[Freesurfer] Error: inputs cannot have multiple frames

[HYE JUNG YOUN]

External Email - Use Caution

Dear Freesurfer developers,

 

I realised some of my recon-alls been processed with the following error: 

ERROR: input(s) cannot have multiple frames!
/Users/mac_01/Desktop/1155_401/mri/orig/001.mgz has 2 frames

 

(I have attached the recon-all.log)

 

I checked the mri info and I think the problem is the dimensions which is
256 x 256 x 211 x 2. 

I'll attach the original commands I used with mri info in txt file in case
it would help you to see where I went wrong. 

 

If anyone has been through this problem or if you know what I can do to fix
this, please let me know. 

 

Best,

H 

 

Thu Mar  3 09:44:42 KST 2022
cd /Users/mac_01/Desktop/1155_401
setenv SUBJECTS_DIR /Users/mac_01/Desktop
/Applications/freesurfer/7.2.0/bin/recon-all -s 1155_401 -i 1155_401.nii -all 
-qcache

subjid 1155_401
setenv SUBJECTS_DIR /Users/mac_01/Desktop
FREESURFER_HOME /Applications/freesurfer/7.2.0
Actual FREESURFER_HOME /Applications/freesurfer/7.2.0
build-stamp.txt: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
Darwin mac-01.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:06:51 
PST 2021; root:xnu-7195.81.3~1/RELEASE_ARM64_T8101 arm64
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8176 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
descriptors  2560 
memorylocked unlimited
maxproc  2666 

PhysMem: 15G used (1437M wired), 93M unused.


program versions used
7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b)
7.2.0

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  
ProgramVersion: 7.2.0  TimeStamp: 2022/03/03-00:44:42-GMT  BuildTime: Jul 13 
2021 22:05:06  BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b  
User: root  Machine: mac-01.local  Platform: Darwin  PlatformVersion: 20.3.0  
CompilerName: Clang  CompilerVersion: 10.0.1
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 
7.2.0  TimeStamp: 2022/03/03-00:44:43-GMT  BuildTime: Jul 13 2021 22:05:06  
BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b  User: root  
Machine: mac-01.local  Platform: Darwin  PlatformVersion: 20.3.0  CompilerName: 
Clang  CompilerVersion: 10.0.1
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label 
-all-info  ProgramVersion: 7.2.0  TimeStamp: 2022/03/03-00:44:43-GMT  
BuildTime: Jul 13 2021 22:05:06  BuildStamp: 
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b  User: root  Machine: 
mac-01.local  Platform: Darwin  PlatformVersion: 20.3.0  CompilerName: Clang  
CompilerVersion: 10.0.1
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  
ProgramVersion: 7.2.0  TimeStamp: 2022/03/03-00:44:43-GMT  BuildTime: Jul 13 
2021 22:05:06  BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b  
User: root  Machine: mac-01.local  Platform: Darwin  PlatformVersion: 20.3.0  
CompilerName: Clang  CompilerVersion: 10.0.1
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  
ProgramVersion: 7.2.0  TimeStamp: 2022/03/03-00:44:43-GMT  BuildTime: Jul 13 
2021 22:05:06  BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b  
User: root  Machine: mac-01.local  Platform: Darwin  PlatformVersion: 20.3.0  
CompilerName: Clang  CompilerVersion: 10.0.1
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  
ProgramVersion: 7.2.0  TimeStamp: 2022/03/03-00:44:43-GMT  BuildTime: Jul 13 
2021 22:05:06  BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b  
User: root  Machine: mac-01.local  Platform: Darwin  PlatformVersion: 20.3.0  
CompilerName: Clang  CompilerVersion: 10.0.1
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  
ProgramVersion: 7.2.0  TimeStamp: 2022/03/03-00:44:44-GMT  BuildTime: Jul 13 
2021 22:05:06  BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b  
User: root  Machine: mac-01.local  Platform: Darwin  PlatformVersion: 20.3.0  
CompilerName: Clang  CompilerVersion: 10.0.1
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  
ProgramVersion: 7.2.0  TimeStamp: 2022/03/03-00:44:44-GMT  BuildTime: Jul 13 
2021 22:05:06  BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b  
User: root  Machine: mac-01.local  Platform: Darwin  PlatformVersion: 20.3.0  
CompilerName: Clang  CompilerVersion: 10.0.1
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  
ProgramVersion: 7.2.0  TimeStamp: 2022/03/03-00:44:44-GMT  BuildTime: Jul 13 
2021 22:05:06  BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b  
User: root  Machine: mac-01.local  Platform: Darwin  PlatformVersion: 20.3.0  
CompilerName: Clang  CompilerVersion: 10.0.1
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.2.0  
TimeStamp: 2022/03/03-00:44:44-GMT  BuildTime: Jul 13 2021 22:05:06  
BuildStamp: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b  User: root  
Machine: mac-01.local  

Re: [Freesurfer] GLM analysis - volume and surface area

[Laura Willers de Souza]

External Email - Use Caution

Sorry about that!
I'm resending with previous emails.

The first message below is the one you didn't know how to respond to because 
you didn't have the previous e-mails.

---

On 2/22/2022 9:15 AM, Laura Willers de Souza wrote:


Thanks so much for the explanation!



There is something different in the analysis of volume and surface area in 
relation to the analysis of cortical thickness? Like some more command, or some 
other detail that must be changed (besides, of course, the flag that specifies 
the measure to be analyzed) - I'm already using permutation in the correction 
of multiple comparisons.



--

On 2/21/2022 15:20 PM, Douglas N. Greve wrote:


Yes, it is. It is confusing when you talk about area and volume since these are 
not point measures like thickness (ie, what is the volume or area of a 
vertex?). The area of a vertex is computed as the mean of the adjacent 
triangles of the vertex. The volume is the mean of the neighboring truncated 
tetrahedra. When you run mris_preproc, it will apply a jacobian correction 
(like VBM). Otherwise, it operates the same as if you had a thickness value at 
the vertex, ie, same GLM, etc. Make sure to use permutation for correction of 
multiple comparisons.

-

On 2/21/2022 12:13 PM, Laura Willers de Souza wrote:

Hello FreeSurfer Developers,


I would like to know if it is correct to perform volume and surface area 
analysis using freesurfer's GLM!?
In several mailing list questions I have already seen instructions for 
performing these types of analysis. But I understand that freesurfer does 
vertex-wise analysis in the 2D surface space. So, it is not clear to me how it 
is possible to evaluate a 3D measurement, as volume, with a 2D method!?
I've also read that surface area analysis via vertex-wise analysis doesn't make 
much sense. The best would be to do ROI-based analysis. Can you explain that to 
me?

Thanks in advance!

Best,
Laura.
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[Freesurfer] FW: Neurotechnology Job Opportunity for the BRAIN Initiative

[Fischl, Bruce]

FYI

From: Talley, Edmund (NIH/NINDS) [E] 
Sent: Wednesday, March 2, 2022 1:08 PM
To: Talley, Edmund (NIH/NINDS) [E] 
Subject: Neurotechnology Job Opportunity for the BRAIN Initiative


External Email - Use Caution

I’m writing with information on a rare opening for a Neurotechnology Program 
Director to manage projects for the BRAIN Initiative.  This is a dream job for 
anyone who wants to shape the development of cutting edge methods to understand 
the brain.

The Brain Research through Advancing Innovative Neurotechnologies® Initiative 
(BRAIN Initiative), along with the NINDS Division of Neuroscience, is seeking 
exceptional candidates for the position of Neurotechnology Program Director 
(Health Scientist Administrator -13/14 or 15).

This is a unique opportunity to advance the Neurotechnology portfolio for the 
BRAIN Initiative, a historic multi-billion-dollar effort to transform 
neuroscience by developing the technologies of the future.  It offers 
collaborations with highly motivated, skilled, and scientifically curious 
colleagues from 10 NIH Institutes and Centers and from partner agencies such as 
NSF and DARPA.  It requires extensive engagement and outreach to the research 
community to assess trends, communicate priorities, and identify new 
opportunities.  Responsibilities include developing new programs, making 
funding recommendations, and direct managerial oversight of grants and research 
cooperative agreements.

The position will be responsible for overseeing a portfolio of grants and 
cooperative agreements to support these scientific areas: neural interface 
technologies that record, modulate, or stimulate neural activity; novel 
materials and neural interface devices; and biotechnologies applied to the 
nervous system (including development of hardware, software, and computational 
techniques). Candidates should possess a doctoral degree and post-doctoral 
training, with expertise in research towards understanding and applying neural 
engineering concepts and technologies. We encourage applications from 
candidates who enjoy working collaboratively and bring a diverse perspective to 
neural engineering research.

Job Post Link: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://www.ninds.nih.gov/About-NINDS/Jobs-At-NINDS/Health-Scientist-Administrator-neural-engineering

Please send a letter of interest and curriculum vitae to Dr. Ned Talley at 
edmund.tal...@nih.gov.



Edmund (Ned) Talley, Ph.D.
Program Director, National Inst. of Neurological Disorders and Stroke (NINDS)
6001 Executive Boulevard, Rockville MD 20852
Phone: 301-496-1917, Email: edmund.tal...@nih.gov

Alert: For BRAIN FOAs that require a Plan for Enhancing Diverse Perspectives 
(PEDP), applications without this new component will be withdrawn prior to 
review.  Evaluation of the PEDP will be made during peer review as part of the 
scorable criteria and will be used to inform funding decisions.  For more 
information:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://braininitiative.nih.gov/about/plan-enhancing-diverse-perspectives-pedp


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[Freesurfer] Question about editing topology errors

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

I have this issue occurring in several hemispheres (See images attached) where 
a “sulcus” is created because the pial crosses where it shouldn’t, and am 
wondering what the best way to edit this is. I don’t think it is a matter of 
adding WM control points as it is not the WM that needs to be corrected but 
rather the pial. My 2nd image shows how the sulci should look in the pial.

Should it be just a matter of removing voxels in the brainmask.mgz and doing

recon-all -autorecon-pial -subjid

I tried this for one subject and it was not happy. Is there a way to add 
control points for the pial?

Thank you!

Trisanna Sprung-Much, PhD
McGill University
Montreal Neurological Institute
--

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Re: [Freesurfer] Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames!

[Knut J Bjuland]

External Email - Use Caution

Hi

I found out that some had made duplicated copy of the same dicom serie and I 
sorted it out with dcm2niix.

Best Regards

Knut Jørgen

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

Sent: Friday, February 25, 2022 7:46 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Checking for (invalid) multi-frame inputs... ERROR: 
input(s) cannot have multiple frames!

I'm not sure what question you are asking

On 2/25/2022 1:17 PM, Knut J Bjuland wrote:

External Email - Use Caution

Dear Freesurfer experts,




I get this error when I am running FreeSurfer.






Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/home/knutjb/subjects/test/mri/orig/001.mgz has 4 frames
If this is a multi-frame MEMPRAGE image,
use mri_concat --rms to combine echo frames.




It has a t1_sag_mprage sequence, and it also give this waning

filesare not found to be different and cannot be sorted.




In addition, I get these errors when importing using recon-all -i file -all -s 
test




INFO: Found 770 files in //20210224_151919/5_t1_sag_mprage
INFO: Scanning for Series Number 5
Scanning Directory
INFO: found 768 files in series
INFO: loading series header info.




When I am running mri_concat --rms I am able to run recon-all -all.




Your sincerely,



Knut Jørgen Bjuland






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[Freesurfer] Permission denied error from -localGI

[Billah, Tashrif]

Hi all,

We are trying to run recon-all with -localGI but running into an unknown 
permission denied error:

$ recon-all -s sub-1001 -localGI

```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
 exit
=


< M A T L A B (R) >
Copyright 1984-2017 The MathWorks, Inc.
R2017a (9.2.0.556344) 64-bit (glnxa64)
March 27, 2017


>> reading filled volume...
/bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for reading
ERROR: loading 
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file 
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

```

Our MATLAB environment is properly setup and we regularly run other 
FreeSurfer-MATLAB commands. So I do not think that is causing the issue.

Best,
Tashrif
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[Freesurfer] mri_binarize error when using trac-all -prep

[Thorn, Kathryn]

External Email - Use Caution

Hello Freesurfer Experts,

I am currently attempting to process a single subject via Tracula v7.2. 
Previously, I used v6.0 to process this same dataset through all three steps of 
Tracula (prep, bedp, and path) with equivalent parameters with no errors.

First, I ran recon-all -all on this subject which finished without error. Then 
I ran segmentThalamicNuclei.sh per instructions on the first page of the 
Tracula user guide - also finished without error. Then I passed the outputs of 
these steps onto trac-all -prep.

tract-all -prep exits with errors after about a minute. The command is unable 
to find the file aparc+aseg+thalnuc.nii.gz. This traces back to an error with 
mri_binarize:

mri_binarize --i 
/Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz 
--o 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
ERROR: must specify minimum and/or maximum threshold or match values

aparc+aseg+thalnuc.nii.gz cannot be found because it is never created. However, 
all expected outputs previous to this file are created in the correct locations 
and trac-all -prep seems to be able to find all of the initial files I supply 
to it.

I've attached the full trac-all -prep output as well as the config file I used 
for full context.

Is there some threshold I need to specify in the config file? I looked at a 
complete example config file and I don't see any field related to this, but 
perhaps I'm missing something.

Or is this perhaps due to some error in my data? Any ideas?

Thank you!

Kayti Thorn
(she/her)
Database Specialist
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425

(base) user1s-iMac-Pro:Tracula_Test user1$ time trac-all -prep -c 
$base/tracula-outputs/${i}/${i}_config.txt

domainname: Command not found.
INFO: SUBJECTS_DIR is /Users/user1/Desktop/QA_Tracula/recon-all-outputs
INFO: Diffusion root is /Users/user1/Desktop/QA_Tracula/tracula-outputs
Actual FREESURFER_HOME /Applications/freesurfer/7.2.0
trac-preproc -c 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/scripts/dmrirc.local 
-log 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/scripts/trac-all.log 
-cmd 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/scripts/trac-all.cmd
#-
/Applications/freesurfer/7.2.0/bin/trac-preproc 
#-
#@# Image corrections Wed Mar  2 08:55:51 EST 2022
rm -f 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvals 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvecs
mri_convert --bvec-voxel 
/Users/user1/Desktop/QA_Tracula/raw-diffusion-data/QA_subj/dwi_preprocessed.nii 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz
mri_convert --bvec-voxel 
/Users/user1/Desktop/QA_Tracula/raw-diffusion-data/QA_subj/dwi_preprocessed.nii 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz 
reading from 
/Users/user1/Desktop/QA_Tracula/raw-diffusion-data/QA_subj/dwi_preprocessed.nii...
TR=8400.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.98918, -0.131599, -0.0648441)
j_ras = (0.120405, 0.980758, -0.153676)
k_ras = (0.08382, 0.144206, 0.985991)
writing to 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz...
rm -f 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvals.tmp
 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvecs.tmp
mv -f 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvecs.tmp
 /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvecs
mv -f 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvals.tmp
 /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvals
orientLAS 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.1.nii.gz
INFO: input image orientation is RAS
INFO: input image determinant is 15.625
mri_convert -oni 88 -onj 88 -onk 60 -oid -0.98918 0.131599 0.0648441 -ojd 
0.120405 0.980758 -0.153676 -okd 0.08382 0.144206 0.985991 -oc 6.55566 26.9913 
11.164 -rt nearest 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.1.nii.gz
mri_convert -oni 88 -onj 88 -onk 60 -oid -0.98918 0.131599 0.0648441 -ojd 
0.120405 0.980758 -0.153676 -okd 0.08382 0.144206 0.985991 -oc 6.55566 26.9913 
11.164 -rt nearest 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz 
/Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.1.nii.gz
 
normalizing out_i_direction: (-0.98918, 0.131599, 0.0648441) -> (-0.98918, 
0.131599, 

[Freesurfer] Linear mixed model for longitudinal data

[Julian Macoveanu]

External Email - Use Caution

Dear all,

This is my first attempt to analyze longitudinal structural data with
freesurfer, and I just do my best to follow the tutorial. I have some
things not clear, so any help would be appreciated.

We have a longitudinal study design with 2 groups, healthy and
patients who were scanned at baseline a second time following a
variable time interval (6 to 36 months). We want to investigate
whether the patient’s cortical thickness/volume progresses differently
compared to controls (group-by-time interaction effects). I chose to
analyze the data with LME due to variable follow-up time, having only
50% of the patients with a second scan, and also having family members
within and between groups.

Questions
1) To account for familial relationship, should I add a family ID as
covariate that stays in the design matrix X and count this covariate
as random effect when the model is fitted? Like this:
lhstats = lme_mass_fit_Rgw(X,[1 2 3],Y,ni,lhTh0,lhRgs,lhsphere);

Where the first 3 covariates in X are counted as random effects: 1 the
intercept, 2 follow-up time and 3 family ID.

The X would further include group, age, sex, TIV, and group*time, the
last one being the interaction term we want to assess using CM.C = [0
0 0 0 0 0 0 1].

Does the X and CM look good to address our research question?

2) It is unclear to me how to perform correction for multiple
comparisons and assess what is significant. I follow this procedure
after constructing X:

[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2 3],Y,ni,lhcortex,3);
[lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere,lhRe,lhTh0,lhcortex,2,95);
lhstats = lme_mass_fit_Rgw(X,[1 2 3],Y,ni,lhTh0,lhRgs,lhsphere);
F_lhstats = lme_mass_F(lhstats,CM);
dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0):

The dvtx is not empty but has 130 vertexes that survive. What I don’t
understand, when constructing the sig.mgh map it appears the dvtx is
not used:
fs_write_fstats(F_lhstats,mri,'sig.mgh','sig');
How can I be sure when I import sig.mgh in Freeview I only look at the
vertexes surviving multiple comparison?

3) Given a few clusters showing an interaction effect which are saved
as sig.mgh and overlaid on surface in freeview, how do I know
(visualize) what is going on in these clusters, like which of the
group means go up or down? (I use FS71 and tksurfer not working). Is
it here that printing out and plotting the betas (of the interaction
term) are useful for?

4) I have a hypothesis to find differences in prefrontal cortex, at
which step would I apply a PFC mask? I have constructed a PFC.label
file by adding corresponding label files.

Thank you,
Julian

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