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Today's Topics:
1. Visualizing transparent surface with non transparent
annotations (Leonardo Tozzi)
2. Failing to execute QDEC (vittal korann)
3. Re: different clusters in mri_surfcluster output versus
viewing in Freeview (Huang, Yujing)
4. Re: segmenThalamicNuclei.sh exited with ERRORS (beh?et ayy?ld?z)
5. Re: Extracting brain volume seperately (Douglas N. Greve)
6. Re: Nuisance regressors (Douglas N. Greve)
7. Please unsubscribe me (Manuela Dorado Novoa)
8. Re: Hole in the insula (Douglas N. Greve)
9. Re: Correlating and/or linear regressing surface overlays
(Douglas N. Greve)
10. Re: different clusters in mri_surfcluster output versus
viewing in Freeview (Smith, Christine)
11. Re: mri_easyreg tool (Iglesias Gonzalez, Juan E.)
12. MGH35 template (Maffei, Chiara,PHD)
13. Re: [External] Re: 7.3.2-patch issues - thalamic segmentation
(Kumar, Avnish)
14. Re: mri_robust_register --minsize (Reuter, Martin,Ph.D.)
15. Re: [External] Re: 7.3.2-patch issues - thalamic segmentation
(Aaron Tanenbaum)
----------------------------------------------------------------------
Message: 1
Date: Wed, 22 Feb 2023 19:34:40 +0000
From: Leonardo Tozzi <ltozzi@stanford.edu>
Subject: [Freesurfer] Visualizing transparent surface with non
transparent annotations
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BYAPR02MB5352E6F3CF76C8B3FC793BD0A9AA9@BYAPR02MB5352.namprd02.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
External Email - Use Caution
Dear Experts,
I would like to use Freeview to achieve the following.
I would like to visualize a transparent brain surface, with only some annotations visible. In other words, I would like the surface to be transparent, but the annotations I choose to visualize to not be transparent.
Is there a way to achieve this?
Thank you,
Leonardo Tozzi, MD, PhD
Director of Computational Neuroscience & Neuroimaging Program
Stanford Center for Precision Mental Health and Wellness
Stanford University
ltozzi@stanford.edu<mailto:ltozzi@stanford.edu> | (650) 5615738
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------------------------------
Message: 2
Date: Wed, 22 Feb 2023 15:13:05 -0500
From: vittal korann <vittalkorann@gmail.com>
Subject: [Freesurfer] Failing to execute QDEC
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CACyMoT34SU_cVpy9CbbTkz4WLUp0sGPLZhU_daECXvBjxsFdkw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi Freesurfer experts,
I am trying to run Qdec on schizophrenia pre and post intervention scans.
I created .dat and .levels files within the qdec folders and loaded the
.dat file into qdec gui.
It is suddenly crashing when I select my design and hit the Analyze button.
And the same error message copied below from the terminal.
Writing to /usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh
--------------------------------------------------------------------------
ERROR: Invalid FreeSurfer license key found in license file
/usr/local/freesurfer/license.txt
If you are outside the NMR-Martinos Center,
go to http://secure-web.cisco.com/15DaQ_a1o5YqT7dopqDTQDqaw-6K4jw9WyiYPYFheSvTtpugAraCBH9rOU4vIGs1TEI43LJjYPoOIj3fAmdDCERFpQ1LHl12LfJ_50bAo89SwWewCqQoT0X5kuU_NBixkFxVrgcva2vKbl2YFXW_xttlI0Ia4oNeAQffEyVzxy_fA9_i-UKawlqhtAeQ7KGVF_kiB9agU6kOjJB8Sm8o_AWVumIklix8kCZQS9O-S0t6dm1tAm9BTTUh71y1to8GfMLqw-MfzjzJw_XKxqQJGVtudNje83w9e91dD9rKkG2PLkemhLEsviXBxq0294sIX5rkf4B0Bl61UaruVV6iL4Q/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
Even though I renewed my license file, the issue still persists.
FYI I did use qdec in the past and am quite comfortable with it.
Also, I attached my license file if anything is missing.
Any help would be appreciated!
With regards
Vittal
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vittalkorann@gmail.com
63593
*CmVKVhaJCkeY
FSuKGHKmQyVMA
------------------------------
Message: 3
Date: Wed, 22 Feb 2023 21:02:30 +0000
From: "Huang, Yujing" <YHUANG43@mgh.harvard.edu>
Subject: Re: [Freesurfer] different clusters in mri_surfcluster output
versus viewing in Freeview
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<MN2PR04MB5982FFEC6A3C3366A39B93999DAA9@MN2PR04MB5982.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
Hi Christine,
Sig = -log(pvalue)
In freeview, the overlay thresholds can be adjusted by clicking 'Configure' button (under the Overlay dropdown menu).
For mri_surfcluster (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster), I think you can try to adjust these options to match freeview: --thmin <>, --thmax <>, --thsign <>, --minarea <>, --no-adjust.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Smith, Christine
Sent: Tuesday, February 21, 2023 6:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] different clusters in mri_surfcluster output versus viewing in Freeview
External Email - Use Caution
Hello,
I am getting a mismatch of clusters when we view cluster results in freeview versus ask for a table of the significant clusters.
I am performing a GLM analysis on Freesurfer to analyze cortical thickness (mri_glmfit). When viewing the significance map with freeview, we set the minimum threshold to 2 for the sig.mgh file.
We also used the same threshold when creating a summary table of the clusters using mri_surfcluster.
mri_surfcluster --in {$dir}/visuospatial_MCI_correlation/sig.mgh --hemi left --thmin 2 --thsign pos --minarea 10 --subject fsaverage --surf inflated --annot BN_Atlas --sum {$dir}/visuospatial_MCI_correlation/left.thickness.clustersummary_BN.txt
We were hoping to use the summary text file to identify the clusters on freeview and their characteristics (e.g., size, x, y, z ccordinates). Unfortunately, the regions that we see for both methods don't match as there are some clusters that we see on the summary text file that we don't see on freeview and vice versa. How can we make the output of these two methods match up? Note that the issue is not the minimum cluster size in the summary table. When we put that to 1 we still get a mismatch.
Please note that in the mri_surfcluster program we can indicate that we only want positive results. We don't see a way to do this in freeview or a way for that to affect the p value in freeview.
Is this possibly the issue? If so, how can we make a picture in freeview that matches our summary table?
Regards,
Christine
--
Christine N. Smith, Ph.D.
Research Service, VA San Diego Healthcare System
Department of Psychiatry, University of California San Diego
VA San Diego Healthcare System
VMRF Building 13
3350 La Jolla Village Drive (151A)
San Diego, CA 92161
T: (858) 552-8585; then press *7128
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------------------------------
Message: 4
Date: Wed, 22 Feb 2023 22:25:48 +0100
From: beh?et ayy?ld?z <behcetayyildizz@gmail.com>
Subject: Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS
To: fsbuild <fsbuild@contbay.com>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAFJQ+MEpL+YXp5Y-PJD_pwxRPv=gJ0-Tb-9ErEUzd6Bj5j++DQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear All,
Thank you very much for your interest. I contacted my system administrator
and he fixed it.
fsbuild <fsbuild@contbay.com>, 22 ?ub 2023 ?ar, 18:04 tarihinde ?unu yazd?:
>
> The best solution (which I think was previously emailed to you) is to have
> an admin/IT person update your system by doing the following:
>
> 1) Copy the link for the freesurfer release install package matching your
> Ubuntu system, e.g., 7.3.2 freesurfer release on Ubuntu 18, 20, 22, from
> https://secure-web.cisco.com/17odrIaeqqXyCFNMITUZLWCsV1nDLwcZvIwAdFfrCgZstaX3KcShsxwtd1nV_0neGCljJYRyrmXB_9FYYWlvzi0aAOKF6-IgKzdLVnoXlPzWf-aVUWxsLEcxHHagKtcYlTSzSaYMEniOiZ9-011NkqMYAmxTbdvalw_Bz9ZkraztvTZRL3LvDUHmsXbxeTCZKy_m1TW09Rd1FMb8MhEzG7sqZ9V5OZBS4HP_DAXX0oTCpyFY8RNIo1COpOW9mVc5vwmYBzSzqyq4nnbGh2OYCHkw3wTT6wskllFFKVAf5rxhJJLBi181Gj0OBWi_ItifA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
>
> 2) Download and install it with,
>
> $ wget <link copied from the web page above>
> .... say wget downloaded the file freesurfer_ubuntu18-7.3.2_amd64.deb ....
> $ sudo apt-get install ./freesurfer_ubuntu18-7.3.2_amd64.deb
>
> That should install libncurses and anything else that's needed
> automatically. Trying to piecemeal run commands to install individual
> system packages like libncurses is asking for more trouble.
>
> - R.
>
> On 2/22/23 10:54, Iglesias Gonzalez, Juan E. (
> JIGLESIASGONZALEZ@mgh.harvard.edu) wrote:
>
> Thanks for the interest in our software!
>
> Could you please try running this command from the terminal?
>
> sudo apt-get install libncurses5
>
> Cheers,
>
> /Eugenio
>
> --
>
> Juan Eugenio Iglesias
>
> http://secure-web.cisco.com/1CD4UMye_OW85IfsE6bQBrNtvpWyCJy2BhTyu2MIEBR_-FzT4qnEOIvuv60AJod7OwbUow5sN8KBnBocp8nrsNl0y1lbMWwxmyTtIn-uTzPbWgYozeNdWRX52yjCNa_DCtcCsXcyetP3rR93lWBi2HU9ML3fLK5AeoZk-2zljmNU0uT3ATORLN2xlu_95yv8lDRlPgueBO5vpLNngwCeC48BsGs7jJDHjJDVbaXiJSl9gtf8WK0qEvAjayRCzl5LcjwgSzWTQM5o-HHB-TEMgWnc2uT3zGYvFuNnFIMnv3LApUMzDvcfFpAeCr-qPthrU/http%3A%2F%2Fwww.jeiglesias.com
>
>
>
> *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of beh?et
> ayy?ld?z <behcetayyildizz@gmail.com>
> *Reply-To: *Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>
> *Date: *Wednesday, February 15, 2023 at 05:36
> *To: *"Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
> *Subject: *[Freesurfer] segmenThalamicNuclei.sh exited with ERRORS
>
>
>
> * External Email - Use Caution *
>
> Dear All,
>
> I was using Linux Ubuntu to perform my analysis. However, they were
> changed with Linux ..... a couple of days ago. And while the
> segmentThalamicNuclei.sh command was running before the change, after the
> change it didn't run and I got the following message.
>
>
>
>
>
> drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$
> segmentThalamicNuclei.sh con_HaJa93
>
> Setting ITK threads to 1
>
> #--------------------------------------------
>
> #@# Thalamic Nuclei processing Wed 15 Feb 2023 11:09:10 AM CET
>
> ------------------------------------------
>
> Setting up environment variables
>
> ---
>
> LD_LIBRARY_PATH is
> ..:/sw/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/sw/freesurfer/7.1.1//MCRv84//bin/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sw/freesurfer/7..1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:
>
> /sw/freesurfer/7.1.1//bin/SegmentThalamicNuclei: error while loading
> shared libraries: libncurses.so.5: cannot open shared object file: No such
> file or directory
>
> 127
>
> Linux causal.brain.mri.tu-muenchen.de
> <http://secure-web.cisco.com/1Q7u7_P_NBkc_6lPG6bKTBeKKKlGXijIY3WOh-az_lej5ouUAxdtd4EmKT_u9Ta4ud8eMwDHlMpBMhNFLQGw8LWF4sEDJlyH6Muh82TsilCRK1ngCD8sjyG-bAu8CT6GY9MyisYmh9yQuNzToAjWnufnO_vOtzf99VuFt0fshgezuEzCh7ol77iCiTtL-r6g3DBhNXWLP_G9X0qe-imQVFcZecK19skmK2_yLx7sH-K6ro7bRrWRzE3teegonbBQVv6CgdfZbtEQB51-157E3hXTYNBhNfuMoLwk1ExcuA4yRb2ATsBgCSvv-JLWOJuv_03h2XiPIQvfiWSc1jUKDtA/http%3A%2F%2Fcausal.brain.mri.tu-muenchen.de>
> 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux
>
>
>
> Do you guys have any idea how to fix it ?
>
>
>
> Thanks in advance.
>
>
>
> --
>
> *Beh?et Ayy?ld?z..*
>
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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h2bzWR_-fmqLc/https%3A%2F%MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
> 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.
>
>
>
--
*Beh?et Ayy?ld?z..*
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------------------------------
Message: 5
Date: Wed, 22 Feb 2023 17:42:42 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Extracting brain volume seperately
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <9b24f86d-e36a-f843-07cf-28adc1a2140f@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
We do not generate a scalp segmentation (but you can use samseg which
generates skull and something like skin). If you want to create a binary
volume with a chosen seg or tissue type = 1 and everything else = 0, you
can use something like
mri_binarize --i aseg.mgz --match 4 5 14 15 43 44 --o csf.mgz
where those numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt
just chose the ones you want
On 2/1/2023 12:00 PM, ???(JIANG Yichuan) wrote:
>
> ????????External Email - Use Caution
>
> Hi Douglas,
>
> Thank you for your reply. I'm a beginner in freesurfer and my previous
> statement was not very clear. My purpose is to generate new .mgz files
> (e.g., scalp.mgz and CSF.mgz, etc.)?that are not in the MRI folder.
>
> Bset regards,
> Yichuan Jiang
>
>
> ------------------?Original?------------------
> *From: *?"Douglas?N.?Greve"<dgreve@MGH.HARVARD.EDU>;
> *Date: *?Wed, Feb 1, 2023 11:00 PM
> *To: *?"freesurfer"<freesurfer@nmr.mgh.harvard.edu>;
> *Subject: *?Re: [Freesurfer] Extracting brain volume seperately
> everything except skull and scalp are in the aseg.stats file. You can
> get skull by running samseg, eg,
> cd subject/mri
> samseg --i orig.mgz --o samseg
> there will be a stats file in the samseg folder with skull volume in it
>
> On 2/1/2023 5:00 AM, ???(JIANG Yichuan) wrote:
>>
>> External Email - Use Caution
>>
>> Dear Experts,
>>
>> How can I extract scalp, skull, csf, gray, and white volume, seperately.
>> Best wishes,
>> Yichuan Jiang
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 6
Date: Wed, 22 Feb 2023 17:46:53 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Nuisance regressors
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <de3e7d8d-177c-4f30-9c32-af9894bc21b0@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
you would add them as task regressors and set up first level contrasts
as you describe. I'm not sure of your last question (ie, second-level
comparison of their effect). Do you want to compare, eg, respiration vs
motion? I'm not sure how you would do that.
On 2/6/2023 5:18 AM, Marilena Wilding wrote:
>
> ????????External Email - Use Caution
>
> Hi Freesurfers!
>
> I would like to compare the effect of different nuisance regressors
> (I.e., cardiac and respiratory signal, motion) on my resting-state
> data. For that I?m adding the respective regressors to my first-level
> GLM. Now, how can I best compute a contrast between the effect of
> different physiological regressors and motion? Would I add them as
> task regressors in 1st level or rather as nuisance regressors and how
> can I get second-level comparison of their effect?
>
> Thanks in advance for your help!
>
> Best,
>
> Maria
>
>
> _______________________________________________
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Message: 7
Date: Wed, 22 Feb 2023 14:49:29 -0800
From: Manuela Dorado Novoa <manuelad@uw.edu>
Subject: [Freesurfer] Please unsubscribe me
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAGhN0Bc=Y02S_AMWrct4D6fZx+7FOYA0nEUe6PPxNZsAS+Cb3Q@mail.gmail.com>
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Hi,
Please, unsubscribe me from your mailing list.
Thank you,
Manuela
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Message: 8
Date: Wed, 22 Feb 2023 18:02:55 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Hole in the insula
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <8772f436-6486-628f-3cc0-eb996ea59685@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
That looks like a GM lesion (maybe some kind of stroke). I don't think
we have a way to fix it.
On 2/7/2023 10:34 AM, Aaron Tanenbaum wrote:
>
> ????????External Email - Use Caution
>
> ?I have this subject that has holes in the insula. Please see
> attached. I was wondering what should freesurfer have classified it as.
>
> _______________________________________________
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Message: 9
Date: Wed, 22 Feb 2023 18:16:35 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Correlating and/or linear regressing surface
overlays
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <7e6d3e12-2129-e4db-6210-260eb0bde7a9@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
It looks like you are doing the right thing. You indicated not to use a
contrast matrix. If you want to test a contrast, I think the matrix
would be [0 1] (I think it adds an offset regressor)
On 2/10/2023 4:50 PM, Finn, Quentin wrote:
>
> ????????External Email - Use Caution
>
> Freesurfer experts,
>
> I have some surface data that I'd like to correlate with some other
> data, although a linear regression would also be fine if I could get
> something like a t-stat out of it.
>
> This data came from two different PET tracers -- voxelwise data was
> resampled via vol2surf onto each subjects cortical surface:
>
> So I have, say, data like this:
>
> tracer1_subj1_lh.mgh
> tracer1_subj2_lh.mgh
> .
> .
> .
> .
> tracer1_subjn_lh.mgh
>
> And then I have another set:
>
> tracer2_subj1_lh.mgh
> tracer2_subj2_lh.mgh
> .
> .
> .
> .
> tracer2_subjn_lh.mgh
>
> I'd really like to just stack them all up with mris_preproc, something
> like this:
>
> mris_preproc --is tracer1_subj1_lh.mgh --istracer1_subj2_lh.mgh?[etc]
> --istracer1_subjn_lh.mgh--out tracer1_lh.mgh --hemi lh --fsgd tracer1.fsgd
> mris_preproc --is tracer2_subj1_lh.mgh --istracer2_subj2_lh.mgh?[etc]
> --istracer2_subjn_lh.mgh--out tracer2_lh.mgh --hemi lh --fsgd tracer1.fsgd
>
> The FSGD's are the same because the subjects are the same.
>
>
> and then run something like...
>
> mri_glmfit? --glmdir tracer1_tracer2_left --y tracer1_lh.mgh --fsgd
> tracer1.fsgd --pvr tracer2.mgh --no-contrasts-ok --surface fsaverage lh
>
> This doesn't have an output that's really what I'm looking for as far
> as I can tell though, there's no fit statistics type overlay in the
> output folder, probably because I'm doing something wrong.
>
> Any help on this would be just wonderful!
>
> -quentin finn
>
>
> Houston Methodist. Leading Medicine.
>
> /U.S. News & World Report/ has named Houston Methodist Hospital the
> Best Hospital in Texas for 11 years in a row. Houston Methodist is the
> No. 1 hospital in Texas and No. 15 in the nation. For more than 100
> years, Houston Methodist has provided the best ? and safest ? clinical
> care, advanced technology and patient experience. That is our promise
> of leading medicine.
>
>
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Message: 10
Date: Thu, 23 Feb 2023 01:59:24 +0000
From: "Smith, Christine" <c4smith@health.ucsd.edu>
Subject: Re: [Freesurfer] different clusters in mri_surfcluster output
versus viewing in Freeview
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BYAPR19MB23757D2AE9E0B2B11407A29EAFAB9@BYAPR19MB2375.namprd19.prod.outlook.com>
Content-Type: text/plain; charset="windows-1252"
External Email - Use Caution
Hi Yujing,
Thank you for explaining that.
I believe that mri_surfcluster is the correct output, in that it is carrying out a one-sided test of significance at 2 (Sig = -log(pvalue), i.e., p < 0.01).
For the Configure options, is there a similar option to allow the threshold to be 2 for a one-sided test?
We have experimented around by setting very high (max) and very low (min) values and we still weren't able to get the clusters identified by mri_surfclust to show up on Freeview, even when we reduce the threshold to account for the fact that it is a two-sided test.
Christine
--
Christine N. Smith, Ph.D.
Research Service, VA San Diego Healthcare System
Department of Psychiatry, University of California San Diego
VA San Diego Healthcare System
VMRF Building 13
3350 La Jolla Village Drive (151A)
San Diego, CA 92161
T: (858) 552-8585; then press *7128
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>
Sent: Wednesday, February 22, 2023 1:02 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] different clusters in mri_surfcluster output versus viewing in Freeview
Hi Christine,
Sig = -log(pvalue)
In freeview, the overlay thresholds can be adjusted by clicking ?Configure? button (under the Overlay dropdown menu).
For mri_surfcluster (https://secure-web.cisco.com/1s-yjkzBiQAThacWUNnIK21XblT9nkT5OPNMThSIWYwFxi8trCStUQVVjrjOiQAMydWH2btfNkaakgOi3WAFT-200lZb-VuqCIOIWVLsKBOETP4jQ-PGabAWJSlRRt0wpVufWFy1wYtyN_mK2grU-yxCd_eTX02y2NrdAmiwSC9soZnMerL9bBkTANEcSZ_nJdBIeRXI7av45Q6n03QwsiqWPNvY93FaN37uUGeO8MuBHwL3gA5SQk3OXXsr2WK2sCKM-SVZL59v6Wjys_Ms8PQkWT-4y5ob98mMWfzdUvtoiHjwiUFuQ4kBHL0H_1u7u-dWOrVviDCzI9p8GKQZeow/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_surfcluster), <https://secure-web.cisco.com/1SBkSnQMGRKnxmygapTCqZX6jLeRJXcnnL-5wJhgqkL2_VAVcpyS1by1j-AFBiwOI52FsDhblV2S0OJyE70K5fK-bUp0v_oQIJ14QNG2S6YUCRdX3iydA9IwwukWCovSe6mEoOCp59-qYrI-eMzf5sG_IcOuDJXblFdBSfFFEEL0EJumi1xVPT2OK_cRm40R-lcNSL9WOvA9W9ggdnZrCyvVYJqQLzo0RovkspNbzPtakAwEsvX0IxpWit7o8PNIHBvWsYIuQPbUulObGRZLB4YKZu6UTGvIsqWBewV2S1PVGoXNfDG-Z1mVj0A_E_qX_E1JpyOTVLVdDhSexD95Iaw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_surfcluster),__;!!LLK065n_VXAQ!nP6YzWkD5kki_fH6eoPxh7GYGISZOCVDkiv
7oh7i7miyEbAYhc-kerXLBeVJsEdOL47Z-BwyKRfHb1Azt_RymKoiIqg$> I think you can try to adjust these options to match freeview: --thmin <>, --thmax <>, --thsign <>, --minarea <>, --no-adjust.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Smith, Christine
Sent: Tuesday, February 21, 2023 6:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] different clusters in mri_surfcluster output versus viewing in Freeview
External Email - Use Caution
Hello,
I am getting a mismatch of clusters when we view cluster results in freeview versus ask for a table of the significant clusters.
I am performing a GLM analysis on Freesurfer to analyze cortical thickness (mri_glmfit). When viewing the significance map with freeview, we set the minimum threshold to 2 for the sig.mgh file.
We also used the same threshold when creating a summary table of the clusters using mri_surfcluster.
mri_surfcluster --in {$dir}/visuospatial_MCI_correlation/sig.mgh --hemi left --thmin 2 --thsign pos --minarea 10 --subject fsaverage --surf inflated --annot BN_Atlas --sum {$dir}/visuospatial_MCI_correlation/left.thickness.clustersummary_BN.txt
We were hoping to use the summary text file to identify the clusters on freeview and their characteristics (e.g., size, x, y, z ccordinates). Unfortunately, the regions that we see for both methods don?t match as there are some clusters that we see on the summary text file that we don?t see on freeview and vice versa. How can we make the output of these two methods match up? Note that the issue is not the minimum cluster size in the summary table. When we put that to 1 we still get a mismatch.
Please note that in the mri_surfcluster program we can indicate that we only want positive results. We don't see a way to do this in freeview or a way for that to affect the p value in freeview.
Is this possibly the issue? If so, how can we make a picture in freeview that matches our summary table?
Regards,
Christine
--
Christine N. Smith, Ph.D.
Research Service, VA San Diego Healthcare System
Department of Psychiatry, University of California San Diego
VA San Diego Healthcare System
VMRF Building 13
3350 La Jolla Village Drive (151A)
San Diego, CA 92161
T: (858) 552-8585; then press *7128
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Message: 11
Date: Thu, 23 Feb 2023 04:26:05 +0000
From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_easyreg tool
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <E9EF26F4-2126-4824-BAC5-BB2F32C7D96F@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Sorry for the late response, I went on vacation the very same day you posted your question.
The floating image is the one you want to deform, and the reference image is the one you use as target for the registration /deformation. In other words: the deformed floating image should overlap with the reference image.
More information here:
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Kind regards,
/Eugenio
--
Juan Eugenio Iglesias
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From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Peters, Johnny Y" <jonathan-peters@uiowa.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, February 10, 2023 at 11:40
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_easyreg tool
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to use the mri_easyreg on the developmental version of freesurfer but I am confused about what .mgz or .nii(.gz) I am supposed to use for the reference image, floating image, and the others. I saw no previous threads on the mailing list addressing my question so I decided to email you. Would you be able to give an example command line using the subject bert in the freesurfer directory?
Thank You
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Message: 12
Date: Thu, 23 Feb 2023 04:58:46 +0000
From: "Maffei, Chiara,PHD" <CMAFFEI@mgh.harvard.edu>
Subject: [Freesurfer] MGH35 template
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <69B8F5C9-97CC-480E-91E3-A368CFC2B74F@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Mark,
Sorry for the late reply.
The population template was built using the FA images only, so there is no corresponding T1 template image.
You can use the transforms stored in dmri/xfms in your TRACULA directory to map the subject?s anatomical images to this template space, or you can set the interreg variable in your dmrirc configuration file to 1 or 2 to have your TRACULA common space be the MNI152 T1 1mm space instead.
I hope this helps,
Chiara
Dear Freesurfer developers,
Hi, this message may have slipped through the cracks, hope someone can help us out on this.
We're looking for the T1 image that goes along with (i.e. in same space, or at least in same participants) as the MGH35_HCP_FA_template image which is used in TRACULA?
Does such a template exist, and if so, would it be possible to share?
Thanks so much!
Mark
____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461
Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wagshul@einsteinmed.ed<mailto:mark.wagshul@einsteinmed.edu>
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Message: 13
Date: Thu, 23 Feb 2023 05:51:39 +0000
From: "Kumar, Avnish" <Avnish.Kumar@mgh.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic
segmentation
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BYAPR04MB47901681193A62E1E16404E8D3AB9@BYAPR04MB4790.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
Hi Katie,
The core.py file has been updated now. Please try downloading it again and applying the same fix<MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2-patch/segment_subregions/> as before.
Best,
Avnish
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Katie Rose Jobson <katie.jobson@temple.edu>
Sent: Monday, February 6, 2023 3:17 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic segmentation
External Email - Use Caution
Hi FS experts,
Apologies for my late follow up.
In reference to the previous conversation, I added the core.py file to the correct subdirectory to complete the thalamic nuclei segmentation. I received an error still, albeit a different error:
Traceback (most recent call last):
File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions", line 6, in <module>
from freesurfer import subregions
File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/__init__.py", line 1, in <module>
from freesurfer.subregions.process import structure_names
File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py", line 8, in <module>
from freesurfer.subregions.thalamus import ThalamicNuclei
File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/thalamus.py", line 9, in <module>
from freesurfer.subregions.core import MeshModel
File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py", line 9, in <module>
from gems.subregions import utils
ImportError: cannot import name 'utils' from 'gems.subregions' (unknown location)
I am assuming this is because the core.py script was previously housed in the '/gems/subregions' subdirectory, and is attempting to import 'utils' from there. Is there any way to edit this file (core.py) to call on this 'utils' function?
Please let me know if I can clarify my question in any way and thank you in advance for your help!
Best Wishes,
Katie
--
Katie Jobson, M.S. | Personal Website<https://secure-web.cisco.com/1ho9yNMxPXcFe1keXWE6wU20yOWqSzwoLYY9yARkmRCu9A8_XhOXs1813M6_RxM-r3s-D_p5KtP47zZHAwIEOLNo2SWUEMb8izbw-aoPMo5VaQrkfHwPEQR-A_1Ndy0swiCQkRPIUc3N5YrjPIPddJbD0uuvB9ahtxvje-xF2ONHK4BV8UxSW4KsdBelaJeRTLEi6OmnEK9n9LxWCfulEB20fM8BR8uo6J-I1HfMdGt94a5FStVqF_XoAkXTpu7BHr_u_tNTaFPaAzGv-YMiazbNylkbOsNOUtl1x9J8dy3t1wyH3YuvujxkpFJyq3Boq/https%3A%2F%2Fkjobson-neuro.github.io%2F>
Ph.D. Student | Cognitive Neuroscience Lab<https://secure-web.cisco.com/1uRVKqr-OerGkjpg37lgmTfI8G88BkyD_v1y97KKQvh5AZ4-HIw6jDi1X-egyGybN70R_3IK7JfG6NBpr7vyUJs6WmRkCn0xt_y_-KnhH46kTj-7Xn600oPlnbidSm5PAMKsicH6XpINAZ0uytQwlGJO10m-1Wubg_6xkcOK3296_lntwqYHR_qBE8jCt_VavyEQlx9OOKNnyIvRNXgfYS1GthgtdQ3D4XNDSGtEHB-GO7JnX5Megar67weLsVe37-oqGC5wOwyl6Uq7To5l5z51YzmCl9D-NB0kzfykkgB-RTA_RD5aGb3uH5vCO16LW/https%3A%2F%2Fsites.temple.edu%2Fcnltu%2F>
Department of Psychology and Neuroscience | Temple University
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Kumar, Avnish <Avnish.Kumar@mgh.harvard.edu>
Sent: Thursday, December 8, 2022 10:19 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [External] Re: [Freesurfer] 7.3.2-patch issues - thalamic segmentation
Hi Katie,
Thank you for pointing this out! Yes, please make changes to the core.py script in your '$FREESURFER/python/packages/freesurfer/subregions/' folder. I will update the patch instructions to reflect this as well.
Best,
Avnish
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Katie Rose Jobson <katie.jobson@temple.edu>
Sent: Wednesday, December 7, 2022 3:35 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] 7.3.2-patch issues - thalamic segmentation
External Email - Use Caution
Hi FS experts,
I am attempting to implement the patch on version 7.3.2 for issues with thalamic segmentation. I followed the instructions found here: 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/pub/dist/freesurfer/7.3.2-patch/readme.txt<https://secure-web.cisco.com/1t1MSwicSbVaKTZz26QQcqNH4nacgccE3ISyro01uNnj95812z_YeG8e-DFrygCnFv6ktzMUExhmiUbDqFCf0KpNXHr5RRUcxC1AVcCaSsWWiaxtTasb5Nv7Ri_-7l4aFJc-3z8v4jMcuMuarQHkVMdfQFpDlwx_JPNCkzIF5bYbOAbLpgF5bFi1S7RGHvbfQJzCvT-GHwedW82ZkC0XRXlRJuOk5tvcxrjxhnlP_J0o1XiFpmUB27GQrmlDo4RruZFSRCORXtarTTjw4Ev2G9p7K_-aX2-nkBsHZuSRRYBIEgbqijea_xNPhBMogTCeJ/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1JULaWPox6hiL5oNotdoE4us3D1hhs0HqpeHRUYFRvLuHPjNtpIrfTSk2Oor44j2FBUk_pFk20EpHFiM3R1FVkDnc65JJPCI2jaG74UkvfjSzqwjWygwvquVzF3AUampB5BRXbiKSY7Eq72Qbr3mY5H5t3RtHvfghMkNSXw1ggCZ3hzozbWLX2XVfU6Y5rB9JzogJtWSki-SikTk1LjM-Zp5AqdAc4RDMLOPK5MS
T93Dqz207lgJp4Isj6YZIOqM1Fms1_LkZdkfuWRZVT-8jSSycyBTF13XHfqQC3TqOL541UgCoyh-f4b9wH1mNOwjdTyfJIP8epMLDFkafQf_-Ow%252Fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Fpub%25252Fdist%25252Ffreesurfer%25252F7.3.2-patch%25252Freadme.txt%26data%3D05%257C01%257Ckatie.jobson%2540temple.edu%257C3795cd2b1f9a46dc040308dad92faa19%257C716e81efb52244738e3110bd02ccf6e5%257C0%257C0%257C638061096005588355%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DHp5cWxnS%252FQSuB9KV%252FgLBR53k3jfPkdqNqn9O5E2haNg%253D%26reserved%3D0> and placed the scripts in their designated directories. However, I received the same error as before. The output indicates that the core.py script is located in the '$FREESURFER/python/packages/freesurfer/subregions/' directory, as opposed to the directory I was instructed to put the core.py script in ('$FREESURFER/python/packages/gems/subregions/').
Should I replace the core.py script within '$FREESURFER/python/packages/freesurfer/subregions/'? Or is there another course of action that I can do that may solve this issue?
Here is the exact error, if that is at all helpful:
Step 2: aligning atlas to reference segmentation
Traceback (most recent call last):
File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions", line 99, in <module>
subregions.run_cross_sectional(args.structure, parameters)
File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py", line 52, in run_cross_sectional
model.align_atlas_to_seg()
File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py", line 240, in align_atlas_to_seg
mask = mask.resize(1, interp='nearest')
TypeError: resize() got an unexpected keyword argument 'interp'
Thank you in advance for your help!
Best Wishes,
Katie
--
Katie Jobson, M.S. | Personal Website<https://secure-web.cisco.com/1qpE5cLLOL2CHnskATS2LqMgtMkQTCjvU4-ECsmcad-ykS4zLMlXgZ588AmpaseiaPCkUvGQ1X4WspXesw0YnXcGOjyj0EijWmOKOXyotE1hV03fl4mXxOVIG2WKrYCf5A1FLFBA_YxNW-rvLNNcfqq56KBAFWvkOZqPUNORHUvLmwM1hJtOq6S-dINpVeZ_kOr4p6JZWf2yK1VRmbot0IkDKqCD3ylXwQZqnGd3xFGJBRyvqcwOgNqdslOi9c3kBXuuMhEYgOogGPHoha0q9Cg-Lq1dVlL0tfo188LWTwffgpnMDCUr0wcNHbRQsI4KU/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1pn78j_bRtnBgT0xpSoaIHzF2FCTjom5RSQL5Coy-3athVw1rlGDJ6sTy7yVFFWJBkSfhVQs-ERcG_L3oXVWMADGT5-tV7LBBMD7EwnhGiZ7MRrBYfbM-Ixh6qioHPgeLskxYOWAtLdvG0uVkpYDbsL4C8Z8zWouSr6bSlWKv0B371bqES3dXSF47F_fPyYE42XsPkmkPY07cWlBAroKO4MyOxUb06ONSnmYxdXAU5ab0f9c9ju6MfbHg4IieU1ECtqao1fw5H-Idta06FlDqn0v-TZczEyQMz_yMfoy_oA9QOWJyEEHIR8J_vHzH15DhUBUgx2gtv0kuE0ZGjebQjQ%252Fhttps%25253A%25252F%25252Fkjobson-neuro.github.io%25252F%26data%3D05%257C01%257Ckatie.jobson%2540temple.edu%257C3795cd2b1f9a46dc040308dad92faa19%257C716
e81efb52244738e3110bd02ccf6e5%257C0%257C0%257C638061096005588355%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DjEfWDE9dwjIKlP1UEcWXaH0JOt7RZpZ3jDLG04rOwkQ%253D%26reserved%3D0>
Ph.D. Student | Cognitive Neuroscience Lab<https://secure-web.cisco.com/12TSjlFST5ClRU5NTmGCTo4cbHr9K_otNLC_UTGVRjTnEqOipmFiPU6ncsH260zbu8XMGDxbprbJihlBWCHuNLKEPzTwtMbjvLVM1N1J_GfvuOQyP82VGJKvv_mhN_my1bKZDe6OUxVOdT8ADJ6ewdd4NnK2HTiOb6QIYpUsqaOG1A7JWhhJzaaButMw8NGfeDvXf4ZR74JzKeAcjeOF8en6J11tcClnh_614PFl6j92ksk2WruYc_yTEFFVqWgCLfNCS3huT3d--QYSYRAzEGkulM6lXmAmuMfVf2oSDRaWseMO20bdLl-MyKDXJ1Z8s/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F13fFt8PE3xjBFNhyYO17_fs-djBanSzBziNRRKhkYNAIjVw3vQ9lQCBGRAJDIhWHwLmtZ2hMLLSzCRhoKz3qo97Q472xVV0I-dmZKJahUOBAnwchKxLdDQOJkxntBsA4NbWyxrDP80dMWcPZDA9hqpjtMzmYRZkXbbJ2F_QL3hqIhlTcczsRrBZermR0RF0-ZR5oKet9KHvjxlgAd8PJgZ573QiqJ96Hgi0xdHBzG9Kh6cYkwtkoU3L-6UGBdsfGFBSQJ1BaGfIWPLl0-CgB5KwOWekN7AXJGHOF6gyZimhtMxIS-7421h7RZu67mW74Jb6sS5UnRLAp7G-p66Jyrlw%252Fhttps%25253A%25252F%25252Fsites.temple.edu%25252Fcnltu%25252F%26data%3D05%257C01%257Ckatie.jobson%2540temple.edu%257C3795cd2b1f9a46dc040308dad92faa
19%257C716e81efb52244738e3110bd02ccf6e5%257C0%257C0%257C638061096005588355%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DsET5lqz9mj2jA3PqXIxjw2nZEIak3%252B7pJn4PEMboBQc%253D%26reserved%3D0>
Department of Psychology and Neuroscience | Temple University
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------------------------------
Message: 14
Date: Thu, 23 Feb 2023 09:18:50 +0000
From: "Reuter, Martin,Ph.D." <MREUTER@mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_robust_register --minsize
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <CAACCCA4-9FCE-4B06-A6E3-8BA607882985@mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"
Hi Sebastien,
Robust register cannot register a slice into a 3D volume. It can only register 3d to 3d (or 2d to 2d, although that has not been tested much).
Sorry,
Martin
On 30. Jan 2023, at 21:09, Proulx, Jean Sebastien <JSPROULX@mgh.harvard.edu> wrote:
Hello,
I am trying to register a full volume to a single slice, and I follow example 3 of mri_robust_register's help. I get the following error:
Input image is smaller than min dimension: 1 < 16
Input dimensions (after conformalizing) MOV: 64 64 64
Input dimensions (after conformalizing) DST: 64 64 1
Specify larger minimum ...
This error stays after adding --minsize 1 or --minsize, despite mri_robust_register recognizing the flag, as suggested by this terminal output:
--minsize: Smallest dimension > 0 .
Registration ran ok when replacing the single-slice with a 40-slice volume.
Any idea on what is going on here?
Thanks a lot for the good work and
Have a good day!
Sebastien
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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------------------------------
Message: 15
Date: Thu, 23 Feb 2023 08:12:12 -0600
From: Aaron Tanenbaum <aaron.b.tanenbaum@gmail.com>
Subject: Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic
segmentation
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAAGp_pz9V6QHi4Hw=nOOtsRh44hvoaXP6+EKbpVWcaAcw-3Gfw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi,
I saw this thread and was wondering about the details of this patch. Does
this patch affect the standard recon-all call or is this meant for a
special flag. Also I was also wondering what issue did it solve?
Thank you.
On Wed, Feb 22, 2023 at 11:52 PM Kumar, Avnish <Avnish.Kumar@mgh.harvard.edu>
wrote:
> Hi Katie,
>
> The core.py file has been updated now. Please try downloading it again and
> applying the same fix
> <https://secure-web.cisco.com/1jL26L7yFavOUgcWfxYm-k3h15hb0c5gOBHa9Fed4BCYLubpwr-niyJ-R1e6v30g6M7KnS_6WZxqflmAWLgjRPfEPSuoq0dklfegUn03H-r36juVobk3F3SYqLW5gq23xrLQiPF5G2vENSKbNdvxNLPIgVwOC0_84R3mVkvdBCElZhtZ5UDlXd0WzMLSjf7gJDbB651AHUCT9wh-91j-A0iUNu79mTXPZtmayJ77YNgMlH9qiSwRzhRT0H2iC6FCqMgCLC7PinAV99aNZo4EAzLIQZNZ4fOtEjm51OZZ4T_077e6kprzhNwFhcMaW-CIBATU8VSigXdH9B-i_aPvXxQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2-patch%2Fsegment_subregions%2F>
> as before.
>
> Best,
> Avnish
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Katie Rose Jobson <
> katie.jobson@temple.edu>
> *Sent:* Monday, February 6, 2023 3:17 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic
> segmentation
>
>
> External Email - Use Caution
>
> Hi FS experts,
>
> Apologies for my late follow up.
>
> In reference to the previous conversation, I added the core.py file to the
> correct subdirectory to complete the thalamic nuclei segmentation. I
> received an error still, albeit a different error:
>
> Traceback (most recent call last):
>
> File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions",
> line 6, in <module>
>
> from freesurfer import subregions
>
> File
> "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/__init__.py",
> line 1, in <module>
>
> from freesurfer.subregions.process import structure_names
>
> File
> "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py",
> line 8, in <module>
>
> from freesurfer.subregions.thalamus import ThalamicNuclei
>
> File
> "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/thalamus.py",
> line 9, in <module>
>
> from freesurfer.subregions.core import MeshModel
>
> File
> "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py",
> line 9, in <module>
>
> from gems.subregions import utils
>
> ImportError: cannot import name 'utils' from 'gems.subregions' (unknown
> location)
>
> I am assuming this is because the core.py script was previously housed in
> the '/gems/subregions' subdirectory, and is attempting to import 'utils'
> from there. Is there any way to edit this file (core.py) to call on this
> 'utils' function?
>
> Please let me know if I can clarify my question in any way and thank you
> in advance for your help!
>
> Best Wishes,
> Katie
> --
> Katie Jobson, M.S. | Personal Website
> <https://secure-web.cisco.com/1ho9yNMxPXcFe1keXWE6wU20yOWqSzwoLYY9yARkmRCu9A8_XhOXs1813M6_RxM-r3s-D_p5KtP47zZHAwIEOLNo2SWUEMb8izbw-aoPMo5VaQrkfHwPEQR-A_1Ndy0swiCQkRPIUc3N5YrjPIPddJbD0uuvB9ahtxvje-xF2ONHK4BV8UxSW4KsdBelaJeRTLEi6OmnEK9n9LxWCfulEB20fM8BR8uo6J-I1HfMdGt94a5FStVqF_XoAkXTpu7BHr_u_tNTaFPaAzGv-YMiazbNylkbOsNOUtl1x9J8dy3t1wyH3YuvujxkpFJyq3Boq/https%3A%2F%2Fkjobson-neuro.github.io%2F>
> Ph.D. Student | Cognitive Neuroscience Lab
> <https://secure-web.cisco.com/1uRVKqr-OerGkjpg37lgmTfI8G88BkyD_v1y97KKQvh5AZ4-HIw6jDi1X-egyGybN70R_3IK7JfG6NBpr7vyUJs6WmRkCn0xt_y_-KnhH46kTj-7Xn600oPlnbidSm5PAMKsicH6XpINAZ0uytQwlGJO10m-1Wubg_6xkcOK3296_lntwqYHR_qBE8jCt_VavyEQlx9OOKNnyIvRNXgfYS1GthgtdQ3D4XNDSGtEHB-GO7JnX5Megar67weLsVe37-oqGC5wOwyl6Uq7To5l5z51YzmCl9D-NB0kzfykkgB-RTA_RD5aGb3uH5vCO16LW/https%3A%2F%2Fsites.temple.edu%2Fcnltu%2F>
> Department of Psychology and Neuroscience | Temple University
>
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Kumar, Avnish <
> Avnish.Kumar@mgh.harvard.edu>
> *Sent:* Thursday, December 8, 2022 10:19 AM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* [External] Re: [Freesurfer] 7.3.2-patch issues - thalamic
> segmentation
>
> Hi Katie,
>
> Thank you for pointing this out! Yes, please make changes to the core.py
> script in your '$FREESURFER/python/packages/freesurfer/subregions/'
> folder. I will update the patch instructions to reflect this as well.
>
> Best,
> Avnish
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Katie Rose Jobson <
> katie.jobson@temple.edu>
> *Sent:* Wednesday, December 7, 2022 3:35 PM
> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* [Freesurfer] 7.3.2-patch issues - thalamic segmentation
>
>
> External Email - Use Caution
>
> Hi FS experts,
>
> I am attempting to implement the patch on version 7.3.2 for issues with
> thalamic segmentation. I followed the instructions found here: *MailScanner
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming
> to be*
> https://secure-web.cisco.com/1mCHS2GkeGhBpJl5i4kLOmiu-VYhuxPl9ZPOae6mcel-DbGhTodG0pu85-hJ2dZg3pCawC2piCcYxYVybSA_J7R75kC3q6czI411rqFoF6W6Vce2V2kXMMelfwwg71rOXC43OpgCsX0SbbvwVZqmKZKhGmHXCtbmmAdxiiC2ev1abaVyk59OSz5oyCJmb5hYi9sQfjMF2pGp0v1X_XO7vhaMK2xrToJTN6fYK48o0_ggPyWMAVe1uLNjbEP7apBMmNNYxRTwSOJqY05tXrLggGl830QzNfEjpWKxpW-T3hxeW81bz4E0m4qs8W2ECl6soUX3wG_hGEI-OVMSTHHf5tQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2-patch%2Freadme.txt
> <https://secure-web.cisco.com/1t1MSwicSbVaKTZz26QQcqNH4nacgccE3ISyro01uNnj95812z_YeG8e-DFrygCnFv6ktzMUExhmiUbDqFCf0KpNXHr5RRUcxC1AVcCaSsWWiaxtTasb5Nv7Ri_-7l4aFJc-3z8v4jMcuMuarQHkVMdfQFpDlwx_JPNCkzIF5bYbOAbLpgF5bFi1S7RGHvbfQJzCvT-GHwedW82ZkC0XRXlRJuOk5tvcxrjxhnlP_J0o1XiFpmUB27GQrmlDo4RruZFSRCORXtarTTjw4Ev2G9p7K_-aX2-nkBsHZuSRRYBIEgbqijea_xNPhBMogTCeJ/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1JULaWPox6hiL5oNotdoE4us3D1hhs0HqpeHRUYFRvLuHPjNtpIrfTSk2Oor44j2FBUk_pFk20EpHFiM3R1FVkDnc65JJPCI2jaG74UkvfjSzqwjWygwvquVzF3AUampB5BRXbiKSY7Eq72Qbr3mY5H5t3RtHvfghMkNSXw1ggCZ3hzozbWLX2XVfU6Y5rB9JzogJtWSki-SikTk1LjM-Zp5AqdAc4RDMLOPK5MST93Dqz207lgJp4Isj6YZIOqM1Fms1_LkZdkfuWRZVT-8jSSycyBTF13XHfqQC3TqOL541UgCoyh-f4b9wH1mNOwjdTyfJIP8epMLDFkafQf_-Ow%252Fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Fpub%25252Fdist%25252Ffreesurfer%25252F7.3.2-patch%25252Freadme.txt%26data%3D05%257C01%257Ckatie.jobson%2540temple.edu%257C3795cd
2b1f9a46dc040308dad92faa19%257C716e81efb52244738e3110bd02ccf6e5%257C0%257C0%257C638061096005588355%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DHp5cWxnS%252FQSuB9KV%252FgLBR53k3jfPkdqNqn9O5E2haNg%253D%26reserved%3D0> and
> placed the scripts in their designated directories. However, I received the
> same error as before. The output indicates that the core.py script is
> located in the '$FREESURFER/python/packages/freesurfer/subregions/'
> directory, as opposed to the directory I was instructed to put the core.py
> script in ('$FREESURFER/python/packages/gems/subregions/').
>
> Should I replace the core.py script within '$FREESURFER/python/packages/freesurfer/subregions/'?
> Or is there another course of action that I can do that may solve this
> issue?
>
> Here is the exact error, if that is at all helpful:
> Step 2: aligning atlas to reference segmentation
> Traceback (most recent call last):
> File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions",
> line 99, in <module>
> subregions.run_cross_sectional(args.structure, parameters)
> File
> "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py",
> line 52, in run_cross_sectional
> model.align_atlas_to_seg()
> File "
> /usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py",
> line 240, in align_atlas_to_seg
> mask = mask.resize(1, interp='nearest')
> TypeError: resize() got an unexpected keyword argument 'interp'
>
> Thank you in advance for your help!
>
> Best Wishes,
> Katie
> --
> Katie Jobson, M.S. | Personal Website
> <https://secure-web.cisco.com/1qpE5cLLOL2CHnskATS2LqMgtMkQTCjvU4-ECsmcad-ykS4zLMlXgZ588AmpaseiaPCkUvGQ1X4WspXesw0YnXcGOjyj0EijWmOKOXyotE1hV03fl4mXxOVIG2WKrYCf5A1FLFBA_YxNW-rvLNNcfqq56KBAFWvkOZqPUNORHUvLmwM1hJtOq6S-dINpVeZ_kOr4p6JZWf2yK1VRmbot0IkDKqCD3ylXwQZqnGd3xFGJBRyvqcwOgNqdslOi9c3kBXuuMhEYgOogGPHoha0q9Cg-Lq1dVlL0tfo188LWTwffgpnMDCUr0wcNHbRQsI4KU/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1pn78j_bRtnBgT0xpSoaIHzF2FCTjom5RSQL5Coy-3athVw1rlGDJ6sTy7yVFFWJBkSfhVQs-ERcG_L3oXVWMADGT5-tV7LBBMD7EwnhGiZ7MRrBYfbM-Ixh6qioHPgeLskxYOWAtLdvG0uVkpYDbsL4C8Z8zWouSr6bSlWKv0B371bqES3dXSF47F_fPyYE42XsPkmkPY07cWlBAroKO4MyOxUb06ONSnmYxdXAU5ab0f9c9ju6MfbHg4IieU1ECtqao1fw5H-Idta06FlDqn0v-TZczEyQMz_yMfoy_oA9QOWJyEEHIR8J_vHzH15DhUBUgx2gtv0kuE0ZGjebQjQ%252Fhttps%25253A%25252F%25252Fkjobson-neuro.github.io%25252F%26data%3D05%257C01%257Ckatie.jobson%2540temple.edu%257C3795cd2b1f9a46dc040308dad92faa19%257C716e81efb52244738e3110bd02ccf6e5%257C0
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> Ph.D. Student | Cognitive Neuroscience Lab
> <https://secure-web.cisco.com/12TSjlFST5ClRU5NTmGCTo4cbHr9K_otNLC_UTGVRjTnEqOipmFiPU6ncsH260zbu8XMGDxbprbJihlBWCHuNLKEPzTwtMbjvLVM1N1J_GfvuOQyP82VGJKvv_mhN_my1bKZDe6OUxVOdT8ADJ6ewdd4NnK2HTiOb6QIYpUsqaOG1A7JWhhJzaaButMw8NGfeDvXf4ZR74JzKeAcjeOF8en6J11tcClnh_614PFl6j92ksk2WruYc_yTEFFVqWgCLfNCS3huT3d--QYSYRAzEGkulM6lXmAmuMfVf2oSDRaWseMO20bdLl-MyKDXJ1Z8s/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F13fFt8PE3xjBFNhyYO17_fs-djBanSzBziNRRKhkYNAIjVw3vQ9lQCBGRAJDIhWHwLmtZ2hMLLSzCRhoKz3qo97Q472xVV0I-dmZKJahUOBAnwchKxLdDQOJkxntBsA4NbWyxrDP80dMWcPZDA9hqpjtMzmYRZkXbbJ2F_QL3hqIhlTcczsRrBZermR0RF0-ZR5oKet9KHvjxlgAd8PJgZ573QiqJ96Hgi0xdHBzG9Kh6cYkwtkoU3L-6UGBdsfGFBSQJ1BaGfIWPLl0-CgB5KwOWekN7AXJGHOF6gyZimhtMxIS-7421h7RZu67mW74Jb6sS5UnRLAp7G-p66Jyrlw%252Fhttps%25253A%25252F%25252Fsites.temple.edu%25252Fcnltu%25252F%26data%3D05%257C01%257Ckatie.jobson%2540temple.edu%257C3795cd2b1f9a46dc040308dad92faa19%257C716e81efb52244738e3110bd02ccf6e5%
257C0%257C0%257C638061096005588355%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DsET5lqz9mj2jA3PqXIxjw2nZEIak3%252B7pJn4PEMboBQc%253D%26reserved%3D0>
> Department of Psychology and Neuroscience | Temple University
>
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