Re: [Freesurfer] Using mri_surf2surf to split files

[Karan Desai]

External Email - Use Caution

Yes, I have attached a link to the previous correspondence from the Freesurfer 
mailing archives here:
https://secure-web.cisco.com/1iDGELrOBJ3D4x9wlujRbDDOmlAxaN5wTKfgu2a-gPCrN-lTjoEg1uHDuP06Ys4S-8OSaulNrVFHnmL1VkLq2xGSlKwDQzHnzi0SP8xvQN-UF2q5msZVt7i-nTE1zINe2rjCjM9k_JSrJOgw9KmCjH2hiw4GgWmdG4GxHInUNvLbbsr8BD3sMZVEueXYtwOoItjzhjTsaZGfQ5JwCMGHE3d0bDe_WgUK2PzJqJNiHN45KXAch6g5GF8x7PZyGF8muztE47EnQtKf0uFchpBSKmw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg68977.html

For more context, I have functional data in an .nii.gz format that was 
pre-processed in FSL, but I need help converting it into functional left and 
right hemisphere surface maps in FreeSurfer for an input to a toolbox. Hope 
this makes sense.



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

Sent: Thursday, January 28, 2021 5:06 PM
To: Karan Desai ; freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Using mri_surf2surf to split files

Sorry, can you include the previous correspondence so that I have context. 
Also, please remember to post to the list

On 1/28/2021 12:07 PM, Karan Desai wrote:

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My bad, I meant to say surfaces. Right now the files are downsampled on
fsaverage4 space and I need to now split it into the respective left/right
hemispheres. For context, these are .nii.gz files currently. Is there a way to
easily do this in Freesurfer?

Best,

Karan Desai
Morey Lab - Duke

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[Freesurfer] Voxel-wise volumes vs APARC volumes

[Mark Wagshul]

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Dear Freesurfer experts,

I'm stuck on something which I think has to do with how Freesurfer calculates 
volumes, but can't quite wrap my head around it, hopefully you can enlighten me.

I have already produced robust results for our data using region-based cortical 
volumes, using aparcstats2table. This is in a group of 55 healthy older adults, 
modeling is using linear mixed effects models. All volumes were normalized with 
the eTIV.

We were hoping on exploring the same models with voxel-wise analyses, and are 
getting wildly different results. Data were created using mri_preproc, 
resampled onto fsaverage, and my assumptions was that because of this 
resampling, we should NOT be normalizing these values to the eTIV. The same 
regions which were highly significant on the region-based analyses and now not 
significant at all, and other regions are now showing up as significant.

Just as a sanity check, I attempted to reproduce the region-based analyses with 
these data using the following simple (I thought!) procedure:


1)  Created an mgz mask of the region I'm interested in, using 
mri_annotation2label and mri_label2label

2)  Read my volume data (#subjects x #vertices) into Matlab

3)  Read my mask into Matlab (yes, I know I can probably do this in 
Freesurfer, but I'm more comfortable with Matlab!)

4)  Multiply them together and take the sum across vertices.

5)  Feed the resultant data back into my LME model.

Two things are puzzling to me. 1) The highly significant results from the old 
LME are no longer significant (at the moment, only checked for two of the 
cortical regions), and 2) The correlation between these new data and the aparc 
volume are OK, although far from perfect (R2 ~ 0.86).

So, I'm obviously missing something here. What is the difference between the 
two volume calculation methods which could explain these discrepancies?

Any help with this would be MOST appreciated!

Best,

Mark

[cid:image004.jpg@01D6F59B.DA0205F0]


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org

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Re: [Freesurfer] Using mri_surf2surf to split files

[Douglas N. Greve]

Sorry, can you include the previous correspondence so that I have 
context. Also, please remember to post to the list


On 1/28/2021 12:07 PM, Karan Desai wrote:


External Email - Use Caution

My bad, I meant to say surfaces. Right now the files are downsampled on
fsaverage4 space and I need to now split it into the respective left/right
hemispheres. For context, these are .nii.gz files currently. Is there a way to
easily do this in Freesurfer?

Best,

Karan Desai
Morey Lab - Duke


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[Freesurfer] Fwd: SAMSEG longitudinal processing questions

[Douglas N. Greve]

Forwarding Stefano's answers...


 Forwarded Message 
Subject:Re: [Freesurfer] SAMSEG longitudinal processing questions
Date:   Thu, 28 Jan 2021 16:45:39 +
From:   Stefano Cerri 
To: Douglas N. Greve 
CC: Koen Van Leemput 



External Email - Use Caution


1) SAMSEG long should compute more consistent longitudinal structural 
volumes than SAMSEG while detecting better volumetric group differences 
(cf. Table 1 and Fig 3 of https://arxiv.org/pdf/2008.05117.pdf). Yes, 
using SBTIV for correcting volume changes from different scanners would 
be beneficial and most probably necessary.


2) The lesion version of SAMSEG long is available in the development 
version. Enabling the lesion extension can be done by adding the same 
flag(s) as for the cross-sectional lesion version (--lesion, see the 
Wiki for details: https://surfer.nmr.mgh.harvard.edu/fswiki/Samseg)


3) We never conducted extensive experiments for the number of burn-in 
and samples for the MCMC scheme, but we found that 50 burn-in and 50 
samples lead to robust and replicable lesion segmentation results. 
Increasing these two numbers might increase the lesion segmentation 
performance, although differences might be minimal and the overall 
computational cost high. We suggest to not decrease these two numbers as 
lesion performance could potentially decrease.


Best,
Stefano




*From:* Douglas N. Greve 
*Sent:* 28 January 2021 16:30
*To:* Koen Van Leemput; Stefano Cerri
*Subject:* Fwd: [Freesurfer] SAMSEG longitudinal processing questions

 Forwarded Message 
Subject:[Freesurfer] SAMSEG longitudinal processing questions
Date:   Thu, 28 Jan 2021 09:37:32 -0500
From:   XY XY 
Reply-To:   Freesurfer support list 
To: freesurfer@nmr.mgh.harvard.edu



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Hi FreeSurfers,

Thank you for sharing the new SAMSEG tool, which I consider a major 
breakthrough in image processing!

I have a few questions about using SAMSEG vs SAMSEG_Long:

1. What volumetric differences should I expect between running SAMSEG on 
individual images, vs. using SAMSEG_Long for the longitudinal analysis? 
Could I use SBTIV to adjust differences between scans?

(all images are FLAIRs preprocessed using mrI_robust_template)

2. Is there currently a way to integrate lesion segmentation into the 
SAMSEG_long’s longitudinal analysis?


3. What is the expected impact of increasing or decreasing -Burn-In and 
-Sample numbers for lesion segmentation?



Thank you for all the help!

Best,

Dave Kamson

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Re: [Freesurfer] Parallel computing for recon-all

[Michael Krause]

External Email - Use Caution

On 1/28/21 6:00 PM, Douglas N. Greve wrote:
> No, use of -threads or -openmp will always trigger the openmp code. The 
> -parallel may introduce other parallel. I did not write this part of the 
> code so I'm not sure, and I think I might have broken the -parallel 
> implementation when I did the last recon-all rewrite

Ah, that's good to know. I will remove the redundancy in our scripts then.

What do you mean by "may have broken"? Broken as in we have to worry about
results? We are currently running a couple of thousand subjects with 7.1.1
and they appear to be running fine so far *with* -parallel and -openmp 4
with an average core utilization of around 2.4 out of the possible 4.

cheers
Michael Krause

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[Freesurfer] data sharing of freesurfer processed data

[STACEY M SCHAEFER]

External Email - Use Caution

Does the freesurfer group have any recommendations or procedures for public 
sharing data that has been processed with freesurfer? In particular, procedures 
to automatically swap out participant IDs to anonymize the data?


Stacey M. Schaefer, Ph.D.
Center for Healthy Minds

University of Wisconsin-Madison

625 W Washington Ave

Madison WI 53703


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Re: [Freesurfer] LME Univariate Analysis

[Boa Sorte Silva, Narlon]

External Email - Use Caution

Just following up on my email below to see if anyone is able to help?

Thanks!
Nárlon Cássio

Nárlon Cássio Boa Sorte Silva, PhD
CIHR/MSFHR Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia
Twitter: @BoaNarlon

On Jan 20, 2021, at 9:20 PM, Boa Sorte Silva, Narlon 
mailto:narlon.si...@ubc.ca>> wrote:

[CAUTION: Non-UBC Email]
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Dear Freesurfer Experts,
Hope this finds you well

I am following the LME tutorial running LME Univariate analysis. I was 
wondering if someone would kindly check my steps below? I wanted to make sure 
specially that my matrix (X) and and contrast (C) were designed accordingly to 
assess group*time interaction.

Study design:
Two groups: 0 = control, 1 = intervention
Time: 0 = baseline, 1 = 6-month follow-up
Outcome of interest: Change in hippocampal volume
Co-Variate: Estimated ICV

Here are the steps I took in Matlab:

# Loading into Matlab Qdec table with 7 columns in this exact order:  fsid, 
fsid-base, time, group, Righ.Hipp, Left.Hipp, estimated_ICV:
Qdec = fReadQdec('qdec-aseg.table.dat');
Qdec = rmQdecCol(Qdec,1);
sID = Qdec(2:end,1);
Qdec = rmQdecCol(Qdec,1);
M = Qdec2num(Qdec);
Y = M(:,3:4);
M = M(:,[1:2 5]); # Here I loaded estimated ICV already into M (as the third 
column), as it will be treated as a covariate later.

# Sorting data according to time
[M,Y,ni] = sortData(M,1,Y,sID);

# Building design matrix X from M, for a simple time by group interaction. Note 
that here, I have the slope column as 1, then I add time and group columns via: 
M(:,1:2), then a column for group*time via: M(:,1).*M(:,2), and finally a 
column for estimated ICV, as the final column in the matrix via: M(:,3). I 
wonder if this is correct?
X = [ones(length(M),1) [M(:, 1:2) M(:,1).*M(:,2) M(:,3)]];

# Determining model parameters, for total hippocampal volume, Left.Hipp, and 
Right.Hipp. Here, since my sample is small (N = 15), I am using 1 random effect 
only.
hipp_vol_stats_tot = lme_fit_FS(X,[1],Y(:,1)+Y(:,2),ni);
hipp_vol_stats_left = lme_fit_FS(X,[1],Y(:,1),ni);
hipp_vol_stats_right = lme_fit_FS(X,[1],Y(:,2),ni);

# Creating contrast (C) matrix for simple group*time interaction controlling 
for estimated ICV. Does this look correct, considering that the last 0 would 
control for estimated ICV?
C = [ 0 0 0 1 0];

# Finally, F test for total, left and right hippocampal volumes
F_C_tot = lme_F(hipp_vol_stats_tot,C);
F_C_left = lme_F(hipp_vol_stats_left,C);
F_C_right = lme_F(hipp_vol_stats_right,C);

Thanks so much for your help!

Nárlon Cássio

Nárlon Cássio Boa Sorte Silva, PhD
CIHR/MSFHR Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia
Twitter: @BoaNarlon

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Re: [Freesurfer] Regarding the developer password.

[fsbuild]

External Email - Use Caution

Hello Anete,
Sending the info to your email shortly.
-R.On Jan 28, 2021, at 08:05, Anete Sneidere  
wrote:External Email - Use 
Caution Hello!I have 
followed the Freesurfer installation guide with VB and Ubuntu but I have not 
been able to log in. It asks for a developers password and I was hoping maybe 
it would be possible for you to send it to me?I noticed many people were 
writing about this issue.Looking forward to hearing from 
you!Anete___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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Re: [Freesurfer] Parallel computing for recon-all

[Douglas N. Greve]

No, use of -threads or -openmp will always trigger the openmp code. The 
-parallel may introduce other parallel. I did not write this part of the 
code so I'm not sure, and I think I might have broken the -parallel 
implementation when I did the last recon-all rewrite

On 1/28/2021 11:23 AM, Michael Krause wrote:
>  External Email - Use Caution
>
>> 1 According to documents, freesurfer is OpenMP code , I use -openmp 8
>> flag like: recon-all -alli -i input.file  -s output.file -openmp 8
>> to tun the recon command on a server, but it doesn't work for me (the
>> running time is very similar for the same subject). Cloud you tell me
>> what is wrong?
> It's my understanding that you also need to specify `-parallel` in
> addition to optional flag for the openmp thread count. At least since
> v6, no?
>
>   
> https://secure-web.cisco.com/1iQveNDdwNTosrnlkwXmvvjJwqsGtnW6NxvHb6cchwZMPFP4GLC1cY28DgYWfxtlbZ2Gosv-sZAbvDcxlokTGdnOIu1nJM0jMb2c8piqb9yE2aGPCKmbZm89O65nTV3e5HtcVenn5l3CKNNxGXAhrJJoEjwh0VdT7FUh66bTUwCh24ii6BBq0v-Ju1512mnjcSOnn_LgoFCj_8RLZERY14L1A2Ve_iEumL9Quafz8aEnq3tO8_1bJMrMrjDuKP71WwkUOoeuud_NU5qAcJpnNzg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
>
> cheers
> Michael Krause
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Parallel computing for recon-all

[Michael Krause]

External Email - Use Caution

> 1 According to documents, freesurfer is OpenMP code , I use -openmp 8
> flag like: recon-all -alli -i input.file  -s output.file -openmp 8 
> to tun the recon command on a server, but it doesn't work for me (the
> running time is very similar for the same subject). Cloud you tell me
> what is wrong?

It's my understanding that you also need to specify `-parallel` in
addition to optional flag for the openmp thread count. At least since
v6, no?

 
https://secure-web.cisco.com/1iQveNDdwNTosrnlkwXmvvjJwqsGtnW6NxvHb6cchwZMPFP4GLC1cY28DgYWfxtlbZ2Gosv-sZAbvDcxlokTGdnOIu1nJM0jMb2c8piqb9yE2aGPCKmbZm89O65nTV3e5HtcVenn5l3CKNNxGXAhrJJoEjwh0VdT7FUh66bTUwCh24ii6BBq0v-Ju1512mnjcSOnn_LgoFCj_8RLZERY14L1A2Ve_iEumL9Quafz8aEnq3tO8_1bJMrMrjDuKP71WwkUOoeuud_NU5qAcJpnNzg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes

cheers
Michael Krause

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[Freesurfer] FW: FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing

[Loreto, Flavia]

External Email - Use Caution

Hi Andrew,

This is the output:

-bash-4.2$   touch /tmp/mytempfile && rm -f /tmp/mytempfile
touch: cannot touch ‘/tmp/mytempfile’: Permission denied

Yes, I am running it through the High Performance Computing (HPC) cluster. Is 
there a way to work around this kind of permission problem?

Many thanks for your help.
Best,
Flavia


From:  on behalf of "Hoopes, Andrew" 

Reply to: Freesurfer support list 
Date: Tuesday, 26 January 2021 at 22:05
To: Freesurfer support list 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

Okay, maybe it’s a permission error. How about the output of the following?

touch /tmp/mytempfile && rm -f /tmp/mytempfile

Also, are you running recon-all on a cluster?
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Loreto, Flavia 

Date: Tuesday, January 26, 2021 at 1:56 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

External Email - Use Caution
Hi Andrew,
Many thanks for your reply. This is what I get if I ls/temp:

-bash-4.2$ ls /tmp
hsperfdata_gc520
hsperfdata_rf1116
hsperfdata_scliffor
pbs.3000969.pbs
systemd-private-845d4b93c36041db9cb4f47a494a5f87-httpd.service-gKdDDc
systemd-private-845d4b93c36041db9cb4f47a494a5f87-httpd.service-ZujPj0
systemd-private-845d4b93c36041db9cb4f47a494a5f87-ntpd.service-sX44ZN
systemd-private-845d4b93c36041db9cb4f47a494a5f87-ntpd.service-ukGmwH

What would you recommend doing?

Thank you.
Best,
Flavia


From:  on behalf of "Hoopes, Andrew" 

Reply to: Freesurfer support list 
Date: Tuesday, 26 January 2021 at 17:32
To: Freesurfer support list 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

Hi Flavia,
Do you have access to /tmp on your system? Can you `ls /tmp`?
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Loreto, Flavia 

Date: Tuesday, January 26, 2021 at 11:29 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

External Email - Use Caution
Hi Douglas,
Here is the result:

-bash-4.2$ ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
-rw-rw 1 floreto rds-000730 925609 Jan 17 04:02 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot

Thank you.
Best,
Flavia


From:  on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 
Date: Tuesday, 26 January 2021 at 16:25
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

Sorry, that first one should have been
ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
left off the "t"
On 1/26/2021 10:55 AM, Loreto, Flavia wrote:

External Email - Use Caution
Dear Douglas,
Thanks for your reply. Please see below the results of those commands:


-bash-4.2$ ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno

ls: cannot access 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno: No 
such file or directory

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001/label

drwxrws--- 2 floreto rds-000730 4096 Jan 17 04:47 
/rds/general/project/imperialapc/live/freesurfer/APC001/label

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001

drwxrws--- 10 floreto rds-000730 4096 Jan 17 12:46 
/rds/general/project/imperialapc/live/freesurfer/APC001

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer

drwxrws--- 3 floreto rds-000730 4096 Jan 16 20:33 
/rds/general/project/imperialapc/live/freesurfer

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live

drwxrws--- 11 root rds-000730 8192 Jan 18 13:06 
/rds/general/project/imperialapc/live

Thank you.
Best,
Flavia


From: 

 on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 

Date: Tuesday, 26 January 2021 at 15:30
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

This email from dgr...@mgh.harvard.edu 
originates from outside Imperial. Do not click on links and attachments unless 
you recognise the sender. If you trust the sender, add them to your safe 
senders 
list

Re: [Freesurfer] question on data quality - examples in appendix

[Douglas N. Greve]

On 1/27/2021 1:34 PM, Nils B. wrote:


External Email - Use Caution

Hello and thank you for you answer,

to the first point: Freesurfer is recognizing this area as Gray 
Matter. Can I just delete this part manually and see if the WM/GM 
pials are correct or would this lead to other problems?
You can do this. It is essentially a skull stripping error, though it is 
really hard to remove because it is between two bits of brain.


To the second point: I mean the tool, which enables me to do manual 
edits like deleting areas. It's the 4th tool from the left in the top 
bar of the Freesurfer GUI.
What editing did you do there? I don't think they look that unusual; 
sometimes you need to look in all  3 dims.


Best regards,

Nils

Am Mi., 27. Jan. 2021 um 00:41 Uhr schrieb Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>:




On 1/26/2021 3:18 PM, Nils B. wrote:


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Hello everyone,

I'm analyzing 1,5T scans and I've two problems with the data
quality of my participants, where I hope you can help me.

1. In two of my scans the participants have blurry areas near the
cerebellum, which makes it nearly impossible for Freesurfer
(Version 7.1) to set the pials correctly (see Appendix: Scan 1).
Is this problem caused by movement while scanning or is there
something i can do?

This looks like it could be the transverse sinus vein and not
brain tissue.


2. Sometimes when I'm using the manual tool "recon-edit" for
manual skullstrips the pials look weird after another recon (see
Appendix: Scan 2, green box).

I'm not sure what you did here. What is the "recon-edit" tool?


I hope you can help me with this.

Best regards,

Nils
-- 


Nils Böer
Research Assistant with Bachelor Degree (WHB)
*Psychology and Movement*
University of Paderborn
Department of Sports and Health
Warburger Str. 100
33098 Paderborn
Room: Sp 1.401

Email: nils.tobia...@gmail.com / nbo...@mail.uni-paderborn.de

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--

Nils Böer
Research Assistant with Bachelor Degree (WHB)
*Psychology and Movement*
University of Paderborn
Department of Sports and Health
Warburger Str. 100
33098 Paderborn
Room: Sp 1.401

Email: nils.tobia...@gmail.com / nbo...@mail.uni-paderborn.de 

Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ 

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

[Douglas N. Greve]

Run
mri_concat input.mgz --rms --o 001.mgz
then pass 001.mgz to recon-all


On 1/28/2021 3:13 AM, 南修司郎 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,
I'm attempting to recon-all a subject, but i got the following error.
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz 
has 4 frames


I checked mri_info, and the dimensions are 256 x 256 x 176 x 4.
I asked the radiation technologist to change the dimensions to 256 x 
256 x 176, but he told me it's impossible because of the multi echo 
sequence.


I'd appreciate if someone help me out with this and resolve this error.

Shujiro Minami M.D., Ph.D.
Dpt. of Otolaryngology National Tokyo Medical Center
2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan
E-mail shujiromin...@me.com 

1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform:Ubuntu 18.04.5 LTS (GNU/Linux 5.4.0-1034-gcp x86_64)
3) uname -a: Linux instance-1 5.4.0-1034-gcp #37~18.04.1-Ubuntu SMP Wed Jan 6 
19:44:48 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached

User: shujirominami  Machine: instance-1  Platform: Linux  PlatformVersion: 
5.4.0-1034-gcp  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  
ProgramVersion: $Name: stable6 $  TimeStamp: 2021/01/27-10:28:02-GMT  
BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_relabel_hypointensities.c,v 
1.13 2015/05/15 18:44:10 nicks Exp $  User: shujirominami  Machine: instance-1  
Platform: Linux  PlatformVersion: 5.4.0-1034-gcp  CompilerName: GCC  
CompilerVersion: 40400
###
GCADIR /usr/local/freesurfer/average
GCA RB_all_2016-05-10.vc700.gca
GCASkull RB_all_withskull_2016-05-10.vc700.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /usr/local/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
###
/home/shujirominami/freesurfer/subjects/todai_test

  mri_convert /home/shujirominami/NIFTI/todai_test.nii.gz 
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz

mri_convert.bin /home/shujirominami/NIFTI/todai_test.nii.gz 
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/shujirominami/NIFTI/todai_test.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, 1)
k_ras = (1, 0, 0)
writing to 
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz...
#
#@# MotionCor Wed Jan 27 10:29:57 UTC 2021
Found 1 runs
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz has 4 frames
If this is a multi-frame MEMPRAGE image,
use mri_concat --rms to combine echo frames.
Linux instance-1 5.4.0-1034-gcp #37~18.04.1-Ubuntu SMP Wed Jan 6 19:44:48 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s todai_test exited with ERRORS at Wed Jan 27 10:30:01 UTC 2021

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] help with labels

[Douglas N. Greve]

You can manully edit the annotation or you can manually edit the AAL 
segmentation to fill in the holes


On 1/28/2021 6:09 AM, Alberto Del Cerro Leon wrote:


External Email - Use Caution

I found the vertex for the holes but how can i modify them or how can 
I solve them?


El mié, 27 ene 2021 a las 16:36, Douglas N. Greve 
(mailto:dgr...@mgh.harvard.edu>>) escribió:


Look at the surface superimposed on the volume along with the AAL
segmentation to make sure that it intersects the segmentation at
all vertices. You can find the vertex numbers for the holes, and
then go specifically to that vertex

On 1/27/2021 6:27 AM, Alberto Del Cerro Leon wrote:


External Email - Use Caution

Hello Freesurfer team, I did an AAL atlas on the surface using
mri_vol2surf, however when I look at this overlay there are many
holes in the labels with vertices that don't belong to any label.
Could u help me with this problem?

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Re: [Freesurfer] recon all

[Douglas N. Greve]

No head motion correction because  there is only one image

On 1/27/2021 6:59 PM, 郑凤莲 wrote:


External Email - Use Caution

Hi experts,
We have segmented hippocampus using Freesurfer 6.0. I have a question 
that is there "head motion correct" in this step? If yes, how does it 
examined?

I am looking forward to your reply. Thanks very much.

Sincerely,
Zheng



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邮箱：zhengfenglian0...@163.com

 



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Re: [Freesurfer] Parallel computing for recon-all

[Douglas N. Greve]

On 1/27/2021 2:02 PM, Wei Shao wrote:


External Email - Use Caution

Hi, Douglas

Thanks for your kind reply.

1 I run the same subject on a server with openmp 8 flags cost 7 hours, 
without openmp 8 flag would be 7h10minutes.

Can you send the two recon-all.log files?


3 Could you be more specific about run them by hand? is this mean I 
run different tasks like skull strip or parcellation separately within 
recon rather than recon-all?
Each step in recon-all can be run separately using command line flags. 
It is not an easy thing to do and not well documented.


Best,
Wei



On Mon, Jan 25, 2021 at 10:17 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:




On 1/20/2021 3:39 PM, Wei Shao wrote:


External Email - Use Caution

Hi, Freesufer experts

My name is wei shao, I have a few questions regarding the
parallel computing of recon-all

1 According to documents, freesurfer is OpenMP code , I use
-openmp 8 flag like: recon-all -alli -i input.file  -s
output.file -openmp 8
to tun the recon command on a server, but it doesn't work for me
(the running time is very similar for the same subject). Cloud
you tell me what is wrong?

Please specify the difference in times.


2 Can Freesufer take advantage of several GPUs?

No


3 Is it possible to open few threads to run recon-all on
different sections parallelly?

Only if you run them by hand


Best,
Wei



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[Freesurfer] SAMSEG longitudinal processing questions

[XY XY]

External Email - Use Caution

Hi FreeSurfers,

Thank you for sharing the new SAMSEG tool, which I consider a major 
breakthrough in image processing!
I have a few questions about using SAMSEG vs SAMSEG_Long:

1. What volumetric differences should I expect between running SAMSEG on 
individual images, vs. using SAMSEG_Long for the longitudinal analysis? 
Could I use SBTIV to adjust differences between scans?
(all images are FLAIRs preprocessed using mrI_robust_template)

2. Is there currently a way to integrate lesion segmentation into the 
SAMSEG_long’s longitudinal analysis?

3. What is the expected impact of increasing or decreasing -Burn-In and -Sample 
numbers for lesion segmentation?


Thank you for all the help!

Best,

Dave Kamson

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[Freesurfer] Regarding the developer password.

[Anete Sneidere]

External Email - Use Caution

 Hello!

I have followed the Freesurfer installation guide with VB and Ubuntu but I
have not been able to log in. It asks for a developers password and I was
hoping maybe it would be possible for you to send it to me?
I noticed many people were writing about this issue.
Looking forward to hearing from you!

Anete
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[Freesurfer] ERROR: input(s) cannot have multiple frames!

[南修司郎]

   External Email - Use Caution


Hello FreeSurfer Developers,
I'm attempting to recon-all a subject, but i got the following error.
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz has 4 frames


I checked mri_info, and the dimensions are 256 x 256 x 176 x 4.

I asked the radiation technologist to change the dimensions to 256 x 256 x 176, 
but he told me it's impossible because of the multi echo sequence.



I'd appreciate if someone help me out with this and resolve this error.



Shujiro Minami M.D., Ph.D.
Dpt. of Otolaryngology National Tokyo Medical Center
2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan
E-mail shujiromin...@me.com



1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu 18.04.5 LTS (GNU/Linux 5.4.0-1034-gcp x86_64)
3) uname -a: Linux instance-1 5.4.0-1034-gcp #37~18.04.1-Ubuntu SMP Wed Jan 6 
19:44:48 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached

User: shujirominami  Machine: instance-1  Platform: Linux  PlatformVersion: 5.4.0-1034-gcp  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/01/27-10:28:02-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $  User: shujirominami  Machine: instance-1  Platform: Linux  PlatformVersion: 5.4.0-1034-gcp  CompilerName: GCC  CompilerVersion: 40400 
###

GCADIR /usr/local/freesurfer/average
GCA RB_all_2016-05-10.vc700.gca
GCASkull RB_all_withskull_2016-05-10.vc700.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /usr/local/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
###
/home/shujirominami/freesurfer/subjects/todai_test

 mri_convert /home/shujirominami/NIFTI/todai_test.nii.gz /home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz 

mri_convert.bin /home/shujirominami/NIFTI/todai_test.nii.gz /home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from /home/shujirominami/NIFTI/todai_test.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, 1)
k_ras = (1, 0, 0)
writing to 
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz...
#
#@# MotionCor Wed Jan 27 10:29:57 UTC 2021
Found 1 runs
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz has 4 frames
If this is a multi-frame MEMPRAGE image,
use mri_concat --rms to combine echo frames.
Linux instance-1 5.4.0-1034-gcp #37~18.04.1-Ubuntu SMP Wed Jan 6 19:44:48 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s todai_test exited with ERRORS at Wed Jan 27 10:30:01 UTC 2021

To report a problem, see 
http://secure-web.cisco.com/1g-5Sw5A-mJK27f9rxSEw4DBgjmZ7KTng5JrfBIPRNQPlEHCK_2tvxt6c4VAFY8M8aXtgjW2wRrVh3lfJWDAObul-ChFw-EgshQxXF7xs8ftorKmKNZOxjPgprRtx6IFZh7BtQIjHj7f0sY7N_qnq-JqdGk-bpGnLlwWT-920Eo3Yp0LBOUU9rTr0sKsCENdJx2LNXqNo969fGvFq3oi1kRepC601NZSMwau1HPSNnCotMYa8YmNLmOhpelXErfVeAzYpgXP0ZLg2ZBwxKf1sCA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
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Re: [Freesurfer] help with labels

[Alberto Del Cerro Leon]

External Email - Use Caution

I found the vertex for the holes but how can i modify them or how can I
solve them?

El mié, 27 ene 2021 a las 16:36, Douglas N. Greve ()
escribió:

> Look at the surface superimposed on the volume along with the AAL
> segmentation to make sure that it intersects the segmentation at all
> vertices. You can find the vertex numbers for the holes, and then go
> specifically to that vertex
>
> On 1/27/2021 6:27 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Hello Freesurfer team, I did an AAL atlas on the surface using
> mri_vol2surf, however when I look at this overlay there are many holes in
> the labels with vertices that don't belong to any label. Could u help me
> with this problem?
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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