Re: [Freesurfer] (no subject)

[Ammon, William]

Hi Saman,

It looks like with the --subjects flag you are pointing Freesurfer to the stats 
directory within a subject directory (where Freesurfer expects the subject 
directory). aparcstats2table and asegstats2table assume a standard Freesurfer 
directory configuration so try entering just the subject directory (one level 
up from stats) is enough and Freesurfer will know to access the proper stats 
files that you specify. Also try and double check your SUBJECTS_DIR.

Cheers,
Bill

From:  on behalf of saman fouladi 

Reply-To: Freesurfer support list 
Date: Tuesday, November 3, 2020 at 12:24 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] (no subject)


External Email - Use Caution
hi

I run in linux command:
"""
aparcstats2table --hemi lh  --subjects /home/team33/MRI4/subj10/stats --parc 
aparc.a2009s  --meas meancurv --tablefile /home/team33/ aparcstats.txt
"""
but show below error an i can not solve it nix:

"""
 File "/usr/local/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
"""

I changed the code several times, but in all cases there is this error.
This error also happens to asegstats2table.

please help me


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Re: [Freesurfer] Meta-analysing brain measure statistics across multiple cohorts using different versions of Freesurfer

[Ammon, William]

Hello,

It is not advisable to mix versions of FreeSurfer as results across different 
versions of FreeSurfer are expected to differ, even if by a little. We 
recommend that the same version of FreeSurfer be used to process every case in 
your dataset. If you were to proceed with an analysis of, for example, a cohort 
processed with 5.3 versus 6.0,  differences in stats could be partially due to 
difference in version.

Cheers,
Bill

From:  on behalf of Stephanie K 

Reply-To: Freesurfer support list 
Date: Wednesday, November 4, 2020 at 3:00 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Meta-analysing brain measure statistics across 
multiple cohorts using different versions of Freesurfer


External Email - Use Caution
Hi,

I am planning on meta-analysing the effects of regional and global cortical 
thickness + surface area, as well as subcortical volumes of 3 cohorts. Two of 
them have been processed using Freesurfer 5.3 and one one of them has been 
Freesurfer 6.0. Is it wrong to meta-analyse them due to differences in the 
pipeline? I would really appreciate your advice.

Thanks
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Re: [Freesurfer] please help me {Disarmed}

[Ammon, William]

Hello,

Are you still getting the error message that “atleast 1 subject must be 
provided”? Or is it a different error message? The screenshot shows you are in 
the directory MRI4 but the command you’ve sent indicates you want to output 
aparcstats.txt to the directory team33.
Make sure to remove the space in “/home/team33/aparcstats.txt”, and that you 
have proper permissions to write to the directory ‘team33’.

Cheers,
Bill

From:  on behalf of saman fouladi 

Reply-To: Freesurfer support list 
Date: Friday, November 6, 2020 at 1:13 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] please help me {Disarmed}


External Email - Use Caution
hi

I found the solution to my problem but the following error occurs

I run in linux command:
"""
aparcstats2table --hemi lh  --subjects /home/team33/MRI4/subj1 --parc 
aparc.a2009s  --meas meancurv --tablefile /home/team33/ aparcstats.txt
"""
but show below error an i can not solve it nix:

"""
 File "/usr/local/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
"""

I changed the code and direction several times, but in all cases there is this 
error.
This error also happens to asegstats2table.

The attached image shows my access to folders.

please help me



On Saturday, October 24, 2020, 7:27:18 PM GMT+3:30, saman fouladi 
 wrote:


thank Bruce

I read several articles and got a little confused.

Can you help me a little if you have any information?

On Saturday, October 24, 2020, 6:04:07 PM GMT+3:30, Fischl, Bruce 
 wrote:



Hi Saman



That’s really a scientific question and up to you!
Bruce



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of saman fouladi
Sent: Saturday, October 24, 2020 7:17 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] please help me



External Email - Use Caution

hi



Which output can I use to predict age after recon-all?



On Friday, October 23, 2020, 11:46:09 PM GMT+3:30, saman fouladi 
mailto:smnfoul...@yahoo.com>> wrote:





yes and replacing -sdir with -sd



thank you very much

On Friday, October 23, 2020, 5:58:11 PM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:





You need a -s before the “subj1”



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Friday, October 23, 2020 2:44 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me



External Email - Use Caution

hi



my code is:



recon-all -i /home/MRI/Training/99060003/T1-image/39501.dcm  subj1 -sdir  
/home/MRI4 -all



ERROR: Flag subj1 unrecognized.
-i /home/nbml-challenge/Training/99060003/T1-image/39501.dcm subj1 -sdir 
/home/team33/MRI4 -all



what is ??





On Thursday, October 22, 2020, 5:40:05 PM GMT+3:30, saman fouladi 
mailto:smnfoul...@yahoo.com>> wrote:





hi Bruce



thank you very very much



On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:





Nifty is a format that a lot of people use (including us) but it is not needed 
for our processing. Pick *one* file in your dicom series and pass it to 
recon-all:





recon-all -i  -s  -sdir  -all



cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Wednesday, October 21, 2020 11:57 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me



External Email - Use Caution

hi



Thank you for your response



I have 60 subject MRI that each  contains 174 dcm file. and i want predict age 
of these subjects. in step one i want extract morphology features and in step2 
create a deep learning model that predict age.



According to what I said, what should I do?



If I have to use recon-all with what code can I do this? And what is the use of 
nifty?



On Wednesday, October 21, 2020, 1:06:50 AM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:





Hi Saman



Recon-all will give you a comprehensive assessment of most macroscopically 
visible structures in the brain. You don’t have to convert to nifty first – 
just point recon-all at a single slice in the proper dicom series (for your 3D 
T1-weighted scan), and it will spend a few hours doing stuff



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Tuesday, October 20, 2020 4:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Frees

Re: [Freesurfer] Canon MRI morphometry protocols

[Ammon, William]

Hello Shujiro,

Our group has never used Canon scanners before, so unfortunately I don’t have 
any Canon-specific protocol I can point you to. Below is the link to our 
suggested T1 structural protocol as we have used/tested on Siemens scanners 
before. You could try to reproduce this protocol on your scanner using these 
parameters:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&do=get&target=FreeSurfer_Suggested_Morphometry_Protocols.pdf

Cheers,
Bill



From:  on behalf of 南修司郎 

Reply-To: Freesurfer support list 
Date: Tuesday, November 10, 2020 at 5:35 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Canon MRI morphometry protocols


External Email - Use Caution
Dear experts

We are trying to take MRI with Canon magnetic resonance for FreeSurfer analysis.
I'd appreciate If you could give me the recommended T1 structural protocol for 
Canon scanners.

Thank you in advance.

Shujiro

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
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Re: [Freesurfer] Include T2 in recon-all command

[Ammon, William]

Hi Rosalia,

You can include T2 images by adding the flags  -T2 /path/to/volume (to point to 
the T2 images) and -T2pial -all (to generate new pial surfaces using T2 images).

You can read more about this 
here
 on our wiki.

Bill Ammon

From:  on behalf of Rosalia Dacosta 
Aguayo 
Reply-To: Freesurfer support list 
Date: Wednesday, March 3, 2021 at 7:36 AM
To: Freesurfer support list 
Subject: [Freesurfer] Include T2 in recon-all command


External Email - Use Caution
Dear Freesurfer community,

I would like to include the T2 image in the recon-all command to improve 
segmentation.

Any idea how I should do this in the following command?

recon-all -s Artico1 -i subj01_anat.nii.gz -all -qcache -3T

Regards,
Rosalia
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Re: [Freesurfer] Include T2 in recon-all command

[Ammon, William]

Sorry for any confusion, I meant that you would include the T2 flag to the end 
of your current recon-all command. So you could have a command that would look 
something like

recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume 
-T2pial -all


So you are inputting both T1 and T2 images. For your command in your first 
message, I think you should just add -T2 /path/to/T2_volume -T2pial.

Hope this helps,
Bill Ammon

From:  on behalf of Rosalia Dacosta 
Aguayo 
Reply-To: Freesurfer support list 
Date: Wednesday, March 3, 2021 at 1:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Include T2 in recon-all command


External Email - Use Caution
Hi William,

I wanted to use both T1 and T2 to do the recon -all -all.

Could it be:


  *   recon-all -subject subjectname -i invol1 <-i invol2> -all



El mié., 3 mar. 2021 17:16, Ammon, William 
mailto:wam...@mgh.harvard.edu>> escribió:
Hi Rosalia,

You can include T2 images by adding the flags  -T2 /path/to/volume (to point to 
the T2 images) and -T2pial -all (to generate new pial surfaces using T2 images).

You can read more about this 
here<https://secure-web.cisco.com/1-kKoxBlghDNt9knl5SHKY-AN5hisd2dv9vY-TyxuuixDypboRpqcOZD4spjJfNrqoQ7lNcImlg2d3KaMoRCCAx07RBL5eYJeluoihgs4VgUpNVlUeSCLfSXJTJWa29ulVt1tCzhDA5L3HbSAWlNzdoZsfrWxve-zkvFgPbZfK_8XhHfkvuuWIVlpTuEq_pyIXpmb_3OOQq-yg-ERdHMRgyfFQmTbUdGpCeCMfNW6NItYcf2ydKUFVaraXcXlb3iKIGaPLQxlB6hThbBwTx0EXw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23UsingT2orFLAIRdatatoimprovepialsurfaces>
 on our wiki.

Bill Ammon

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Rosalia Dacosta Aguayo 
mailto:rdacos...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, March 3, 2021 at 7:36 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Include T2 in recon-all command


External Email - Use Caution
Dear Freesurfer community,

I would like to include the T2 image in the recon-all command to improve 
segmentation.

Any idea how I should do this in the following command?

recon-all -s Artico1 -i subj01_anat.nii.gz -all -qcache -3T

Regards,
Rosalia
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