[Freesurfer] Pass code to expand the archive of Free surfer 7.2.0

[krystaly]

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Dear Free Surfer expert,


Would you please send me the pass code for opening the archive of FS 7.2.0?


Thanks for your attention!


Yours sincerely,

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

[Douglas N. Greve]

Hi, sorry for the late response. No, there is nothing else you have to 
do. Using perm is a really good idea with volume and area, so glad to 
hear that is what you are doing.

best
doug


On 3/10/2022 8:21 AM, Laura Willers de Souza wrote:


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Of course!

To do GLM for volume and surface area analysis, is there any change in 
commands in relation tocortical thickness analysis? 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.


Many thanks!

--

On 3/09/2022 15:20 PM, Douglas N. Greve wrote:

Can you just ask the question again so I don't have to sort it out myself?


---

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 
sincethese are not point measures like thickness (ie, what is the 
volume orarea of a vertex?). The area of a vertex is computed as the 
mean of theadjacent triangles of the vertex. The volume is the mean of 
theneighboring truncated tetrahedra. When you run mris_preproc, it 
willapply a jacobian correction (like VBM). Otherwise, it operates the 
sameas if you had a thickness value at the vertex, ie, same GLM, etc. 
Makesure 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
surfacearea analysis using freesurfer's GLM!?

In several mailing list questions I have already seen instructions
forperforming these types of analysis. But I understand that
freesurferdoes vertex-wise analysis in the 2D surface space. So,
it is not clearto me how it is possible to evaluate a 3D
measurement, as volume, witha 2D method!?

I've also read that surface area analysis via vertex-wise
analysisdoesn't make much sense. The best would be to do ROI-based
analysis.Can you explain that to me?

Thanks in advance!

Att,

*Laura Willers de Souza *

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil

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Re: [Freesurfer] WM error near the right putamen

[Douglas N. Greve]

This is actually a bug in version 7.[012]. This area is probably not 
valid anyway. We'll have a fix in 7.3


On 3/21/2022 7:31 PM, Gabor Perlaki wrote:


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Dear all,

fswiki suggests that " There are regions where the surfaces are not 
intended to be accurate that you should be aware of: Areas around the 
hippocampus and amygdala. "


I also found inaccuracy of the WM surface near the putamen and 
accumbens regions. WM surface goes into the putamen (please see the 
attached picture). Do I need to fix this error or is it normal? Are 
the thickness of ctx-rh-medialorbitofrontal and the volume of right 
putamen valid in this case?

Thank you in advance,
Gabor


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Re: [Freesurfer] lh.pial and rh.pial is 0Kb, I cannot open them by using freesurfer

[Douglas N. Greve]

On 3/24/2022 4:49 PM, Muhammed Görünen wrote:


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Hi,

I run recon-all process for a subject's T1 data. At the end, the pial 
files are 0Kb and I cannot open them from python.
Did it end with an error? Did you run out of space? What version of FS? 
Can you send the recon-all.log file?
What would be the problem here? Also, is there any difference between 
pial file and pial.T1 file? I will be happy if you can answer.

The ?h.pial should be a symbolic link to ?h.pial.T1


Best,
--Muhammed

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Re: [Freesurfer] [External] Re: [External] Re: classes for GLM analysis

[Douglas N. Greve]

it does not suprise me that 2014 is not working as that is pretty old. 
I've been using 2018 and that seems to work.


On 3/24/2022 9:31 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


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It is seemingly working in matlab R2021b rather than matlab R2014a. 
Can you confirm this? Otherwise that should be noted in the wiki


Get Outlook for iOS 



*From:* Zeng,Victor (BIDMC - Keshavan - Psychiatry) 


*Sent:* Wednesday, March 16, 2022 5:52:54 PM
*To:* Freesurfer support list 
*Subject:* Re: [External] Re: [Freesurfer] [External] Re: classes for 
GLM analysis
Sorry for the different approach - but I just propensity matched 
people for now so I don't have to deal with so many confounding 
variables. Now I am trying to do multiple correction, with 
mriglmfit-sim not working because of high FWHM (you can ignore my 
other email about that...). So therefore, I am trying palm, and come 
up with this error:


Running PALM alpha119 using MATLAB 8.3.0.532 (R2014a) with the 
following options:
-i 
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisMGH/Replication/rh.pial_lgi.NCBT1_.10.mgh
-m 
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisGLM/Replication/rh.pial_lgi.NCBT1_.10.glmdir/mask.mgh

-d design.mat
-t design.con
-logp
-n 1000
-C 1.958920
-o fsp
-twotail
-s 
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white 
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white.avg.area.mgh

Found FSL in /usr/share/fsl/5.0
Found FreeSurfer in /usr/local/freesurfer/dev7
Found SPM in /home/gamma/spm8
Loading surface 1/1: 
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white
Reading input 1/1: 
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisMGH/Replication/rh.pial_lgi.NCBT1_.10.mgh

Reading design matrix and contrasts.
Elapsed time parsing inputs: ~ 7.22525 seconds.
Number of possible permutations is 9.7768e+204.
Generating 1000 shufflings (permutations only).
Building null distribution.
0.1% [Design 1/1, Contrast 1/1, Shuffling 1/1000, Modality 1/1]
/bin/sh: line 1: 14553 Illegal instruction     matlab -display iconic 
< run_palm.m

error: cannot find expected palm output "fsp_clustere_tstat_fwep.mgz"


This is with Freesurfer dev 20211206. Thanks and sorry for so many 
questions lately

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

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


*Sent:* Wednesday, March 16, 2022 6:09 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* [External] Re: [Freesurfer] [External] Re: classes for GLM 
analysis

Can't tell without the fsgd file

On 3/7/2022 8:30 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


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Just to double check the numbers - I seem to have been getting into 
an error in how many columns in the FSGD it is expecting.


I have 9 different sites, 4 different patient groups, and M/F -> 72 
classes.
I also am covarying for four different factors, so the contrast 
matrix I am making is 72*(4+1) long. Since I want to regress out the 
four factors completely, only the first 72 numbers in 360 contrast 
matters. My FSGD file has 4 columns e.g like


Input GP0001 NCBostonM 60 12000 -0.01 -0.02

It says ERROR: gdfReadV1: Input line 1, subjid = GP0001
Found 4 variables, expected. 10

Where is this 10 coming from?


Get Outlook for iOS 



*From:* Zeng,Victor (BIDMC - Keshavan - Psychiatry) 
 

Re: [Freesurfer] Question about calculation of pial area in DKatlas

[Douglas N. Greve]

On 3/24/2022 2:53 AM, Dongyue Zhou wrote:


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Dear FreeSurfer experts:
 I want to calculate mean pial surface area in DKatlas in individual 
space.And I know the function read_annotation.m in $FREESURFER_HOME/matlab for 
loading this atlas.
And if I can load sub/surf/?h.area.pial as the area in each vertice and 
calculate mean pial area by dividing sum PSA of all vertices in one ROI by the 
number of vertices in this ROI?

That should work

But why my result is not the same as result in sub/stats/?h.aparc.stats ?  Does 
the column named surface area represent mean PSA in each ROI?
The value in aparc.stats is the total, not the mean. I'm not sure why 
you would want the mean.




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Re: [Freesurfer] mri_vol2vol anatomical to functional

[Douglas N. Greve]

I'm not sure I understand what you are saying or what the problem is. 
Can you provide the actual command line you are using, all the terminal 
output, and a picture that shows what the problem is?

On 3/23/2022 2:46 PM, Manenti, Giorgio wrote:
>  External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I am getting problems to transform my xh.ribbon.mgh from anatomical 
> 256x256x256 to functional 104x104x69 space.
>
> When converting the ribbon via “ mri_vol2vol —reg REGfile —mov INPUT —targ 
> funcTEMPLATE —o OUTPUT “ and checking via freeview, i am getting the right 
> functional space dimensions but the INPUT and OUTPUT .mgz are never 
> overlapping. Why am i getting this misplacement ? Is this problem due to the 
> register file i provide or maybe it is just a visualisation error (perhaps 
> freeview is not the best way to check the conversion).
>
> I tried to change REGfile by providing the 1) init.register.dof6.dat and 2) 
> register.dof6.lta (changing “—reg with —lta”). I am getting an almost perfect 
> merge when using the .lta file but still the two volumes are misaligned.
> I tried mri_label2vol as well, but as expected i got worse results.
>
> To provide a minimum more detail, after recon-all i process the anatomy with 
> the longitudinal recon. At that point i use the longitudinal anatomy to 
> register the functional data, which i process by 1) mk-template 2) topup & 
> applytopup.
>
> Many thanks in advance
> Warm regards
>
> Giorgio
>
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Re: [Freesurfer] mri_segment_hypothalamic_subunits error: Illegal instruction 4

[Douglas N. Greve]

You're command line is incomplete (it needs more than just --s). Run it 
with --help and/or visit the wiki page


On 3/23/2022 2:40 PM, Alice Tao wrote:


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Thank you so much for the response! Unfortunately, that is the full 
command line and output:


$ mri_segment_hypothalamic_subunits --s
Illegal instruction: 4

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias 
Gonzalez, Juan E. 

*Sent:* Wednesday, March 23, 2022 10:51 AM
*To:* Freesurfer support list 
*Subject:* [EXTERNAL] Re: [Freesurfer] 
mri_segment_hypothalamic_subunits error: Illegal instruction 4

Dear Alice,

Can you please send us your full command line and output?

Cheers,

/E


Juan Eugenio Iglesias
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* http://www.jeiglesias.com 
 




On Mar 23, 2022, at 10:41, Alice Tao  wrote:

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Hello FreeSurfer Developers,

I'm attempting to use the mri_segment_hypothalamic_subunits tool on 
subjects that have been analyzed with recon-all as described on the 
wiki page (*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits 
), 
but I received the following error when I run the 
mri_segment_hypothalamic_subunits command 
(mri_segment_hypothalamic_subunits--s):


  Illegal instruction: 4

Does anyone have any suggestions on how to trouble-shoot this 
problem? recon-all does not seem to have any issues.


1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
2) Platform: macOS Monterey, version 12.2.1

Thank you!
Alice
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Re: [Freesurfer] repeated measures ANOVA 2x2 covariate

[Douglas N. Greve]

Probably the easiest thing to do since you have only two time points is 
to compute the difference between the two, then just do a simple group 
analysis where you include the covariates that you want.


On 3/23/2022 10:00 AM, Agurne Sampedro Calvete wrote:


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Dear FreeSurfer experts,

I am doing a repeated measures ANOVA 2x2 (2 groups and 2 time points) 
and I would like to include in the analysis a covariate that is 
constant over the 2 times (e.g., baseline medication).

I would like to see a "group x time x covariate" interaction.

What should the design look like? I know that without covariate the 
design is as follows:


GroupDescriptorFile 1

Class Subject1

Class Subject2

Variables    Tp1vsTp2.Group1   Tp1vsTp2.Grroup2

Input   Subject1_time1  Subject1 1 0

Input   Subject1_time2  Subject1 -1    0

Input   Subject2_time1  Subject2 0 1

Input   Subject2_time2  Subject02  0 -1

Design matrix:

1 0 1 0

1 0 -1 0

0 1 0 1

0 1 0 -1


Contrasts (.mtx files):
Tp1vsTp2.Group1        0 0 1 0
Tp1vsTp2.Group2        0 0 0 -1
Interaction (timexgroup) 0 0 1 -1


However, I do not know how I could include the interaction with that 
covariate.


Thank you very much in advance.

Kind regards,

Agurne



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Re: [Freesurfer] qdec analysis error

[Douglas N. Greve]

Sorry, we are not supporting qdec anymore. You will need to use the 
command-line stream


On 3/23/2022 8:02 AM, David wrote:


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Hello FreeSurfer Developers,

I have a problem. Can you help me

freesurfer version : 6.0.0

Load qdec when I run qdec.table.dat, the data is loaded correctly, but 
when I design, I choose discrete and continuous factors for analysis

The error log is as follows
：

Input table: /media/root/Backup_Plus2/new/RECON/qdec/qdec5.table.dat
Subj#, SubjID, Data...
    1 bd1 d Male 15.00 8.00
    2 bd2 d Female 19.00 13.00
    3 bd3 d Male 25.00 9.00
    4 bd4 d Male 17.00 12.00
    5 bd5 d Male 16.00 10.00
    6 bd6 m Female 22.00 12.00
    7 bd7 d Male 17.00 11.00
    8 bd8 d Female 19.00 13.00
    9 bd9 m Female 26.00 7.00
   10 bd10 m Male 53.00 15.00
   11 bd11 m Female 56.00 4.00
   12 bd12 d Female 21.00 14.00
   13 bd13 m Female 19.00 12.00
   14 bd14 m Female 32.00 15.00
   15 bd15 d Male 21.00 9.00
   16 bd16 d Male 16.00 10.00
   17 bd17 d Male 15.00 11.00
   18 bd18 d Female 32.00 10.00
   19 bd19 d Female 20.00 15.00
   20 bd20 d Female 17.00 11.00
   21 bd22 m Male 22.00 11.00
   22 bd23 m Female 28.00 6.00
   23 bd24 d Male 26.00 11.00
   24 bd25 m Female 24.00 9.00
   25 bd26 m Female 30.00 6.00
   26 bd27 m Female 20.00 12.00
   27 bd28 d Female 28.00 16.00
   28 bd29 m Female 18.00 12.00
   29 bd30 d Male 21.00 15.00
   30 bd31 d Female 30.00 16.00
   31 bd32 d Male 18.00 11.00
   32 bd33 d Female 16.00 10.00
   33 bd34 d Male 21.00 11.00
   34 bd35 d Female 15.00 10.00
   35 bd36 d Female 16.00 10.00
   36 bd37 d Male 19.00 14.00
   37 bd39 d Male 16.00 10.00
   38 bd40 m Female 20.00 14.00
   39 bd41 m Female 21.00 15.00
   40 bd42 d Male 23.00 9.00
   41 bd43 m Male 27.00 9.00
   42 bd44 d Female 15.00 8.00
   43 bd45 m Male 19.00 9.00
   44 bd46 d Female 16.00 11.00
   45 bd47 m Female 23.00 15.00
   46 bd48 m Male 18.00 13.00
   47 bd49 d Female 22.00 15.00
   48 bd50 d Female 17.00 11.00
   49 bd51 d Male 17.00 10.00
   50 bd52 d Male 27.00 15.00
   51 bd53 m Male 16.00 9.00
   52 bd54 d Male 18.00 12.00
   53 bd55 d Female 18.00 11.00
   54 bd56 m Female 16.00 10.00
   55 bd57 d Male 16.00 9.00
   56 bd58 m Male 22.00 9.00
   57 bd59 m Male 16.00 8.00
   58 bd60 d Male 16.00 9.00
   59 bd61 m Female 18.00 10.00
   60 bd62 d Female 15.00 9.00
   61 hc1 h Male 52.00 7.00
   62 hc2 h Female 24.00 10.00
   63 hc3 h Male 45.00 7.00
   64 hc4 h Female 18.00 13.00
   65 hc5 h Female 19.00 10.00
   66 hc6 h Female 17.00 12.00
   67 hc7 h Female 19.00 7.00
   68 hc8 h Male 48.00 5.00
   69 hc9 h Female 53.00 6.00
   70 hc10 h Female 52.00 15.00
   71 hc11 h Female 19.00 12.00
   72 hc12 h Female 18.00 12.00
   73 hc13 h Female 20.00 12.00
   74 hc14 h Female 18.00 12.00
   75 hc15 h Female 19.00 13.00
   76 hc16 h Female 18.00 11.00
   77 hc17 h Female 19.00 12.00
   78 hc18 h Female 19.00 12.00
   79 hc19 h Female 19.00 12.00
   80 hc20 h Female 19.00 12.00
   81 hc21 h Female 18.00 12.00
   82 hc22 h Female 18.00 12.00
   83 hc23 h Female 18.00 11.00
   84 hc24 h Female 18.00 12.00
   85 hc25 h Female 18.00 12.00
   86 hc26 h Female 18.00 11.00
   87 hc27 h Female 18.00 12.00
   88 hc28 h Female 18.00 12.00
   89 hc29 h Female 18.00 11.00
   90 hc30 h Male 20.00 12.00
   91 hc31 h Female 29.00 17.00
   92 hc32 h Female 16.00 10.00
   93 hc33 h Female 17.00 10.00
   94 hc34 h Female 26.00 14.00
   95 hc35 h Female 24.00 17.00
   96 hc36 h Female 22.00 17.00
   97 hc37 h Male 25.00 17.00
   98 hc38 h Male 24.00 17.00
   99 hc39 h Male 25.00 17.00
1  groups  discrete 3
    1  d
    2  m
    3  h
2  gender  discrete 2
    1  Male
    2  Female
3  age  continuous 0
4  edu  continuous 0
    Continuous Factors: Mean: StdDev:
    --- - ---
    age    22.293 9.015
    edu    11.374 2.827

Number of subjects:   99
Number of factors:    4 (2 discrete, 2 continuous)
Number of classes:    6
Number of regressors: 18

Data table loading completed successfully.
SUBJECTS_DIR 

Re: [Freesurfer] Negative eTIV

[Douglas N. Greve]

Check the talairach registration (talairch.xfm). It must be badly messed up

On 3/23/2022 4:47 AM, lqcheng2017 wrote:


External Email - Use Caution

Dear experts,

I extracted the eTIV using the mri_segstats, but it showed negative 
value. How could I solve this problem?


Thank you very much.


cmdline mri_segstats --subject Gelb --etiv-only
UseRobust  0
atlas_icv (eTIV) = -2105 mm^3    (det: -925.465454 )


Best,
Luqi


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Re: [Freesurfer] Freesurfer mri_convert

[Douglas N. Greve]

please send the command line, log file, version of FS, etc

On 3/22/2022 11:59 AM, Zoe O'Brien-Moran wrote:


External Email - Use Caution

Dear FS Experts

I am having continued issues with the mri_normalize function on MPRAGE 
data


I get an error message:
3d normalization pass 1 of 2
error: No such file or directory
error: MRInormFindControlPoints: could not find enough control points
error: No such file or directory
error: MRInormFindControlPoints failed

Can you advise on any reason this may be happening?

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Re: [Freesurfer] Tkregister2 not opening GUI

[Douglas N. Greve]

Does /Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/surf/lh.white 
exist and do you have permission to read it? If yes to both, then try 
running it with --debug as the first option, then send all the terminal 
output



On 3/21/2022 5:02 PM, Isabelle Deschamps wrote:


External Email - Use Caution

I did try tkregisterfv, but I get the following error:

cannot find 
/Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/surf/lh.white


[MacBook-Pro-4:~] Isa% tkregisterfv --fstal --s S0010_FS

According to the tutorial, if I leave the –surfs out, the command 
should work but it does not.


I also tried running it with the –surf I get the same error.

I have only ran the following commands so far:

foreach i ("S0010" "S0028" "S0039" "S0057" "S0074" "S0081" "S0096" 
"S0120" "S0131" "S0139" "S0146" "S0152" "S0163" "S0168" "S0171" 
"S0179" "S0205" "S0250" "S0262" "S0263" "S0272" "S0299" "S0300" 
"S0313" "S0328" "S0363" "S0372" "S0375" "S0378" "S0391" "S0409" 
"S0418" "S0419" "S0432" "S0442" "S0448" "S0451" "S0471" "S0481" 
"S0493" "S0504" "S0509" "S0524" "S0525" "S0528" "S0537" "S0544" 
"S0557" "S0589" "S0601" "S0650" "S0669" "S0676" "S0682" "S0715" 
"S0727" "S0738" "S0741" "S0747" "S0762" "S0768" "S0770" "S0800" 
"S0809" "S0837" "S0839" "S0861" "S0888" "S0896" "S0933" "S0949" 
"S0955" "S0982" "S0988" "S1031" "S1058" "S1082" "S1088" "S1091" 
"S1128" "S1133")


recon-all -i /Volumes/CopyPaste/fMRI/fMRI/Freesurfer/"$i".anat.nii.gz 
-subjid "$i"_FS


end

I wanted to verify the registration at this point, but I can.

Thank you for your help,

isabelle

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


*Date: *Thursday, March 17, 2022 at 22:51
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] Tkregister2 not opening GUI

*CAUTION:* This email originated from outside of Georgian College. Do 
not click links or open attachments unless you recognize the sender 
and know the content is safe.


Can you try tkregisterfv ? The old tk tools are not supported any 
more. tkregisterfv uses freeview


On 3/17/2022 6:03 AM, Nathan Kindred (PGR) wrote:

*External Email - Use Caution *

Hi Isabelle,

It’s been a couple of years since I ran FreeSurfer on a Mac, but I
also have had this issue before and it was due to the macOS. I
don’t know if anything has changed recently but if not then the
only solution would be to try to install an older macOS that will
support 32bit apps.

Best,

Nathan

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

 on behalf of
Isabelle Deschamps 

*Date: *Wednesday, 16 March 2022 at 19:20
*To: *freesurfer@nmr.mgh.harvard.edu


*Subject: *[Freesurfer] FW: Tkregister2 not opening GUI

⚠ External sender. Take care when opening links or attachments. Do
not provide your login details.

*External Email - Use Caution *

Good afternoon,

I am following up on my question regarding the GUI for TKregister2
and TKregister2_Cmld not opening.

Is there another way to open the GUI?

Thank you kindly for your help,

isabelle

*From: *Isabelle Deschamps 

*Date: *Thursday, March 10, 2022 at 14:52
*To: *freesurfer@nmr.mgh.harvard.edu


*Subject: *Tkregister2 not opening GUI

Good afternoon,

I am trying to verify the registration and for some reason the GUI
is not opening.

I am using a Macbook Pro running macOS Montery with a 2.4 Gz
Quad-Core Intel Core i5

I have Freesurfer version: maOS-7.2.0

I do not get an error when I run TKregister2 or TKregister_cmld

This is the output that I get without the GUI opening

No target volume specified, assuming FreeSurfer orig volume.

targetvolume orig

movable volume (null)

reg file(null)

LoadVol0

ZeroCRAS1

7.2.0

Diagnostic Level -1

% % % % % % % % avi2talxfm

talairach.xfm -

1.008570.02020-0.00990-0.12365;

-0.017891.032510.24795-28.10577;

0.02556-0.306601.209133.54973;< /span>

0.00.00.01.0;

INFO: loading target
/Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/mri/orig.mgz

Zeroing CRAS of target

new xfm -

1.008570.02020-0.009901.93629;< /span>

-0.017891.032510.24795-11.46406;

0.02556-0.306601.20913-50.28331;

0.00.00.01.0;

-

Ttarg: 

-1.00.00.0128.0;

-0.00.01.0-128.0;

0.0-1.00.0128.0;

0.00.00.01.0;

INFO: loading movable
/Applications/freesurfer/7.2.0/average/mni305.cor.mgz

Tmov: 

Re: [Freesurfer] Permission denied error from -localGI

[Douglas N. Greve]

What version of FS are you running?

On 3/20/2022 8:47 PM, Billah, Tashrif wrote:
It does not exist and cannot be created in a shared cluster. Is there 
a way to define a different folder for 
/scratch/tp24093955057547375.load_mgh.m.mgh?


===
Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

Do you have permission to /scratch? Does it exist?

===
Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

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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Re: [Freesurfer] vertexwise correlation between the two maps and atlases in volume (MNI) to surface

[Douglas N. Greve]

On 3/17/2022 4:41 PM, std...@virgilio.it wrote:


External Email - Use Caution

Hi list,

a) I have two maps, one's of rs-fMRI functional connectivity (by 
FS-FAST) and one's of receptor density (from a PET-Atlas). Both the 
maps are in surface space. How can I measure the vertexwise 
correlation between the two maps?


You can use the per-vertex option (--pvr) in mri_glmfit. Search through 
the mail archives to find how to use it



b) How can I move some atlases in volume (MNI) to surface?
I have tried to use:

mri_vol2surf --src ATLAS_vol.nii --regheader fsaverage --projfrac 0.5 
--hemi lh --out ATLAS_surface.nii


but the results are inconsistent.

Probably easiest to just run recon-all on the MNI152 volume, then map it 
to that output



Thanks


Stefano


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Re: [Freesurfer] Turning Significant Cluster (sig.cluster.summary or sig.mgh) into binary .nii ROI

[Douglas N. Greve]

Are you trying to create a volume-based binary mask or a surface-based 
mask? From the commands below, it looks like surface (but why would you 
need it to be in nii?). In the surface case, you can just

mri_binarize --i ocn.mgh --match clusterno --o clusterno.mask.nii
where "ocn" is the ocn file created by mri_glmfit-sim and clusterno is 
the number of the cluster



On 3/16/2022 3:00 PM, Emily Popa wrote:


External Email - Use Caution

Hello, I am just following up on my previous question. To put it more 
shortly (I apologize for making the question so long before), I am 
just searching for a way to convert a significant cluster from a group 
analysis into a binary .nii mask so I can use the mask (after some 
registration steps) to perform ASL analysis in that specific ROI for 
the same subjects (in FSL).


Best,

Emily S. Popa, M.S.

Staff Research Associate II, Neuroimaging

Pacific Brain Health Center | Pacific Neuroscience Institute 
Foundation | Providence Saint John’s Health Center


1301 20^th  St. #250 Santa Monica, CA. 90404

(408) 750-7971 (M)

cid3519*image001.jpg@01D7EC78.96AA1AC0 
cid3519*image002.jpg@01D7EC78.96AA1AC0 
cid3519*image003.jpg@01D7EC78.96AA1AC0 
cid3519*image004.jpg@01D7EC78.96AA1AC0 
cid3519*image005.jpg@01D7EC78.96AA1AC0 



*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Emily Popa 


*Date: *Thursday, March 10, 2022 at 2:31 PM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *[Freesurfer] Turning Significant Cluster 
(sig.cluster.summary or sig.mgh) into binary .nii ROI


*External Email - Use Caution *

Hello,

I have been struggling to figure out a way to get the significant 
results of a freesurfer group analysis (just one significant cluster) 
from either the sig.cluster.summary or sig.mgh file into a binarized 
ROI in .nii format. I used mri_glmfit to perform the cortical 
thickness analysis on sMRI data and found the significant cluster only 
in the left hemisphere. I tried to follow some instructions I found on 
the FreeSurfer site, however, at the first step/line below 
(mri_volsynth) the –delta-crsf input was referred to on the site as 
the vertex number, but on the –help documentation, it was specified 
that this input should be: col row slice frame : 0-based. Looking at 
the cluster summary file, for the significant cluster there is a 
maximum vertex, but I am not sure if this is the vertex number I 
should be using.


mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness 
--pdf delta --delta-crsf 5 9 5 1 --o delta.sm00.mgh


mris_fwhm --smooth-only --subject fsaverage --hemi lh --i 
delta.sm00.mgh --niters 10 --o delta.sm10.mgh


mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh

When trying the first line above for mri_volsynth, I get this error: 
Segmentation fault: 11 (so I think my input