Re: [Freesurfer] segmentHA_T2.sh longitudinal version?

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Daniel,
Such a script doesn’t exist yet (it’s in the to-do list). The reason why it’s 
not a straightforward extension of segmentHA_T1.sh is that resampling the 
anisotropic T2s to a common space is not a good idea, given the differences in 
orientation. There are ways of getting around this problem; I just haven’t 
found the time to do it, yet…
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Daniel Callow 

Reply-To: Freesurfer support list 
Date: Monday, 29 July 2019 at 21:48
To: Freesurfer support list 
Subject: [Freesurfer] segmentHA_T2.sh longitudinal version?


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Hello,

I have recently used segmentHA_T1_long.sh and was pleased with the segmentation 
results. However, I now have a longitudinal data set that has additional T2 
high-resolution scans of the hippocampus as well as T1's. I know there is a 
segmentHA_T2.sh script to incorporate these types of scans. However, there 
doesn't seem to be a longitudinal version for this. Is this something that is 
being worked on? Or is there another reason that T2 should not be used with 
longitudinal analysis?

Thank you for any advice you can provide,

Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298
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Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found {Disarmed}

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Nope, unless you rerun your subjects, which you totally shouldn’t  (just run 
segmentHA_T1.sh)
And of course, install on a different directory than 6.0 
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of "Chen, Christine" 

Reply-To: Freesurfer support list 
Date: Friday, 26 July 2019 at 12:04
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command 
not found


External Email - Use Caution
Hello,

Thank you for the response! I just want to double check before I install the 
development version, will installing the development version amend, delete, or 
override any of the previous FreeSurfer files or scripts we have with the 
non-development version? Thank you in advance.

Best,
CC

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, 
Eugenio
Sent: Friday, July 26, 2019 11:10 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command 
not found

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Dear CC,
You need the development version of FreeSurfer, since the amygdala was added to 
the atlas after the 6.0 release.
Kind regards,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeiglesias.com=02%7C01%7C%7Ca308e94491bc48d78eed08d711e2e037%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C1%7C636997538438104312=RdJA5s7mvqmGFKznklunjbfduLw35DZEq3FIRSU51gs%3D=0>


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Chen, Christine" 
mailto:ch...@kennedykrieger.org>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 26 July 2019 at 09:47
To: "'freesurfer@nmr.mgh.harvard.edu'" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not 
found


External Email - Use Caution
To whom it may concern,

I am trying to run hippocampal and amygdala segmentation 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala=02%7C01%7C%7Ca308e94491bc48d78eed08d711e2e037%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C1%7C636997538438114306=nqRWqZOXt5TrF6IFPP8Nt6vambpplaQ7WLn2h8jBcak%3D=0>)
 on FreeSurfer v6.0 
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c). I was able to run 
recon-all, however I am unable to run segmentHA_T1.sh because the command 
doesn't exist in $FREESURFER_HOME/bin. Instead, there is segmentSF_T1.sh. I've 
tried searching the email listings for information comparing the two scripts, 
but haven't been able to find much.

In order to run the hippocampal and amygdala segmentation, am I able to use 
segmentSF_T1.sh instead of segmentHA_T1.sh? Is there a more recent version of 
Freesurfer I have to install that includes segmentHA_T1.sh?

Thank you in advance for the help.

Best,
CC


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Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear CC,
You need the development version of FreeSurfer, since the amygdala was added to 
the atlas after the 6.0 release.
Kind regards,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of "Chen, Christine" 

Reply-To: Freesurfer support list 
Date: Friday, 26 July 2019 at 09:47
To: "'freesurfer@nmr.mgh.harvard.edu'" 
Subject: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not 
found


External Email - Use Caution
To whom it may concern,

I am trying to run hippocampal and amygdala segmentation 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala)
 on FreeSurfer v6.0 
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c). I was able to run 
recon-all, however I am unable to run segmentHA_T1.sh because the command 
doesn't exist in $FREESURFER_HOME/bin. Instead, there is segmentSF_T1.sh. I've 
tried searching the email listings for information comparing the two scripts, 
but haven't been able to find much.

In order to run the hippocampal and amygdala segmentation, am I able to use 
segmentSF_T1.sh instead of segmentHA_T1.sh? Is there a more recent version of 
Freesurfer I have to install that includes segmentHA_T1.sh?

Thank you in advance for the help.

Best,
CC


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Please note that e-mail communication is not encrypted by default. You have the 
right to request further emails be encrypted by notifying the sender. Your 
continued use of e-mail constitutes your acknowledgment of these 
confidentiality and security limitations. If you are not the intended 
recipient, be advised that any unauthorized use, disclosure, copying, 
distribution, or the taking of any action in reliance on the contents of this 
information is strictly prohibited. If you have received this e-mail in error, 
please immediately notify the sender via telephone or return e-mail.

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Re: [Freesurfer] Pixel values in Brainstem segmentation {Disarmed}

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi again,
mri_convert will give you the voxel size, which is isotropic. Multiply 2 of the 
dimensions and you’ve got the area.
Also: rather than counting pixels from the discrete segmentation, I highly 
recommend that you produce soft segmentations as explained in my previous 
email. Then, you can weigh the area of each pixel in each slice by it’s 
probability.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Min Zhang 

Reply-To: Freesurfer support list 
Date: Tuesday, 16 July 2019 at 11:28
To: Freesurfer support list 
Subject: Re: [Freesurfer] Pixel values in Brainstem segmentation


External Email - Use Caution
Hi, Eugenia

I need the real area size of the brainstem in one slice, I can calculate the 
total pixels in the area from brainstemSsLabels.v10.mgz, I need the real pixel 
size of it, than I can calculate the real area size. Many Thanks!

Best
Jackie

On Tue, Jul 16, 2019 at 11:16 AM Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution
Dear Jackie,
You may want to use the soft segmentations; you can obtain them by setting the 
environment variable WRITE_POSTERIORS to 1 before running the code, see:
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBrainstemSubstructures=02%7C01%7C%7C57107bbc455449bc08aa08d70a024bb5%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636988877291022044=VfgJV4O%2F3mbmdk3baaSZyXVAIM0p2AfY8WSqaLvZ%2B20%3D=0>
Also: you can obtain the voxel size with:
mri_info brainstemSsLabels.v10.mgz
Cheers,
/E


--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeiglesias.com=02%7C01%7C%7C57107bbc455449bc08aa08d70a024bb5%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636988877291032039=uGg%2BWF942tA6GrHgPtWV1psavUg%2FBn%2F9RtDywLNJcuQ%3D=0>


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Min Zhang 
mailto:jacqueline.m.zh...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 16 July 2019 at 09:58
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Pixel values in Brainstem segmentation


External Email - Use Caution

To whom it may concern

I used the freesufer brainstem segmentation, and I want to calculate the area 
of the segmented brainstem by slices. Would you like to let me know the pixel 
value of all three directions.  I used the result in brainstemSsLabels.v10.mgz. 
Many Thanks!

Best

Jackie
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Re: [Freesurfer] Pixel values in Brainstem segmentation

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Jackie,
You may want to use the soft segmentations; you can obtain them by setting the 
environment variable WRITE_POSTERIORS to 1 before running the code, see:
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures
Also: you can obtain the voxel size with:
mri_info brainstemSsLabels.v10.mgz
Cheers,
/E


--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Min Zhang 

Reply-To: Freesurfer support list 
Date: Tuesday, 16 July 2019 at 09:58
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Pixel values in Brainstem segmentation


External Email - Use Caution

To whom it may concern

I used the freesufer brainstem segmentation, and I want to calculate the area 
of the segmented brainstem by slices. Would you like to let me know the pixel 
value of all three directions.  I used the result in brainstemSsLabels.v10.mgz. 
Many Thanks!

Best

Jackie
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Re: [Freesurfer] Doubts in hippocampal subfields labeling {Disarmed}

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks, Antonin.
The ASEG has definitely oversegmented the hippo. Those large regions were ASEG 
and the subfield module disagree are mostly partial voluming of the lateral 
ventricle and the cerebral white matter or the fimbria, and are thus NOT 
hippocampus. Having said that, it is also true that the subfield module 
undersegments the fimbria a bit; I’m pretty sure this is because some of the 
fimbria voxels (the most lateral ones) get assigned to the  alveus instead 
(which we don’t shown in the segmentation, as it’s not very reliable…)
I hope this helps,
/Eugenio


--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Antonin Skoch 

Reply-To: Antonin Skoch , Freesurfer support list 

Date: Thursday, 4 July 2019 at 07:31
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Doubts in hippocampal subfields labeling


External Email - Use Caution

Dear Eugenio,

I have uploaded the subject as file hippocampal_subfields_labeling.tar.gz to 
your server surfer.nmr.mgh.harvard.edu.
RAS coordinates of the unlabeled area are -31,-27,-9.
Thank you in advance,

Antonin



Dear Antonin,

It is difficult to see what’s going on in the images you sent. Would you mind

uploading the subject, or at least sending us the image without the

segmentation overlaid (and ideally, a sagittal view as well)?

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com





From:  on behalf of Antonin Skoch



Reply-To: Antonin Skoch , Freesurfer support list



Date: Tuesday, 2 July 2019 at 21:43

To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: [Freesurfer] Doubts in hippocampal subfields labeling





External Email - Use Caution

Dear experts,



I noticed that systematically in most of my subjects there is area in

hippocampal region, labeled in aseg as hippocampus, but NOT labeled as

hippocampus in hippocampal subfields segmentation (it has zero value there).

See screenshots with norm.mgz overlaid by 1) aseg, 2) hippocampal subfields

segmentation.



According to T1 and T2 signal, it should neither be white matter and also

probably not a ventricle/CSF. Neocortex is not located here.

It has similar signal intensity as hippocampus, so I think that it should be

hippocampus, but I am puzzled by hippocampal subfields segmentation results

there. Why it is not labeled?



Could you please help me to clarify this? My concern is to correctly label this

area.

I could upload the example subject if it is of any help.



Regards,



Antonin Skoch
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Re: [Freesurfer] Doubts in hippocampal subfields labeling

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Antonin,
It is difficult to see what’s going on in the images you sent. Would you mind 
uploading the subject, or at least sending us the image without the 
segmentation overlaid (and ideally, a sagittal view as well)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Antonin Skoch 

Reply-To: Antonin Skoch , Freesurfer support list 

Date: Tuesday, 2 July 2019 at 21:43
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Doubts in hippocampal subfields labeling


External Email - Use Caution
Dear experts,

I noticed that systematically in most of my subjects there is area in 
hippocampal region, labeled in aseg as hippocampus, but NOT labeled as 
hippocampus in hippocampal subfields segmentation (it has zero value there).
See screenshots with norm.mgz overlaid by 1) aseg, 2) hippocampal subfields 
segmentation.

According to T1 and T2 signal, it should neither be white matter and also 
probably not a ventricle/CSF. Neocortex is not located here.
It has similar signal intensity as hippocampus, so I think that it should be 
hippocampus, but I am puzzled by hippocampal subfields segmentation results 
there. Why it is not labeled?

Could you please help me to clarify this? My concern is to correctly label this 
area.
I could upload the example subject if it is of any help.

Regards,

Antonin Skoch
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Re: [Freesurfer] T2 seq. for hippocampus ?? {Disarmed}

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

1x1x3 is a no-no.
The 1x1x1 FLAIR may or may not help; it’s hard to tell (especially without 
seeing the images!).
But I would try both T1 and T1+FLAIR, and see what happens ;-)

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Aaron Tanenbaum 

Reply-To: Freesurfer support list 
Date: Tuesday, 25 June 2019 at 15:23
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2 seq. for hippocampus ??


External Email - Use Caution
Sorry sent that last email by accident. Here is the finished version

Eugenio,
You said the T1+T2 would be best. The T2 Nik has is not 1mm isotropic but the 
Flair is.  Is a FLAIR in general not beneficial. Can you please elaborate.

On Tue, Jun 25, 2019 at 2:20 PM Aaron Tanenbaum 
mailto:aaron.b.tanenb...@gmail.com>> wrote:
Eugenio,
You said the T1+T2 would be best. The T2 Nik has is not 1mm isotropic but the 
Flair is.  Is a FLAIR in general not benifisiol

On Fri, May 18, 2018 at 2:02 PM Anik Dar 
mailto:aniqa...@gmail.com>> wrote:

External Email - Use Caution
Hi All,

I have 1x1x3 cubic mm T2 and 1x1x1 cubic mm FLAIR, in addition to 1x1x1 cubic 
mm MPRAGE. Can you please let me know whether I should use only T1 or should I 
use one of the additional seq. for hippocampal subfield segmentation ?

cheers

Nik
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Re: [Freesurfer] Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear David,

These are all great questions.

ASEG covers more voxels: the segmentations from the HA module are leaner than 
their ASEG counterparts (the volumes are very highly correlated, though). This 
is because the HA module operates at higher resolution, and also because an 
algorithm is expected to have more false positives when you need to label 
*every voxel* as something.

Large portions of AAA are marked as cerebral cortex: when building the amygdala 
atlas, our anatomy experts noticed that parts of the amygdala were labelled as 
cortex by ASEG. This was corrected in the HA module, which we believe is more 
accurate in that region.

Mismatch between segmentations and volumes: these can happen because the volume 
is not computed with the hard segmentations (i.e., simply counting voxels), but 
using soft segmentations instead. So, there are voxels that may contribute to 
the volume but do not appear in the segmentation because another label was more 
likely at that location.

I hope this helps.

/Eugenio



--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of David S Lee 

Reply-To: Freesurfer support list 
Date: Tuesday, 25 June 2019 at 15:03
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Reposting a Question RE: Hippocampal/Amygdala 
subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors


External Email - Use Caution
Hello Bruce,

Thanks for responding back. To your question RE: "what does the aseg look like 
in those cases? That is, is it the hippo/amygdala stuff failing or is the root 
cause further back in the stream (something that caused a bad aseg)"

In all 5 cases I mentioned, ASEG looks fine. In other words, ASEG masks for 
both Amygdala and Hippocampus cover the appropriate voxels relative to 
subjects' T1 space. However, in all cases (116 subjects I looked at) the latest 
subfield segmentation seem to *underestimate these regions, meaning ASEG always 
covers more voxels.

Along those lines, large portions of AAA regions are usually marked as 
"Cerebral Cortex" in ASEG. And the biggest issue again is that though AAA for 3 
subjects are not visible in subfield segmentation mask, I get volumetric 
output. In one case (Screenshot attached), R AAA has single voxel allocated, 
yet the volume is greater than the Left side which covers more space.

Also for the 2 cases in which medial nuclei are marked as Putamen (Screenshot 
attached), ASEG of putamen and amygdala looks good, but the problematic voxels 
are darker compared to neighboring voxels (Screenshot attached). This could be 
tissue damage and/or incorrect identification of "vessel".

What would be your recommendation to resolve these issues?

Thanks for your time,


--
David S. Lee
Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Re: [Freesurfer] I have a question for "Segmentation of thalamic nuclei."

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Gwang-Won,
What version are you using? What’s the output of “recon-all –version”?
Cheers,
/Eugenio


--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Gwang-Won Kim 

Reply-To: Freesurfer support list 
Date: Friday, 21 June 2019 at 15:25
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] I have a question for "Segmentation of thalamic nuclei."


External Email - Use Caution

Dear there,

I tried to process “Segmentation of thalamic nuclei” using source the 
FreeSurfer development version.
I filled out “segmentThalamicNuclei.sh  bert  [SUBJECTS_DIR]”.
In two computer, there were massages “segmentThamicNuclei.sh: Command not 
found” and “bash: segmentThamicNuclei.sh: command not found”, respectively.
How do I resolve this problem?

Best,
Gwang-Won Kim

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Re: [Freesurfer] hippocampal subfields error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

OK yes this is a problem with the main recon-all stream. It’d have been a 
miracle for the subfield module to recover from that…
At this point, I’ll defer to Doug / Bruce.
Cheers,
/E
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of "Mennecke, 
Angelika" 
Reply-To: Freesurfer support list 
Date: Monday, 17 June 2019 at 10:11
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields error


External Email - Use Caution
Dear Eugenio,

attached you’ll find the picture. Looks as though the left hippocampus has 
erroneously been attributed to gray matter.

Cheers, Angelika

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Iglesias 
Gonzalez, Eugenio
Gesendet: Montag, 17. Juni 2019 15:49
An: Freesurfer support list
Betreff: Re: [Freesurfer] hippocampal subfields error


External Email - Use Caution
Dear Angelika,
Can you please send us a screenshot of the inaccurate T1 segmentation?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of "Mennecke, 
Angelika" 
Reply-To: Freesurfer support list 
Date: Monday, 17 June 2019 at 06:36
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal subfields error


External Email - Use Caution
Hi all,

I’m doing hippocampal subfields analysis with freesurfer 6.0 with T1 and high 
resolution T2 data from a 7T MRT. With at least one of my datasets Matlab 
throws an error during the hippocampal-subfields-T2 –pipeline:

Making Unknown map to reduced label 14
Computing hyperparameters for estimation of Gaussians of T2 data
Error using |
Inputs must have the same size.

Error in segmentSubjectT2_autoEstimateAlveusML (line 1064)

With other patients, the pipeline on the T2 images is correctly working without 
errors. I’m wondering what is causing this error and whether there is something 
I can do to avoid it?

As far as I can see, the only difference between the “error” dataset and the 
others is that hippocampal subfields-T1 is also not calculated correctly. It 
finishes without errors, but the final result does not cover the hippocampus 
correctly (probably due to a T1-hypointense cyst in the hippocampus of that 
patient).

Best regards,

Angelika
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Re: [Freesurfer] hippocampal subfields error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Angelika,
Can you please send us a screenshot of the inaccurate T1 segmentation?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of "Mennecke, 
Angelika" 
Reply-To: Freesurfer support list 
Date: Monday, 17 June 2019 at 06:36
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal subfields error


External Email - Use Caution
Hi all,

I’m doing hippocampal subfields analysis with freesurfer 6.0 with T1 and high 
resolution T2 data from a 7T MRT. With at least one of my datasets Matlab 
throws an error during the hippocampal-subfields-T2 –pipeline:

Making Unknown map to reduced label 14
Computing hyperparameters for estimation of Gaussians of T2 data
Error using |
Inputs must have the same size.

Error in segmentSubjectT2_autoEstimateAlveusML (line 1064)

With other patients, the pipeline on the T2 images is correctly working without 
errors. I’m wondering what is causing this error and whether there is something 
I can do to avoid it?

As far as I can see, the only difference between the “error” dataset and the 
others is that hippocampal subfields-T1 is also not calculated correctly. It 
finishes without errors, but the final result does not cover the hippocampus 
correctly (probably due to a T1-hypointense cyst in the hippocampus of that 
patient).

Best regards,

Angelika
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Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Yes! The changes will probably be tiny, though.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Boris Rauchmann 

Reply-To: Freesurfer support list 
Date: Wednesday, 5 June 2019 at 15:12
To: Freesurfer support list 
Subject: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the 
amygdala


External Email - Use Caution
Dear all,

depends the Segmentation of hippocampal subfields and nuclei of the amygdala 
pipeline on the fs-recon all pipeline? I made some changes mainly by defining 
control points to fix intensity normalization in my dataset and rerun recon 
all. I´m not sure if I also have to rerun the subfields pipeline now?

Thanks,
Boris

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Re: [Freesurfer] longitudinal subfields exited with ERRORS

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Jaime,
This is indeed a funny error. The left side runs to completion, and then the 
right side dies right away…
Is the problem reproducible? Does it happen with other subjects, too?
Kind regards,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Jaime Gomez 

Reply-To: Freesurfer support list 
Date: Wednesday, 29 May 2019 at 03:52
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] longitudinal subfields exited with ERRORS


External Email - Use Caution

Hello FreeSurfer Developers,



I'm trying to run segmentHA_T1_long.sh

  ERROR: MATLAB is exiting because of fatal error
/Applications/freesurfer/bin/run_SegmentSubfieldsT1Longitudinal.sh: line 37: 
49858 Killed: 9
"${exe_dir}"/SegmentSubfieldsT1Longitudinal.app/Contents/MacOS/SegmentSubfieldsT1Longitudinal
 $args
Darwin jaimes-Mac-Pro.local 18.2.0 Darwin Kernel Version 18.2.0:
Fri Oct  5 19:41:49 PDT 2018; root:xnu-4903.221.2~2/RELEASE_X86_64 x86_64

longitudinal subfields exited with ERRORS at Tue May 28 17:53:02 CEST 2019


I've searched the list and no similar errors have been reported.
Does anyone have any thoughts on how to trouble-shoot this one?
Also, Ive attached the recon-all.log in case it's of any use.



1) freesurfer-darwin-OSX-ElCapitan-dev-20190328-6241d26

2) Platform: macOS 10.14.1 (18B75)

3) Darwin jaimes-Mac-Pro.local 18.2.0 Darwin Kernel Version 18.2.0:
Fri Oct  5 19:41:49 PDT 2018; root:xnu-4903.221.2~2/RELEASE_X86_64 x86_64:16 
UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

4) long-hippocampal-subfields-T1.log: see attached

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Re: [Freesurfer] brainstem - partial volume effects

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Dusan,
Volumes are computed from soft segmentations, which ameliorates the problems 
with partial voluming with the surrounding CSF.
Kind regards,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Dusan Hirjak 

Reply-To: Freesurfer support list 
Date: Thursday, 16 May 2019 at 16:21
To: Freesurfer support list , 
"freesurfer-requ...@nmr.mgh.harvard.edu" 

Subject: [Freesurfer] brainstem - partial volume effects


External Email - Use Caution
Dear Freesurfer experts,

I have one question regarding the partial volume effects on brainstem volume 
when using Freesurfer 6.0 brainstem tool: Could partial volume effects in a 
comparatively small sample (n=92) have an influence on the results (group 
difference in SCP volumes)? How should I deal with this effect? Any suggestions 
are welcome.

best regards

Dusan

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Re: [Freesurfer] Thalamus segmentation {Disarmed}

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Zheng,
The reticular nucleus is in the atlas and we use it to fit it to the image, but 
its segmentation is not always reliable and that’s why we don’t provide it (nor 
its volume).
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of 郑凤莲 

Reply-To: Freesurfer support list 
Date: Wednesday, 15 May 2019 at 11:11
To: Freesurfer support list 
Subject: [Freesurfer] Thalamus segmentation {Disarmed}


External Email - Use Caution
Dear Experts,
When I used the recent FS version for thalamus segmentation, I have segmented 
it sucessfully. However, in the .txt file, there are no the volume of 
lateraldorsal and reticular nuclei. Is there any error in my processing steps? 
I don't know the reason for this cese.
I am looking forward to your reply. Thanks very much in advance.
Sincerely,
Zheng

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[Image removed by sender.]

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[Freesurfer] Postdoc position available

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear all,

We are looking for a postdoc in our ERC project, with two main purposes. First, 
to improve the 3D histology reconstruction tools that we have been developing 
to build an ultra-high resolution atlas of the brain using histology. And 
second, to collaborate in the development of segmentation techniques to apply 
the atlas to the automated analysis of in vivo MRI scans, which hope to 
integrate with FreeSurfer. Our research line is moving toward the integration 
of classic model-based algorithms with modern deep learning techniques (see for 
instance https://arxiv.org/abs/1904.11319).

The postdoc will join the Centre for Medical Image Computing (CMIC) at 
University College London (UCL), which will be soon co-located with the new UCL 
 Artificial Intelligence Centre, located on High Holborn in central London. In 
addition, the postdoc will have the opportunity of visiting our lab at the 
Martinos Center in Boston.

More information here:

www.jeiglesias.com

https://tinyurl.com/y4hv275f


--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

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Re: [Freesurfer] Hippocampal subfields segmentation template

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Wu,
The “templates” are probabilistic atlases with no image intensities. All you 
can look at is images like the ones in the top panel of Figure 5 in the paper.
If you want to generate these, let me know and I’ll show you instructions (it’s 
a bit tricky, because it requires  combining different versions of FreeSurfer….)
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Dongsheng Wu 

Reply-To: Freesurfer support list 
Date: Tuesday, 30 April 2019 at 04:38
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields segmentation template


External Email - Use Caution
Dear FS developers,

I uesd the ''recon-all command'' to get the volumes of the hippocampal 
subfields, and we would like to perform further analysis with  these subfields 
in MNI. Could you show us the templates which are used to perform hippocampal 
segmentation (CA1, CA3, HATA, etc.)?


Best wishes,
Wu





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Re: [Freesurfer] Thalamic segmentation

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Zheng
One of the other developers can help you with Freeview.
But, as a workaround, you can always use an earlier version of Freeview, and 
load the lookup table of the Dev version.
Cheers
Eugenio

Sent from mobile, please excuse brevity and typos

--

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 郑凤莲 

Sent: Thursday, April 18, 2019 5:59:15 AM
To: Freesurfer support list
Subject: [Freesurfer] Thalamic segmentation


External Email - Use Caution

Hi Expert,

In the latest version of FS, I have segmented the thalamic successfully. But I 
can't use Freeview to show the segmentation map. There is an error :"freeview: 
/usr/lib/libpng15.so.15:version 'PNG15_0' not found (required by 
/opt/freesurfer/bin/../lib/qt/lib/libQt5Gui.so.5)". May be I didn't install the 
latest version of Freeview. However, I can't find this version on 
Freesurferwiki.  Could you share me the install steps and the latest version? 
Thanks very much for your help.

Sincerely,
Zheng





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Re: [Freesurfer] Hippocampal subfield version

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Emily,
I suspect that you’re mixing versions. Please make sure that you source the dev 
version.
Cheers,
/E

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Emily Schwartz 

Reply-To: Freesurfer support list 
Date: Thursday, 11 April 2019 at 13:02
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal subfield version


External Email - Use Caution
Hi Eugenio,

Thank you so much. I downloaded the development version, but when I run
"segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]," 
it says command not found.

After I download the runtime2014 version, I get the MCRv84 folder, but when I 
try to run a subject through the hippocampal subfield it gives me an error and 
tells me to download runtime2012b. Once I do that I also get the MCRv80 folder 
and am able to run the hippocampal segmentation, but I assume this is the 2017 
version since I cannot run the amygdala segmentation. I am not sure what I am 
doing wrong when I download the 2018 dev version.

Best,
Emily

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, 
Eugenio [e.igles...@ucl.ac.uk]
Sent: Thursday, April 04, 2019 5:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfield version

External Email - Use Caution
Hi Emily,
You need to download the dev version, but run the subfield/amygdala volume on 
cases reconned with FS6.0.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Emily Schwartz 

Reply-To: Freesurfer support list 
Date: Wednesday, 3 April 2019 at 15:44
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfield version


External Email - Use Caution
Hello FS experts,

I was planning to use the hippocampal subfield segmentation module in 
FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei 
of the amygdala segmentation, but realized I need to download the development 
version in order to do that. Is there any reason why I shouldn't use the 
development version over the 6.0 release?

Thank you in advance.

Best,
Emily


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Re: [Freesurfer] Hippocampal subfield version

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Emily,
You need to download the dev version, but run the subfield/amygdala volume on 
cases reconned with FS6.0.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Emily Schwartz 

Reply-To: Freesurfer support list 
Date: Wednesday, 3 April 2019 at 15:44
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfield version


External Email - Use Caution
Hello FS experts,

I was planning to use the hippocampal subfield segmentation module in 
FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei 
of the amygdala segmentation, but realized I need to download the development 
version in order to do that. Is there any reason why I shouldn't use the 
development version over the 6.0 release?

Thank you in advance.

Best,
Emily


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Re: [Freesurfer] segmentHA_T1.sh

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

How about quantifyHAsubregions.sh?
Cheers,
/E

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Daniel Callow 

Reply-To: Freesurfer support list 
Date: Monday, 1 April 2019 at 13:19
To: Freesurfer support list 
Subject: [Freesurfer] segmentHA_T1.sh


External Email - Use Caution
I thought a solution like this might work but there seems to be an issue 
reading in the file.

I tried using mri_segstats on the .mgz file like this to create the stats file 
as this is what I do for my dt_recon results however it doesn't seem to work 
when I just want the volume stats?


mri_segstats --seg 
/Volumes/DANIEL/freesurf/${cond}.${subj}.long.base_${subj}/mri/lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz
 --ctab /Applications/freesurfer_dev/FreeSurferColorLUT.txt --id 226 --id 231 
--id 232 --sum ${SUBJECTS_DIR}/${cond}.${subj}/stats/lhipp_volume.stats





Any ideas on how to make this work or a potential other work around.



Best,
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298
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Re: [Freesurfer] segmentHA_T1_long.sh HBT issue

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Daniel,
This is weird. Can you please send us
lh.hippoAmygLabels-T1.long.v21.*.mgz
for a sample subject?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Daniel Callow 

Reply-To: Freesurfer support list 
Date: Friday, 29 March 2019 at 11:56
To: Freesurfer support list 
Subject: [Freesurfer] segmentHA_T1_long.sh HBT issue


External Email - Use Caution
Hello,

I have run  segmentHA_T1_long.sh from the developer freesurfer version and am 
looking to segment and visualize the head body and tail of the left and right 
hippocampus.

However, when looking at the 
lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz and other files for each 
subject I see only amygdala and subfield segmentations. How do I use the 
outputs to create a head body and tail segmentation that I can visualize and 
extract values from?

Best,
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298
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Re: [Freesurfer] Conversion of thalamic nuclei labels {Disarmed}

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks, Valentina.
The thalamic nuclei were included in the FreeSurfer lookup table in the 
development version, so I doubt they’d be included in the FreeSurfer HSV. Is it 
possible to add them manually?
Also: why don’t you use Freeview to visualize your niftis?
Cheers,
/E

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com


From: Valentina Mancini 
Date: Wednesday, 27 March 2019 at 10:08
To: "Iglesias Gonzalez, Eugenio" , Freesurfer support 
list 
Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels


Hi Eugenio,



Yes, when I move the cursor I can see different pixel values corresponding to 
the different areas of the thalamus.

In FSLeyes you can select different lookup tables, and there is one called 
"Freeseurfer HSV", but it doesn't work anyway.



However, I used FSLeyes only because it was the default programm to open nifti 
files, but it was the same in SPM ad Conn.

Can you please suggest me any other way to open the nifti file with its lookup 
table?

As I was planning to use it in SPM, the ideal would be to manage to visualize 
the different subnuclei in SPM/Conn.



Best,





Valentina

____
Da: Iglesias Gonzalez, Eugenio 
Inviato: mercoledì 27 marzo 2019 14:55:00
A: Freesurfer support list
Cc: Valentina Mancini
Oggetto: Re: [Freesurfer] Conversion of thalamic nuclei labels

Hi Valentina,
I've never used FSLeyes but I suspect you'd need a lookup table to visualize 
the nuclei properly. Do you see different pixel values when you move your 
cursor over the different areas of the thalamus in FSLeyes?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeiglesias.com=02%7C01%7Ce.iglesias%40ucl.ac.uk%7Cfd1e3c21f6bb420769df08d6b2bdb777%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636892925227688578=QTSNSIU2i8dYs0sShmUrI7vitjOBg62WZSiQGKiQt9A%3D=0>


On 27/03/2019, 09:53, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Bruce Fischl"  wrote:

and your full command line for conversion?
    On Wed, 27 Mar 2019, Iglesias
Gonzalez, Eugenio wrote:

>
> External Email - Use Caution
>
> Dear Valentina
> Resolution should not be affected by MRI_convert. Can you please send us 
an example/screen capture?
> Cheers
> Eugenio
>
> Sent from mobile, please excuse brevity and typos
>
> 

> From: Valentina Mancini 
> Sent: Wednesday, March 27, 2019 5:56:34 AM
    > To: freesurfer@nmr.mgh.harvard.edu
> Cc: Iglesias Gonzalez, Eugenio
> Subject: Conversion of thalamic nuclei labels
>
> Dear all,
>
>
> I ran the thalamic segmentation implemented in FreeSurfer and, according 
to visual inspection, I got
> nice results with a good delineation of all the nuclei.
>
> Then, I wanted to use the label of the thalamic nuclei to select an ROI 
in the MGN and the MD to
> perform functional connectivity with cortical regions in SPM.
>
> Therefore, I converted the outputs of the segmentation
> (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into 
nifti files by using the
> command "mri_convert .mgz  .nii".
>
> However, the resulting labels of the thalamus have a different resolution 
and I cannot visualize
> anymore the different thalamic subnuclei but only the entire thalamus.
>
>
>
> Do you have any suggestion to convert thalamic labels into nifti without 
losing the different
> subnuclei?
>
> Do you think that the thalamic segmentation is accurate enough to be used 
to perform functional
> connectivity?
>
>
>
> Thank you and best regards,
>
>
>
> Valentina Mancini
>
>
>
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Re: [Freesurfer] Conversion of thalamic nuclei labels

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Valentina,
I've never used FSLeyes but I suspect you'd need a lookup table to visualize 
the nuclei properly. Do you see different pixel values when you move your 
cursor over the different areas of the thalamus in FSLeyes?
Cheers,
/Eugenio

-- 
Juan Eugenio Iglesias
 
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
 
Research staff
Martinos Center for Biomedical Imaging 
Massachusetts General Hospital 
 
Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology
 
Lecturer on Radiology
Harvard Medical School
 
http://www.jeiglesias.com 
 

On 27/03/2019, 09:53, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Bruce Fischl"  wrote:

and your full command line for conversion?
On Wed, 27 Mar 2019, Iglesias 
    Gonzalez, Eugenio wrote:

> 
> External Email - Use Caution
> 
> Dear Valentina
> Resolution should not be affected by MRI_convert. Can you please send us 
an example/screen capture?
> Cheers
> Eugenio
> 
> Sent from mobile, please excuse brevity and typos
> 
> 

> From: Valentina Mancini 
> Sent: Wednesday, March 27, 2019 5:56:34 AM
    > To: freesurfer@nmr.mgh.harvard.edu
> Cc: Iglesias Gonzalez, Eugenio
> Subject: Conversion of thalamic nuclei labels  
> 
> Dear all,
> 
> 
> I ran the thalamic segmentation implemented in FreeSurfer and, according 
to visual inspection, I got
> nice results with a good delineation of all the nuclei.
> 
> Then, I wanted to use the label of the thalamic nuclei to select an ROI 
in the MGN and the MD to
> perform functional connectivity with cortical regions in SPM.
> 
> Therefore, I converted the outputs of the segmentation
> (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into 
nifti files by using the
> command "mri_convert .mgz  .nii".
> 
> However, the resulting labels of the thalamus have a different resolution 
and I cannot visualize
> anymore the different thalamic subnuclei but only the entire thalamus.
> 
>  
> 
> Do you have any suggestion to convert thalamic labels into nifti without 
losing the different
> subnuclei?
> 
> Do you think that the thalamic segmentation is accurate enough to be used 
to perform functional
> connectivity?
> 
> 
> 
> Thank you and best regards,
> 
> 
> 
> Valentina Mancini
> 
> 
>


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Re: [Freesurfer] Conversion of thalamic nuclei labels

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Valentina
Resolution should not be affected by MRI_convert. Can you please send us an 
example/screen capture?
Cheers
Eugenio

Sent from mobile, please excuse brevity and typos


From: Valentina Mancini 
Sent: Wednesday, March 27, 2019 5:56:34 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Iglesias Gonzalez, Eugenio
Subject: Conversion of thalamic nuclei labels


Dear all,


I ran the thalamic segmentation implemented in FreeSurfer and, according to 
visual inspection, I got nice results with a good delineation of all the nuclei.

Then, I wanted to use the label of the thalamic nuclei to select an ROI in the 
MGN and the MD to perform functional connectivity with cortical regions in SPM.

Therefore, I converted the outputs of the segmentation 
(ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into nifti 
files by using the command "mri_convert .mgz  .nii".

However, the resulting labels of the thalamus have a different resolution and I 
cannot visualize anymore the different thalamic subnuclei but only the entire 
thalamus.



Do you have any suggestion to convert thalamic labels into nifti without losing 
the different subnuclei?

Do you think that the thalamic segmentation is accurate enough to be used to 
perform functional connectivity?



Thank you and best regards,



Valentina Mancini
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Re: [Freesurfer] Thalamic nuclei segmentation

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Zheng,
Did the segmentation run to completion?
Can you please send us the output?
Cheers
Eugenio

Sent from mobile, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 郑凤莲 

Sent: Wednesday, March 27, 2019 3:09:21 AM
To: Freesurfer support list
Subject: [Freesurfer] Thalamic nuclei segmentation


External Email - Use Caution

Hi experts,
I have segmented the thalamic nuclei into 25 nuclei using the new FS version. 
However, when I input "freeview -v nu.mgz -v 
ThalamicNuclei.v10.T1.mgz:colormap=lut ", there is no 3D atlas in Freeview, 
just nu.mgz. What's the matter? Please help me. I am looking forward to your 
reply. Thanks very much.
Sincerely,
Zheng




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Re: [Freesurfer] segmentHA_T1_long.sh error {Disarmed}

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Daniel,
Can you please give us some more information? How did you call the script? Did 
you get any other output? Did the running case complete without errors?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com


From:  on behalf of Daniel Callow 

Reply-To: Freesurfer support list 
Date: Sunday, 24 March 2019 at 13:28
To: Freesurfer support list 
Subject: [Freesurfer] segmentHA_T1_long.sh error


External Email - Use Caution
Hello,

When trying to run the segmentHA_T1_long.sh command on my data I get the 
following error log posted below (I ran several versions of a for loop and got 
issues with all of them). I closed out the matlab browsers and am retrying the 
code again to see if it is reproducible and so afar it is running. I just 
wanted to get an idea if this is a known problem.

Best,
Daniel


   Segmentation violation detected at Sat Mar 23 18:31:18 2019


Configuration:
  Crash Decoding : Disabled
  Current Visual : Quartz
  Default Encoding   : ISO-8859-1
  MATLAB Architecture: maci64
  MATLAB Root: /Applications/freesurfer_dev/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 
20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
  Processor ID   : x86 Family 6 Model 44 Stepping 2, GenuineIntel
  Software OpenGL: 0
  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java 
HotSpot(TM) 64-Bit Server VM mixed mode
  Window System  : Quartz

Fault Count: 1


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 7f9c4806f000  RBX = 7f9c4806f000
  RCX = 79ab52d0  RDX = 00011392e97e
  RSP = 7f9c4806f000  RBP = 9b6309ab52d0
  RSI = 7f9c47637ba0  RDI = 

   R8 = 7f9c4a0a3270   R9 = 7f9c4806f000
  R10 = 00011e59176a  R11 = 
  R12 = 79ab5330  R13 = 00011377c3c7
  R14 = 79ab53a0  R15 = 00011e591777

  RIP = 0001188c5f40  RFL = 7f9c4a0a3270

   CS = 9b6300305bc3   FS = 00011e59176a   GS = 7f9c4806f1e8

Stack Trace (from fault):
[  0] 0x0001075f6e64 
/Applications/freesurfer_dev/MCRv84//bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052
[  1] 0x0001075faa2a 
/Applications/freesurfer_dev/MCRv84//bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906
[  2] 0x0001075fa477 
/Applications/freesurfer_dev/MCRv84//bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119
[  3] 0x00010c443b7a 
/Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146
[  4] 0x00010c443e58 
/Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880
[  5] 0x00010c441733 
/Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275
[  6] 0x7fffbac1cb3a   
/usr/lib/system/libsystem_platform.dylib+00011066 _sigtramp+0026
[  7] 0x00011377d6f8 
/Applications/freesurfer_dev/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568
 _ZN23JNI_ArgumentPusherVaArg7iterateEy+
[  8] 0x00011376dd67 
/Applications/freesurfer_dev/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679
 jni_GetMethodID+0126
[  9] 0x00010f8ca271 
/Applications/freesurfer_dev/MCRv84//bin/maci64/libmwjmi.dylib+00160369 
_Z12mljGetMethodP7_jclassPKcS2_+0049
[ 10] 0x00011ddec366 
/Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+00598886 
_ZN2ui14JavaScreenData20getPrimaryScreenRectEv+0150
[ 11] 0x00011ddf1ef4 
/Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+00622324 
_ZN10ScreenImpl13getScreenSizeEv+0036
[ 12] 0x00011ddf02e2 
/Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+00615138 
_ZNK2ui24RootScreenAndPointerImpl13getScreenSizeEv+0018
[ 13] 0x00011ddf4f58 
/Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+00634712 
_ZN2ui4Root17getScreenSizeImplEPN4mcos11COSPropInfoEPNS1_9COSClientEPNS1_12COSInterfaceE+0040
[ 14] 0x00011e22bd13 
/Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+05053715 

Re: [Freesurfer] Thalamic nuclei longitudinal analysis

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Antti,
There’s no specific longitudinal version of the thalamic nuclei yet (hopefully 
one day…)
You could naively segment the subjects in a cross-sectional fashion, but I’d 
highly recommend that you run the main longitudinal stream first 
(https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) and then run 
the thalamic module on the longitudinally processed subjects.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com


From:  on behalf of Antti Cajanus 

Reply-To: Freesurfer support list 
Date: Wednesday, 13 March 2019 at 08:46
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Thalamic nuclei longitudinal analysis


External Email - Use Caution
Dear FS experts,

I'm using the thalamic nuclei segmentation on T1-images. Is it possible to 
perform longitudinal analysis with this data, or could I just segment the 
different time points separately to see volume reduction of specific nuclei?

Best,
Antti Cajanus
PhD student
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Re: [Freesurfer] Thalamic Nuclei {Disarmed}

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Zheng,
You’ll need a more recent dev version to use the thalamic nucle segmentation.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com


From:  on behalf of 郑凤莲 

Reply-To: Freesurfer support list 
Date: Tuesday, 12 March 2019 at 04:13
To: Freesurfer support list 
Subject: [Freesurfer] Thalamic Nuclei {Disarmed}


External Email - Use Caution
Hi Experts,
I am using Freesurfer dev version for the segmentation of thalamic nulei. 
Previously, I have used this version for amygdala and hippocampus segmentation. 
However, the segmentThalamicNuclei.sh file can't be found in this version. Is 
there another new version for the thalamic? Could you share me the new version?
Thanks very much in advance. Look forward to your reply.
Sincerely,
Zheng

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"maas.mail.163.com" claiming to be 

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邮箱：zhengfenglian0...@163.com


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Re: [Freesurfer] hippocampus subfield division

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Yixin,
Yes, give segmentHA_T1.sh a shot. You need to install the development version 
of FreeSurfer, though.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com


From:  on behalf of Yixin Ma 

Reply-To: Freesurfer support list 
Date: Monday, 11 February 2019 at 10:01
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampus subfield division


External Email - Use Caution
Hi Freesurfer experts,

I'm writing to ask about the hippocampus subfield division again. Last time, I 
gave you an example of the subject that I failed to run the hippocampal 
subfield division, and you told me that you were able to run the hippocampus 
subfield on your laptop. I was using the older command of recon-all -all -s 
bert -hippocampal-subfields-T1. Should I try to use the newer version: 
segmentHA_T1.sh bert [SUBJECTS_DIR]. Is that possible FreeSurfer upgrading is 
the reason that I failed to run a subject on my server recently (but I was able 
to run it before). Also, can I ask where can I find the file of segmentHA_T1.sh?

Thanks for your help.

Cheers,

Yixin
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Re: [Freesurfer] Thalamic segmentation questions

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Manoj,

First question:
The one without the suffix is defined at higher resolution, on a voxel grid 
that does not correspond to the standard FS space (where norm.mgz, aseg.mgz, 
etc. live).
The one with the suffix lives on the voxel grid of norm.mgz, aseg.mgz, etc
Both of them live in the physical RAS coordinates or the other volumes, that’s 
why they look similar when you open them of FreeView. But if you zoom in 
enough, you’ll notice that the one without the suffix has higher resolution.

Second question:
Yes, you first need to register, manually or (preferably) automatically, e.g., 
with BBregister, mri_robust_register, etc.
Then, you can run:mri_convert   moving.nii.gz  deformed.nii.gz  -rl  nu.mgz 
-at  [YOURTRANSFORMFILE.LTA]  -rt nearest

I hope this helps.

/Eugenio


--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com


From:  on behalf of Manoj Saranathan 

Reply-To: Freesurfer support list 
Date: Tuesday, 29 January 2019 at 19:15
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Thalamic segmentation questions


External Email - Use Caution
The thalamic nuclei segmentation produces 2 mgz files. One has the FS suffix 
and other does not. Is the latter without the FS in the native space? If I 
import and view in freeview, they look same. I want it in native space so I can 
do some Dice calculations.

My manual segmentations are on a different data set very close to but not 
necessarily perfectly aligned to the T1 data set used in recon-all. I can use 
the mri_conver -rl 'reslice like' option but it does not do any registrations 
does it? It just reslices it in the orientation of the file argument to -rl 
right. I assume have to manually affine register and propagate the warps if 
they are not aligned?

Thanks,
manoj



From: Manoj Saranathan
Sent: Tuesday, January 29, 2019 5:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Thalamic segmentation questions

The thalamic nuclei segmentation produces 2 mgz files. One has the FS suffix 
and other does not. Is the latter without the FS in the native space? If I 
import and view in freeview, they look same. I want it in native space so I can 
do some Dice calculations.

My manual segmentations are on a different data set very close to but not 
necessarily perfectly aligned to the T1 data set used in recon-all. I can use 
the mri_conver -rl 'reslice like' option but it does not do any registrations 
does it? It just reslices it in the orientation of the file argument to -rl 
right. I assume have to manually affine register and propagate the warps if 
they are not aligned?

Thanks,
manoj


From: Manoj Saranathan
Sent: Tuesday, January 29, 2019 5:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Thalamic segmentation questions

The thalamic registration produces 2 mgz files. One has the FS suffix and other 
does not. Is the latter without the FS in the native space? If I import and 
view in freeview, they look same. I want it in native space so I can do some 
Dice with manual segmentation.

The 'reslice like' option of mri_convert does not do any registrations does it? 
It just reslices it in the orientation of the file argument to -rl right. I 
assume have to manually register and propagate the warps if they are not 
aligned.

Thanks,
manoj



Manoj Saranathan
Associate Professor, Dept. of Medical Imaging
University of Arizona
Ph: 520-626-6531
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Re: [Freesurfer] Hippocampus subfield division error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks, Yixin.
It just ran to completion on my machine with FreeSurfer 6.0. Let me know if you 
want me to send you the output.
Did you notice this problem on other subjects?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com


From:  on behalf of Yixin Ma 

Reply-To: Freesurfer support list 
Date: Tuesday, 22 January 2019 at 10:09
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Hippocampus subfield division error


External Email - Use Caution
Hi Dr.
[Image removed by sender.] 
00246.zip[Image
 removed by sender.]
Iglesias

I have the problem of hippocampus subfield division not working. You mentioned 
that  I can upload one of the subjects as an example. I'm not sure what kinds 
of file do you want, so I uploaded the folder of the FreeSurfer reconstruction 
results, as attached. Thank you again for your help.

Best regards,

Yixin

On Fri, Jan 18, 2019 at 12:28 PM Yixin Ma 
mailto:yixin...@gmail.com>> wrote:
Hi,

The hippocampus subfields division problem happens on more than one subjects 
(~10). However, I have successfully run it on one subject (which is a little 
earlier in time, before I failed to run recent 10 subjects). Thank you for your 
help.

Best regards,

Yixin

-- Forwarded message -
From: Yixin Ma mailto:yixin...@gmail.com>>
Date: Fri, Jan 18, 2019 at 11:04 AM
Subject: Hippocampus subfield division error
To: mailto:freesurfer@nmr.mgh.harvard.edu>>

Hi FreeSurfer experts,

I'm writing to ask about the hippocampus subfields division in FreeSurfer 6.0.

I got an error message as attached, could you please help me with which part 
might have gone wrong? This subject's other recon-all worked but not for 
hippocampus subfields division.

Thank you for your help.

Best regards,

Yixin

[ > In segmentSubjectT1_autoEstimateAlveusML at 325]
Reading contexts of file 
/usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt
--
Making Lateral-nucleus map to reduced label 1
Making Paralaminar-nucleus map to reduced label 1
Making Basal-nucleus map to reduced label 1
Making Accessory-Basal-nucleus map to reduced label 1
Making Corticoamygdaloid-transitio map to reduced label 1
Making Central-nucleus map to reduced label 1
Making Cortical-nucleus map to reduced label 1
Making Medial-nucleus map to reduced label 1
Making Anterior-amygdaloid-area-AAA map to reduced label 1
--
Making alveus map to reduced label 2
Making Hippocampal_tail map to reduced label 2
Making HATA map to reduced label 2
Making fimbria map to reduced label 2
Making parasubiculum map to reduced label 2
Making hippocampal-fissure map to reduced label 2
--
Making Left-Cerebral-Cortex map to reduced label 3
--
Making Left-Cerebral-White-Matter map to reduced label 4
--
Making Left-Lateral-Ventricle map to reduced label 5
--
Making Left-choroid-plexus map to reduced label 6
--
Making Unknown map to reduced label 7
--
Making Left-VentralDC map to reduced label 8
--
Making Left-Putamen map to reduced label 9
--
Making Left-Pallidum map to reduced label 10
--
Making Left-Thalamus-Proper map to reduced label 11
--
Making Left-Accumbens-area map to reduced label 12
--
Making Left-Caudate map to reduced label 13
Error using segmentSubjectT1_autoEstimateAlveusML (line 348)
The vector of prior probabilities in the mesh nodes must always sum to one over 
all classes
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Re: [Freesurfer] Hippocampus subfield division error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks! Can you please upload one of the subjects that fail?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com


From:  on behalf of Yixin Ma 

Reply-To: Freesurfer support list 
Date: Friday, 18 January 2019 at 12:28
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Hippocampus subfield division error


External Email - Use Caution
Hi,

The hippocampus subfields division problem happens on more than one subjects 
(~10). However, I have successfully run it on one subject (which is a little 
earlier in time, before I failed to run recent 10 subjects). Thank you for your 
help.

Best regards,

Yixin

-- Forwarded message -
From: Yixin Ma mailto:yixin...@gmail.com>>
Date: Fri, Jan 18, 2019 at 11:04 AM
Subject: Hippocampus subfield division error
To: mailto:freesurfer@nmr.mgh.harvard.edu>>

Hi FreeSurfer experts,

I'm writing to ask about the hippocampus subfields division in FreeSurfer 6.0.

I got an error message as attached, could you please help me with which part 
might have gone wrong? This subject's other recon-all worked but not for 
hippocampus subfields division.

Thank you for your help.

Best regards,

Yixin

[ > In segmentSubjectT1_autoEstimateAlveusML at 325]
Reading contexts of file 
/usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt
--
Making Lateral-nucleus map to reduced label 1
Making Paralaminar-nucleus map to reduced label 1
Making Basal-nucleus map to reduced label 1
Making Accessory-Basal-nucleus map to reduced label 1
Making Corticoamygdaloid-transitio map to reduced label 1
Making Central-nucleus map to reduced label 1
Making Cortical-nucleus map to reduced label 1
Making Medial-nucleus map to reduced label 1
Making Anterior-amygdaloid-area-AAA map to reduced label 1
--
Making alveus map to reduced label 2
Making Hippocampal_tail map to reduced label 2
Making HATA map to reduced label 2
Making fimbria map to reduced label 2
Making parasubiculum map to reduced label 2
Making hippocampal-fissure map to reduced label 2
--
Making Left-Cerebral-Cortex map to reduced label 3
--
Making Left-Cerebral-White-Matter map to reduced label 4
--
Making Left-Lateral-Ventricle map to reduced label 5
--
Making Left-choroid-plexus map to reduced label 6
--
Making Unknown map to reduced label 7
--
Making Left-VentralDC map to reduced label 8
--
Making Left-Putamen map to reduced label 9
--
Making Left-Pallidum map to reduced label 10
--
Making Left-Thalamus-Proper map to reduced label 11
--
Making Left-Accumbens-area map to reduced label 12
--
Making Left-Caudate map to reduced label 13
Error using segmentSubjectT1_autoEstimateAlveusML (line 348)
The vector of prior probabilities in the mesh nodes must always sum to one over 
all classes
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Re: [Freesurfer] Hippocampus subfield division error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Yixin,
Does this happen for all subjects, or only one?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com


From:  on behalf of Yixin Ma 

Reply-To: Freesurfer support list 
Date: Friday, 18 January 2019 at 11:06
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampus subfield division error


External Email - Use Caution
Hi FreeSurfer experts,

I'm writing to ask about the hippocampus subfields division in FreeSurfer 6.0.

I got an error message as attached, could you please help me with which part 
might have gone wrong? This subject's other recon-all worked but not for 
hippocampus subfields division.

Thank you for your help.

Best regards,

Yixin

[ > In segmentSubjectT1_autoEstimateAlveusML at 325]
Reading contexts of file 
/usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt
--
Making Lateral-nucleus map to reduced label 1
Making Paralaminar-nucleus map to reduced label 1
Making Basal-nucleus map to reduced label 1
Making Accessory-Basal-nucleus map to reduced label 1
Making Corticoamygdaloid-transitio map to reduced label 1
Making Central-nucleus map to reduced label 1
Making Cortical-nucleus map to reduced label 1
Making Medial-nucleus map to reduced label 1
Making Anterior-amygdaloid-area-AAA map to reduced label 1
--
Making alveus map to reduced label 2
Making Hippocampal_tail map to reduced label 2
Making HATA map to reduced label 2
Making fimbria map to reduced label 2
Making parasubiculum map to reduced label 2
Making hippocampal-fissure map to reduced label 2
--
Making Left-Cerebral-Cortex map to reduced label 3
--
Making Left-Cerebral-White-Matter map to reduced label 4
--
Making Left-Lateral-Ventricle map to reduced label 5
--
Making Left-choroid-plexus map to reduced label 6
--
Making Unknown map to reduced label 7
--
Making Left-VentralDC map to reduced label 8
--
Making Left-Putamen map to reduced label 9
--
Making Left-Pallidum map to reduced label 10
--
Making Left-Thalamus-Proper map to reduced label 11
--
Making Left-Accumbens-area map to reduced label 12
--
Making Left-Caudate map to reduced label 13
Error using segmentSubjectT1_autoEstimateAlveusML (line 348)
The vector of prior probabilities in the mesh nodes must always sum to one over 
all classes
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Re: [Freesurfer] Longitudinal subfields segmentation single time point

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks a lot for your email, Saskia.
Does this happen for more than one subject? Can you reproduce the error?
Cheers,
/E

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com


From:  on behalf of "Koch, S.B.J. 
(Saskia)" 
Reply-To: Freesurfer support list 
Date: Friday, 18 January 2019 at 09:46
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Longitudinal subfields segmentation single time point


External Email - Use Caution

Dear FreeSurfer Developers,



I am attempting to run the longitudinal hippocampal subfields segmentation, 
using the development version of FreeSurfer. This works perfect for subjects 
with multiple data time points, but I get the following error for subjects for 
which I have a single data time point (see attachment for the error log):



***

 Global iteration 2

***

   * Estimating subject-specific atlas *

Error using kvlGEMSMatlab

/autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/Matlab/kvlMatlabObjectArray.cxx:82:

itk::ERROR: MatlabObjectArray(0x7f8686741c40): Trying to access non-existing 
object (25)

Error in kvlGetOptimizer (line 11)

Error in SegmentSubfieldsT1Longitudinal (line 1155)

Is it possible to run this longitudinal module on subjects with a single time 
point? Any thoughts on how to troubleshoot this?



FreeSurfer version: freesurfer-Linux-centos7_x86_64-dev-20180118-d073f7e

Platform: CentOS Linux 7 (Core)

Uname -a: Linux mentat003.dccn.nl 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 
20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux



Thanks for your help!

Saskia
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Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during segmentation {Disarmed}

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Rachel,
Sorry I missed your previous email.
Would you mind uploading your subject(s), so I can take a look?
Cheers,
/E

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com


From:  on behalf of Rachel Phillips 

Reply-To: Freesurfer support list 
Date: Wednesday, 16 January 2019 at 09:37
To: Freesurfer support list 
Subject: Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during 
segmentation {Disarmed}


External Email - Use Caution

Any guidance on this error is appreciated. I am still receiving the same output 
stated earlier.



Rachel Phillips


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rachel Phillips 

Sent: Monday, January 7, 2019 9:11:47 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during 
segmentation {Disarmed}


External Email - Use Caution

Version 6.0



Thanks,

Rachel


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: Monday, January 7, 2019 2:50:57 AM
To: freesurfer@nmr.mgh.harvard.edu; Freesurfer support list
Cc: Courtney Haswell
Subject: Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during 
segmentation {Disarmed}


External Email - Use Caution
Hi Rachel
This is very weird. What exact version are you using? 6.0 or dev?
Cheers
Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital and Harvard Medical School
Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

MailScanner has detected a possible fraud attempt from " 
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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rachel Phillips 

Sent: Friday, January 4, 2019 7:43:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Courtney Haswell
Subject: [Freesurfer] Longitudinal Hippocampal Subfields - error during 
segmentation


External Email - Use Caution

Hello,



I have run a longitudinal sample (up to 4 timepoints per subject) through the 
Freesurfer 6.0 longitudinal processing pipeline, and currently I am attempting 
to produce the longitudinal hippocampal subfield segmentation with the 
following command: longHippoSubfieldsT1.sh  [SubjectsDirectory]. I am 
receiving the following error: "Error using SegmentSubfeldsT1Longitudinal (line 
441) The vector of prior probabilities in the mesh nodes must always sum to one 
over all classes".



Below is an example of the output that precedes this error:


[> In SegmentSubfieldsT1Longitudinal at 418]
Reading contexts of file 
/usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt
--
Making Lateral-nucleus map to reduced label 1
Making Paralaminar-nucleus map to reduced label 1
Making Basal-nucleus map to reduced label 1
Making Accessory-Basal-nucleus map to reduced label 1
Making Corticoamygdaloid-transitio map to reduced label 1
Making Central-nucleus map to reduced label 1
Making Cortical-nucleus map to reduced label 1
Making Medial-nucleus map to reduced label 1
Making Anterior-amygdaloid-area-AAA map to reduced label 1
--
Making alveus map to reduced label 2
Making Hippocampal_tail map to reduced label 2
Making HATA map to reduced label 2
Making fimbria map to reduced label 2
Making parasubiculum map to reduced label 2
Making hippocampal-fissure map to reduced label 2
--
Making Left-Cerebral-Cortex map to reduced label 3
--
Making Left-Cerebral-White-Matter map to reduced label 4
--
Making Left-Lateral-Ventricle map to reduced label 5
--
Making Left-choroid-plexus map to reduced label 6
--
Making Unknown map to reduced label 7
--
Making Left-VentralDC map to reduced label 8
--
Making Left-Putamen map to reduced label 9
--
Making Left-Pallidum map to reduced label 10
--
Making Left-Thalamus-Proper map to reduced label 11
--
Making Left-Accumbens-area map to reduced label 12
--
Making Left-Caudate map to redu

Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during segmentation {Disarmed}

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Rachel
This is very weird. What exact version are you using? 6.0 or dev?
Cheers
Eugenio

Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital and Harvard Medical School

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology


www.jeiglesias.comwww.jeiglesias.com>




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rachel Phillips 

Sent: Friday, January 4, 2019 7:43:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Courtney Haswell
Subject: [Freesurfer] Longitudinal Hippocampal Subfields - error during 
segmentation


External Email - Use Caution

Hello,


I have run a longitudinal sample (up to 4 timepoints per subject) through the 
Freesurfer 6.0 longitudinal processing pipeline, and currently I am attempting 
to produce the longitudinal hippocampal subfield segmentation with the 
following command: longHippoSubfieldsT1.sh  [SubjectsDirectory]. I am 
receiving the following error: "Error using SegmentSubfeldsT1Longitudinal (line 
441) The vector of prior probabilities in the mesh nodes must always sum to one 
over all classes".


Below is an example of the output that precedes this error:


[> In SegmentSubfieldsT1Longitudinal at 418]
Reading contexts of file 
/usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt
--
Making Lateral-nucleus map to reduced label 1
Making Paralaminar-nucleus map to reduced label 1
Making Basal-nucleus map to reduced label 1
Making Accessory-Basal-nucleus map to reduced label 1
Making Corticoamygdaloid-transitio map to reduced label 1
Making Central-nucleus map to reduced label 1
Making Cortical-nucleus map to reduced label 1
Making Medial-nucleus map to reduced label 1
Making Anterior-amygdaloid-area-AAA map to reduced label 1
--
Making alveus map to reduced label 2
Making Hippocampal_tail map to reduced label 2
Making HATA map to reduced label 2
Making fimbria map to reduced label 2
Making parasubiculum map to reduced label 2
Making hippocampal-fissure map to reduced label 2
--
Making Left-Cerebral-Cortex map to reduced label 3
--
Making Left-Cerebral-White-Matter map to reduced label 4
--
Making Left-Lateral-Ventricle map to reduced label 5
--
Making Left-choroid-plexus map to reduced label 6
--
Making Unknown map to reduced label 7
--
Making Left-VentralDC map to reduced label 8
--
Making Left-Putamen map to reduced label 9
--
Making Left-Pallidum map to reduced label 10
--
Making Left-Thalamus-Proper map to reduced label 11
--
Making Left-Accumbens-area map to reduced label 12
--
Making Left-Caudate map to reduced label 13
Error using SegmentSubfieldsT1Longitudinal (line 441)
The vector of prior probabilities in the mesh nodes must always sum to one over 
all classes

Any guidance on this error would be greatly appreciated.

Thanks,
Rachel
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Re: [Freesurfer] thalamus_proper or whole_thalamus volume measurement?

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Corinna,
The reason for this is that the volumes correspond to two different analyses.
The volumes from the two sources are highly correlated, though, so it shouldn’t 
make almost any difference to use one or the other – but it you’re doing any 
analysis with the nuclei, I would use the one from the thalamic tool, for 
consistency.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital and Harvard Medical School

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

http://www.jeiglesias.com



From:  on behalf of Corinna Bauer 

Reply-To: Freesurfer support list 
Date: Monday, 17 December 2018 at 12:34
To: Mailing Freesurfer List 
Subject: [Freesurfer] thalamus_proper or whole_thalamus volume measurement?


External Email - Use Caution
Dear all,

For the new thalamus nuclei segmentation there is a measurement for the whole 
left and right thalami. The values are different from the thalamus_proper 
values.

Which output should be reported as the volume for the whole thalamus?

Thank you

Corinna
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Re: [Freesurfer] Classification of amygdala subregions using Freesurfers new Algorithm

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Sally,
As you've mentioned, different approaches have been used in the literature 
comprising different nuclei into different groups. The exact details are in the 
paper, but what you wrote sounds about right.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

http://www.jeiglesias.com



From: Sally Grace 
Date: Monday, 10 December 2018 at 16:31
To: "freesurfer@nmr.mgh.harvard.edu" 
Cc: "Iglesias Gonzalez, Eugenio" 
Subject: Classification of amygdala subregions using Freesurfers new Algorithm


Dear Eugenio and experts,



I have run the segmentation of the hippocampus subfields and nuclei of the 
amygdala using the latest algorithm implemented in the development version of 
Freesurfer. We have a priori hypotheses regarding the basolateral amygdala.



I understand that you have broken the amygdala output down into the distinct 
subregions, e.g., the basal, lateral and accessory basal amygdala nuclei.  
Based on this reference 
https://www.physiology.org/doi/pdf/10.1152/physrev.2.2003, my understanding 
is that the "basolateral nucleus" is comprised of the basal and lateral nucleus 
of the amygdala and the "basolateral nuclei" (aka. basolateral complex) 
comprises basal, lateral and accessory basal nuclei.


So, I can create a variable called the "basolateral nucleus" (by adding 
together the basal + lateral) and the "basolateral complex" (by adding together 
basal + lateral + accessory basal). Is this assumption correct?

Kind regards,
Sally.


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Re: [Freesurfer] segmentHA_T2 newbie questions

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear K


  1.  No
  2.  No, just the subject name; the subjects directory is specified separately.
  3.  Points at a file.
  4.  Yes.
Cheers,
/E

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

http://www.jeiglesias.com



From:  on behalf of Freesurfer 

Reply-To: Freesurfer support list 
Date: Tuesday, 11 December 2018 at 15:24
To: Freesurfer support list 
Subject: [Freesurfer] segmentHA_T2 newbie questions


External Email - Use Caution
Hi,

Trying to run the HippoAmig segmentation with T1-w and T2-w files for the first 
time and I have a few basic questions I could not resolve looking on the FS 
wiki:

1. Does the T2-w image need to be first recon-all processed like the T1-w?

On the wiki the command line is:

segmentHA_T2.sh  bert  FILE_ADDITIONAL_SCAN   ANALYSIS_ID  USE_T1

2. Does “bert” correspond to the directory for recon-all subject “bert” after 
been processed?

3. Does the FILE_ADDITIONAL_SCAN need to be a nit scan or should it point to 
the freesurfer directory post recon-all (this is kind of related to question #1 
I realize).

4. In ANALYSIS_IS can I type just “T2”?


Thanks!

K
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Re: [Freesurfer] Segmentation of hippocampal subfields on FS v6 stable data?

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Nope, please don't rerun the recon-all with dev. Just run the hippo+amyg module 
on the 6.0-reconned data.
Cheers,
/Eugenio

-- 
Juan Eugenio Iglesias
 
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology
 
http://www.jeiglesias.com
 
 

On 30/11/2018, 09:13, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
ts...@rcmd.org"  wrote:

External Email - Use Caution

Dear FreeSurfer experts,


we would like to use the 'Segmentation of hippocampal subfields and nuclei 
of the amygdala' feature [1] that is available in the development version of 
FreeSurfer.

However, we already pre-processed all subjects from the study using 
recon-all from FreeSurfer v6.0 stable.

Can we apply the hippocampal subfields methods to the data pre-processed 
with the stable version, or should we run recon-all again using the dev version 
before we proceed?

Thanks,

Tim

[1] 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and 
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] hippocampal subfield question

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Arkadiy,
Technically you should do it after, but the changes will be tiny, so it’s 
probably fine to do it before (as long as you’re consistent across subjects).
Cheers,
/E

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

http://www.jeiglesias.com



From:  on behalf of "Maksimovskiy, 
Arkadiy" 
Reply-To: Freesurfer support list 
Date: Thursday, 29 November 2018 at 17:13
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal subfield question

Dear Experts,

I was wondering if it is important to wait for the manual edits to be done on a 
dataset before running hippocampal subfield analyses. I believe that recon-all 
processing is sufficient, and edits can be done in parallel. But wanted to make 
sure that they will not affect the nuclei/subfield segmentation.

Thank you for your help,
Arkadiy

--
Arkadiy L. Maksimovskiy, Ph.D.
Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
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Re: [Freesurfer] segmentHA_T2.sh: amygdala recon-all command stoped.

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

While I guess it’d technically be possible to use the SAMSEG tools to obtain an 
initial ASEG, and then modify the hippocampal tool slightly to accommodate this 
change, I think that I’ll say that no, at this moment it is not possible – but 
maybe we should look into this in the future.
Sorry if this is not the answer you’d have liked to hear…
/E

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

http://www.jeiglesias.com



From:  on behalf of qimo601 

Reply-To: Freesurfer support list 
Date: Tuesday, 27 November 2018 at 00:29
To: Freesurfer support list 
Subject: Re: [Freesurfer] segmentHA_T2.sh: amygdala recon-all command stoped.


External Email - Use Caution


Dear Juan Eugenio Iglesias:
   Thanks for the response.
I have a question about T1 and T2 data, whether they must be scanned by 
the same patient?
Because I have no T1 sequence data. If i want to get the hippocampal 
subfields of T2 data, can I use T1 data of  patient A  to recon-all and T2 data 
of another patient B to segment ?

Thank you very much.
Confused beginner.
Qimo


At 2018-11-26 23:45:17, "Iglesias Gonzalez, Eugenio"  
wrote:


External Email - Use Caution
Dear Qimo,
You do need a T1 volume to run the main recon-all; sorry if the wiki wasn’t 
clear enough. It is true that segmenta_T2.sh only uses the intensities of the 
FLAIR scan, but a  recon-all processed T1 is still necessary.
Cheers,
/E

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

http://www.jeiglesias.com



From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of qimo601 mailto:qimo...@126.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, 26 November 2018 at 06:49
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] segmentHA_T2.sh: amygdala recon-all command stoped.


External Email - Use Caution

hi,FreeSurfer experts.
I am trying to use segmentHA_T2.sh command to segment the T2 FLAIR Sequence MRI 
Data.
Also I am now only having T2 Data.
But there was a mistake in the first step. Sincerely ask for help.

(1)First I use recon-all command to generate the subject file from my nii 
file.But it stop in Correct Defect step.
I have run three times after 48 hours. It also stop there.
I dont't know why.
Can you help me?

my command:
recon-all -all -i nii-004/ADNI_004_3D_FLAIR.nii.gz -s Subj004 -itkthreads 4

The output of the terminal is as follows：
CORRECTING DEFECT 45 (vertices=24, convex hull=53, v0=135114)
After retessellation of defect 45 (v0=135114), euler #=96 (83072,238273,155297) 
: difference with theory (-19) = -115
CORRECTING DEFECT 46 (vertices=97, convex hull=30, v0=136402)
After retessellation of defect 46 (v0=136402), euler #=97 (83078,238301,155320) 
: difference with theory (-18) = -115
CORRECTING DEFECT 47 (vertices=74, convex hull=24, v0=138982)
After retessellation of defect 47 (v0=138982), euler #=98 (83088,238338,155348) 
: difference with theory (-17) = -115
CORRECTING DEFECT 48 (vertices=83, convex hull=55, v0=139717)
After retessellation of defect 48 (v0=139717), euler #=99 (83098,238391,155392) 
: difference with theory (-16) = -115
CORRECTING DEFECT 49 (vertices=141431, convex hull=17606, v0=149662)

(2)Because of the above mistakes, I haven't tried the next step yet.
segmentHA_T2.sh subject004 ADNI_004_3D_FLAIR.nii.gz  T2 0

(3)Attached is the log(recon-all.log).

(4)My envientment as follows:
Ubuntu 16.04 amd_x64
freesurfer-linux-centos6_x86_64-dev.tar.gz(21-Nov-2018)
My data type: 3D-FLAIR (Pixel Spacing X=1.0 mm; Pixel Spacing Y=1.0 mm; Pulse 
Sequence=SE/IR; Slice Thickness=1.200476837158 mm; TE=441.0 ms; TI=1650.0 
ms; TR=4800.0 ms; Weighting=T2;)




Thanks,

Qimo











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Re: [Freesurfer] segmentHA_T2.sh: amygdala recon-all command stoped.

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Qimo,
You do need a T1 volume to run the main recon-all; sorry if the wiki wasn’t 
clear enough. It is true that segmenta_T2.sh only uses the intensities of the 
FLAIR scan, but a  recon-all processed T1 is still necessary.
Cheers,
/E

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

http://www.jeiglesias.com



From:  on behalf of qimo601 

Reply-To: Freesurfer support list 
Date: Monday, 26 November 2018 at 06:49
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] segmentHA_T2.sh: amygdala recon-all command stoped.


External Email - Use Caution

hi,FreeSurfer experts.
I am trying to use segmentHA_T2.sh command to segment the T2 FLAIR Sequence MRI 
Data.
Also I am now only having T2 Data.
But there was a mistake in the first step. Sincerely ask for help.

(1)First I use recon-all command to generate the subject file from my nii 
file.But it stop in Correct Defect step.
I have run three times after 48 hours. It also stop there.
I dont't know why.
Can you help me?

my command:
recon-all -all -i nii-004/ADNI_004_3D_FLAIR.nii.gz -s Subj004 -itkthreads 4

The output of the terminal is as follows：
CORRECTING DEFECT 45 (vertices=24, convex hull=53, v0=135114)
After retessellation of defect 45 (v0=135114), euler #=96 (83072,238273,155297) 
: difference with theory (-19) = -115
CORRECTING DEFECT 46 (vertices=97, convex hull=30, v0=136402)
After retessellation of defect 46 (v0=136402), euler #=97 (83078,238301,155320) 
: difference with theory (-18) = -115
CORRECTING DEFECT 47 (vertices=74, convex hull=24, v0=138982)
After retessellation of defect 47 (v0=138982), euler #=98 (83088,238338,155348) 
: difference with theory (-17) = -115
CORRECTING DEFECT 48 (vertices=83, convex hull=55, v0=139717)
After retessellation of defect 48 (v0=139717), euler #=99 (83098,238391,155392) 
: difference with theory (-16) = -115
CORRECTING DEFECT 49 (vertices=141431, convex hull=17606, v0=149662)

(2)Because of the above mistakes, I haven't tried the next step yet.
segmentHA_T2.sh subject004 ADNI_004_3D_FLAIR.nii.gz  T2 0

(3)Attached is the log(recon-all.log).

(4)My envientment as follows:
Ubuntu 16.04 amd_x64
freesurfer-linux-centos6_x86_64-dev.tar.gz(21-Nov-2018)
My data type: 3D-FLAIR (Pixel Spacing X=1.0 mm; Pixel Spacing Y=1.0 mm; Pulse 
Sequence=SE/IR; Slice Thickness=1.200476837158 mm; TE=441.0 ms; TI=1650.0 
ms; TR=4800.0 ms; Weighting=T2;)



Thanks,

Qimo





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Re: [Freesurfer] thalamic nuclei additional scan error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Zhac,
Apologies for the mistake in the wiki. As explained in the error message, the 
subjects directory is the second argument. Also, if you are using a T2 scan, I 
would replace t1 by t2 in the last argument.
The call should be:
(For a T1 additional scan)
segmentThalamicNuclei.sh MS14 /Applications/freesurfer/subjects/   
/Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t1
(For a T2 additional scan)
segmentThalamicNuclei.sh MS14 /Applications/freesurfer/subjects/   
/Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t2
Cheers,
/Eugenio

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

http://www.jeiglesias.com



From:  on behalf of zhac looch 

Reply-To: Freesurfer support list 
Date: Friday, 23 November 2018 at 16:32
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] thalamic nuclei additional scan error


External Email - Use Caution
Hi Freesurfer Team,

I want to add additional scan my thalamic segmentation. but my code is not 
working. where is the error in my code?

thanks for help

my code:
segmentThalamicNuclei.sh MS14 
/Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t1

my error:


Usage:



   segmentThalamicNuclei.sh SUBJECT_ID [SUBJECT_DIR] [ADDITIONAL_VOL   
ANALYSIS_ID   BBREGISTER_MODE]



Or, for help



   segmentThalamicNuclei.sh --help

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Re: [Freesurfer] loading and rendering the Amygdala nuclei only in Freeview

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Erik,
If you render labels >7000, you shouldn’t see a rendering of the subfields – 
but they will indeed remain visible in the orthogonal views. If you want to get 
rid of them, you can use mri_threshold:
mri_threshold 
lh.hippoAmygLabels-T1-HippoAMYT1andT2FLAIR.v20.FS60.FSvoxelSpace.mgz6999  
onlyAmyg.mgz
Cheers,
/Eugenio

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

http://www.jeiglesias.com



From:  on behalf of Erik O'Hanlon 

Reply-To: Freesurfer support list 
Date: Friday, 16 November 2018 at 08:15
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] loading and rendering the Amygdala nuclei only in Freeview


External Email - Use Caution

Hi FS Experts,



I'm trying to make some images of my amygdala nuclei in freeview and selected 
my T1 as background and then loaded up 
lh.hippoAmygLabels-T1-HippoAMYT1andT2FLAIR.v20.FS60.FSvoxelSpace.mgz image 
which loads up perfectly. I selected the "show existing labels " and the 
freesurfer colour LUT but when I select the range for 7001-7015 for amygdala 
only, the hippocampal subfields are still there. Is there a way to only load 
the amygdala nuclei. I'm sure it's something simple I'm just not doing, but I 
can't seem to get it to work.



Any pointers gladly accepted



Thanks



Erik





Erik O'Hanlon
Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.com

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022


[cid:AS_BRONZE_IIDD_65c26b0a-ea45-42c8-956e-5d84e884e4e6.png]
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Re: [Freesurfer] Longitudinal brainstem structures / thalamic nuclei

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Niels,
There is, but not in the short term. For the time being, you can run the module 
on longitudinally processed subjects.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
http://www.jeiglesias.com



From:  on behalf of Niels Bergsland 

Reply-To: Freesurfer support list 
Date: Monday, 5 November 2018 at 11:33
To: Freesurfer Mailing List 
Subject: [Freesurfer] Longitudinal brainstem structures / thalamic nuclei


External Email - Use Caution
Hi Eugenio,
Just wanted to ask quickly if there is plan to implement longitudinal 
processing for the brainstem structures and thalamic nuclei modules?
Thanks!
Niels
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Re: [Freesurfer] Segmentation of thalamic nuclei - no reticular nucleus

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi HSK
We use it in the model fitting but do not segment it due to the absolute lack 
of contrast with the white matter.
Kind regards,
Eugenio

--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
http://www.jeiglesias.com



From:  on behalf of Hyun Seok Kim 

Reply-To: Freesurfer support list 
Date: Tuesday, 30 October 2018 at 17:10
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Segmentation of thalamic nuclei - no reticular nucleus


External Email - Use Caution
Dear all,

I ran thalamic nuclei segmentation tool using the 
"freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa" version. The segmented 
thalamic nuclei were visualized well by FreeView and were able to find most 
nuclei. But there is no reticular nucleus (R). I also checked the existence of 
the reticular nucleus with the following matlab code, but it did not exist.

y = MRIread('ThalamicNuclei.v10.T1.FSvoxelSpace.mgz');
find(y.vol == 8125)

Is there any way to find the reticular nucleus?


Best regards,

Hyun Seok Kim

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Re: [Freesurfer] Matlab Segmentation error when running hippocampal segmentation in dev version

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Jaime,
Can you please send us the output you get between calling the command and the 
error?
Cheers,
/E

--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
http://www.jeiglesias.com



From:  on behalf of Jaime Gomez 

Reply-To: Freesurfer support list 
Date: Tuesday, 30 October 2018 at 12:33
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Matlab Segmentation error when running hippocampal 
segmentation in dev version


External Email - Use Caution

Hi,
I think I have the same or similar error than
[Freesurfer] error in hippocampal subfields and nuclei of amygdala 
segmentation
I am running segmentHA_T1.sh for one subject and I get this matlab segmentation 
error bellow:
I have 16GB memory in a MacOS, and when the process finished with the error I 
still have 7 GB of memory free to use.
I installed the Matlab R2014b runtime as it is explained 
here
 and I have a Matlab 2016 installed.


Thanks!
Jaime


   Segmentation violation detected at Tue Oct 30 13:06:09 2018


Configuration:
  Crash Decoding : Disabled
  Current Visual : Quartz
  Default Encoding   : ISO-8859-1
  MATLAB Architecture: maci64
  MATLAB Root: /Applications/freesurfer/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 
20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64
  Processor ID   : x86 Family 6 Model 62 Stepping 4, GenuineIntel
  Software OpenGL: 0
  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java 
HotSpot(TM) 64-Bit Server VM mixed mode
  Window System  : Quartz

Fault Count: 1


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 7fb47210a800  RBX = 7fb47210a800
  RCX = 750c92f0  RDX = 000112fb097e
  RSP = 7fb47210a800  RBP = 9b63050c92f0
  RSI = 7fb470d3f910  RDI = 

   R8 = 7fb47691da70   R9 = 7fb47210a800
  R10 = 00011d44376a  R11 = 
  R12 = 750c9350  R13 = 000112dfe3c7
  R14 = 750c93c0  R15 = 00011d443777

  RIP = 000117f94f40  RFL = 7fb47691da70

   CS = 9b6300305bc3   FS = 00011d44376a   GS = 7fb47210a9e8

Stack Trace (from fault):
[  0] 0x000107817e64 
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052
[  1] 0x00010781ba2a 
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906
[  2] 0x00010781b477 
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119
[  3] 0x00010e399b7a 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146
[  4] 0x00010e399e58 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880
[  5] 0x00010e397733 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275
[  6] 0x7fff6b0d9b3d   
/usr/lib/system/libsystem_platform.dylib+00019261 _sigtramp+0029
[  7] 0x000112dff6f8 
/Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568
 _ZN23JNI_ArgumentPusherVaArg7iterateEy+
[  8] 0x000112defd67 
/Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679
 jni_GetMethodID+0126
[  9] 0x0001117b1271 
/Applications/freesurfer/MCRv84//bin/maci64/libmwjmi.dylib+00160369 
_Z12mljGetMethodP7_jclassPKcS2_+0049
[ 10] 0x00011cc9e366 
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00598886 
_ZN2ui14JavaScreenData20getPrimaryScreenRectEv+0150
[ 11] 0x00011cca3ef4 
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00622324 
_ZN10ScreenImpl13getScreenSizeEv+0036
[ 12] 0x00011cca22e2 
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00615138 
_ZNK2ui24RootScreenAndPointerImpl13getScreenSizeEv+0018
[ 13] 0x00011cca6f58 
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00634712 
_ZN2ui4Root17getScreenSizeImplEPN4mcos11COSPropInfoEPNS1_9COSClientEPNS1_12COSInterfaceE+0040
[ 14] 0x00011d0ddd13 
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+05053715 

Re: [Freesurfer] segmentHA_T1 error DYLD_LIBRARY_PATH

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

It seems it could be a version conflict. Please try unsetting DYLD_LIBRARY_PATH.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
http://www.jeiglesias.com



From:  on behalf of Jaime Gomez 

Reply-To: Freesurfer support list 
Date: Tuesday, 30 October 2018 at 11:10
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] segmentHA_T1 error DYLD_LIBRARY_PATH


External Email - Use Caution

Hi,

I have this error when I try to run segmentHA_T1.sh
It seems that it sets up the wrong DYLD_LIBRARY_PATH, the one I have in my 
bash_profile is
/Applications/MATLAB_R2016a.app/bin/maci64:/Applications/MATLAB_R2016a.app/sys/os/maci64:/Applications/MATLAB_R2016a.app/bin/maci64:/Applications/MATLAB_R2016a.app/sys/os/maci64:

[~/val...V/003_SAG_3D_IR] $ segmentHA_T1.sh sujeto_uno
#
#@# Hippocampal Subfields processing (T1) left Tue Oct 30 12:04:16 CET 2018
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64:
dyld: Library not loaded: @loader_path/libmwmclmcrrt.8.0.dylib
  Referenced from: 
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
  Reason: image not found
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
38:  7887 Abort trap: 6   
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 $args
#
--

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Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Gouyang
There's no T2 longitudinal pipeline available at the moment.
In its absence, what you're doing is the way to go ;-)

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Chen Guoyang (IMH) 

Sent: Tuesday, October 30, 2018 4:00:54 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform 
file {Disarmed}


External Email - Use Caution
Hi Martin,

Thanks for the input! It worked perfectly.

A follow up question:

I understand that for T1 hippocampal subfield segmentation, Freesurfer has a 
longitudinal module for it (segmentHA_T1.long.sh)

Does freesurfer have a longitudinal module for T1+T2 hippocampal segmentations?

If such a module is not available, will just like to consult you guys whether 
are our current processing steps appropriate for longitudinal comparisons:

1.   Run the longitudinal pipeline (FSv6.0) across all our subjects and 
each of their timepoints, example:

recon-all –long Subject1_timepoint1 Subject1_base

recon-all –long Subject1_timepoint2 Subject1_base

2.   Run segmentHA_T2.sh across each longitudinal scan of each of our 
subjects, example:
segmentHA_T2.sh Subject1_timepoint1 Subject1_timepoint1.long.Subject1_base 
Subject1_timepoint1_T2.nii T2 1
segmentHA_T2.sh Subject1_timepoint2 Subject1_timepoint2.long.Subject1_base 
Subject1_timepoint2_T2.nii T2 1

Thanks!

Yours Sincerely,
Guoyang

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter
Sent: Saturday, 27 October, 2018 4:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform 
file

Hi,

Looks like the input is a multi frame image. Should only be single frame.

Best Martin

On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

It seems like a problem with mri_robust_register.
Martin, any ideas?

--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
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From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Chen Guoyang (IMH)" 
mailto:guoyang_c...@imh.com.sg>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 26 October 2018 at 11:35
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file

External Email - Use Caution
Dear Freesurfer experts,

I am currently attempting to include an additional T2 MRI scan in the 
segmentation of our T1 scan. The freesurfer version that I'm using is the 
freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version).

However, I ran into this issue, ERROR: cannot find transform file. I've pasted 
the output below.

Will like your advices for the this matter.

Thanks!

Sincerely,
Guoyang

OS Darwin
Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct  4 
00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64
--

#
#@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib:
Registering norm.mgz to additional volume
/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass single 
frame MRI target /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii.

/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz
 --maskmov 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//wholeBrainMask.mgz
 --dst /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii --lta 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta
 --noinit --cost NMI -nosym >/dev/null: Signal 127
ERROR: cannot find transform file 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/

Re: [Freesurfer] error in hippocampal subfields and nuclei of amygdala segmentation

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear J
How much RAM memory do you have?
Andrew: do you think this might be the problem?
Cheers
E


Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 오진영 

Sent: Tuesday, October 30, 2018 5:51:22 AM
To: Freesurfer support list
Subject: [Freesurfer] error in hippocampal subfields and nuclei of amygdala 
segmentation


External Email - Use Caution

Dear freesurfer experts,

I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala 
with segmentHA_T1.sh command.
I already run segmentation of hippocampal subfields and nuclei of amygdala 
several times, however, after segment nuclei of amygdala in left hemisphere and 
before segment nuclei of amygdala in right hemisphere, there appears same error 
"MATLAB is exiting because of fatal error" and hippocampal subfields 
segmentation stops.
Ignoring and Trying the same command few more times, I can make it to segment 
subfields of amygdala, but I am still wondering if I can run segmentHA_T1.sh 
without any error.

Following is the repeated error with the few lines:


#

#@# Hippocampal Subfields processing (T1) right 2018년 10월 30일 화요일 14시 07분 17초 
KST

--

Setting up environment variables

---

DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:

PostVMInit failed to initialize com.mathworks.mwswing.MJStartupForDesktop




   Segmentation violation detected at Tue Oct 30 14:07:20 2018




Configuration:

  Crash Decoding : Disabled

  Current Visual : Quartz

  Default Encoding   : US-ASCII

  MATLAB Architecture: maci64

  MATLAB Root: /Applications/freesurfer/MCRv84

  MATLAB Version : 8.4.0.150421 (R2014b)

  Operating System   : Darwin 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 
22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64

  Processor ID   : x86 Family 6 Model 158 Stepping 9, GenuineIntel

  Software OpenGL: 0

  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java 
HotSpot(TM) 64-Bit Server VM mixed mode

  Window System  : Quartz


Fault Count: 2



Abnormal termination:

Segmentation violation


Register State (from fault):

  RAX = 7fafcba4f000  RBX = 7fafcba4f000

  RCX = 7cdf72d0  RDX = 000111cba97e

  RSP = 7fafcba4f000  RBP = 9b630cdf72d0

  RSI = 7fafcdb8a9b0  RDI = 


   R8 = 7fafcc2dc270   R9 = 7fafcba4f000

  R10 = 00011bd1f76a  R11 = 

  R12 = 7cdf7330  R13 = 000111b083c7

  R14 = 7cdf73a0  R15 = 00011bd1f777


  RIP = 000116ca6f40  RFL = 7fafcc2dc270


   CS = 9b6300305bc3   FS = 00011bd1f76a   GS = 7fafcba4f1e8


Stack Trace (from fault):

[  0] 0x000105f76e64 
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052

[  1] 0x000105f7aa2a 
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906

[  2] 0x000105f7a477 
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119

[  3] 0x00010d041b7a 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146

[  4] 0x00010d041e58 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880

[  5] 0x00010d03f733 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275

[  6] 0x7fff74b75f5a   
/usr/lib/system/libsystem_platform.dylib+8026 _sigtramp+0026

[  7] 0x000111b096f8 
/Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568
 _ZN23JNI_ArgumentPusherVaArg7iterateEy+

[  8] 0x000111af9d67 
/Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679
 jni_GetMethodID+0126

[  9] 0x0001104dd271 
/Applications/freesurfer/MCRv84//bin/maci64/libmwjmi.dylib+00160369 
_Z12mljGetMethodP7_jclassPKcS2_+0049

[ 10] 0x00011b57a366 
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00598886 
_ZN2ui14JavaScreenData20getPrimaryScreenRectEv+0150

[ 11] 0x00011b57fef4 
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00622324 
_ZN10ScreenImpl13getScreenSizeEv+0036

[ 12] 0x00011b57e2e2 
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00615138 

Re: [Freesurfer] subfield normalization vs. covarying for whole hippocampal volume

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Lauren,
This is a very interesting question!
Site harmonization matters aside (there’s a vast literature on it), whether you 
correct by ICV or whole hippocampal volume essentially answers to different 
questions:
- ICV: you’re asking whether there’s an effect of X on subfield Y.
- whole hippo volume: you’re asking whether X has an effect on the fraction of 
hippocampal volume attributed to Y.
Both questions are interesting; it depends on what you’re trying to answer.
Of course, if you’re correcting by whole hippocampal volume, then don’t correct 
by ICV…
I hope this helps!
/Eugenio

--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
http://www.jeiglesias.com



From:  on behalf of Lauren Salminen 

Reply-To: Freesurfer support list 
Date: Friday, 26 October 2018 at 22:40
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] subfield normalization vs. covarying for whole 
hippocampal volume


External Email - Use Caution
Hello,

I’m working on a multi-site hippocampal subfields project (FSv. 6) and am 
wondering if it is “better” to normalize subfield volumes by dividing each 
subfield by whole hippocampal volume, or covary for hippocampal volume as an 
independent predictor variable in the regression models.

Ultimately the goal is to determine the degree that each subfield may be 
uniquely associated with my target predictor variable, and we would like to 
know if this effect can be observed independent of potential differences in the 
whole hippocampus.  Traditionally we have covaried for whole hippocampal 
volume, but I’ve found more interesting effects by normalizing each subfield to 
their hippocampal volume.

Any guidance is appreciated.

Thank you!



Lauren E. Salminen, Ph.D.
Imaging Genetics Center
Stevens Neuroimaging and Informatics Institute
Keck School of Medicine
University of Southern California
http://igc.ini.usc.edu/



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Re: [Freesurfer] Error in segmentHA_T1.sh

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

No worries! Your LD_LIBRARY_PATH configuration made my day 


--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
http://www.jeiglesias.com



From:  on behalf of "Scheffler, F, Mev 
[fre...@sun.ac.za]" 
Reply-To: Freesurfer support list 
Date: Friday, 26 October 2018 at 17:35
To: Freesurfer support list 
Subject: Re: [Freesurfer] Error in segmentHA_T1.sh


External Email - Use Caution
Sorry, scratch that. Apparently it just didn’t realise that my subjects were in 
a subdirectory in the subjects directory.

Running now.

Note to self: “Think before you click send”

Kind regards,



FREDA SCHEFFLER

Research Assistant / PhD Candidate


[email.jpg]


MA Research Psychology
Faculty of Medicine and Health Sciences
Fakulteit Geneeskunde en Gesondheidswetenskappe
Universiteit Stellenbosch University
PO Box | Posbus 241, Cape Town | Kaapstad, 8000
Francie van Zijl Drive | -rylaan, Tygerberg, 7505
South Africa | Suid-Afrika

Tel:  +27 21 938 9771
Email | E-pos:  fre...@sun.ac.za




From:  on behalf of "Scheffler, F, Mev 
[fre...@sun.ac.za]" 
Reply-To: Freesurfer support list 
Date: Friday, 26 October 2018 at 18:24
To: Freesurfer support list 
Subject: [Freesurfer] Error in segmentHA_T1.sh


External Email - Use Caution
Dear Freesurfer Developers

I’ve run recon-all -all on a batch of 20 subjects on a linux based high 
performance computing setup and am now trying to run the segmentHA_T1 on them 
as well.

It sets up the environment and then complains about myMRIread and Error in 
segmentSubjectT1_autoEstimateAlveusML (line 157)

Here is the command line output:


#

#@# Hippocampal Subfields processing (T1) left Fri Oct 26 18:06:27 SAST 2018

--

Setting up environment variables

---


LD_LIBRARY_PATH is









Error using myMRIread (line 16)

Error in myMRIread: temporary directory does not exist



Error in segmentSubjectT1_autoEstimateAlveusML (line 157)





@#@FSTIME  2018:10:26:18:06:27 run_segmentSubjectT1_autoEstimateAlveusML.sh N 
13 e 107.33 S 6.58 U 8.77 P 14% M 145072 F 14363 R 298922 W 0 c 179 w 32314 I 
33416 O 0 L 0.02 5.50 14.86

@#@FSLOADPOST 2018:10:26:18:08:14 run_segmentSubjectT1_autoEstimateAlveusML.sh 
N 13 0.78 4.16 13.38

Linux cnode0070 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 
x86_64 x86_64 x86_64 GNU/Linux



T1 hippocampal subfields exited with ERRORS at Fri Oct 26 18:08:15 SAST 2018



What am I doing wrong here?

Thanks very much.

Kind regards,



FREDA SCHEFFLER

Research Assistant / PhD Candidate


[email.jpg]


MA Research Psychology
Faculty of Medicine and Health Sciences
Fakulteit Geneeskunde en Gesondheidswetenskappe
Universiteit Stellenbosch University
PO Box | Posbus 241, Cape Town | Kaapstad, 8000
Francie van Zijl Drive | -rylaan, Tygerberg, 7505
South Africa | Suid-Afrika

Tel:  +27 21 938 9771
Email | E-pos:  fre...@sun.ac.za



[Image removed by sender. 
http://cdn.sun.ac.za/100/ProductionFooter.jpg]

The integrity and confidentiality of this email are governed by these terms. 
Disclaimer
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende 
bepalings bereël. Vrywaringsklousule
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Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

It seems like a problem with mri_robust_register.
Martin, any ideas?

--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
http://www.jeiglesias.com



From:  on behalf of "Chen Guoyang 
(IMH)" 
Reply-To: Freesurfer support list 
Date: Friday, 26 October 2018 at 11:35
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file


External Email - Use Caution

Dear Freesurfer experts,



I am currently attempting to include an additional T2 MRI scan in the 
segmentation of our T1 scan. The freesurfer version that I'm using is the 
freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version).



However, I ran into this issue, ERROR: cannot find transform file. I've pasted 
the output below.



Will like your advices for the this matter.



Thanks!



Sincerely,

Guoyang


OS Darwin
Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct  4 
00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64
--

#
#@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib:
Registering norm.mgz to additional volume
/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass single 
frame MRI target /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii.

/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz
 --maskmov 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//wholeBrainMask.mgz
 --dst /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii --lta 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta
 --noinit --cost NMI -nosym >/dev/null: Signal 127
ERROR: cannot find transform file 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta
gunzip: can't stat: 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz
 
(/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz.gz):
 No such file or directory
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)



Error in myMRIread>myMRIread_aux (line 92)



Error in myMRIread (line 63)



Error in segmentSubjectT1T2_autoEstimateAlveusML (line 207)



MATLAB:badSwitchExpression
Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct  4 
00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64

T2 hippocampal subfields exited with ERRORS at Fri Oct 26 17:50:18 +08 2018

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Re: [Freesurfer] Disjointed thalamic nuclei segmentation

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks, Niels.
It is definitely a matter of hyperintensity of voxels close to the lateral 
boundary, particularly in the anterior region (which has a fuzzy boundary with 
the white matter in first place). Whether these hyperintensities are due to MS 
pathology, that I do not know (I’m really not the person to tell…).
These could be cleaned up with postprocessing (e.g., filling holes, or using a 
Markov Random Field), but the impact on the volumes would be negligible.
Cheers,
/Eugenio


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: Niels Bergsland 
Date: Wednesday, 10 October 2018 at 15:42
To: "Iglesias Gonzalez, Eugenio" 
Subject: Re: [Freesurfer] Disjointed thalamic nuclei segmentation

Hi Eugenio,
Thanks for the lightning fast response! :)
I've attached them here. It looks like it might actually be the opposite in 
this case in that the voxels here are darker. Some of the cases are MS patients 
and so it's conceivable that they have thalamic lesions. Admittedly though, I 
have not really spent time in the past looking for thalamic lesions on 
T1-weighted images and this hasn't been an issue in the past since the thalamic 
segmentation in the aseg doesn't end up being affected by these voxels with 
lower intensities. If you would like to look at some other cases or need other 
outputs, just let me know and I'm happy to send them along!

Thanks again,
Niels

On Wed, Oct 10, 2018 at 4:30 PM Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution
Thanks, Niels.
I suspect the problem is that, for some reason, such voxels have much brighter 
intensity than their surroundings, and are classified as white matter / 
reticular nucleus. But that shouldn’t be happening that far from the lateral 
boundary of the thalamus…
Can you please send us norm.mgz and the thalamic segmentation file, so I can 
take a look?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Niels Bergsland mailto:theni...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, 10 October 2018 at 15:22
To: Freesurfer Mailing List 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Disjointed thalamic nuclei segmentation


External Email - Use Caution
Hi Eugenio,
Thank you again for the fantastic thalamic nuclei segmentation tool!

I'm going through and QC'ing a batch of subjects that were processed through 
the pipeline. Data was originally processed with freesurfer-6.0.0 and then 
processed through the thalamic nuclei stream (dev-20180818-e30e6f9).

I have found that for some cases, there are some isolated patches of voxels 
that are disconnected and seemingly in the wrong place. I've noticed it 
primarily for the MDm and my impression is that it tends to happen more in the 
right hemisphere. I've attached a sample image to show you what I mean. The red 
cross has been placed on a set of these voxels.  It is not the case that they 
are connected in 3D.

Any input is appreciated and thanks again! If it can be useful, I'm happy to 
upload the data

-Niels
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Re: [Freesurfer] Disjointed thalamic nuclei segmentation

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks, Niels.
I suspect the problem is that, for some reason, such voxels have much brighter 
intensity than their surroundings, and are classified as white matter / 
reticular nucleus. But that shouldn’t be happening that far from the lateral 
boundary of the thalamus…
Can you please send us norm.mgz and the thalamic segmentation file, so I can 
take a look?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Niels Bergsland 

Reply-To: Freesurfer support list 
Date: Wednesday, 10 October 2018 at 15:22
To: Freesurfer Mailing List 
Subject: [Freesurfer] Disjointed thalamic nuclei segmentation


External Email - Use Caution
Hi Eugenio,
Thank you again for the fantastic thalamic nuclei segmentation tool!

I'm going through and QC'ing a batch of subjects that were processed through 
the pipeline. Data was originally processed with freesurfer-6.0.0 and then 
processed through the thalamic nuclei stream (dev-20180818-e30e6f9).

I have found that for some cases, there are some isolated patches of voxels 
that are disconnected and seemingly in the wrong place. I've noticed it 
primarily for the MDm and my impression is that it tends to happen more in the 
right hemisphere. I've attached a sample image to show you what I mean. The red 
cross has been placed on a set of these voxels.  It is not the case that they 
are connected in 3D.

Any input is appreciated and thanks again! If it can be useful, I'm happy to 
upload the data

-Niels
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Re: [Freesurfer] Fwd: Hippocampal-Amygdala subfields error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Miguel Angel,
Ideally, one would always run all the subjects on the same platform. If this is 
completely impractical due to computational limitations, then it is very 
important to:
-  spread the groups across platforms, e.g., avoid running all controls on one 
platform, and all diseased on another, or e.g., all younger subjects on one 
platform, and older on another. In you don’t do this, you will never know 
whether detected effects are due to actual differences in brain structure, or 
processing platforms.
AND
- include the platform as a covariate in subsequent analysis.
I hope this helps,
/Eugenio


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Miguel Ángel Rivas 
Fernández 
Reply-To: Freesurfer support list 
Date: Wednesday, 10 October 2018 at 11:12
To: Freesurfer support list 
Subject: [Freesurfer] Fwd: Hippocampal-Amygdala subfields error


External Email - Use Caution

Hi everyone,


Here a question and an answer of FreeSurfer experts that would be for interest.


- Could there be any difference in accuracy when the recon-all is executed on 
two Mac computers that have a different processor? that is,  it is preferable 
to execute the recon-all of all the subjects in the same computer?. Sorry for 
this absurd question but I would be sure about this.



- Regarding the second question: it is a really good one. Would you mind 
posting it on the FreeSurfer list? Short answer is: same machine.



Best

-- Forwarded message -
From: Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>>
Date: mié., 10 oct. 2018 a las 11:53
Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error
To: Miguel Ángel Rivas Fernández 
mailto:miguelrivasf...@gmail.com>>
Cc: Hoopes, Andrew mailto:ahoo...@mgh.harvard.edu>>

Hi again, MA.
I totally forgot to attach the binary.
The thing is that I don’t have it on my hard drive, so I need to recompile it, 
but our MAC server seems to be down   rrr
Andrew: any ideas why breck is not responding?
MA: sorry for the delay; we’ll definitely get to the bottom of this.

Regarding the second question: it is a really good one. Would you mind posting 
it on the FreeSurfer list? Short answer is: same machine.

Cheers,

/Eugenio



--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: Miguel Ángel Rivas Fernández 
mailto:miguelrivasf...@gmail.com>>
Date: Wednesday, 10 October 2018 at 09:39
To: "Iglesias Gonzalez, Eugenio" 
mailto:e.igles...@ucl.ac.uk>>
Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error

Hi Eugenio,

It´s possible that you have forgotten to attach the file in this email? because 
I don´t find anywhere.

Another question, could there be any difference in accuracy when the recon-all 
is executed on two Mac computers that have a different processor? that is,  it 
is preferable to execute the recon-all of all the subjects in the same 
computer?. Sorry for this absurd question but I would be sure about this.


Best,

El mié., 3 oct. 2018 a las 19:52, Iglesias Gonzalez, Eugenio 
(mailto:e.igles...@ucl.ac.uk>>) escribió:
Allrighty, here are the instructions

(depending on the location of FREESURFER_HOME, the following commands might 
need to be preceded by “sudo”)
1. Save the attached file to a directory of your choice. From the terminal, cd 
into that directory.
2. Decompress with:   tar xvf segmentSubjectT2_autoEstimateAlveusML.tar.gz
3. Move existing version of the code:mv 
$FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app   
$FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app.old
4. Replace with new version:   mv ./segmentSubjectT2_autoEstimateAlveusML.app   
$FREESURFER_HOME/bin/
5. Rerun the code

If this doesn’t work, you can revert the changes with:

  1.  Delete new version with:rm –rf  
$FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app
  2.  Restore previous version:   mv   
$FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app.old   
$FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app

If it works:  there’s no need to rerun the subjects that didn’t crash.

Please let us know what happens!

Cheers,

/E


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: Miguel Ángel Rivas Fernández 
mailto:miguelrivasf...@gmail.com>>
Date: Wednesday, 3 October 2018 at 18:32
To: "Iglesias Gonzalez, Eugenio" 
mailto:e.igles...@ucl.ac.uk>>
Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error


Hi Eugenio,

I ran the command with the 

Re: [Freesurfer] Thalamic Nuclei segmentation results

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Vasudev,

What lookup table are you using to visualize the results? Are you using 
FreeView from the development version, and visualizing the segmentation with 
the default lookup table?

Cheers,

/Eugenio


Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Dev vasu 

Sent: Tuesday, October 9, 2018 10:06:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Thalamic Nuclei segmentation results


External Email - Use Caution

Dear all,

I have used Freesurfer pipeline for Thalamic  Nuclei segmentation, the results 
of segmentation appear to be very poor, i am annexing the results , please 
kindly review if there is any thing wrong with the segmentation results.


Thanks
Vasudev
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Re: [Freesurfer] hippocampal subfields

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks, Marcel. Can you please send us the whole output (can be found in the 
log file)
Cheers,
/E

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Marcel Heers 

Reply-To: Freesurfer support list 
Date: Monday, 8 October 2018 at 20:45
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal subfields


External Email - Use Caution
Dear Eugenio,

there is one error in the error.log: 'Could not set locale'.

Best regards

Marcel
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Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Glad to hear.
As much as it exists to solve problems, it’s also nice to get positive news on 
the list every once in a while.
Cheers,
/E

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Pradeep 

Reply-To: Freesurfer support list 
Date: Monday, 8 October 2018 at 18:51
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal segmentation with an additional scan 
ERROR kvlGEMSMatlab


External Email - Use Caution
Hi Iglesias,

It turns out that my input images are in different orientation and I had a hard 
time reorienting them.
Starting from dicom images and using mri_convert to bring them to nifti format 
seem to fix the problem
The hippocampal subfiled segmentation program with the additional high 
resolution scan works!


Thank you for all the help!

Pradeep

On Thu, Oct 4, 2018 at 11:28 AM Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution
Thanks!
Did you check whether the T2 and the T1 were correctly registered? You can 
check out the animated gif under mri/transforms in the subject’s directory.
Cheers,
/E

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Pradeep mailto:tprad...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 4 October 2018 at 19:21
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Hippocampal segmentation with an additional scan 
ERROR kvlGEMSMatlab


External Email - Use Caution
I have tried this for two subjects and got the same error.

Thanks,
Pradeep

On Thu, Oct 4, 2018 at 11:14 AM Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution
Dear Pradeep,
Did you get this error on several subjects, or only one?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Pradeep mailto:tprad...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 4 October 2018 at 19:12
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Hippocampal segmentation with an additional scan ERROR 
kvlGEMSMatlab


External Email - Use Caution
Hello,

I am trying to run the hippocampal segmentation with an additional Hi-res scan 
using the following command

recon-all -s  -hippocampal-subfields-T2   
and got the following error


Error using kvlGEMSMatlab
/autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211:
itk::ERROR: Region ImageRegion (0x7f67011c5dd0)
  Dimension: 3
  Index: [0, 845, 0]
  Size: [105, 18446744073709550952, 20]
 is outside of buffered region ImageRegion (0x7f6573ca8bb8)
  Dimension: 3
  Index: [0, 0, 0]
  Size: [526, 181, 526]

Error in kvlReadCroppedImage (line 11)
Error in segmentSubjectT2_autoEstimateAlveusML (line 838)
Started at Thu Oct 4 09:35:38 MST 2018
Ended   at Thu Oct 4 09:57:35 MST 2018
#@#%# recon-all-run-time-hours 0.366
recon-all -s subject_id finished without error at Thu Oct  4 09:57:36 MST 2018
done


I came across a similar error in the forums and using the most recent version 
seem to have worked for some, but it did not help in my case.

Freesurfer version I am using
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a

with matlab run time from 2012b as suggested
I have also tried to use 2014b runtime which exited right away.

Thank you for your help,
Pradeep





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Re: [Freesurfer] Hippocampal/Amygdala subfield segmentation error - Freesurfer devel-20180612

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Sally,
It is indeed the linear registration used to initialize the atlas deformation 
that is going crazy. Do you think you could upload the subject, so we can take 
a look?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Sally Grace 

Reply-To: Freesurfer support list 
Date: Monday, 8 October 2018 at 06:21
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal/Amygdala subfield segmentation error - 
Freesurfer devel-20180612


External Email - Use Caution
Dear experts,
I am running the hippocampal/amygdala segmentation on T1's preprocessed in 
-reconall in FS 5.3 using FS devel-20180612 using the command segmentHA_T1.sh 
bert [SUBJECTS_DIR]
This has worked successfully for roughly 1000 participants but for one 
participant I keep getting the error below, despite several troubleshooting 
attempts. The error appears to be "Fitting mesh to synthetic image resulted in 
no deformation"  - I have had a look at the hippocampus masks and they appear 
to be registered incorrectly, despite the grey matter volume output from 
-reconall having no errors. Do you have any idea what I can do to troubleshoot 
or fix this?
Thanks in advance,
Sally.

Error Log:

--
USER valentil
HOST m3a007
PROCESSID 29440
PROCESSOR x86_64
OS Linux
Linux m3a007 3.10.0-514.26.1.el7.x86_64 #1 SMP Thu Jun 29 16:05:25 UTC 2017 
x86_64 x86_64 x86_64 GNU/Linux
--

#
#@# Hippocampal Subfields processing (T1) left Tue Sep 25 10:18:56 AEST 2018
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/devel-20180612/MCRv84//runtime/glnxa64:/usr/local/freesurfer/devel-20180612/MCRv84//bin/glnxa64:/usr/local/freesurfer/devel-20180612/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/devel-20180612/lib/tcltktixblt:/usr/local/freesurfer/devel-20180612/lib/qt/lib:/usr/local/freesurfer/devel-20180612/lib/petsc/lib:/usr/local/freesurfer/devel-20180612/lib/KWWidgets/lib/KWWidgets:/usr/local/freesurfer/devel-20180612/lib/cuda/lib64:/usr/local/freesurfer/devel-20180612/lib/cuda/lib:/usr/local/freesurfer/devel-20180612/lib/bem:/usr/local/freesurfer/devel-20180612/lib:/usr/local/freesurfer/devel-20180612/lib/vtk/lib/vtk-5.6:/usr/local/fsl/5.0.11/fsl/lib:/usr/local/libjpeg-turbo/1.4.2/lib64:/usr/local/cuda/7.5/extras/CUPTI/lib64:/usr/local/cuda/7.5/lib64:/usr/local/cuda/7.5/lib:/usr/local/cuda/7.5/lib64/stubs:/opt/munge-0.5.11/lib:/opt/slurm-17.11.4/lib:/opt/slurm-17.11.4/lib/slurm:/usr/local/tigervnc/1.8.0/lib64:/usr/local/tigervnc/1.8.0/lib:/opt/munge-0.5.11/lib:/opt/slurm-17.11.4/lib:/opt/slurm-17.11.4/lib/slurm::/usr/local/freesurfer/devel-20180612/MCRv84//sys/opengl/lib/glnxa64:/usr/local/freesurfer/devel-20180612/lib/tcltktixblt:/usr/local/freesurfer/devel-20180612/lib/qt/lib:/usr/local/freesurfer/devel-20180612/lib/petsc/lib:/usr/local/freesurfer/devel-20180612/lib/KWWidgets/lib/KWWidgets:/usr/local/freesurfer/devel-20180612/lib/cuda/lib64:/usr/local/freesurfer/devel-20180612/lib/cuda/lib:/usr/local/freesurfer/devel-20180612/lib/bem:/usr/local/freesurfer/devel-20180612/lib:/usr/local/freesurfer/devel-20180612/lib/vtk/lib/vtk-5.6:/usr/local/fsl/5.0.11/fsl/lib:/usr/local/libjpeg-turbo/1.4.2/lib64:/usr/local/cuda/7.5/extras/CUPTI/lib64:/usr/local/cuda/7.5/lib64:/usr/local/cuda/7.5/lib:/usr/local/cuda/7.5/lib64/stubs:/opt/munge-0.5.11/lib:/opt/slurm-17.11.4/lib:/opt/slurm-17.11.4/lib/slurm:/usr/local/tigervnc/1.8.0/lib64:/usr/local/tigervnc/1.8.0/lib:/opt/munge-0.5.11/lib:/opt/slurm-17.11.4/lib:/opt/slurm-17.11.4/lib/slurm:
Registering imageDump.mgz to hippocampal mask from ASEG
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

--mov: Using imageDump.mgz as movable/source volume.
--dst: Using 
/home/valentil/kg98/Valentina/ENIGMA_sex_differences/Scripts/rerun_reconall/NIAAA_MRI00032_1-out/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz
 as target volume.
--lta: Output transform as trash.lta .
--mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz !
--sat: Using saturation 50 in M-estimator!

reading source 'imageDump.mgz'...
reading target 
'/home/valentil/kg98/Valentina/ENIGMA_sex_differences/Scripts/rerun_reconall/NIAAA_MRI00032_1-out/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz'...

Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE )
   Type Source : 0  Type Target : 3  ensure both FLOAT (3)
   Reordering axes in mov to better fit dst... ( -1 3 -2 )
MRIreorder() ---
xdim=-1 ydim=3 zdim=-2
src 131 241 99, 0.25 0.25 0.25
dst 131 99 241, 0.25 0.25 0.25
 Determinant after swap : 0.015625
   Mov: (0.25, 0.25, 0.25)mm  and dim (131, 99, 241)
   Dst: (1, 

Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks!
Did you check whether the T2 and the T1 were correctly registered? You can 
check out the animated gif under mri/transforms in the subject’s directory.
Cheers,
/E

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Pradeep 

Reply-To: Freesurfer support list 
Date: Thursday, 4 October 2018 at 19:21
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal segmentation with an additional scan 
ERROR kvlGEMSMatlab


External Email - Use Caution
I have tried this for two subjects and got the same error.

Thanks,
Pradeep

On Thu, Oct 4, 2018 at 11:14 AM Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution
Dear Pradeep,
Did you get this error on several subjects, or only one?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Pradeep mailto:tprad...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 4 October 2018 at 19:12
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Hippocampal segmentation with an additional scan ERROR 
kvlGEMSMatlab


External Email - Use Caution
Hello,

I am trying to run the hippocampal segmentation with an additional Hi-res scan 
using the following command

recon-all -s  -hippocampal-subfields-T2   
and got the following error


Error using kvlGEMSMatlab
/autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211:
itk::ERROR: Region ImageRegion (0x7f67011c5dd0)
  Dimension: 3
  Index: [0, 845, 0]
  Size: [105, 18446744073709550952, 20]
 is outside of buffered region ImageRegion (0x7f6573ca8bb8)
  Dimension: 3
  Index: [0, 0, 0]
  Size: [526, 181, 526]

Error in kvlReadCroppedImage (line 11)
Error in segmentSubjectT2_autoEstimateAlveusML (line 838)
Started at Thu Oct 4 09:35:38 MST 2018
Ended   at Thu Oct 4 09:57:35 MST 2018
#@#%# recon-all-run-time-hours 0.366
recon-all -s subject_id finished without error at Thu Oct  4 09:57:36 MST 2018
done


I came across a similar error in the forums and using the most recent version 
seem to have worked for some, but it did not help in my case.

Freesurfer version I am using
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a

with matlab run time from 2012b as suggested
I have also tried to use 2014b runtime which exited right away.

Thank you for your help,
Pradeep





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Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Pradeep,
Did you get this error on several subjects, or only one?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Pradeep 

Reply-To: Freesurfer support list 
Date: Thursday, 4 October 2018 at 19:12
To: Freesurfer support list 
Subject: [Freesurfer] Hippocampal segmentation with an additional scan ERROR 
kvlGEMSMatlab


External Email - Use Caution
Hello,

I am trying to run the hippocampal segmentation with an additional Hi-res scan 
using the following command

recon-all -s  -hippocampal-subfields-T2   
and got the following error


Error using kvlGEMSMatlab
/autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211:
itk::ERROR: Region ImageRegion (0x7f67011c5dd0)
  Dimension: 3
  Index: [0, 845, 0]
  Size: [105, 18446744073709550952, 20]
 is outside of buffered region ImageRegion (0x7f6573ca8bb8)
  Dimension: 3
  Index: [0, 0, 0]
  Size: [526, 181, 526]

Error in kvlReadCroppedImage (line 11)
Error in segmentSubjectT2_autoEstimateAlveusML (line 838)
Started at Thu Oct 4 09:35:38 MST 2018
Ended   at Thu Oct 4 09:57:35 MST 2018
#@#%# recon-all-run-time-hours 0.366
recon-all -s subject_id finished without error at Thu Oct  4 09:57:36 MST 2018
done


I came across a similar error in the forums and using the most recent version 
seem to have worked for some, but it did not help in my case.

Freesurfer version I am using
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a

with matlab run time from 2012b as suggested
I have also tried to use 2014b runtime which exited right away.

Thank you for your help,
Pradeep





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Re: [Freesurfer] hippocampal subfields error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

That sounds pretty weird… Did you get any error messages on the Linux server?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Marcel Heers 

Reply-To: Freesurfer support list 
Date: Wednesday, 3 October 2018 at 20:11
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal subfields error


External Email - Use Caution
Dear Eugenio,

I am currently testing the newest version of your hippocampal subfield analysis 
script. If I process the data on my macbook the files 
hipposubfields.lh.T2.v21.file_ID contain the volumes of the different nuclei, 
but on the linux server these files remain empty. On the server I installed 
freesurfer as local user. Do you have any suggestions how to check what might 
go wrong?

Thanks for your help!

Marcel
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Re: [Freesurfer] amygdala segmentation atlas influence

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks, Raj.
I’d argue that, if the volumes of the nuclei were completely driven by the 
global volume of the amygdala, e.g., in an extreme case, V_nuc = alpha  x  
V_whole, then the effect size of the nucleus at hand would be the same as for 
the whole amygdala. Whether such effect size is higher or lower than the “real” 
effect size in presence of perfect segmentation… depends on the nucleus ;-)
Doug: any thoughts?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: "Dr Rajendra Morey, M.D." 
Date: Monday, 1 October 2018 at 21:53
To: "Iglesias Gonzalez, Eugenio" , Freesurfer support 
list 
Subject: RE: [Freesurfer] amygdala segmentation atlas influence

Hi Eugenio
Thanks for your response it is helpful. In the dataset that I just analyzed 
with about 375 scans I suspect that the segmentation for some nuclei is heavily 
driven by the atlas. This is resulting in relatively low variance in both the 
patient group and the control group. The implication is that the between-group 
statistical test is overly sensitive and therefore produces higher than the 
expected chance   of a significant result. Is this a reasonable concern.

The counterargument is that the means of the two groups are closer to each 
other than the true means because of a heavy reliance on the atlas.  The 
implication here is that the between group statistical test is going to be more 
conservative than the true difference. Or does it mean the significance  of the 
test is not affected but that the effect size is artificially low. Let me know 
your thoughts!

Thanks
raj

From: Iglesias Gonzalez, Eugenio [mailto:e.igles...@ucl.ac.uk]
Sent: Sunday, September 30, 2018 10:44 AM
To: Freesurfer support list 
Cc: Dr Rajendra Morey, M.D. 
Subject: Re: [Freesurfer] amygdala segmentation atlas influence

Dear Raj,
A few years ago, we published a paper on how Monte Carlo sampling could be used 
to quantify this. Unfortunately, the method was incredibly slow and difficult 
to tune, and the performance gain was tiny, so we never put it in FreeSurfer. 
But this is a direction I’m still interested in, and which I’m planning to 
revisit in the future.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Emily K Clarke mailto:ek...@duke.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, 26 September 2018 at 15:15
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: "Dr Rajendra Morey, M.D." 
mailto:rajendra.mo...@duke.edu>>
Subject: [Freesurfer] amygdala segmentation atlas influence


External Email - Use Caution

Hello all,

I have run the amygdala segmentation in my datasets to obtain volumes of 
nuclei. I am aware from the fswiki that the volumes should be interpreted with 
caution because of the reliance on the atlas. When running FS, is there a way 
to get some metric about how much the segmentation relied on the atlas relative 
information from the T1 being segmented. If this metric is not available to the 
user, is some version of it calculated by the software and therefore available 
internally. Thanks in advance for your help!

raj
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Re: [Freesurfer] cannot stat volumesAmygdala.txt

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi again, John,
The amygdala segmentation only because available in development versions newer 
than FreeSurfer 6.0.
Please try again with the latest dev. You don’t need to re-run recon-all; you 
can run the hippo+amygdala volume on subjects processed with 6.0.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of John 
Papatriantafyllou 
Reply-To: Freesurfer support list 
Date: Sunday, 30 September 2018 at 22:15
To: Freesurfer support list 
Subject: Re: [Freesurfer] cannot stat volumesAmygdala.txt


External Email - Use Caution
Hi
it is
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
John



On Sun, Sep 30, 2018 at 2:50 PM Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution
Hi Jon,
What exact version are you using? Is it a recent development version?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of John Papatriantafyllou 
mailto:epikti...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, 30 September 2018 at 09:29
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] cannot stat volumesAmygdala.txt


External Email - Use Caution
dear Freesurfers,
after processing hippocampal subfields i cannot get amygdala stats.
Instead i get the following massage
cannot stat  volumesAmygdala.txt
Any suggestions?
John

PS i run freesurfer under neurodebian system on pc with windows 10


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Re: [Freesurfer] amygdala segmentation atlas influence

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Raj,
A few years ago, we published a paper on how Monte Carlo sampling could be used 
to quantify this. Unfortunately, the method was incredibly slow and difficult 
to tune, and the performance gain was tiny, so we never put it in FreeSurfer. 
But this is a direction I’m still interested in, and which I’m planning to 
revisit in the future.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Emily K Clarke 

Reply-To: Freesurfer support list 
Date: Wednesday, 26 September 2018 at 15:15
To: "freesurfer@nmr.mgh.harvard.edu" 
Cc: "Dr Rajendra Morey, M.D." 
Subject: [Freesurfer] amygdala segmentation atlas influence


External Email - Use Caution

Hello all,

I have run the amygdala segmentation in my datasets to obtain volumes of 
nuclei. I am aware from the fswiki that the volumes should be interpreted with 
caution because of the reliance on the atlas. When running FS, is there a way 
to get some metric about how much the segmentation relied on the atlas relative 
information from the T1 being segmented. If this metric is not available to the 
user, is some version of it calculated by the software and therefore available 
internally. Thanks in advance for your help!

raj
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Re: [Freesurfer] cannot stat volumesAmygdala.txt

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Jon,
What exact version are you using? Is it a recent development version?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of John 
Papatriantafyllou 
Reply-To: Freesurfer support list 
Date: Sunday, 30 September 2018 at 09:29
To: Freesurfer support list 
Subject: [Freesurfer] cannot stat volumesAmygdala.txt


External Email - Use Caution
dear Freesurfers,
after processing hippocampal subfields i cannot get amygdala stats.
Instead i get the following massage
cannot stat  volumesAmygdala.txt
Any suggestions?
John

PS i run freesurfer under neurodebian system on pc with windows 10


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Re: [Freesurfer] matlab MEXFile error in thalamic nuclei segmentation script

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Carme,
This has to do with the CentOS version.
Please try the version compiled on CentOS6 (that should fix the problem).
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Carme Uribe Codesal 

Reply-To: Freesurfer support list 
Date: Friday, 21 September 2018 at 10:03
To: Freesurfer support list 
Subject: [Freesurfer] matlab MEXFile error in thalamic nuclei segmentation 
script


External Email - Use Caution
Dear FreeSurfer users,

I am trying to run the Thalamic nuclei and the hippocampal/amygdala 
segmentation scripts but there is an error with the matlab license.
The error message is:

LD_LIBRARY_PATH is 
.:/nas01/users/carme/freesurfer/MCRv84//runtime/glnxa64:/nas01/users/carme/freesurfer/MCRv84//bin/glnxa64:/nas01/users/carme/freesurfer/MCRv84//sys/os/glnxa64:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/libexec/NX3/lib64/Xinerama:/usr/lib/nx/X11
Invalid MEX-file 
'/tmp/MCR_714808722/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64':
 /lib64/libc.so.6: version `GLIBC_2.14' not found (required by 
/tmp/MCR_714808722/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64)

Error in kvlClear (line 11)

Error in SegmentThalamicNuclei (line 203)

MATLAB:invalidMEXFile

Thanks!

Carme Uribe
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Re: [Freesurfer] Hippocampal-Amygdala subfields error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Wow sorry about this. I have to carefully check whether it’s a different / 
related bug, or if the fix only made it to the Linux version. Is it happening 
for all subjects, or only some?
I’m traveling / on vacation these days but will take a look as soon as I can.
Cheers,
/E

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Miguel Ángel Rivas 
Fernández 
Reply-To: Freesurfer support list 
Date: Sunday, 16 September 2018 at 15:52
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error


External Email - Use Caution

Hi Eugenio,

I have downloaded the most recent dev version ( 
freesurfer-darwin-OSX-ElCapitan-dev.tar.gz<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-darwin-OSX-ElCapitan-dev.tar.gz>
 ) from here  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev and I 
get the same error.

My version of Mac is Mac OS High Sierra Version 10.13.3


Fitting mesh to image data mask took 683.6633 seconds
Transforming points
Transforming points
Wrote image to file image.mgz
INFO: dst volume info differs from the one stored in lta.  gets modified now.
volume geometry:
extent  : (691, 691, 473)
voxel   : ( 0.,  0.,  0.)
x_(ras) : ( 0., -1.,  0.)
y_(ras) : (-0.0047,  0.,  1.)
z_(ras) : ( 1.,  0.,  0.0047)
c_(ras) : ( 4.2397, 13.6233, 12.2196)
file: T2isotropic.mgz
volume geometry:
extent  : (640, 640, 225)
voxel   : ( 0.3594,  0.3594,  0.7000)
x_(ras) : ( 0., -1.,  0.)
y_(ras) : (-0.0047,  0.,  1.)
z_(ras) : ( 1.,  0.,  0.0047)
c_(ras) : ( 4.2397, 13.6234, 12.2196)
file: /Applications/freesurfer/subjects/5095/mri/orig/T2.nii
Constructing image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information 
(/Applications/freesurfer/subjects/5095/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does not contain MRI parameters
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)



MATLAB:subsassignnumelmismatch
Darwin rmnlab1.inv.usc.es<http://rmnlab1.inv.usc.es> 17.4.0 Darwin Kernel 
Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; 
root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64

T2 hippocampal subfields exited with ERRORS at domingo, 16 de septiembre de 
2018, 15:35:35 CEST

For more details, see the log file 
/Applications/freesurfer/subjects/5095/scripts/hippocampal-subfields-T2.HIPO-AMI.log






What could be the problem?


Thanks in advance,

Best wishes,


El vie., 14 sept. 2018 a las 0:40, Iglesias Gonzalez, Eugenio 
(mailto:e.igles...@ucl.ac.uk>>) escribió:

External Email - Use Caution
Hi Miguel Angel,
This bug was recently fixed in the dev version. If you download the most recent 
one, you won’t have this problem.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Miguel Ángel Rivas Fernández 
mailto:miguelrivasf...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 13 September 2018 at 21:12
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Hippocampal-Amygdala subfields error


External Email - Use Caution

Hello Freesurfer devs,

I ran the hippocampal and amygdala subfields command in my sample and I get the 
following error in several subjects:

Constructing image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information 
(/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does not contain MRI parameters
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)Constructing 
image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information 
(/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does not contain MRI parameters
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)

MATLAB:subsassignnumelmismatch
Darwin rmnlab1.inv.usc.es<http://rmnlab1.inv.usc.es> 17.4.0 Darwin Kern

Re: [Freesurfer] Hippocampal-Amygdala subfields error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Miguel Angel,
This bug was recently fixed in the dev version. If you download the most recent 
one, you won’t have this problem.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Miguel Ángel Rivas 
Fernández 
Reply-To: Freesurfer support list 
Date: Thursday, 13 September 2018 at 21:12
To: Freesurfer support list 
Subject: [Freesurfer] Hippocampal-Amygdala subfields error


External Email - Use Caution

Hello Freesurfer devs,

I ran the hippocampal and amygdala subfields command in my sample and I get the 
following error in several subjects:

Constructing image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information 
(/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does not contain MRI parameters
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)Constructing 
image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information 
(/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does not contain MRI parameters
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)

MATLAB:subsassignnumelmismatch
Darwin rmnlab1.inv.usc.es 17.4.0 Darwin Kernel 
Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; 
root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64

T2 hippocampal subfields exited with ERRORS at jueves, 13 de septiembre de 
2018, 21:37:33 CEST



What would be the reason?


Thanks in advance,


Best wishes,

--
Miguel Ángel Rivas Fernández
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Re: [Freesurfer] Minimum FS version for thalamic segmentation

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Niels
5.1 should do but please let us know if it doesn't!
Cheers
E

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Niels Bergsland 

Sent: Wednesday, September 12, 2018 1:25:18 PM
To: Freesurfer Mailing List
Subject: [Freesurfer] Minimum FS version for thalamic segmentation


External Email - Use Caution

Hi Eugenio,
Just a quick question - is there a minimum version of FS that is required to 
run the thalamic nuclei segmentation? I am just thinking about some old 
datasets that we have that were run with FS 5.1.
Thanks and best wishes,
Niels
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Re: [Freesurfer] Amygdala subfields segmentation

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev


Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Miguel Ángel Rivas 
Fernández 
Sent: Tuesday, September 11, 2018 5:59:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Amygdala subfields segmentation


External Email - Use Caution

Hi Eugenio,


Where can I find the link for download the latest dev version?


The latest version is this?:

freesurfer-darwin-OSX-ElCapitan-dev.tar.gz


Thanks in advance,


Best,


El mar., 11 sept. 2018 a las 17:47, Iglesias Gonzalez, Eugenio 
(mailto:e.igles...@ucl.ac.uk>>) escribió:

External Email - Use Caution

Dear MA
Please download the latest dev version and the command will be there
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Miguel Ángel Rivas Fernández 
mailto:miguelrivasf...@gmail.com>>
Sent: Tuesday, September 11, 2018 12:20:55 PM
To: Freesurfer support list
Subject: [Freesurfer] Amygdala subfields segmentation


External Email - Use Caution

Hi Freesurfer developes,

I am trying to execute the hippocampal and amygdala segmentation command " 
segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]" 
but freesurfer gave to me this error command not found.


However, when I use the command that segment only the hippocampal subfields 
(recon-all -s  -hippocampal-subfields-T2  ) I don´t have any problem.


What would be the reason?


Thanks in advance.


Best,

--
Miguel Ángel Rivas Fernández
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


--
Miguel Ángel Rivas Fernández
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Re: [Freesurfer] Amygdala subfields segmentation

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear MA
Please download the latest dev version and the command will be there
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Miguel Ángel Rivas 
Fernández 
Sent: Tuesday, September 11, 2018 12:20:55 PM
To: Freesurfer support list
Subject: [Freesurfer] Amygdala subfields segmentation


External Email - Use Caution

Hi Freesurfer developes,

I am trying to execute the hippocampal and amygdala segmentation command " 
segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]" 
but freesurfer gave to me this error command not found.


However, when I use the command that segment only the hippocampal subfields 
(recon-all -s  -hippocampal-subfields-T2  ) I don´t have any problem.


What would be the reason?


Thanks in advance.


Best,

--
Miguel Ángel Rivas Fernández
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Using the new Thalamus tool

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

10-15 mins or so

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Erik O'Hanlon 

Sent: Tuesday, September 11, 2018 12:32:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Using the new Thalamus tool


External Email - Use Caution

Thanks Eugenio,


I'll intall the latest dev version so. How long does it typically take to run a 
subject through the thalamus pipeline typically?


Thanks again for the prompt reply. Very much appreciated.


Cheers


Erik


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: 10 September 2018 18:00:20
To: freesurfer@nmr.mgh.harvard.edu; Freesurfer support list
Subject: Re: [Freesurfer] Using the new Thalamus tool


External Email - Use Caution

Dear Erik,
Installing only the thalamic tool is technically possible but requires a level 
of hacking that i don't want to encourage or support ;-)
Please install the new dev on a separate directory, and make FREESURFER_HOME 
point to that the directory (and source freesurfer) to run the thalamic tool. 
No need to rerun recon-all on the subjects.
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Erik O'Hanlon 

Sent: Thursday, September 6, 2018 3:44:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using the new Thalamus tool


External Email - Use Caution

Hi FS Experts


I've run my data through the brainstem, hippocampus and amygdala following the 
usual Recon_all and using the developmental version downloaded and stalled 
around Jan2018. I'd like to use the new thalamus tool and am wondering if I 
need to do a full install of the latest DEV version to do so. As I am still 
working on certain aspects of the analyses I've run so far, I don't want to 
overwrite my main FS installation mid analysis. Is it possible to download the 
toolbox and add it to my current dev version or is it best just to do another 
install with teh complete new Dev version?  Is it possible to run the Thalamus 
analysis as an addtional component without having to rerun the recon_all again?


Thanks and regards


Erik

Erik O'Hanlon
Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/>


Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022<http://www.rcsi.ie/strategy2018>


[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]


Erik O'Hanlon
Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/>


Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022<http://www.rcsi.ie/strategy2018>


[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

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Re: [Freesurfer] thalamic segmentation

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Vinny,
The anatomical definitions can be found in the paper, which is open access (see 
Table 2):
https://www.sciencedirect.com/science/article/pii/S1053811918307109
Kind regards
Eugenio



Sent from my phone, please excuse brevity and typos






From: Vinny K
Sent: Monday, September 10, 10:35
Subject: Re: [Freesurfer] thalamic segmentation
To: freesurfer@nmr.mgh.harvard.edu


External Email - Use Caution
Hi,

I ran recon-all to generate the required files for the thalamic segmentation 
tool 
(http://freesurfer.net/fswiki/ThalamicNuclei)
 using the latest development version of Freesurfer (06/09/2018) linux-cent06.  
The segmented thalamic nuclei were visualized but I could not find a table 
listing the thalamic nuclei and its associated label to help identify the 
specific nuclei.

Any help would be greatly appreciated.

Thanks,

Vinny


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Re: [Freesurfer] amygdala segmentation using additional scan error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Jinyoung
Sorry for the slow response but I'm traveling these days
I believe this is a bug that was fixed in the dev version 2-3 weeks ago. Would 
you mind trying the latest dev, and checking whether that solves the problem?
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 오진영 

Sent: Wednesday, September 5, 2018 6:13:48 AM
To: Freesurfer support list
Subject: [Freesurfer] amygdala segmentation using additional scan error


External Email - Use Caution

Hello, freesurfer experts

I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala 
with additional scan.
I already ran segmentation of hippocampal subfields and nuclei of amygdala with 
only T1 image, using segmentHA_T1.sh command and succeeded.
After success of segmentation of amygdala with T1 image, I tried to run 
segmentation again with additional scan(T2 image) to get more reliable results.
However, when I use command segmentHA_T2.sh, I got the following error:

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 2628)


And the last few lines before the error are below:

Fitting mesh to image data mask took 264.2808 seconds

Transforming points

Transforming points

Wrote image to file image1.mgz

Wrote image to file image2.mgz

INFO: dst volume info differs from the one stored in lta.  gets modified now.

volume geometry:

extent  : (232, 469, 208)

voxel   : ( 0.,  0.,  0.)

x_(ras) : ( 0., -1.,  0.)

y_(ras) : ( 0.,  0., -1.)

z_(ras) : ( 1.,  0.,  0.)

c_(ras) : (-21.1788, -1.8961,  3.8447)

file: T2isotropic.mgz

volume geometry:

extent  : (256, 256, 256)

voxel   : ( 1.,  1.,  1.)

x_(ras) : ( 0., -1.,  0.)

y_(ras) : ( 0.,  0., -1.)

z_(ras) : ( 1.,  0.,  0.)

c_(ras) : ( 2.3212,  8.6039, -21.1553)

file: /Users/mnd_mac/Desktop/JY_surfer/sub_05_T2.nii

Constructing image-to-world transform from header information (asmr1.mgz)

Constructing image-to-world transform from header information 
(/Users/mnd_mac/Desktop/JY_surfer//recon_sub_05/tmp/hippoSF_T1T2_v21_T2_left/imageDump.mgz)

Wrote image to file asmr2.mgz

This file does not contain MRI parameters

This file does not contain MRI parameters

This file does not contain MRI parameters

In an assignment  A(:) = B, the number of elements in A and B must be the same.


Error in segmentSubjectT1T2_autoEstimateAlveusML (line 2628)




MATLAB:subsassignnumelmismatch

Darwin MnD-macui-iMac.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 
22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64

and I have no idea how to solve this problem out.

I use the dev version of freesurfer.
T1 scan image and T2 scan image of participant were taken on the same day.

If you have any recommendations, please send me the email back.

Thanks!

Jinyoung
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Re: [Freesurfer] Using the new Thalamus tool

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Erik,
Installing only the thalamic tool is technically possible but requires a level 
of hacking that i don't want to encourage or support ;-)
Please install the new dev on a separate directory, and make FREESURFER_HOME 
point to that the directory (and source freesurfer) to run the thalamic tool. 
No need to rerun recon-all on the subjects.
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Erik O'Hanlon 

Sent: Thursday, September 6, 2018 3:44:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using the new Thalamus tool


External Email - Use Caution

Hi FS Experts


I've run my data through the brainstem, hippocampus and amygdala following the 
usual Recon_all and using the developmental version downloaded and stalled 
around Jan2018. I'd like to use the new thalamus tool and am wondering if I 
need to do a full install of the latest DEV version to do so. As I am still 
working on certain aspects of the analyses I've run so far, I don't want to 
overwrite my main FS installation mid analysis. Is it possible to download the 
toolbox and add it to my current dev version or is it best just to do another 
install with teh complete new Dev version?  Is it possible to run the Thalamus 
analysis as an addtional component without having to rerun the recon_all again?


Thanks and regards


Erik

Erik O'Hanlon
Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.com


Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022


[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

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Re: [Freesurfer] hippocampus subfields with T2

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Um this is an empirical question. I would try with and without, and then 
decide.
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alexopoulos, Dimitrios 

Sent: Thursday, August 30, 2018 9:38:50 PM
To: Freesurfer support list
Subject: [Freesurfer] hippocampus subfields with T2


External Email - Use Caution
We have a cohort of 10yo subjects for which we have acquired a 0.85mm isotropic 
T1-mprage and a 1mm isotropic T2-space.
Is it possible or even recommended to try and generate better hippocampal 
segmentation in fressurfer 6.0 using both the T1 and T2,
or does the T2 need to be of equal or better resolution than the T1?

Jim


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
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Re: [Freesurfer] questions about hippocampus subfield error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

The subfield part never started. Recon-all died earlier.
Andrew: any ideas?

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 姜时泽 

Reply-To: Freesurfer support list 
Date: Friday, 24 August 2018 at 15:14
To: Freesurfer support list 
Subject: Re: [Freesurfer] questions about hippocampus subfield error


External Email - Use Caution
Hi Eugenio
I did not find the log file you mentioned. Attached is all log file within 
script directory. Would you please help me to figure out what was wrong?
Thank you so much
Best wishes
Shize




在 2018-08-24 15:50:44，"Iglesias Gonzalez, Eugenio"  写道：


External Email - Use Caution
I am really confused. There are no errors in the subfield module in that log.
Can you please send me the file hippocampal-subfields-T1.log, which should be 
found in the scripts directory (inside the subject’s directory)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 姜时泽 mailto:jiangshize1...@163.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 23 August 2018 at 23:02
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] questions about hippocampus subfield error


External Email - Use Caution
Hi Juan
Thank you for your kindly help. Attached is the log file with error. I am not 
sure if this is the file for hippocampus subfield segmentation.
Thank you very much
Shize





在 2018-08-24 05:08:35，"Iglesias Gonzalez, Eugenio" 
mailto:e.igles...@ucl.ac.uk>> 写道：



External Email - Use Caution

Thanks! Can you please send us the log of the hippocampal subfield 
segmentation? It should be in the same directory as the recon-all log.

Cheers,

/E



Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/




From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 姜时泽 mailto:jiangshize1...@163.com>>
Sent: Thursday, August 23, 2018 5:08:51 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] questions about hippocampus subfield error


External Email - Use Caution
Hi Eugenio,
Yes, If I run without the hippocampal subfield flag. Recon-all complete without 
any error. So I am confused what is wrong with this.
Thank you
Shize





在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio" 
mailto:e.igles...@ucl.ac.uk>> 写道：



External Email - Use Caution

Hi Shize,

Does recon-all complete when you run it without the hippocampal subfield flag? 
It doesn’t look like an error in the subfield module to me …

Cheers,

/Eugenio



--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/





From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 姜时泽 mailto:jiangshize1...@163.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 23 August 2018 at 15:10
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] questions about hippocampus subfield error



External Email - Use Caution

Dear freesurfer experts,

I am trying to run recon-all with -hippocampal-subfields-T1 flag to get 
hippocampal subfield information. I tried many times but always finish with 
error. The MRI data is obtained from GE750 MRI machine. The resolution is 
1mm*1mm*1mm.

below is the commands I used to run freesurfer and attached is the recon-all 
log file.

recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 
-brainstem-structures -3T -qcache -all

I am not sure if there are something wrong with my inputs.

Thank you all

all the best

Shize






--

Shize Jiang
Fudan University,
Department of neurosurgery, Huashan Hospital, Shanghai Medical College
Shanghai,200032,P.R.China
Mobile: (86)18317079839
E-Mail: sjian...@fudan.edu.cn<mailto:sjian...@fudan.edu.cn>











[ge removed by sender.]























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The information in this e-mail is intended only for the person to whom it is
addressed. If yo

Re: [Freesurfer] questions about hippocampus subfield error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

I am really confused. There are no errors in the subfield module in that log.
Can you please send me the file hippocampal-subfields-T1.log, which should be 
found in the scripts directory (inside the subject’s directory)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 姜时泽 

Reply-To: Freesurfer support list 
Date: Thursday, 23 August 2018 at 23:02
To: Freesurfer support list 
Subject: Re: [Freesurfer] questions about hippocampus subfield error


External Email - Use Caution
Hi Juan
Thank you for your kindly help. Attached is the log file with error. I am not 
sure if this is the file for hippocampus subfield segmentation.
Thank you very much
Shize




在 2018-08-24 05:08:35，"Iglesias Gonzalez, Eugenio"  写道：


External Email - Use Caution

Thanks! Can you please send us the log of the hippocampal subfield 
segmentation? It should be in the same directory as the recon-all log.

Cheers,

/E



Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/




From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 姜时泽 mailto:jiangshize1...@163.com>>
Sent: Thursday, August 23, 2018 5:08:51 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] questions about hippocampus subfield error


External Email - Use Caution
Hi Eugenio,
Yes, If I run without the hippocampal subfield flag. Recon-all complete without 
any error. So I am confused what is wrong with this.
Thank you
Shize




在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio" 
mailto:e.igles...@ucl.ac.uk>> 写道：


External Email - Use Caution

Hi Shize,

Does recon-all complete when you run it without the hippocampal subfield flag? 
It doesn’t look like an error in the subfield module to me …

Cheers,

/Eugenio



--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/





From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 姜时泽 mailto:jiangshize1...@163.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 23 August 2018 at 15:10
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] questions about hippocampus subfield error



External Email - Use Caution

Dear freesurfer experts,

I am trying to run recon-all with -hippocampal-subfields-T1 flag to get 
hippocampal subfield information. I tried many times but always finish with 
error. The MRI data is obtained from GE750 MRI machine. The resolution is 
1mm*1mm*1mm.

below is the commands I used to run freesurfer and attached is the recon-all 
log file.

recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 
-brainstem-structures -3T -qcache -all

I am not sure if there are something wrong with my inputs.

Thank you all

all the best

Shize





--

Shize Jiang
Fudan University,
Department of neurosurgery, Huashan Hospital, Shanghai Medical College
Shanghai,200032,P.R.China
Mobile: (86)18317079839
E-Mail: sjian...@fudan.edu.cn<mailto:sjian...@fudan.edu.cn>










[age removed by sender.]















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Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] questions about hippocampus subfield error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks! Can you please send us the log of the hippocampal subfield 
segmentation? It should be in the same directory as the recon-all log.

Cheers,

/E


Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 姜时泽 

Sent: Thursday, August 23, 2018 5:08:51 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] questions about hippocampus subfield error


External Email - Use Caution

Hi Eugenio,
Yes, If I run without the hippocampal subfield flag. Recon-all complete without 
any error. So I am confused what is wrong with this.
Thank you
Shize





在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio"  写道：

External Email - Use Caution

Hi Shize,

Does recon-all complete when you run it without the hippocampal subfield flag? 
It doesn’t look like an error in the subfield module to me …

Cheers,

/Eugenio



--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/





From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 姜时泽 mailto:jiangshize1...@163.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 23 August 2018 at 15:10
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] questions about hippocampus subfield error



External Email - Use Caution

Dear freesurfer experts,

I am trying to run recon-all with -hippocampal-subfields-T1 flag to get 
hippocampal subfield information. I tried many times but always finish with 
error. The MRI data is obtained from GE750 MRI machine. The resolution is 
1mm*1mm*1mm.


below is the commands I used to run freesurfer and attached is the recon-all 
log file.


recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 
-brainstem-structures -3T -qcache -all

I am not sure if there are something wrong with my inputs.


Thank you all

all the best

Shize






--

Shize Jiang
Fudan University,
Department of neurosurgery, Huashan Hospital, Shanghai Medical College
Shanghai,200032,P.R.China
Mobile: (86)18317079839
E-Mail: sjian...@fudan.edu.cn<mailto:sjian...@fudan.edu.cn>












[mage removed by sender.]










___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] questions about hippocampus subfield error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Shize,
Does recon-all complete when you run it without the hippocampal subfield flag? 
It doesn’t look like an error in the subfield module to me …
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 姜时泽 

Reply-To: Freesurfer support list 
Date: Thursday, 23 August 2018 at 15:10
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] questions about hippocampus subfield error


External Email - Use Caution
Dear freesurfer experts,
I am trying to run recon-all with -hippocampal-subfields-T1 flag to get 
hippocampal subfield information. I tried many times but always finish with 
error. The MRI data is obtained from GE750 MRI machine. The resolution is 
1mm*1mm*1mm.

below is the commands I used to run freesurfer and attached is the recon-all 
log file.

recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 
-brainstem-structures -3T -qcache -all
I am not sure if there are something wrong with my inputs.

Thank you all
all the best
Shize





--

Shize Jiang
Fudan University,
Department of neurosurgery, Huashan Hospital, Shanghai Medical College
Shanghai,200032,P.R.China
Mobile: (86)18317079839
E-Mail: sjian...@fudan.edu.cn











[mage removed by sender.]






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Re: [Freesurfer] hippocampal subfield segmentation

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Ryan,

Is it possible that you're mixing versions of FreeSurfer in your PATH and/or 
LD_LIBRARY_PATH? Maybe you could try unsetting them before you source 
FreeSurfer?

Cheers,

/Eugenio


Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Nillo, Ryan Michael R 

Sent: Tuesday, August 21, 2018 9:58:25 PM
To: Freesurfer support list
Subject: [Freesurfer] hippocampal subfield segmentation


External Email - Use Caution

Hello FreeSurfer users,

I want to segment hippocampal subfields, but did not have much luck running it. 
I downloaded the matlab compiler runtime according to this: 
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime. Now, there is a 
directory called MCRv80 in my FREESURFER_HOME. The first error says 
kvlAutoCrop: command not found. However, $FREESURFER_HOME.bin is on my path. 
Does anything seem incorrect?

My path looks like this:
/data/sugrue2/rnillo/tools:/data/sugrue2/rnillo:/netopt/afni:/working/sdl_analysis/software/dcm2niix/build/bin:/netopt/rhel7/versions/cmtk/lib/cmtk/bin:/working/sdl_analysis/software/vtk-dicom/build/bin:/netopt/dicom/bin:/working/sdl_analysis/software/ANTs/antsbin/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/mni/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/share/bin/local/sdl/fix:/netopt/rhel7/fsl/bin:/working/sdl_analysis/software/git_pipeline/CommandLineProg:/netopt/share/local/bin/sdl/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/bin:/usr/local/sbin:/working/sdl_analysis/software/git_unwarp:/working/sdl_analysis/software/parallel:/working/sdl_analysis/software/git_tools:/working/sdl_analysis/software/anaconda3/bin:/bin:/sbin:/usr/bin::/netopt/rhel7/bin:/netopt/rhel7/bin/local:/netopt/share/bin:/netopt/share/bin/local:/netopt/bin:/netopt/bin/local:/netopt/dicom/bin:/netopt/rhel7/matlab/bin:/netopt/ctf/bin:/netopt/share/hosts::/netopt/caret/bin:/netopt/afni:/netopt/freesurfer/bin/Linux:/netopt/freesurfer/bin/noarch:/netopt/sybase/12.5.3/OCS-12_5/bin:/netopt/rhel7/fsl/bin:/netopt/sge_n1ge6/bin/lx24-amd64:/netopt/rhel7/tivoli/tsm/client/ba/bin::/netopt/share/bin/local/sdl:/netopt/bin/local/brain:/netopt/share/bin/local/brain:/netopt/bin/local/ncl:/netopt/share/bin/local/ncl:.
MatlabRuntime - Free Surfer 
Wiki
surfer.nmr.mgh.harvard.edu
Matlab Runtime. The brainstem and hippocampal subfield modules in FreeSurfer 
6.0 and the development version require the Matlab R2012b (v8.0) runtime (note 
that development versions from January 2018 onwards require the Matlab R2014b - 
v8.4 - runtime instead).




ERROR MESSAGE:

#
#@# Hippocampal Subfields processing (T1 only) left Tue Aug 21 13:45:25 PDT 2018
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/runtime/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/bin/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/os/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/working/sdl_analysis/software/freesurfer6/freesurfer/bin:
Warning: Unable to open display '10.48.0.125:0'.  You will not be able to 
display graphics on the screen.
Registering imageDump.mgz to hippocampal mask from ASEG
/working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlAutoCrop: line 3: 
kvlAutoCrop.bin: command not found
gzip: 
/data/sugrue2/MTS/sub_0006_T1_20160920_1723/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz:
 No such file or directory
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)



Error in myMRIread>myMRIread_aux (line 92)



Error in myMRIread (line 63)



Error in segmentSubjectT1_autoEstimateAlveusML (line 158)



MATLAB:badSwitchExpression
#
#@# Hippocampal Subfields processing (T1 only) right Tue Aug 21 13:45:43 PDT 
2018
--
Setting up environment variables
---
LD_LIBRARY_PATH is 

Re: [Freesurfer] segmentHA_T1.sh exits with error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Antonin,
Thanks again for letting us know you had this problem; it turned out to be a 
small, silly bug in the code. I will fix it ASAP, and the updated code should 
be on the dev version in the next few days.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Antonin Skoch 

Reply-To: Freesurfer support list 
Date: Friday, 17 August 2018 at 18:16
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] segmentHA_T1.sh exits with error


External Email - Use Caution
Dear experts,

I am running segmentHA_T1.sh. In about 3 subjects from 200, the script exits 
with following error:

In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT1_autoEstimateAlveusML (line 1856)

MATLAB:subsassignnumelmismatch
Command exited with non-zero status 255

Full log file is attached. I have also uploaded whole subject (named 
segmentHA_T1_error.tar.gz ), including content of temporary directory  
hippoSF_T1_v21_right, to your server.

I am using dev version, build 2018-07-28. I am using customized recon-all, but 
it should not relate to this error. Could you please look at this issue?

Regards,

Antonin Skoch
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Re: [Freesurfer] Freesurfer v6.0: Using FLAIR for hippocampal subfields

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Without having seen your FLAIR scans, I’d say probably not, but it’s an 
empirical question; give them a go! ;-)

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Ole Johan Evjenth 
Sørhaug 
Reply-To: Freesurfer support list 
Date: Monday, 20 August 2018 at 13:17
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Freesurfer v6.0: Using FLAIR for hippocampal subfields


External Email - Use Caution
Dear freesurfer experts,

I'm interested in doing subfield segmentations of the hippocampus in version 
6.0. What I am specifically interested in, is that if I can expect better 
segmentations if I use a 1mm isotropic FLAIR series in addition to the 1mm 
isotropic T1 series, rather than using the T1 series alone.

Regards
Ole Johan Sørhaug
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Re: [Freesurfer] segmentHA_T1.sh exits with error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Antonin,
Can you please send me a listing of the files in:
/hydra-db/hydra_io/vypocty/freeSurfer/A_analysis_HPC_PFC/A_links_all/ESO_C00577_20160303_1246_1/tmp/hippoSF_T1_v21_right/
Kind regards,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Antonin Skoch 

Reply-To: Freesurfer support list 
Date: Friday, 17 August 2018 at 18:16
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] segmentHA_T1.sh exits with error


External Email - Use Caution
Dear experts,

I am running segmentHA_T1.sh. In about 3 subjects from 200, the script exits 
with following error:

In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT1_autoEstimateAlveusML (line 1856)

MATLAB:subsassignnumelmismatch
Command exited with non-zero status 255

Full log file is attached. I have also uploaded whole subject (named 
segmentHA_T1_error.tar.gz ), including content of temporary directory  
hippoSF_T1_v21_right, to your server.

I am using dev version, build 2018-07-28. I am using customized recon-all, but 
it should not relate to this error. Could you please look at this issue?

Regards,

Antonin Skoch
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Re: [Freesurfer] Hippocampal subfield registration question.

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Jamie,
It’s a message from mri_robust_register in the initialization of the atlas 
position. If the finaloutput looks reasonable (which it mostly likely will), 
don’t worry too much.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Jamie Hanson 

Reply-To: Freesurfer support list 
Date: Friday, 10 August 2018 at 17:13
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfield registration question.


External Email - Use Caution

Dear FS List,

I was just started to run hippocampal subfield segmentation and had a question 
about registration (and a related output warning).
In the ~5 test subjects I've tried the SF routine, I get a warning early on 
that says--

**
*
* WARNING: Registration did not converge in 5 steps!
*  Problem might be ill posed.
*  Please inspect output manually!
*
**

Two questions--
1) Is that anything to be concerned about?
2) If so, are there relevant documents regarding checking the outputs to flag 
potential poor registration/segmentation?

Any information or thoughts are greatly appreciated!
Thanks much!

All the best,
Jamie.

--
Jamie Hanson
Assistant Professor, Psychology
Research Scientist, Learning Research and Development Center
University of Pittsburgh
Personal website: jamiehanson.org
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[Freesurfer] New segmentation of thalamic nuclei

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear FreeSurfer users,

It is my pleasure to announce that our new tool to segment the thalamic nuclei 
from structural MR scans is available in the development version of FreeSurfer. 
The tool relies on an atlas derived from manual annotations made on 
histological sections. The module can analyze the main FreeSurfer T1 scan, but 
also supports MR images with contrasts other than T1 – as long as the 
corresponding T1 has been processed with recon-all. If you’ve got images 
processed with an earlier version of FreeSurfer, you don’t need to process them 
again with the development version; you can directly run the new module on your 
existing processed subjects.

You can find the documentation, including a link to a preprint of the paper, in 
the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei

As with any other FreeSurfer tool (particularly those that have been recently 
released), we appreciate any feedback that you might have.

Kind regards,

/Eugenio


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

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Re: [Freesurfer] Mismatching hippocampal output

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Sophie. No output is better than the other. If you have run all your 
subjects with both, I'd say to take the average!

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Dean, Sophie 

Sent: Wednesday, August 8, 2018 6:15:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Mismatching hippocampal output


External Email - Use Caution

Dear FreeSurfer developers,



As I understand it is recommended data is processed using the same OS. However, 
it also states on the FreeSurfer webpage that there is an exception for some 
post-processing tools.



Recon-all was first done with:

FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Platform: Darwin Kernel Version 17.4.0



Post-processing for hippocampal segmentation was done separately on two 
different machines with different operating systems:

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Platform: Linux Version 2.6.32-696.23.1.el6.x86_64

2) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Platform: Darwin Kernel Version 17.7.0



Both have slightly different volume outputs. Is this difference due to 
software/OS differences? Which output would you recommend using?



I have attached recon-all logs in case they are of use for my inquest.



With thanks and kind regards,

Sophie

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Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Vasudev,
It is expected that you get different volume estimates with different atlases 
(FreeSurfer vs CobraLab), as the manual delineation protocols that were used to 
create them are very different (e.g., see Yushkevich et al., NeuroImage, 2015).
Regarding the differences in p-values between the two methods:
- Do you get a similar effect size / pval when looking at the whole hippocampus?
- Are the volumes of the subfields given by one method highly correlated with 
the volumes given by the other?
- Did you QC the output, for both methods?
- How different were the results you got? While you mention statistical 
significance vs not, I wouldn’t be alarmed if the p-value was 0.04 vs 0.06, 
whereas 0.1 vs 0.5 would be much more worrying.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Dev vasu 

Reply-To: Freesurfer support list 
Date: Thursday, 2 August 2018 at 19:18
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Anterior / Posterior Partition in Hippocampus 
parcellation atlas


External Email - Use Caution
Dear All,

I have a problem with the Freesurfer hippocampal longitudinal segmentation 
results , when i have done segmentation using following algorithm ( 
https://github.com/CobraLab/antsRegistration-MAGeT) with no anterior/posterior 
partitioning ( Head/body/tail ) , on my subject pool the volumes that i have 
obtained for each subfield is very different from the volumes of corresponding 
subfields that i am getting when i have done subfield segmentation using 
freesurfer. I think algorithm does influence the segmentation procedure, if 
this is the case then i am getting different results for histology based 
segmentation using https://github.com/CobraLab/antsRegistration-MAGeT and 
freesurfer.


When i compare the subfield volumes between healthy and disease patients  that 
i have obtained using first segmentation procedure using ANTS-MAGeT , i notice 
statistical significance   in subfields like CA1,CA2-CA3 but when i do the same 
using freesurfer based algorithm i notice no statistical significance in these 
subfields.

Do you think the algorithm has any influence on segmentation to such a level 
that we get completely different results on two occasions.


Thanks
Vasudev


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Re: [Freesurfer] hippocampal subfields segmentation error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Jin,
6.0 does not segment the nuclei of the amygdala; you can ignore that line, 
assuming the code runs to completion (I am assuming it does?)
If you want to segment the nuclei of the amygdala, you’ll have to download the 
development version:
http://freesurfer.net/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 오진영 

Reply-To: Freesurfer support list 
Date: Monday, 30 July 2018 at 09:29
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields segmentation error


External Email - Use Caution
Dear Eugenio,

Thanks for your reply.
I am running version "freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" of 
freesurfer.
As the log is so long, I attached whole log as a text file and I just copied 
few lines before the error below:


WorldToImageTransform after cropping:

AffineTransform (0x128c17790)

  RTTI typeinfo:   itk::AffineTransform

  Reference Count: 1

  Modified Time: 377450804

  Debug: Off

  Object Name:

  Observers:

none

  Matrix:

-3.3 8.73125e-11 2.22045e-16

-8.4821e-14 -2.67186e-12 -3.3

5.55112e-16 3.3 1.97674e-10

  Offset: [15.4608, 101.71, 117.525]

  Center: [0, 0, 0]

  Translation: [15.4608, 101.71, 117.525]

  Inverse:

-0.3 4.85723e-17 9.7012e-12

8.32667e-17 2.19633e-11 0.3

9.42996e-15 -0.3 -2.96735e-13

  Singular: 0

I am WriteImage and I'm running!

Wrote image to file asmr2.mgz

This file does not contain MRI parameters

This file does not contain MRI parameters

numberOfLabels: 25

Rasterizing mesh...here: 25

here2: 25

done

mri_convert.bin discreteLabels.mgz discreteLabelsResampledT1.mgz -rt nearest 
-odt float -rl 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz

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

reading from discreteLabels.mgz...

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

i_ras = (-1, 0, 2.84217e-14)

j_ras = (0, 6.58905e-11, -1)

k_ras = (2.91038e-11, 1, -8.90815e-13)

reading template info from volume 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz...

Reslicing using nearest

writing to discreteLabelsResampledT1.mgz...

mv: rename volumesAmygdala.txt to 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt:
 No such file or directory

Thank you so much.
Hope to hear you soon!

Jin Young

2018-07-30 17:01 GMT+09:00 Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>>:

External Email - Use Caution
Dear Jinyoung,
Can you please send us the log, or at least the last few lines before the error?
Also, which exact version are you using? 6.0 or dev?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 오진영 mailto:jinyoung.oh...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, 30 July 2018 at 06:41
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: JongHyun Lee mailto:jonghyunlee1...@gmail.com>>
Subject: [Freesurfer] hippocampal subfields segmentation error


External Email - Use Caution
Hello, freesurfer experts

I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala 
by using "segmentSF_T1.sh" command.
I have downloaded the newest development version(freesurfer v.6.0) and license, 
as well as the required matlab runtime.

However, I am getting the following error:
mv: rename volumesAmygdala.txt to 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt:
 No such file or directory

and I have no idea how to find the text file and solve this problem out.
If you have any idea or recommends, please send me the e-mail back.

Thanks!

Jinyoung


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Re: [Freesurfer] hippocampal subfields segmentation error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Jinyoung,
Can you please send us the log, or at least the last few lines before the error?
Also, which exact version are you using? 6.0 or dev?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 오진영 

Reply-To: Freesurfer support list 
Date: Monday, 30 July 2018 at 06:41
To: "freesurfer@nmr.mgh.harvard.edu" 
Cc: JongHyun Lee 
Subject: [Freesurfer] hippocampal subfields segmentation error


External Email - Use Caution
Hello, freesurfer experts

I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala 
by using "segmentSF_T1.sh" command.
I have downloaded the newest development version(freesurfer v.6.0) and license, 
as well as the required matlab runtime.

However, I am getting the following error:
mv: rename volumesAmygdala.txt to 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt:
 No such file or directory

and I have no idea how to find the text file and solve this problem out.
If you have any idea or recommends, please send me the e-mail back.

Thanks!

Jinyoung

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Re: [Freesurfer] Label numbers for thalamic nuclei

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear KT,
They range from 8100 to 8300.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of ?? ? 

Reply-To: Freesurfer support list 
Date: Friday, 20 July 2018 at 08:17
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Label numbers for thalamic nuclei


External Email - Use Caution

Dear Freesurfer Team,



I have been using  segmentation of thalamic nuclei from the Freesurfer dev 
version(freesurfer-linux-centos7_x86_64-dev).

I see some thalamus labels in FreeSurferColorLUT.txt(#8001-8014), but I can't 
find label numbers for 25 different nuclei. Where could I find those numbers?



Thanks in advance,

Kayeong Tak
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Re: [Freesurfer] Re?? Re?? Re??segmentHA_T2.sh

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks! I am fairly confident it's a memory issue, then. Do you have access to 
a machine with more RAM you can test the code on?

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of  <530337...@qq.com>
Sent: Thursday, July 19, 2018 5:27:46 AM
To: Freesurfer support list
Subject: [Freesurfer] Re?? Re?? Re??segmentHA_T2.sh


External Email - Use Caution

I tried to run"segmentHA_T2.sh subject001 T2.nii T2 0" and "segmentHA_T1.sh 
subject003", it's well done! When run
Thanks,
Fiona

--  ------
??: "Iglesias Gonzalez, Eugenio";
: 2018??7??18??(??) 8:35
??: "Freesurfer support 
list";"Freesurfersupport 
list";
: Re: [Freesurfer] Re?? Re??segmentHA_T2.sh


External Email - Use Caution

Thanks!
Do you have the same problem if you use the T2 alone? For instance
segmentHA_T2.sh subject001 T2.nii T2 0



Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of  <530337...@qq.com>
Sent: Wednesday, July 18, 2018 1:21:25 PM
To: Freesurfer support list
Subject: [Freesurfer] Re?? Re??segmentHA_T2.sh


External Email - Use Caution

Dear Eugenio,
I tried 3 subjects ,it dies at the same step ,and it stops there all the time 
even 3 days. No error reported here.
Thanks ,
Fiona Ding.

------ ???? --
??: "Iglesias Gonzalez, Eugenio";
: 2018??7??18??(??) 7:29
??: "Freesurfer support list";
: Re: [Freesurfer] Re??segmentHA_T2.sh


External Email - Use Caution
Thanks, Fiona.
Is the error reproducible? Does it always die at the same step? Do you get the 
same problem with other subjects?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of  
<530337...@qq.com>
Reply-To: Freesurfer support list 
Date: Wednesday, 18 July 2018 at 10:15
To: freesurfer 
Subject: [Freesurfer] Re??segmentHA_T2.sh


External Email - Use Caution
hello??
I think RAM is enough??my computer is imac pro.There is 16G DDDR3. This process 
takes up about 1-2G. The total RAM occupied is 5G. Thanks Fiona Ding.

 External Email - Use Caution  Weird! Maybe you ran out of RAM 
memory?



--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com<http://www.jeiglesias.com/>

http://cmictig.cs.ucl.ac.uk/





From: 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
at 
nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
on behalf of  
<530337973<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
at qq.com<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>

Reply-To: Freesurfer support list 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
at 
nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>

Date: Tuesday, 17 July 2018 at 13:40

To: freesurfer 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
at 
nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>

Subject: [Freesurfer] segmentHA_T2.sh





External Email - Use Caution

Dear  freesurfer experts,

when i run the command??segmentHA_T2.sh subject001 T2.nii T2 1?? ,it runs as 
following:

--

Making Left-Thalamus-Proper map to reduced label 10

--

Making Left-choroid-plexus map to reduced label 11

--

Making Left-VentralDC map to reduced label 12

--

Making Left-Accumbens-area map to reduced label 13

--

Making Unknown map to reduced label 14

Computing hyperparameters for estimation of Gaussians parameters

znzreadInt: znzread failed

No such file or directory

Estimating typical intensities of molecular layer and alveus

numberOfLabels: 2

Rasterizing mesh...here: 2

here2: 2

done

Smoothing mesh collection with kernel size 1.50 ...Smoothing class: 0

Smoothing class: 1

Smoothing class: 2

Smoothing class: 3

Smoothing class: 4

Smoothing class: 5

Smoothing class: 6

Smoothing class: 7

Smoothing class: 8

Smoothing class: 9

Smoothing class: 10

Smoothing class: 11

Smoothing class: 12

Smoothing class: 13

done

numberOfImages = 2

Image: 0

Image: 2

Iteration 1 of 7

1 0.00035804

2 0.089592



fianally,it stop here and can't run anymore,no error reported??I didn't know 
what??s wrong??

What can i do??

Thanks very much

Fiona Ding
_

Re: [Freesurfer] Re?? Re??segmentHA_T2.sh

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks!
Do you have the same problem if you use the T2 alone? For instance
segmentHA_T2.sh subject001 T2.nii T2 0



Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of  <530337...@qq.com>
Sent: Wednesday, July 18, 2018 1:21:25 PM
To: Freesurfer support list
Subject: [Freesurfer] Re?? Re??segmentHA_T2.sh


External Email - Use Caution

Dear Eugenio,
I tried 3 subjects ,it dies at the same step ,and it stops there all the time 
even 3 days. No error reported here.
Thanks ,
Fiona Ding.

--  --
??????: "Iglesias Gonzalez, Eugenio";
: 2018??7??18??(??) 7:29
??: "Freesurfer support list";
: Re: [Freesurfer] Re??segmentHA_T2.sh


External Email - Use Caution
Thanks, Fiona.
Is the error reproducible? Does it always die at the same step? Do you get the 
same problem with other subjects?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of  
<530337...@qq.com>
Reply-To: Freesurfer support list 
Date: Wednesday, 18 July 2018 at 10:15
To: freesurfer 
Subject: [Freesurfer] Re??segmentHA_T2.sh


External Email - Use Caution
hello??
I think RAM is enough??my computer is imac pro.There is 16G DDDR3. This process 
takes up about 1-2G. The total RAM occupied is 5G. Thanks Fiona Ding.

 External Email - Use Caution  Weird! Maybe you ran out of RAM 
memory?



--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com<http://www.jeiglesias.com/>

http://cmictig.cs.ucl.ac.uk/





From: 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
at 
nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
on behalf of  
<530337973<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
at qq.com<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>

Reply-To: Freesurfer support list 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
at 
nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>

Date: Tuesday, 17 July 2018 at 13:40

To: freesurfer 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
at 
nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>

Subject: [Freesurfer] segmentHA_T2.sh





External Email - Use Caution

Dear  freesurfer experts,

when i run the command??segmentHA_T2.sh subject001 T2.nii T2 1?? ,it runs as 
following:

--

Making Left-Thalamus-Proper map to reduced label 10

--

Making Left-choroid-plexus map to reduced label 11

--

Making Left-VentralDC map to reduced label 12

--

Making Left-Accumbens-area map to reduced label 13

--

Making Unknown map to reduced label 14

Computing hyperparameters for estimation of Gaussians parameters

znzreadInt: znzread failed

No such file or directory

Estimating typical intensities of molecular layer and alveus

numberOfLabels: 2

Rasterizing mesh...here: 2

here2: 2

done

Smoothing mesh collection with kernel size 1.50 ...Smoothing class: 0

Smoothing class: 1

Smoothing class: 2

Smoothing class: 3

Smoothing class: 4

Smoothing class: 5

Smoothing class: 6

Smoothing class: 7

Smoothing class: 8

Smoothing class: 9

Smoothing class: 10

Smoothing class: 11

Smoothing class: 12

Smoothing class: 13

done

numberOfImages = 2

Image: 0

Image: 2

Iteration 1 of 7

1 0.00035804

2 0.089592



fianally,it stop here and can't run anymore,no error reported??I didn't know 
what??s wrong??

What can i do??

Thanks very much

Fiona Ding
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Re：segmentHA_T2.sh

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks, Fiona.
Is the error reproducible? Does it always die at the same step? Do you get the 
same problem with other subjects?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 墨初 
<530337...@qq.com>
Reply-To: Freesurfer support list 
Date: Wednesday, 18 July 2018 at 10:15
To: freesurfer 
Subject: [Freesurfer] Re：segmentHA_T2.sh


External Email - Use Caution
hello，
I think RAM is enough。my computer is imac pro.There is 16G DDDR3. This process 
takes up about 1-2G. The total RAM occupied is 5G. Thanks Fiona Ding.

 External Email - Use Caution  Weird! Maybe you ran out of RAM 
memory?



--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/





From: 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
at 
nmr.mgh.harvard.edu>
on behalf of 墨初 
<530337973
at qq.com>

Reply-To: Freesurfer support list 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
at 
nmr.mgh.harvard.edu>

Date: Tuesday, 17 July 2018 at 13:40

To: freesurfer 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
at 
nmr.mgh.harvard.edu>

Subject: [Freesurfer] segmentHA_T2.sh





External Email - Use Caution

Dear  freesurfer experts,

when i run the command“segmentHA_T2.sh subject001 T2.nii T2 1” ,it runs as 
following:

--

Making Left-Thalamus-Proper map to reduced label 10

--

Making Left-choroid-plexus map to reduced label 11

--

Making Left-VentralDC map to reduced label 12

--

Making Left-Accumbens-area map to reduced label 13

--

Making Unknown map to reduced label 14

Computing hyperparameters for estimation of Gaussians parameters

znzreadInt: znzread failed

No such file or directory

Estimating typical intensities of molecular layer and alveus

numberOfLabels: 2

Rasterizing mesh...here: 2

here2: 2

done

Smoothing mesh collection with kernel size 1.50 ...Smoothing class: 0

Smoothing class: 1

Smoothing class: 2

Smoothing class: 3

Smoothing class: 4

Smoothing class: 5

Smoothing class: 6

Smoothing class: 7

Smoothing class: 8

Smoothing class: 9

Smoothing class: 10

Smoothing class: 11

Smoothing class: 12

Smoothing class: 13

done

numberOfImages = 2

Image: 0

Image: 2

Iteration 1 of 7

1 0.00035804

2 0.089592



fianally,it stop here and can't run anymore,no error reported。I didn't know 
what‘s wrong？

What can i do？

Thanks very much

Fiona Ding
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] segmentHA_T2.sh

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Weird! Maybe you ran out of RAM memory?

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 墨初 
<530337...@qq.com>
Reply-To: Freesurfer support list 
Date: Tuesday, 17 July 2018 at 13:40
To: freesurfer 
Subject: [Freesurfer] segmentHA_T2.sh


External Email - Use Caution
Dear  freesurfer experts,
when i run the command“segmentHA_T2.sh subject001 T2.nii T2 1” ,it runs as 
following:
--
 Making Left-Thalamus-Proper map to reduced label 10
--
Making Left-choroid-plexus map to reduced label 11
--
Making Left-VentralDC map to reduced label 12
--
Making Left-Accumbens-area map to reduced label 13
--
Making Unknown map to reduced label 14
Computing hyperparameters for estimation of Gaussians parameters
znzreadInt: znzread failed
No such file or directory
Estimating typical intensities of molecular layer and alveus
numberOfLabels: 2
Rasterizing mesh...here: 2
here2: 2
done
Smoothing mesh collection with kernel size 1.50 ...Smoothing class: 0
Smoothing class: 1
Smoothing class: 2
Smoothing class: 3
Smoothing class: 4
Smoothing class: 5
Smoothing class: 6
Smoothing class: 7
Smoothing class: 8
Smoothing class: 9
Smoothing class: 10
Smoothing class: 11
Smoothing class: 12
Smoothing class: 13
done
numberOfImages = 2
Image: 0
Image: 2
Iteration 1 of 7
1 0.00035804
2 0.089592

fianally,it stop here and can't run anymore,no error reported。I didn't know 
what‘s wrong？
What can i do？
Thanks very much
Fiona Ding


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.