MRI data that I got via CD. Dicom files
> did not have .dcm extension, so I used a program and they turned into
> a .dcm image.
>
> My reconall run for around 2 hours, after I got an error:
>
> Counting frames
> nframes = 481
> nslices = 1
> ndcmfiles = 481
> PE Dir = UNKNOWN (dicom read)
> Loading pixel data
> JPEG compressed, decompressing
> cd /home/banu/usr/local/freesurfer/subjects/sepsis1dicomwritebelow
> fsdcmdecompress --i
> /home/banu/Documents/Sepsis/yeni_dicom_write_below/F_000001.dcm --o
> /tmp/banu.tmp.decompressed.dcm.1TXZUy --jpeg >&
> /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out
> ERROR: 512, see /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out for
> more details
> Linux banuf 4.15.0-51-generic #55-Ubuntu SMP Wed May 15 14:27:21 UTC
> 2019 x86_64 x86_64 x86_64 GNU/Linux
>
>
> Before that, I got many Warnings about imagenumber, tag serial number,
> seriesnumber, tag, ect. In case you want I can share the whole log
> file. I am wondering if there was sth wrong with my .dcm format. If
> yes, how I can solve this problem? It seems like there was sth wrong
> with tags, but I really cannot solve the problem.
>
> Many thanks!
> Have a nice and healthy week!
> Banu
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 12
Date: Tue, 6 Apr 2021 13:22:57 +0000
From: "Coleman, Katherine" <kcoleman0@bwh.harvard.edu>
Subject: [Freesurfer] unsubscribe
To: "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
Message-ID: <218EBD99-160A-4937-B1A6-D7EDEF09AA39@bwh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"
Hello,
Please remove me from the free surfer forum mailing list.
Thank you,
Katherine
Katherine Coleman, MS
Research Assistant II
Mood Trajectories and Outcomes Laboratory
Department of Psychiatry
[cid:image001.jpg@01D6CE33.2A446E30]
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Message: 13
Date: Tue, 6 Apr 2021 09:25:59 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_gtmpvc error Checking tissue type ERROR:
CheckSegTissueType() tissue type for seg
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <014bcfc7-3d2b-0314-24f2-8d7280900b66@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
You will need to create a new color table. This is not hard, but not
easy either. First, there should be a color table already there. I'm not
sure what that will be like; it might have your segments in it, it might
not. It might be easier to run gtmseg with the standard options and look
at the color table, then try to replicate it with your segmentation
On 4/5/2021 6:43 AM, Bahar Hazal Yal??nkaya wrote:
>
> ????????External Email - Use Caution
>
> Hello Freesurfer"s Developers,
>
> I am trying to follow */PetSurfer/* (*MailScanner has detected a
> possible fraud attempt from "secure-web.cisco.com" claiming to be*
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
> <https://secure-web.cisco.com/1oGyZvXtztP0MX30hKqio2fJStw1wQuIW11p5b1b0CkNwSGz7RCQalhqGZJFfIT2Ob3QQETtldwxv9y8xYVYGSkRdQ_GjplqWAGkIFRP1S40sf8UfJTbg-jdroEwAQvGW-9HmP1fatTZ8h3DhbPvM4MaRIdn-gicol4f85-JI5PjVoycwQ5z0q2oYvFmz9DuRwGJZg7EiKqmfCLYhXNUOPOwhpm1kKKikeaQrRAVCr4-WbYz4Z0GXBVuflZqXa84PEzxVj0uL51CZ_xoDuhu3DA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer>)
> to apply PVC to Pet images.
> Default pipeline is working however, whenever i try to use another
> atlas, Schaefer parcellation,?mri_gtmpvc command I get following error:
> WARNING: LTAconcat(): inverting LTA 1 to match geometry
>
> Replacing 18
>
> Pruning ctab
>
> tissue type schema
>
> Checking tissue type
>
> ERROR: CheckSegTissueType() tissue type for seg 258 Head-ExtraCerebral
> not set
>
> Failed tissue type check
>
>
> I have searched to list several people who have issued similar errors
> but unfortunately i could not find any solution that works for me.
> Below you can find commands I used:
>
> $ gtmseg --s subject--o gtmseg.mgz
> --ctx-annotSchaefer2018_400Parcels_7Networks_order.annot 1000 2000
> --ctab Schaefer2018_400Parcels_7Networks_order_LUT.txt
> $ mri_coreg --s subject --mov AbetaPre.nii.gz --reg AbetaPre.reg.lta
> $ mri_gtmpvc --i AbetaPre.nii.gz --psf 8 --reg AbetaPre.reg.lta
> --regheader --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01
> --mgx .01 --km-ref 8 47 --o gtmpvc.output
> Also I checked the run of gtmseg via "*tkmeditfv*" where i can
> visualise 258 Head-ExtraCerebral, and additionally I checked
> *gtmseg.ctab *file also 258 Head-ExtraCerebral in the list.
> I will be happy to hear from you.
> Kind regards.
> --
> Ph.D. Bahar Hazal Yal??nkaya
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------
Message: 14
Date: Tue, 6 Apr 2021 09:28:21 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Problem with freesurfer measures
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <bee9db6e-332d-d5d6-fe10-0e8697f03490@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
It is normal that those give different results. I would expect them to
be extremely close to each other, so small that the difference does not
matter. But if you had to take one, I'd take the output of
mris_anatomical_stats
On 4/5/2021 11:47 AM, Alberto Del Cerro Leon wrote:
>
> ????????External Email - Use Caution
>
> To obtain de stats from mri_anatomical stats i used
> />>mris_anatomical_stats -a
> /usr/local/freesurfer/subjects/218/label/rh.myAAL.annot
> -f///usr/local/freesurfer/subjects/218/stats/rh.myAAL.stats -b 218 rh/
> In another hand, the workflow to obatian?the stats from mri_segstats was:
> >>/mri_aparc2aseg --s 218 --labelwm --hypo-as-wm --rip-unknown --volmask
> --o /usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz //--annot myAAL/
> />>//mri_segstats --seg
> /usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz//--ctab
> /home/neuroimage/fsl/FreeSurfer/wmAALColorLUT.txt --sum
> /usr/local/freesurfer/subjects/218/stats/wmmyAAL.stats /
> /-//-pv /usr/local/freesurfer/subjects/218/mri/norm.mgz --excludeid 0
> --brainmask /usr/local/freesurfer/subjects/218/mri/brainmask.mgz --in
> /usr/local/freesurfer/subjects/218/mri/norm.mgz/
> /--in-intensity-name norm --in-intensity-units MR --subject 218
> --surf-wm-vol --etiv/
>
> El lun, 5 abr 2021 a las 15:50, Douglas N. Greve
> (<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribi?:
>
> What are your command lines?
>
> On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote:
>>
>> ????????External Email - Use Caution
>>
>> Thanks a lot, It works!, now I have obtained values to ctx and wm
>> volumes for each area. However when I look at the gray matter
>> volume values calculated by mri_anatomical stats, the results are
>> pretty similar to the ctx-ROIs calculated by mri_segstats, but
>> not the same. It is normal? In that case what measure will be
>> more suitable?
>>
>> El lun, 29 mar 2021 a las 5:22, Douglas N. Greve
>> (<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribi?:
>>
>> You'll need to create your own color table by adding 3000 to
>> the left hemi structures and 4000 to the right hemi
>> structures. Look at the 3000s and 4000s in
>> $FREESURFER_HOME/FreeSurferColorLUT.txt
>>
>>
>> On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote:
>>>
>>> ????????External Email - Use Caution
>>>
>>> Hello Douglas, i tried but when i look at the wmparc.mgz
>>> created by the code >>mri_aparc2aseg --s 215 --labelwm
>>> --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz
>>> --annot myAAL it takes the index and the names from
>>> FreeSurferColorLUT instead of the names in the colorLUT
>>> associated?with myAAL.annot then the ROIs are disorganized.
>>> Could you help me with this problem?
>>>
>>> El jue, 25 mar 2021 a las 14:59, Douglas N. Greve
>>> (<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>)
>>> escribi?:
>>>
>>> Look in recon-all.log to find the command that creates
>>> the wmparc.mgz. Run that command changing the aparc
>>> annot to your annot and the output to a new file name.
>>> Look in wmparc.stats; at the top will be an mri_segstats
>>> command line. Copy that command line changing the file
>>> names as needed.
>>>
>>> On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:
>>>>
>>>> ????????External Email - Use Caution
>>>>
>>>> Thanks!, how can I obtain the white matter volume stats
>>>> using my annotation file?
>>>>
>>>> El mar, 16 mar 2021 a las 16:59, Douglas N. Greve
>>>> (<dgreve@mgh.harvard.edu
>>>> <mailto:dgreve@mgh.harvard.edu>>) escribi?:
>>>>
>>>> I think they will give very similar results, but my
>>>> guess is that #1 is a little better
>>>>
>>>> On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
>>>>>
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> I want to use the annotation file created by
>>>>> myself in fsaverage to calculate the anatomical
>>>>> stats, but i dont?know what is the best workflow.
>>>>>
>>>>> 1. Convert the annotation file to each subject
>>>>> space using mri_sur2surf and using
>>>>> mri_anatomical_stats in each subject
>>>>> 2. Convert the surface of each subject to
>>>>> fsaverage space and use mri_segstats to obtain the
>>>>> data, in this case i dont?know what surface i have
>>>>> to convert to fsaverage space to do it (i can see
>>>>> thickness (lh/rh.thickness) and volume
>>>>> (lh/rh.volume) but not folding index and white
>>>>> matter volume)
>>>>>
>>>>> Any idea?
>>>>>
>>>>> El lun, 8 mar 2021 a las 16:04, Fischl, Bruce
>>>>> (<BFISCHL@mgh.harvard.edu
>>>>> <mailto:BFISCHL@mgh.harvard.edu>>) escribi?:
>>>>>
>>>>> Hi Alberto
>>>>>
>>>>> 1. And 4. Are not properties of single
>>>>> surfaces ? they are computed from the
>>>>> white and the pial. For 2 and 3 that is
>>>>> really up to you
>>>>>
>>>>> Cheers
>>>>> Bruce
>>>>>
>>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
>>>>> <freesurfer-bounces@nmr.mgh.harvard.edu
>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
>>>>> *On Behalf Of *Alberto Del Cerro Leon
>>>>> *Sent:* Monday, March 8, 2021 7:02 AM
>>>>> *To:* Freesurfer support list
>>>>> <freesurfer@nmr.mgh.harvard.edu
>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>>> *Subject:* [Freesurfer] Problem with
>>>>> freesurfer measures
>>>>>
>>>>> *????????External Email - Use Caution *
>>>>>
>>>>> Hello Freesurfer team, I am using an
>>>>> annotation file that i've created previously
>>>>> to obtain the measures of some ROIs. To do
>>>>> that i am using de commands mri_surf2surf and
>>>>> mri_segstats. I want to obtain the following
>>>>> measures:
>>>>>
>>>>> 1. Gray and White Matter Volume
>>>>>
>>>>> 2. Folding Index
>>>>>
>>>>> 3. Curvature measures
>>>>>
>>>>> 4. Thickness
>>>>>
>>>>> However I don't know what surface in the surf
>>>>> folder of each subject I have to use. Could u
>>>>> help me?
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>> *MailScanner has detected a possible fraud
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>>>>> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>> <https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD5cHD7GRwSEtVGA5l0wVfI-qwadg-4V9ONf5EZ0kiLcRjW6DVI_Rd2ZeqiMxXTIBEnUxA3T9NzdNSt8iXVZ7cyXIzeEsQeBhrig9ume-iTSL61o9NJ8xeYD0zqzkN5beVGaw6yxXpHYMufcuWsp7li3hf1daYTVoJEiUno9_8hA_Q7xVe54KZ585zoXC2r43bYx3pxJ56xQU1iAEqLf5WArPGhqVAV_6TmQ9v8C2Xw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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>
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------------------------------
Message: 15
Date: Tue, 6 Apr 2021 09:29:20 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Website Ports
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <1d438758-e598-6101-209b-5b14bd1ec83a@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
why do you need to connect to the web site? that is not needed to run FS
On 4/5/2021 3:20 PM, Swearingen, Hannah wrote:
>
> ????????External Email - Use Caution
>
> Hi,
>
> I am setting up an Access Control List for an isolated VLAN in which
> my center's neuroimaging computing workstations will be connected to
> our hospital's network for data back-up.
>
> We want to be able to connect to Freesurfer's?website while connected
> to the VLAN, and we need to supply which ports the website accesses. I
> used nmap to scan and see which ports are open, and I found this:
>
> PORT ? STATE? SERVICE
>
> 21/tcp open ? ftp
>
> 80/tcp open ? http
>
> 443/tcp open ? https
>
>
>
> Our hospital's IT is unsure if the FTP port can be opened without a
> security breach, and they are wondering?if we will still be able to
> access the website without the 21/FTP port opened?
>
>
> Can anyone provide me with that information?
>
>
> Thanks,
>
> Hannah
>
>
> --
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------
Message: 16
Date: Tue, 6 Apr 2021 09:30:17 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_average_surface fails
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <a6bc5f6a-0e93-3d9b-3070-2d16d56f648e@mgh.harvard.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
Do you have write permissions to
/Applications/freesurfer/subjects
Of not on a mac
On 4/6/2021 6:39 AM, ????????? wrote:
> External Email - Use Caution
>
> Hi,
> I am trying to make an average subject but when the process reaches mris_average_surface it fails as seen below.
> My command was as follow:
> make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
> Can you please guide me to solve this issue.
>
> Thanks
>
> Mudathir
>
> ###########################################
> #@# Making average lh.white surface ---------------------
> Tue Apr 6 19:23:39 JST 2021
> /Applications/freesurfer/subjects/avgsubject
> mris_make_average_surface -i 7 -o white -sdir-out /Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
> reading vertex positions from white...
> ---------------------------------------------------
> hemi = lh
> avg_surf_name = white
> canon_surf_name = sphere.reg
> out_sname = avgsubject
> xform = talairach.xfm
> ---------------------------------------------------
>
>
> Is a directory
> Is a directory
> ERROR: creating directory /
> ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surf
> mris_average_surface failed
> ERROR: make_average_surface
> #################################################
>
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 17
Date: Tue, 6 Apr 2021 09:33:30 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] 2mm thick image for hippocampal
segmentation.
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <715750d4-45f9-180c-d2ae-e0a485e61ffc@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Twice the same image at 1x1x1, then use mri_robust_template to register
and average them together
On 4/6/2021 8:10 AM, Ramesh Babu wrote:
>
> ????????External Email - Use Caution
>
> Dear Eugenio and Philipp,
>
> Thank you very much for your suggestions. Could you please give more
> input on "acquire the T1WI double and average it after coregistration,
> this increases the SNR".
>
> Should aquire twise the same sequence with 1x1x2 voxel dimension?
>
> Thanks
> Ramesh
>
>
> On Fri, 2 Apr, 2021, 9:00 PM Iglesias Gonzalez, Juan E.,
> <JIGLESIASGONZALEZ@mgh.harvard.edu
> <mailto:JIGLESIASGONZALEZ@mgh.harvard.edu>> wrote:
>
> That all sounds right, thanks a lot Philipp!
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> *MailScanner has detected a possible fraud attempt from
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> <http://secure-web.cisco.com/1yAlNRge1To1jCEouu9JnBYJFnIJRo-86GCJ4EIWmAyj8pkkdBifGwyirgDc1KI-N6H7_dg4rBnLgE3CaKBeQuxL7GotNy9SzxKSD4OusIQrdGgcD_E0ObeWLPWYbYhFPgBDLEjcGPr-D8PT-k8bLD71quTve1q2fA_-MJY73fb-zPWX2QNDMT39_ceuRLWK8XGl18IGjSIXm6QeDK2erHCdQTO-rww0uRlSIph9mtjeVoEggFnM0sluSy0XceT-MPg9TJwCFg8RuNNq4J20pSw/http%3A%2F%2Fwww.jeiglesias.com>
>
>
> *From: *<freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of
> "Saemann, Philipp" <saemann@psych.mpg.de
> <mailto:saemann@psych.mpg.de>>
> *Reply-To: *Freesurfer support list
> <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> *Date: *Friday, April 2, 2021 at 03:51
> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>, Umesh Rurdrapatna
> <umeshrs@gmail.com <mailto:umeshrs@gmail.com>>
> *Subject: *Re: [Freesurfer] 2mm thick image for hippocampal
> segmentation.
>
> *????????External Email - Use Caution *
>
> Hi,
>
> I try to answer but Eugenio may also add comments. Several points
> that are important:
>
> -?1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm
> can manage.
>
> - Post-aquisition reslicing to a higher resolution does not really
> increase the information content. Internally the algorithm works
> at a much higher resolution, anyway.
>
> - If possible, switch to 3 Tesla.
>
> - If possible and this is a prospective study, add a coronal T2
> image and use the bi-channel option. See papers of Iglesias et al.
> on this.
>
> - What you could also?do on a?1.5 T is acquire the T1WI double and
> average it after coregistration, this increases the SNR.
>
> - Generally, isometric resolutions are good due to the symmetry,
> of course.
>
> - Also on 1.5 T, you may go bit below 1 mm with good head
> immobilization, and a longer scanning time. BRAVO in general is a
> good T1 option.
>
> Best,
>
> Philipp
>
> ------------------------------------------------------------------------
>
> *Von:*freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> <freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> im Auftrag von
> Ramesh Babu <mgrameshbabu2013@gmail.com
> <mailto:mgrameshbabu2013@gmail.com>>
> *Gesendet:* Freitag, 2. April 2021 09:29
> *An:* Freesurfer support list; Umesh Rurdrapatna
> *Betreff:* Re: [Freesurfer] 2mm thick image for hippocampal
> segmentation.
>
> *????????External Email - Use Caution *
>
> Dear experts,
>
> Sorry for reposting. I am expecting some response from experts, so
> that I can proceed with confidence.
>
> For our project work, we are looking for hippocampal??and its
> subfield?volumes. Using GE 1.5T scanner, we?tried a 3D BRAVO
> sequence with 1x1x1 resolution, 256x256x160 dimension with 8* flip
> angle which produced images with a lot of noise. Then we tried the
> same sequence?with 1x1x2 resolution, and 256x256x80 FOV, which
> produced a clean image without?noise. When we reformatted?the
> images, it produces 0.5x0.5x1 resolution with 512x512x172 dimension.
>
> Is this sequence good for hippocampal volume estimation and
> subfield segmentation (also for whole-brain VBM analysis)?
>
> Could you please suggest to me a correct sequence, if need to be
> changed?
>
> Regards
>
> Ramesh
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> *MailScanner has detected a possible fraud attempt from
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> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://secure-web.cisco.com/1IXus-BXNwSxxsWt0Hl4GNJkM1JdHvv3SmnEoV0r7QyM62LQaQ7GOor7RtRN0aQzfhFM7lc_9Uu5fcLfv9rDBmaLelquFxD0i5EeJz7dRB1fSkcrH9OXh7CcxyQUdtB4YnGDLHG1bIPRqDN88-MQD4DLOCFxhRwE-yMzpgybXDc7HTRizMdSWlMKBuA-Ut2s6ZjmZ1o1v6hOcCdFt73IOXO-n12alCMDKQF2h4U1gnWzOiaxIt45LuwnOsHIljxgM20xQqjqxBim8X_oH_yng5Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------
Message: 18
Date: Tue, 6 Apr 2021 13:38:37 +0000
From: Daniel Gutstein <daniel.gutstein@northwestern.edu>
Subject: [Freesurfer] Freesurfer Versions - Zeros in the Cortex
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2F5F4F23-A758-4F12-B303-EBD66FEF346F@northwestern.edu>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hello,
We are looking at the vertex-wise thickness measures for participants within the fsaverage space. There are a number of indices within the cortex that have thickness values of 0 in the thickness.fsaverage.mgh surface files. In FreeSurfer version 5.1, those same indices no longer have thickness 0 in the corresponding rh and lh fwhm smoothed thickness surface files due to the smoothing effect. However, in versions 6 and 7.1.1, the indices with 0 values remain 0 even in the fwhm smoothed files. Do you know why it was chosen that smoothing should have no impact on zeros in the later versions of FreeSurfer? Also, if we are interested in impacting the zeros from the later versions, is there a methodology which you would recommend?
Thanks,
Daniel
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------------------------------
Message: 19
Date: Tue, 6 Apr 2021 15:41:36 +0200
From: Bahar Hazal Yal??nkaya <baharhazalyalcinkaya@gmail.com>
Subject: Re: [Freesurfer] mri_gtmpvc error Checking tissue type ERROR:
CheckSegTissueType() tissue type for seg
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAGZFL9eVvG1+FhoUqK24DG=ahiMfYhQ2AGA5UbzfXDHZKA056g@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Thanks for response, color table and annotations are there "--ctx-annot
Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab
Schaefer2018_400Parcels_7Networks_order_LUT.txt", gtmseg did not gave an
error, you can see at attachments. (Also I can see 258 Head
segmentation in *gtmseg.ctab
*file) also mri_coreg is working well (see also attachments). The problem
is the "*mri_gtmpvc*" command where it fails while checking tissue types
more precisely it complains about Head segmentation.
I run with standard options. I checked everything I can think of, each file
and image seems to be similar but still could not find a proper solution.
Is there anything specific I need to check?
Thanks in advance,
Kind regards
On Tue, Apr 6, 2021 at 3:26 PM Douglas N. Greve <dgreve@mgh.harvard.edu>
wrote:
> You will need to create a new color table. This is not hard, but not easy
> either. First, there should be a color table already there. I'm not sure
> what that will be like; it might have your segments in it, it might not. It
> might be easier to run gtmseg with the standard options and look at the
> color table, then try to replicate it with your segmentation
>
> On 4/5/2021 6:43 AM, Bahar Hazal Yal??nkaya wrote:
>
> External Email - Use Caution
> Hello Freesurfer"s Developers,
>
> I am trying to follow *PetSurfer* (*MailScanner has detected a possible
> fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1MVnuTs8K837n1EabeVA8Fk2FSlKYqIyoMOZLNUEUFjVIs1owR3RKcjhBG3XokQo740Eq6q6HEZtsCWVX7BXJtFgR2OzEWsDdDj1riYwlCUgHoZoHtDhMyYsgkd60rqqQ9azZMrOCdUKh-iuUzxz54tG5-2HAEYjJrNgEJd-FXTzybf3cqPYug0ayvoKmGMdYIHfC_cTKcbYBqFEf2LoquV4rOsJotKFJm5Rtwf_HunRIvt7iUXW7s1oFB_7nKaijQbqYLTifws-10GMnNBMkDQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer
> <https://secure-web.cisco.com/1oGyZvXtztP0MX30hKqio2fJStw1wQuIW11p5b1b0CkNwSGz7RCQalhqGZJFfIT2Ob3QQETtldwxv9y8xYVYGSkRdQ_GjplqWAGkIFRP1S40sf8UfJTbg-jdroEwAQvGW-9HmP1fatTZ8h3DhbPvM4MaRIdn-gicol4f85-JI5PjVoycwQ5z0q2oYvFmz9DuRwGJZg7EiKqmfCLYhXNUOPOwhpm1kKKikeaQrRAVCr4-WbYz4Z0GXBVuflZqXa84PEzxVj0uL51CZ_xoDuhu3DA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer>)
> to apply PVC to Pet images.
> Default pipeline is working however, whenever i try to use another atlas,
> Schaefer parcellation, mri_gtmpvc command I get following error:
>
> WARNING: LTAconcat(): inverting LTA 1 to match geometry
>
> Replacing 18
>
> Pruning ctab
>
> tissue type schema
>
> Checking tissue type
>
> ERROR: CheckSegTissueType() tissue type for seg 258 Head-ExtraCerebral not
> set
>
> Failed tissue type check
>
> I have searched to list several people who have issued similar errors but
> unfortunately i could not find any solution that works for me. Below you
> can find commands I used:
>
> $ gtmseg --s subject --o gtmseg.mgz --ctx-annot
> Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab
> Schaefer2018_400Parcels_7Networks_order_LUT.txt
> $ mri_coreg --s subject --mov AbetaPre.nii.gz --reg AbetaPre.reg.lta
> $ mri_gtmpvc --i AbetaPre.nii.gz --psf 8 --reg AbetaPre.reg.lta
> --regheader --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx
> .01 --km-ref 8 47 --o gtmpvc.output
> Also I checked the run of gtmseg via "*tkmeditfv*" where i can visualise 258
> Head-ExtraCerebral, and additionally I checked *gtmseg.ctab *file also 258
> Head-ExtraCerebral in the list.
> I will be happy to hear from you.
> Kind regards.
> --
> Ph.D. Bahar Hazal Yal??nkaya
>
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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> https://secure-web.cisco.com/14cq6eGfvOcpfd9Y3vfBGA7p9Xc5PZeusO6xBxdl8k8go_naRsMxqzInFfDfwXqr6X3L2gvhxFOD1H7AqmaSe25DCQnn5EE763m9AYP-xtv7kA7l2KsaIIGge2I2JmWmriWYx9o0qAbdIELvL7SIJHMSrGrFczppuvppirbL6_AOXcUA8-WmphAP2r5jrHz-jV_ooq3O7ekh6WMvFmVHIz6Bwoy-oRL34X2Yyg55MNnhAJXX5758vDMxC3fx6013vLB7O0-KpYwzWTXm9TMgsRg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
--
Ph.D. Bahar Hazal Yal??nkaya
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