Re: [Freesurfer] Subregion Segmentation of thalamus for TRACULA

[Iglesias Gonzalez, Juan E.]

Dear Makenna (and rest of users)

Thanks for spotting this bug, and for bearing with us while we transition to 
the new, Matlab-free code.

Renaming should be fine for now but we’ll certainly fix this on our end ASAP.

Kind regards,

Juan Eugenio Iglesias
http://www.jeiglesias.com

On Jul 28, 2022, at 18:15, Makenna B McGill 
mailto:makennamcg...@utexas.edu>> wrote:

Hi FreeSurfer Developers,

I'm trying to run TRACULA in FreeSurfer v7.3 on OS Monterey.

I was unable to download R2014b Runtime on my newer OS, so instead of the 
segmentThalamicNuclei.sh script, I tried running the newer segmentation tool 
segment_subregions thalamus 
(https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation).

This was successful, but trac-all looks for the 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz file, whereas the subregion segmentation 
produces the file ThalamicNuclei.FSvoxelSpace.mgz.

I'm wondering two things: (1) is the new segmentation tool compatible with 
trac-all (the wiki says the results will be very close but not identical), and 
(2) if so, would it be appropriate to rename/link the file so that trac-all can 
find it, as this user did with the ThalamicNuclei.v13 file 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg73065.html)?

Thank you in advance for any suggestions you might have, and please let me know 
if anything needs clarified.

Best,
Makenna

Makenna McGill (she/her)
Doctoral Student in Clinical Psychology
University of Texas at Austin
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Re: [Freesurfer] Problem with hypothalamus subunits?

[Iglesias Gonzalez, Juan E.]

It should be identical but if you want to rerun 1 or 2 subjects for peace of 
mind, you should totally do it. Or even rerun your whole dataset; the 
algorithms runs pretty fast anyway ;-)

Juan Eugenio Iglesias
http://www.jeiglesias.com

On Jul 28, 2022, at 16:43, Zeng, Victor (BIDMC - Keshavan - Psychiatry) 
mailto:vz...@bidmc.harvard.edu>> wrote:

External Email - Use Caution

If the brain scans went through successfully already, in an older dev version, 
do they need to be reprocessed?

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Iglesias Gonzalez, Juan E. 
mailto:jiglesiasgonza...@mgh.harvard.edu>>
Sent: Thursday, July 28, 2022 11:28 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [External] Re: [Freesurfer] Problem with hypothalamus subunits?

Thanks for reporting this bug, Victor. I just fixed it. The fix will be 
propagated to the development version in the next couple of days but, if you 
want, you can keep using the version you’ve got by adding the flag --crop 1000  
(where 1000 is a number bigger than your image size in any dimension). That 
will have the same effect as the fix.

Cheers,

Eugenio

Juan Eugenio Iglesias
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://www.jeiglesias.com

On Jul 27, 2022, at 15:03, Zeng, Victor (BIDMC - Keshavan - Psychiatry) 
mailto:vz...@bidmc.harvard.edu>> wrote:

External Email - Use Caution

Hi all,
I've downloaded a new dev version of FS 7/19/2022 - and I receive an error with 
running subunits:

mri_segment_hypothalamic_subunits --s 10893/
using 1 thread
/mnt/QBERT/freesurfer/python/scripts/mri_segment_hypothalamic_subunits:1023: 
DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has 
a more predictable return type. To obtain get_data() behavior going forward, 
use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise  as of 
version: 5.0
  volume = np.squeeze(x.get_data())
predicting 1/1

the following problem occured when preprocessing image //0893/mri/nu.mgz :
'NoneType' object is not subscriptable
resuming program execution


segmentation  saved in://10893/mri/hypothalamic_subunits_seg.v1.mgz
volumes saved in:  //10893/mri/hypothalamic_subunits_volumes.v1.csv
resampled images saved in: 
//10893/mri/hypothalamic_subunits_nu_resampled_1mm.v1.mgz

If you use this tool in a publication, please cite:
Automated segmentation of the hypothalamus and associated subunits in brain MRI
B. Billot, M. Bocchetta, E. Todd, A. V. Dalca, J. D. Rohrer, J. E. Iglesias
NeuroImage 2020



Is this a problem with tensorflow? It does not seem clear. No files are 
actually being written

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
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Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

[Douglas N. Greve]

Can you send us a sample case?

On 7/28/2022 8:58 PM, Miriam Taza wrote:

Nothing strange about them.
They’re T1w scans 1x1x1mm3

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


*Sent:* Thursday, July 28, 2022 1:25 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain
Have you looked at the input volume to see if there is anything 
strange about them? What kind of scans are you passing to it? What is 
the resolution?


On 7/25/2022 9:03 PM, Miriam Taza wrote:


External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were 
not picked up after running ScLimbic. These are healthy adults and 
their scans look good. Also, I noticed often when this occurs NAcc is 
also 0 or other regions.
I am concerned if there is a systematic issue with left volumes 
ending up smaller than they should relative to right.


Thanks,
Miriam

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Re: [Freesurfer] Subregion Segmentation of thalamus for TRACULA

[Makenna B McGill]

External Email - Use Caution

Hi Juan,

Thank you for the response! I did rename the file
to ThalamicNuclei.v12.T1.FSvoxelSpace.mgz as you suggested, however I run
into the following error when running trac-all prep in v7.3:

trac-all -prep -c
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/config/tracula_config.txt
-noqa
...

input
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg.nii.gz

frame  0

nErode3d   2

nErode2d   0

output
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg_mask.nii.gz

Binarizing based on threshold

min0.5

max+infinity

binval1

binvalnot 0

fstart = 0, fend = 0, nframes = 1

Found 1169534 values in range

Dilating 4 voxels in 3d

Eroding 2 voxels in 3d

Counting number of voxels in first frame

Found 1609388 voxels in final mask

Writing output to
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg_mask.nii.gz

Count: 1609388 1609388.00 16777216 9.592700

mri_binarize done

printf: illegal option -- -

usage: printf format [arguments ...]

mri_binarize --i
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/aparc+aseg.mgz
--o
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz

ERROR: must specify minimum and/or maximum threshold or match values

mri_concat --i
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
--i
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
--max --o
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz

ninputs = 2

Checking inputs

error: niiRead(): error opening file
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz

ERROR: reading
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz

mri_binarize --i
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/aparc+aseg.mgz
--match 2 41 7 46 172 177 77 --o
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter.nii.gz

The file
/Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
was never created, which based on this response (
https://secure-web.cisco.com/13t_KJAXtZcpC_gOfCll4FYtVMXaIkjdLA8U-v2sJUFPyB8mHuFe_ecupkoIne9WFljgyemgbeM49fV0_G_O87MttbYzzSbfjfTPJDITPjhKzTHi-URG2yOs3f8Ci5_354W1QkfuohMCg9h_mMPdTvFuMnQMX9B4KjiOh_WE7oSw6fV2hhSQcag9wZXG1T2AA_xoXw9x_sGzaQyaUS0otafBfEI5qnyRnJSDWdcw3qb8f48MR4Jn6g73iZp3XpVSuDrwLXLeq-fT02uB1Y7BAteH-8BnYAskY16uVMQWk9B98nzcy2nAVoKNfpkyH8oE0lsaUxCLli-sYquztoDsLEQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg72181.html)
seems to be because of issues with using the
mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz file. I've attached my
configuration file and the trac-all log, although this error section
appears to be missing from the log file.

Any suggestions you might have would be greatly appreciated!

Best,
Makenna

*Makenna McGill *(she/her)
Doctoral Student in Clinical Psychology
University of Texas at Austin


On Fri, Jul 29, 2022 at 7:53 AM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:

> Dear Makenna (and rest of users)
>
> Thanks for spotting this bug, and for bearing with us while we transition
> to the new, Matlab-free code.
>
> Renaming should be fine for now but we’ll certainly fix this on our end
> ASAP.
>
> Kind regards,
>
> Juan Eugenio Iglesias
> http://secure-web.cisco.com/1n-OaOnfhvsxFVcU07U1St5F0bdZPJNaj2ZTuvmVj-1O05DCLl-Zi6V5A4V-oiU9hpdWaeh4b8bLkO4LqnJKi7lVoSqlyaPCk4D7Vdp86e5_kh_57lHqAxE-85GLrRxn6SI5zcSoHGsXOTGEknZq2bXNkbtHdzu13NueCV4wBvZVxMp1MD7j3k3WnW2TtcjeGE_GLE6etudAheFwYfGqpTBkzBS0zhsokZpNggCT3p7XWFOBUBV-FBGdkB3kxbHoFXX8NjpiMG9byOgZ30DxQ14xCfIS_WvMHwqSD_QfnmH_KT94Habrp9eNwQBli-RBy/http%3A%2F%2Fwww.jeiglesias.com
>
> On Jul 28, 2022, at 18:15, Makenna B McGill 
> wrote:
>
> Hi FreeSurfer Developers,
>
> I'm trying to run TRACULA in FreeSurfer v7.3 on OS Monterey.
>
> I was unable to download R2014b Runtime on my newer OS, so instead of the
> segmentThalamicNuclei.sh script, I tried running the newer segmentation
> tool segment_subregions thalamus (
> https://secure-web.cisco.com/1f16U4BOMTLy2zx3wBKG1xKc1x-zFBuasQvMGTtF9DhO_xA1qJChqY9VVvHNgF--g7u2R6MW5TVFcO298nuOOG7PiBtl3O99Ls5nQz7tfEsn2izhwmFrDXf3akzXxmioVbB0YYhbL9Zx3xOSNFTZUWgEBX1pDKDk8-GiWTGC59ehht7j7tOLUib3ByXn_3FzERnkhlWfGV1qMf1ICn79me5k3loveqm93_7iiMlQYmwwp0BooIVxPXSvk_lwB5qtGCGKsU7w27azCBMq95lnNlHeWl10fXKqsD5cMV3gThM2pJXbDeEhIQdztZ6CFYmvBhtD6VK_HXf5OqO3OC5bT7A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSubregionSegmentation).
>
> This was successf