Re: [Freesurfer] error in "recon-all -all -s subject -hippocampal-subfields-T1": exited with errors

[Douglas N. Greve]

You have to run through all of recon-all before running the subfields, 
so just add -all to the command line


On 6/22/2020 2:06 PM, Shimura, Yuki wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compute calculate hippocampal volumes, as described 
on the MultiModal FMRI tutorial "Segmentation of hippocampal 
subfields"(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields), 
but I get the following error when I run the following command:


Command:
recon-all -s subject -hippocampal-subfields-T1

Error:
recon-all -s TNU_AIDAZ_3002_T1 exited with ERRORS at Mon Jun 22 
15:42:08 JST 2020

(TNU_AIDAZ_3002_T1 is the subject name)

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.

Here are few contexts:
a) I had the following command for recon-all for my subject:
recon-all -i ${SUBJECTS_DIR}/subject_structual_image_file.nii -s 
subject -all -qcache -3T

b) this was done without an error
c) now I want to do "
recon-all -s subject -hippocampal-subfields-T1"

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) Platform: CentOS release 6.7 (Final)
3) recon-all.log: see attached


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Re: [Freesurfer] PhD Position - Early MRI and childhood outcomes - Liggins Institute, Auckland

[Eleanor Kennedy]

External Email - Use Caution

Updated link: 
https://www.findaphd.com/phds/project/early-mri-and-childhood-outcomes/?p122350


Hello,

We are seeking a PhD candidate at the Liggins Institute, University of Auckland 
with Prof Jane Harding. Research at the Liggins Institute focuses on early life 
determinants of long-term health and covers a broad range of disciplines from 
basic science through to clinical trials and translational research.

Project Description:

MRI is increasingly being used in preterm newborns to assess early brain injury 
and brain maturation, but its relationship to later development is unclear. We 
plan to determine the relationship between early MRI and later development in 
children who as babies took part in clinical trials of additional nutrition, or 
of magnesium sulphate administration to prevent cerebral palsy. If early MRI is 
predictive of particular problems such as cerebral palsy, it could be used in 
the future to identify babies at risk and allow early intervention.

The project will involve neonatal MRI (DTI, fMRI and structural scans). 
Assessments of children at two years of age for cognitive, language, motor and 
executive function.

We are looking for candidates with a degree in a health, psychology or 
education-related discipline and some experience with MRI analysis.

For more information, see the Find a Thesis entry here: 
https://www.findathesis.auckland.ac.nz/research-entry/10464530

Thanks,


Eleanor Kennedy
Research Fellow
Liggins Institute

DDI +64 9 923 6701 Ext 86701
E eleanor.kenn...@auckland.ac.nz  W 
www.liggins.auckland.ac.nz
A The University of Auckland, Building 503, Level 2, 85 Park Road, Auckland
P Private Bag 92019, Auckland 1142, NZ

[Liggins Logo Colour_small]


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[Freesurfer] PhD Position - Early MRI and childhood outcomes - Liggins Institute, Auckland

[Eleanor Kennedy]

External Email - Use Caution

Hello,

We are seeking a PhD candidate at the Liggins Institute, University of Auckland 
with Prof Jane Harding. Research at the Liggins Institute focuses on early life 
determinants of long-term health and covers a broad range of disciplines from 
basic science through to clinical trials and translational research.

Project Description:

MRI is increasingly being used in preterm newborns to assess early brain injury 
and brain maturation, but its relationship to later development is unclear. We 
plan to determine the relationship between early MRI and later development in 
children who as babies took part in clinical trials of additional nutrition, or 
of magnesium sulphate administration to prevent cerebral palsy. If early MRI is 
predictive of particular problems such as cerebral palsy, it could be used in 
the future to identify babies at risk and allow early intervention.

The project will involve neonatal MRI (DTI, fMRI and structural scans). 
Assessments of children at two years of age for cognitive, language, motor and 
executive function.

We are looking for candidates with a degree in a health, psychology or 
education-related discipline and some experience with MRI analysis.

For more information, see the Find a Thesis entry here: 
https://www.findathesis.auckland.ac.nz/research-entry/10464530

Thanks,


Eleanor Kennedy
Research Fellow
Liggins Institute

DDI +64 9 923 6701 Ext 86701
E eleanor.kenn...@auckland.ac.nz  W 
www.liggins.auckland.ac.nz
A The University of Auckland, Building 503, Level 2, 85 Park Road, Auckland
P Private Bag 92019, Auckland 1142, NZ

[Liggins Logo Colour_small]


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Re: [Freesurfer] Longitudinal Stream Problem

[Danielian, Laura (NIH/NINDS) [E]]

External Email - Use Caution

Interesting – I never did any editing directly on the original 
brain.finalsurfs.mgz.  I only did cerebellar edits on the 
brain.finalsurfs.manedit.mgz copy of brain.finalsurfs.mgz.  Looks like those 
edits copied over somehow.

Regardless, it sounds like this will be easy to correct.  Where can I find an 
unedited copy of brain.finalsurfs.mgz and when/how would I reintegrate that 
into the processing stream?

Thanks,
Laura



From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 
Date: Monday, June 22, 2020 at 12:13 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Longitudinal Stream Problem


It looks like someone edited the brain.finalsurfs.mgz. In the attached is the 
image of the brain.final... You can see where the brain is missing. The white 
surface (green line) stops at that edge. When I used the unedited brain, the 
surfaces went to the right place (yellow surface)
On 6/22/2020 9:21 AM, Danielian, Laura (NIH/NINDS) [E] wrote:

External Email - Use Caution
Thanks Douglas.  I could send other problem data sets too if it would help.  
Just let me know.

Thanks,
Laura


From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 

Date: Friday, June 19, 2020 at 6:10 PM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Longitudinal Stream Problem

OK, I have it now and am able to verify the problem. It's really strange -- I 
don't know why it is behaving like this. It may take me a few days to dig into.
On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E] wrote:

External Email - Use Caution
Sorry I’m not sure why it didn’t upload.  I just tried it again.  
danielianall.tar.gz  - Should include all parts.  EM2 is the cross-sectional.  
EM is the base.  EM2.long.EM is the long.  I also tried sending just the base 
again.  danielianbase.tar.gz.

Thanks,

Laura

From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 

Date: Thursday, June 18, 2020 at 9:12 AM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Longitudinal Stream Problem

I have not seen that file appear. Can you re-upload it?
On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote:

External Email - Use Caution
Hi Douglas,

OK I just uploaded the base separately.  danielianbase.tar.gz  I thought it was 
part of the original bundle.  Sorry!

Laura


From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 

Date: Tuesday, June 16, 2020 at 10:10 AM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Longitudinal Stream Problem

I have your data, but it does not have the base image. Can you upload that as 
well?
On 6/15/2020 5:15 PM, Danielian, Laura (NIH/NINDS) [E] wrote:

External Email - Use Caution
Hi Douglas,

I just upload the files as danielian.tar.gz.  I didn’t notice any damage or 
artifact on this particular brain or the others that had this same problem.  
This subject is a healthy control and most of the subjects (3 of 4) that are 
having this problem are healthy.  For each we used 2 T1s for the original 
cross-sectional input.  The cross was reconstructed fine as was the base and 
the 2 other longitudinal timepoints for this same subject.  The same is the 
case with the others I’m having trouble with – all of the their other 
timepoints are fine for the cross/base/longitudinal surfaces.  The warped 
surfaces are always lower posterior (cerebellum adjacent) and sometimes also 
temporal.  Upper cortical and frontal regions are unaffected.

Thanks for your help!

Laura



From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 

Date: Friday, June 12, 2020 at 10:35 AM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Longitudinal Stream Problem

Hard to tell from just that view. Was there a lot of brain change with that 
time point? Or was there an MRI artifact? If no to both, then you can upload 
all the cross, the base, and that one long. Follow instructions below (you can 
make one tarball for all subjects)

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subjects.tar.gz ./subject1 ./subject2
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put 

Re: [Freesurfer] How to make surface cuts / flatmaps. Alternative for tksurfer in 2020?

[Chris Klink]

External Email - Use Caution

Someone messaged me that in the latsest FS7 we can now do this in Freeview.
Awesome! I don't think a lot of people know about this. Spread the word!

-- Chris Klink (sent from a phone)
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Re: [Freesurfer] Longitudinal Stream Problem

[Danielian, Laura (NIH/NINDS) [E]]

External Email - Use Caution

Thanks Douglas.  I could send other problem data sets too if it would help.  
Just let me know.

Thanks,
Laura


From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 
Date: Friday, June 19, 2020 at 6:10 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Longitudinal Stream Problem

OK, I have it now and am able to verify the problem. It's really strange -- I 
don't know why it is behaving like this. It may take me a few days to dig into.
On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E] wrote:

External Email - Use Caution
Sorry I’m not sure why it didn’t upload.  I just tried it again.  
danielianall.tar.gz  - Should include all parts.  EM2 is the cross-sectional.  
EM is the base.  EM2.long.EM is the long.  I also tried sending just the base 
again.  danielianbase.tar.gz.

Thanks,

Laura

From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 

Date: Thursday, June 18, 2020 at 9:12 AM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Longitudinal Stream Problem

I have not seen that file appear. Can you re-upload it?
On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote:

External Email - Use Caution
Hi Douglas,

OK I just uploaded the base separately.  danielianbase.tar.gz  I thought it was 
part of the original bundle.  Sorry!

Laura


From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 

Date: Tuesday, June 16, 2020 at 10:10 AM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Longitudinal Stream Problem

I have your data, but it does not have the base image. Can you upload that as 
well?
On 6/15/2020 5:15 PM, Danielian, Laura (NIH/NINDS) [E] wrote:

External Email - Use Caution
Hi Douglas,

I just upload the files as danielian.tar.gz.  I didn’t notice any damage or 
artifact on this particular brain or the others that had this same problem.  
This subject is a healthy control and most of the subjects (3 of 4) that are 
having this problem are healthy.  For each we used 2 T1s for the original 
cross-sectional input.  The cross was reconstructed fine as was the base and 
the 2 other longitudinal timepoints for this same subject.  The same is the 
case with the others I’m having trouble with – all of the their other 
timepoints are fine for the cross/base/longitudinal surfaces.  The warped 
surfaces are always lower posterior (cerebellum adjacent) and sometimes also 
temporal.  Upper cortical and frontal regions are unaffected.

Thanks for your help!

Laura



From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 

Date: Friday, June 12, 2020 at 10:35 AM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Longitudinal Stream Problem

Hard to tell from just that view. Was there a lot of brain change with that 
time point? Or was there an MRI artifact? If no to both, then you can upload 
all the cross, the base, and that one long. Follow instructions below (you can 
make one tarball for all subjects)

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subjects.tar.gz ./subject1 ./subject2
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subjects.tar.gz
Send an email that the file has been and the name of the file.







On 6/9/2020 6:32 PM, Danielian, Laura (NIH/NINDS) [E] wrote:

External Email - Use Caution
Hi, I’ve finished processing a data set that included longitudinal data and I’m 
having a problem with a small percentage of the longitudinal timepoints.  To 
review what I’ve done, I edited all of the individual (cross-sectional) 
timepoints until the wm and pial surfaces were correct, then created the base 
and edited that until it looked good, and then created the longitudinal files 
for each cross-sectional timepoint.  Most of these did not need editing and 
some needed slight edits to either wm or brainmask which corrected the 
longitudinal surfaces.

However, in a small handful of cases, the wm/pial surfaces were so distorted 
that editing would not fix the problem.  In these cases, longitudinal surfaces 
were very different from both the original cross-section and base.  I’ve tried 
to attach a file that shows an example – it might only affect a small portion 
of the brain but in these cases I don’t think I could edit it to improve the 
surfaces.  In the example I 

Re: [Freesurfer] Longitudinal Stream Problem

[Douglas N. Greve]

It looks like someone edited the brain.finalsurfs.mgz. In the attached 
is the image of the brain.final... You can see where the brain is 
missing. The white surface (green line) stops at that edge. When I used 
the unedited brain, the surfaces went to the right place (yellow surface)


On 6/22/2020 9:21 AM, Danielian, Laura (NIH/NINDS) [E] wrote:


External Email - Use Caution

Thanks Douglas.  I could send other problem data sets too if it would 
help.  Just let me know.


Thanks,

Laura

*From: *"Douglas N. Greve" 
*Reply-To: *Freesurfer support list 
*Date: *Friday, June 19, 2020 at 6:10 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Longitudinal Stream Problem

OK, I have it now and am able to verify the problem. It's really 
strange -- I don't know why it is behaving like this. It may take me a 
few days to dig into.


On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E] wrote:

*External Email - Use Caution *

Sorry I’m not sure why it didn’t upload.  I just tried it again.
danielianall.tar.gz  - Should include all parts.  EM2 is the
cross-sectional.  EM is the base.  EM2.long.EM is the long.  I
also tried sending just the base again. danielianbase.tar.gz.

Thanks,

Laura

*From: *"Douglas N. Greve" 

*Reply-To: *Freesurfer support list


*Date: *Thursday, June 18, 2020 at 9:12 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"



*Subject: *Re: [Freesurfer] Longitudinal Stream Problem

I have not seen that file appear. Can you re-upload it?

On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote:

*External Email - Use Caution *

Hi Douglas,

OK I just uploaded the base separately.  danielianbase.tar.gz 
I thought it was part of the original bundle.  Sorry!

Laura

*From: *"Douglas N. Greve" 

*Reply-To: *Freesurfer support list


*Date: *Tuesday, June 16, 2020 at 10:10 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"



*Subject: *Re: [Freesurfer] Longitudinal Stream Problem

I have your data, but it does not have the base image. Can you
upload that as well?

On 6/15/2020 5:15 PM, Danielian, Laura (NIH/NINDS) [E] wrote:

*External Email - Use Caution *

Hi Douglas,

I just upload the files as danielian.tar.gz.  I didn’t
notice any damage or artifact on this particular brain or
the others that had this same problem.  This subject is a
healthy control and most of the subjects (3 of 4) that are
having this problem are healthy.  For each we used 2 T1s
for the original cross-sectional input.  The cross was
reconstructed fine as was the base and the 2 other
longitudinal timepoints for this same subject. The same is
the case with the others I’m having trouble with – all of
the their other timepoints are fine for the
cross/base/longitudinal surfaces.  The warped surfaces are
always lower posterior (cerebellum adjacent) and sometimes
also temporal.  Upper cortical and frontal regions are
unaffected.

Thanks for your help!

Laura

*From: *"Douglas N. Greve" 

*Reply-To: *Freesurfer support list


*Date: *Friday, June 12, 2020 at 10:35 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"



*Subject: *Re: [Freesurfer] Longitudinal Stream Problem

Hard to tell from just that view. Was there a lot of brain
change with that time point? Or was there an MRI artifact?
If no to both, then you can upload all the cross, the
base, and that one long. Follow instructions below (you
can make one tarball for all subjects)

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subjects.tar.gz ./subject1 ./subject2
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subjects.tar.gz
  

Re: [Freesurfer] QDEC analyses

[Douglas N. Greve]

Sorry, I can't remember whether the qdec correction for mult comp 
included an option to specify that there were two hemispheres. If not, 
you can take the cluster p-value that you get from qdec and multiply it 
by 2 (bonferonni correction for 2 hemis), this is mentioned in Greve and 
Fischl, 2017, NI. False positive rates in surface-based anatomical analysis


On 6/22/2020 11:07 AM, xunzhang_hmrrc wrote:


External Email - Use Caution

Thanks for your timely response.
To assess the two group differences in cortical thickness, whole-brain 
vertex-wise analyses were performed using the graphical user interface 
of FreeSurfer known as QDEC. We used a general linear model to compare 
the thickness between the patients and healthy controls with age and 
sex as covariates. The Monte Carlo Null-Z Simulation was conducted to 
control for multiple comparisons (cluster-wise corrected P< 0.05). 
But, as we all know, QDEC analyses have always be done for the two 
hemispheres separately, so the multiple comparisons are also conducted 
for two hemispheres separately, which, the reviewer assumed, is 
different from multiple comparisons for the whole brain? So, could you 
please provide some perspective and citation about the validation for 
such design of QDEC (i.e., the right and left hemisphere were tested 
separately)?





-- Original --
*From:* "Douglas N. Greve";
*Date:* Mon, Jun 22, 2020 10:17 AM
*To:* "freesurfer";
*Subject:* Re: [Freesurfer] QDEC analyses

How you did you do your analysis? As an exploratory/map-based 
analysis? Or as an ROI analysis? How did you correct for multiple 
comparisons? Generally, in a map-based analysis, the correction for 
multiple comparisons incorporates the fact that there are two 
hemispheres being tested.



On 6/20/2020 10:04 PM, xunzhang_hmrrc wrote:


    External Email - Use Caution

Hello Freesurfer developers,

Recently, I have used QDEC of freesurfer 6.0.0 to examine the 
cortical thickness differences between two groups, and the manuscript 
has been submitted to a journal. One reviewer raised a question -"The 
manuscript stated that the right and left hemisphere were tested 
separately. Could the authors provide an explanation for this? I 
assume that testing over 68 (all ROIs) vs testing separately left and 
right (34 ROIs) would have an effect?" Unfornately, I don't know how 
to responde to this reviewer, so I would like to ask for your help. I 
just followed the tutorials of QDEC 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysisV6.0), 
and I found QDEC analyses have always be done for the two hemispheres 
separately. So, could you please provide some perspective and 
citation about the validation for such design of QDEC?


Thank you in advance for your assistance,

Best regards,




Xun



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Re: [Freesurfer] QDEC analyses

[xunzhang_hmrrc]

External Email - Use Caution

Thanks for your timely response. 
To assess the two group differences in cortical thickness, whole-brain 
vertex-wise analyses were performed using the graphical user interface of 
FreeSurfer known as QDEC. We used a general linear model to compare the 
thickness between the patients and healthy controls with age and sex as 
covariates. The Monte Carlo Null-Z Simulation was conducted to control for 
multiple comparisons (cluster-wise corrected P< 0.05). But, as we all know, 
QDEC analyses have always be done for the two hemispheres 
separately, so the multiple comparisons are also conducted for two 
hemispheres separately, which, the reviewer assumed, is different from multiple 
comparisons for the whole brain? So, could you please provide some 
perspective and citation about the validation for such design of
 QDEC (i.e., the right and left hemisphere were tested  
   separately)?

 





-- Original --
From:"Douglas N. Greve"http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysisV6.0),
 and I found QDEC analyses have always be done for the two 
hemispheres separately. So, could you please provide some 
perspective and citation about the validation for such design of
 QDEC?
 
 
Thank you in advance for your assistance,
 
Best regards,
 
   



   
   
Xun
 
 
   
 
   
   
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Re: [Freesurfer] recon-all for macaque brain

[Minqing Jiang]

External Email - Use Caution

Dear Chris and Douglas,

Thank you for the help! I would try the hires and precon_all. One more quesion, 
now I have a much better recon result from adult macaque brain. But when I 
performed MRI in 1 years old macaque. Recon-all barely can generate result, 
either with error or very bad segmentation. We are using TI 1100ms, 
TR3000/TE3.29 and FOV 128*128. Is there any way to segment young monkeys 
better? Thanks again.

bests,
Minqing


Hi Minqing Jiang,

Getting a macaque brain through Freesurfer requires a bit of manual
tinkering. We have a description of how we do it on GitHub:
https://github.com/VisionandCognition/NHP-Freesurfer

There's also precon_all (https://github.com/recoveringyank/precon_all)
which I haven't personally used yet, but I've seen results and it looks
very promising!

 ?Good luck!

Chris



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Re: [Freesurfer] Recon-all error output

[Douglas N. Greve]

If you look at the recon-all.log file, you will see

Include the flag -cw256 with recon-all

So try that

On 6/22/2020 10:03 AM, Frank Chau wrote:


External Email - Use Caution

**

Dear Freesurfer experts,


I ran Recon-all on a batch of subject. Only one Recon-all error 
results were generated which the process just last for few minutes. 
There just 2 mgz file in mri folder of the subject output directory 
were generated. I re-run recon-all on the same subject, same result 
was got again. May I know the cause of this error?


I upload the output result, log history and the T1.nii to the 
following share link, please feel free the check them:




https://www.dropbox.com/sh/lhbzct444n8ek8z/AADbtfyYEBNWZ4yYXPw7ejmwa?dl=0

Thank you.


Regards


Frank

---

*FRANK  C Y CHAU*


Research assistant

Division of Neurology

Department of Medicine


Tel: +852 6340 2553

Fax: 2872 5828


E-mail : cyfr...@hku.hk 



Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam 
Road, Hong Kong



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Re: [Freesurfer] Error with -qcache

[Douglas N. Greve]

This means that you probably edited the subject but did not fully 
regenerate the surfaces


On 6/22/2020 9:46 AM, Mateus Aranha wrote:


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Dear FS team,

I'm running -qcache on my subjects before group analysis and I get the 
following error for 2 of the subjects:


ERROR: number of vertices in 
/home/neuroimagen7/Desktop/SoccerPlayers/ReconFiles/recon_T1/edits/ANON0266_recon_T1/surf/lh.thickness 
does not match surface (139424,138940)

ERROR: reading curvature file

The remaining subjects are fine!

Thank you!
Mateus

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[Freesurfer] Recon-all error output

[Frank Chau]

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Dear Freesurfer experts,


I ran Recon-all on a batch of subject. Only one Recon-all error results were 
generated which the process just last for few minutes. There just 2 mgz file in 
mri folder of the subject output directory were generated. I re-run recon-all 
on the same subject, same result was got again. May I know the cause of this 
error?

I upload the output result, log history and the T1.nii to the following share 
link, please feel free the check them:



https://www.dropbox.com/sh/lhbzct444n8ek8z/AADbtfyYEBNWZ4yYXPw7ejmwa?dl=0

Thank you.


Regards


Frank

---

FRANK  C Y CHAU


Research assistant

Division of Neurology

Department of Medicine


Tel: +852 6340 2553

Fax: 2872 5828


E-mail : cyfr...@hku.hk



Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
Hong Kong
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[Freesurfer] Error with -qcache

[Mateus Aranha]

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Dear FS team,

I'm running -qcache on my subjects before group analysis and I get the
following error for 2 of the subjects:

ERROR: number of vertices in
/home/neuroimagen7/Desktop/SoccerPlayers/ReconFiles/recon_T1/edits/ANON0266_recon_T1/surf/lh.thickness
does not match surface (139424,138940)
ERROR: reading curvature file

The remaining subjects are fine!

Thank you!
Mateus
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Re: [Freesurfer] Freeview - Load custom overlay from terminal

[Wang, Ruopeng]

Hi Ricardo,

I will add those options to the command-line.

Best,
Ruopeng

On Jun 21, 2020, at 3:15 PM, Loucao, Ricardo 
mailto:r.lou...@fz-juelich.de>> wrote:


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Hi Ruopeng,

You were correct - for some reason the version I built was 2.0.
I’ve downloaded a built version of freesurfer v7.1.0 and now I can successfully 
use the flag.

Another question if I may: is there a way to toggle the “clear lower”/“clear 
higher” option also from the terminal?

Thank you in advance!
Best regards,
Ricardo

Date: Thu, 18 Jun 2020 13:28:56 +
From: "Wang, Ruopeng" mailto:rwa...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview - Load custom overlay from terminal
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: 
mailto:fe2c8592-cfc2-41fd-9bb0-b4763ca86...@mgh.harvard.edu>>
Content-Type: text/plain; charset="utf-8"

Hi Ricardo,

The way you use the flag is correct. But have you made sure that you were 
actually running the latest version that you built? You can check freeview?s 
build time from About menu.

Best,
Ruopeng

Date: Thu, 18 Jun 2020 08:15:44 +
From: "Loucao, Ricardo" mailto:r.lou...@fz-juelich.de>>
Subject: [Freesurfer] Freeview - Load custom overlay from terminal
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: 
<25d279e0-2256-47b0-b05a-1f470a1b3...@fz-juelich.de>
Content-Type: text/plain; charset="utf-8"

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Dear FS experts,

I?m trying to load a surface with a custom overlay directly from the terminal 
using the sub-option ?overlay_custom? but it returns ?Unrecognized sub-option 
flag ?overlay_custom??. I checked the source code on GitHub and found the flag 
to be present and implemented. I also built the freeview app from the GitHub 
(as it could be that my version did not have that sub-option) but I got the 
same return message.

Upon inspecting the code further, I figured the way this flag works is via 
quadruplets of the form ?val, r, g, b?. However, I also noticed that this 
return message comes when the overlay_custom sub-option is empty 
(freeview/MainWindow.cpp: line 3484). It seems to me like I might be using the 
flag improperly. Here?s an example of how I am using it:
?:overlay_custom=0.85,255,0,0,0.875,0,255,255,0.90,0,0,255?

Do you have any hints for me on how to deal with this?

Thank you very much in advance!
Best regards,
Ricardo




Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt



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Re: [Freesurfer] recon-all for macaque brain

[Chris Klink]

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Hi Minqing Jiang,

Getting a macaque brain through Freesurfer requires a bit of manual 
tinkering. We have a description of how we do it on GitHub: 
https://github.com/VisionandCognition/NHP-Freesurfer

There's also precon_all (https://github.com/recoveringyank/precon_all) 
which I haven't personally used yet, but I've seen results and it looks 
very promising!

  Good luck!

Chris

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[Freesurfer] How to make surface cuts / flatmaps. Alternative for tksurfer in 2020?

[Chris Klink]

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How do people create flatmaps these days? It's getting more and more of 
a hassle to work with tksurfer (won't work on 64bit only Mac, throws tcl 
& tix errors on Linux in Freesurfer 7). I'm currently running tksurfer 
on Linux in FS6, that I basically only keep around for that purpose. I 
read on the mailing list that tkmedit and tksurfer are pretty much 
deprecated, but I've looked in Freeview and can't find a way to make 
cuts there. I must be missing something?

Is there some other way of doing it? Should I dive into pycortex' 
Blender based approach? What are the options in 2020?

Best,
Chris

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