Re: [Freesurfer] Recon-all Error

2021-01-19 Thread Garcia Pallares, Erendira Xenia 
Hi Dimitri,

Could you indicate the recon command that you ran? You could try rerunning the 
recon-all command in the directory with one of the dicom files for the T1 image.

I’ve posted an example command below:

recon-all -all -i I50 -s  Subj001

• The file after the “-i” flag indicates your input dicom file (I50)
• The file after the “-s” flag represents the output directory (Subj001) after 
you have run recon-all

If you have more than one dicom file that you’d like to run through the recon 
pipeline you can add -i flags for each additional dicom.

You can find additional information on the 
Freesurfer
 wiki

Let me know if you have more questions.

Best regards,

Ren


From: freesurfer-boun...@nmr.mgh.harvard.edu 

Date: Wednesday, January 6, 2021 at 21:34
To: Freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Recon-all Error

External Email - Use Caution
Hello! I’m experiencing an error while I try to use recon-all in a T1 MRI 
image, the following error message appears:
“[...]
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading mri_src from norm.mgz...
error: 
mghRead(/home/developer/Desktop/BIBE_2020/Simulated_MRI/HC/rf0/t1_icbm_normal_1mm_pn1_rf0/mri/norm.mgz,
 -1): could not open file
error: mri_normalize: could not open source file norm.mgz”
Thanks!
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Re: [Freesurfer] Recon-all log

2021-01-19 Thread Mora, Jocelyn S. 
Hi Luisa,

There seems to be an error opening the T1.mgz file. Is there a T1.mgz file in 
your mri folder?

Best,
Jocelyn

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bohorquez Montoya, Luisa 

Sent: Monday, January 18, 2021 10:58 AM
To: Freesurfer support list 
Subject: [Freesurfer] Recon-all log


External Email - Use Caution

Good morning freesurfer, I am new using recon all. Would you mind to help me 
with this error I am getting? What should I do?



Attached is the log and here is my command.



recon-all \

-subject ${ANATDIR} \

-i ${ANATDIR}/${subject}/*Ax_FSPGR_3D_GR.nii.gz \

-T2 ${ANATDIR}/${subject}/*Ax_T2_FLAIR_SE_IR.nii.gz \

-T2pial \

-parallel -openmp 12 \



Thank you so much for your time



Luisa Bohorquez, PhD.

Department of Psychiatry,

Medical College of Wisconsin.


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[Freesurfer] HCP T1w scans on FreeSurfer 7.1

2021-01-19 Thread Trisanna Sprung-Much 
External Email - Use Caution

Hi there

If I want to run some HCP subjects that are 0.5mm iso T1w scans (MPRAGE) in 
FreeSurfer 7.1, would I simply use the following flags, or am I missing 
something?

 -3T -MPRAGE -hires

Do we need an expert file with version 7.1 to specify the number of iterations 
for surface inflation or is this now done automatically?

Thank you
Trisanna
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[Freesurfer] Cannot find rh.white.H

2021-01-19 Thread Andy Worth 
External Email - Use Caution

Hello,

We're seeing this error a lot: "Cannot find rh.white.H" which is generated
here
.

It does not occur if -parallel is turned off.

I see that reconbatchjobs does "exec" on the commands sequentially in the
order of the list, but it runs each in the background:

exec $JOB >> $LOG 2>&1 &


so I thought it might just be slightly possible that these two commands:

  set cmd1 = (rm -f $hemi.white.$suffix)

  set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix)

could end up in a race condition where the file is linked and then
immediately removed if somehow the ln command is executed before the rm
command.

However, I tried reproducing this behavior with a test script but the rm
always happens before the ln.

Any help would be appreciated!

Thanks,

Andy Worth
Scientific Solutions Engineer
he, him, his

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Re: [Freesurfer] Cannot find rh.white.H

2021-01-19 Thread Fischl, Bruce 
Hi Andy

I think the rh.white.H is generated by mris_curvature. Does that help?

Cheers,
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Andy Worth
Sent: Tuesday, January 19, 2021 5:29 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Cannot find rh.white.H


External Email - Use Caution
Hello,

We're seeing this error a lot: "Cannot find rh.white.H" which is generated 
here.

It does not occur if -parallel is turned off.

I see that reconbatchjobs does "exec" on the commands sequentially in the order 
of the list, but it runs each in the background:

exec $JOB >> $LOG 2>&1 &

so I thought it might just be slightly possible that these two commands:


  set cmd1 = (rm -f $hemi.white.$suffix)

  set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix)

could end up in a race condition where the file is linked and then immediately 
removed if somehow the ln command is executed before the rm command.

However, I tried reproducing this behavior with a test script but the rm always 
happens before the ln.

Any help would be appreciated!

Thanks,

Andy Worth
Scientific Solutions Engineer
he, him, his
[https://secure-web.cisco.com/1YriYUvcgCSjRhC6yGeZ5vu_KysFv12VbE-P3WRYMut0v4dV5ZLR8MvWGUaa793niFj0dFyrx1Q6R_6ywkKWHzWY_c19RzETcRJS4x5y66xdtc1cDH235ZWSyN2zx3loPwx8XdLAC8gvP8QOO1Oj0gx4uxiXCDKC2wFY-tb4JgWLPrDrSNN-S6wN0WEom-ZfbujWPJrzylnmiuXFChuep6ROueyv5d-m6UBjUbry6P3gOXvc8RL-9ciCZHIFhaf3WWhYC3Zgn6ooOXcbz58SPcg/https%3A%2F%2Fdrive.google.com%2Fuc%3Fid%3D1oozBEoFHbBP_5xYyw59-9YNoEOsX6Ghd%26export%3Ddownload]
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[Freesurfer] BIDS-PET extension request for comments - closes on Friday, Feb. 12

2021-01-19 Thread Franklin Feingold 
External Email - Use Caution

We are happy to announce that the Positron emission tomography BIDS extension 
is finally nearing it’s completion. Hence, we are seeking final community 
feedback for the PET BIDS standard. We are looking for feedback on GitHub and 
specifically to the BIDS-PET extension proposal ( 
https://secure-web.cisco.com/18Ho2R5GZxtyWMrxs5QijrXyOtATKVsoJi_C5x9ERZG379ee_cw7JF7r45dJV2da4LKI2NNRUy9sGqah-0cOa_Bc6VSabeo33t46e_9DaMfJKU7ABLBpfZi8xyjKlATTBjt3gCWs6LYpvicFDaC2SqlEAh0fst1B0fuFvvxNwmNStQCKL_VuZ5juKj4WMyJ6SQF_m71Ckd4bnPVMjSAKsBqaUku6rb8c7-HjPz3nAxkut6Nk9Cz99XhAwIel-nBHS0CxuBxjGuOt3JAvot58rjA/https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-specification%2Fpull%2F633
 ). We have also developed an extension for the validator ( 
https://secure-web.cisco.com/1DgfuUr_8N83-nl-GVdF77jT1sDjVqo-4lsli0XrQ3TOkX5yBoCPoGPYIcPjA_Mnxq_RGrsSoqd_oscs1RZqwh1YuXHb37SJh2GSyfoppehVK2lmz2N5MdwZb-wXjGZoTccWH2Xn2uLEKpUKtzgynUSbIADxpulOf3HsDMOLzioqVA-uHeYbnEODVQyqxun6-m3c6RQM9PWFRTjB5y6mhnqc_rjKmVk8HCHEC3ZbBEyFNMdPK6Mhm5yezOhfhymmekFO0qYOpK1wqgvFedOi81g/https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-validator%2Fpull%2F1088
 ) and added PET examples into BIDS examples ( 
https://secure-web.cisco.com/1wcZumOdpBZTibGDOVnAaiUqg8mWF2RuYFeqp6qHGuwgbxUau4PqYYVaD-iLy8iEUT9Ow3hDrJ2uOJwYkjl1iIrKYdwILaW1qwdGo49Ib4fqHhgehv_a7NHZF_rnIrw8P-gJlhBj9OBSUL7fgedLPv-V4K20sjuEIZgtDFf7QA5ykX_6zWs5GoGK9JyiN14TCflmgIdhEyUVrh_Vzt1NAXF49o7DCJNI6CCjgFmc_LaPq98tmEBbPLq8xMY0f5t6_8hNtNAh6xVsLm5TZ_g/https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-examples%2Ftree%2Fbep009_pet
 ). The community review will close on Friday (Feb. 12) at 11:59pm PT (pacific 
time).



This BIDS extension seeks to establish how PET data and additional metadata are 
organized within the BIDS structure. This encompasses the recent guidelines for 
brain PET data in publications and in archives provided in the consensus paper 
(Knudsen et al. 2020, 
https://secure-web.cisco.com/1MIWMgeigCAuC-K3Vo4dwvsJCklRfo3-nj_Avatf4FkWMOawTcPrfz1RKd1svX27cs-AjgpYIDrT63jb2G-muHjpKjiTvRq9d8jWYqnymru7rWxU5AnEJzNmanBs13iOBNazfJMm7u0fn_KnB_piCvSUWv9DSw07hQ1VhtnH5lPDgItXKmYx0u8LSm-OdWkWVHpKlfVgfEY4E78qT2J21Y5k2IQIJavfMCucEhWg6ptZjsvh6WR1x-vABTj3nhSI7YMXArof-rba5j3Zuzlj6yQ/https%3A%2F%2Fjournals.sagepub.com%2Fdoi%2F10.1177%2F0271678X20905433
 ), including blood and metabolite data.



The final review entails a two week period for public commenting, with a 
possibility of extension for unresolved discussion. Once public comments are 
concluded, there will be a one week freeze, during which only critical issues 
will be considered. (Please see our release protocol for more details,  
https://secure-web.cisco.com/1YsYtZpSMYV6IeNX0JH4epLt99zW9k-K7bPF3XTD3j9llSkw4RQYmhVa8F6dBd-6zh3ZNcWn3d8DZtTXK8cvk_1BZXRDOZBLIh34dNQz20Se-0CgDMDLErCyKt4eoYvmZfexu7PPsD0qkWUE3LVvmzmmCE4o6hR1Y0rZDJHZhAC-dDNLFtPrCHCLfcUNuK3L4YUWDW_y0JExHZe4rD6c2zl7NJBBR9jLNlRF0uCLs7g8fQATsS5Xe9JkWDKODGuRIkqeiqzXH7YeG0yN-9g3nKQ/https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-specification%2Fblob%2Fmaster%2FRelease_Protocol.md
 )



We are looking forward to hearing from you,

Melanie Ganz (BEP 009 lead) and team
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Re: [Freesurfer] Error in longitudinal pipeline

2021-01-19 Thread vittal korann 
External Email - Use Caution

Hi Kersten,

I followed your mail and even also I got stuck at the contrast matrix i.e
CM:
I have given the code below which I used to execute the longitudinal
pipeline.

[aseg, asegrows,asegcols] =  fast_ldtable(['aseg.long.table']);
asegcols=cellstr(asegcols);
[Y,mri] = fs_read_Y('rh.thickness_sm10.mgh');
rhsphere =
fs_read_surf('/usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere');
rhcortex =
fs_read_label('/usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label');
Qdec = fReadQdec('long.qdec.table.dat');
Qdec = rmQdecCol(Qdec,1);
sID = Qdec(2:end,1);
Qdec = rmQdecCol(Qdec,1);
M = Qdec2num(Qdec);
[M,Y,ni] = sortData(M,1,Y,sID);
Y(:,all(Y==0))=[];
%lme_lowessPlot(M(:,1),Y(:,1)+Y(:,2),0.70,M(:,2));

X = [ones(length(M),1) M M(:,1).*M(:,2)];
[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,[],3);
%[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,[],5);
[lhRgs,lhRgMeans] = lme_mass_RgGrow(rhsphere,lhRe,lhTh0,[],2,95);
%[lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere,lhRe,lhTh0,[],2,95);

lhstats = lme_mass_fit_Rgw(X,[1 2],Y,ni,lhTh0,lhRgs,rhsphere);
lhTh0_1RF = lme_mass_fit_EMinit(X,[1],Y,ni,rhcortex,3);
lhstats_1RF = lme_mass_fit_Rgw(X,[1],Y,ni,lhTh0_1RF,lhRgs,rhsphere);
LR_pval = lme_mass_LR(lhstats,lhstats_1RF,1);
CM = [0 1 0 0 0 0 0];

F_lhstats = lme_mass_F(lhstats,CM);

My design matrix i.e X has 7 columns ['subjID(1)', 'time_years', 'Age',
'Years_of_education', 'Gender', 'ICV', 'time_yearsXAge' ]
So I kept the contrast vector as CM = [0 1 0 0 0 0 0] (if you remember my
mails, this study doesn't have a control group).
Matlab threw an error for this design and the same is highlighted below:


>
>
> *F_lhstats = lme_mass_F(lhstats,CM);Error using lme_mass_F (line 44)The
> number of elements (contrasts) in CM must be equal to the number of
> locations (length(stats))length(stats)= 149995 *


> *length(CM)= 7*


I know it may sound silly but I am really stuck at this point in time.
Would be glad if you could let me know where I am going off the path!

Thanks,
Vittal


On Fri, Dec 11, 2020 at 10:29 PM vittal korann 
wrote:

> Thanks, Kersten.
>
> I am sorry, I didn't see your response in the FS blog.
> I will go through it once and let you know!
>
> Once again thanks a lot for your kind mail!
>
> With regards
> Vittal
>
>
>
> On Thu, Dec 10, 2020 at 6:35 PM Diers, Kersten /DZNE <
> kersten.di...@dzne.de> wrote:
>
>> Hello Vittal,
>>
>> I am (again) attaching my response to your message. This response has
>> been on the freesurfer list since Nov 30, maybe you did not see it?
>>
>> Best, Kersten
>>
>> *From:* Diers, Kersten /DZNE
>> *Sent:* Monday, November 30, 2020 6:27 PM
>> *To:* Freesurfer support list
>> *Subject:* Re: Longitudinal pipeline
>>
>> Hello VIttal,
>>
>> thanks for the info about the design.
>>
>> You wrote before that the Matlab variable X (i.e., the design matrix) has
>> a dimension of 47x6. X is a translation of the study design into a
>> numerical matrix, which is part of the statistical model. In your case, I
>> assume that he first column is a vector of ones (i.e. the
>> intercept/constant of the statistical model), and that the other columns
>> reflect the numerical data in the table that you sent, in the same order.
>> Correct me if I am wrong.
>>
>> Now, the contrast "matrix“ specifies the questions that you want to ask
>> to the data, i.e. the effect of a certain variable (or sometimes
>> combinations of variables) onto the outcome variable Y. I put "matrix" in
>> quotes, because in many cases a simple vector is sufficient; contrasts need
>> not necessarily be specified as a matrix, and contrasts specified as a
>> matrix are typically more complex than those specified by a vector.
>>
>> In any case, the contrast vector/matrix needs to have as many
>> elements/columns as there are columns in X, because the elements/columns
>> oft the contrast vector/matrix will be matched with (and therefore need to
>> correspond to) the columns of X. I.e. the nth element/column in your
>> contrast vector/matrix refers to the nth predictor variable in the
>> statistical model, i.e. the nth column of X. There are 6 columns in X in
>> your case.
>>
>> The entries in the contrast vector/matrix represent weights that you
>> assign to each variable in order to test for its effect. One often (but not
>> always or necessarily) uses +1 to test for a positive relation of the
>> chosen variable on Y, -1 for a negative effect, and zero for not
>> considering a variable for a given contrast. Therefore, the simplest
>> contrast is a vector with a single non-zero entry, and this already allows
>> for the testing of effects. In other cases, contrasts can have more than
>> one non-zero entry, or can be formulated as a matrix, but we don’t need
>> this at the moment.
>>
>> The major issue with your design in its current form is that you will not
>> be able to distinguish effects of time from effects of treatment, due to
>> the absence of a control grou