Re: [Freesurfer] Hippocampus subfield LUT

[Douglas N. Greve]

Look in $FREESURFER/FreeSurferLUT.txt
This has those indices (and a lot more). If you want just the hippo SF 
indices, you can run something like

mri_segstats --seg hipposf.mgz --ctab-default --sum sum.dat
The indices will be in sum.dat

On 5/14/2024 11:04 AM, karl landheer wrote:


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Hello, I am looking for the LUT which converts the indices in images 
like lh.hippoAmygLabels-T.v22.mgz to region name. Is this available 
anywhere? I can’t find it


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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

[Douglas N. Greve]

The first one will test for a difference between group offset/intercept 
accounting for age, gender, episodes, and residuals. By setting a 
regressor contrast element to 0, one accounts for that variable because 
the variable appears in the model that is fit to the data (and so its 
effects already removed from other variables). One more thing: I would 
recommend incorporating gender in the class structure not as a 
continuous variable. So you would have 4 classes: PatentientsMale, 
PatientsFemale, HCMale, HCFemale then use contrast [0.5 0.5 -0.5 -0.5 0 
0 0 0 0 ...]


On 5/9/2024 3:26 PM, Liliana Wu wrote:


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Hello!

I am having trouble with creating my contrast files. I did go over 
FsfdExamples (*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples 
). 
However, I am unsure how should I create my contrast files if I want 
do a 2 group comparison while controlling 4 covariates:


Class:

Patients, healthy control

variables are:

Age,gender,episodes,residuals,

Here is how I set up my contrast files:

1 -1 0 0 0 0 0 0 0 0  - Contrast1 (measure group differences)

1 -1 0.125 0.125 0.125 0.125 0.125 0.125 0.125 0.125 – Contrast 2 
(measure group differences while accounting for covariates)


For some reason I think I am setting up those contrast files wrong… 
Any help is appreciated.


Best,

Liliana


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Re: [Freesurfer] surface and cortical thickness normalization

[Douglas N. Greve]

The reason I suggested scaling by eTIV is an analogy with a box of 
paper. The surface area of the paper in the box scales linearly with the 
volume in the box (twice the volume, twice the paper, twice the area). I 
vaguely remember doing a test of this, but, if I did, it has been a 
while. probably using eTIV^(2/3) works well too. I don't think it is so 
important that it be unitless (though maybe it is easier at review time).


On 5/3/2024 10:56 AM, Fischl, Bruce R.,PHD wrote:


Hi Yunus

I think typically you would normalize by eTIV^(2/3), which would 
result in a dimensionless scaling


Cheers

Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *yunus soleymani

*Sent:* Friday, May 3, 2024 3:31 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] surface and cortical thickness normalization

*External Email - Use Caution *

Hello,

I hope you are doing well. Yesterday, I had some questions regarding 
normalization in Freesurfer. Thanks to Dr. Douglas N. Greve, I 
received answers for all of them. However, I still have one more 
question.


When I normalize brain surfaces to eTIV, they appear to be in two 
different units (mm2 and mm3). Will this be a problem? Additionally, I 
would like to know your thoughts on normalizing cortical thicknesses. 
Do you think they should be normalized to eTIV, or would it be better 
to normalize them to the mean cortical thickness of each subject?


I would greatly appreciate your response.

Thank you,
Yunus


*Yunus Soleymani*
**
*Ph.D. Candidate of Neuroimaging *
*/Tehran University of Medical Sciences/*
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Re: [Freesurfer] Difference between 2 ways to set up fsgd file and contrasts

[Douglas N. Greve]

They are not identical, for  sure. In general, I discourage people from 
modeling categorical variables (eg, Group1/2 below) as continuous 
variables because you make assumptions that might not be reasonable (eg, 
females will have twice the thickness as males). I would use the first 
method.


On 5/2/2024 8:20 PM, Lydia Chung wrote:


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Hi FS support team,

I am going to be using mri_glmfit to test 1) main effects (which 
regions show differences in cortical thickness between group 1 and 
group 2) and 2) interaction effects (does the relationship between IV 
and DV depend on moderator). Depending on the model, the IV is 
sometimes a binary categorical variable and sometimes a continuous 
variable. The moderator is always continuous. So, interaction effects 
are either continuous x continuous OR categorical x continuous.


One thing I'm trying to understand is whether the two examples below 
are basically two different approaches that answer the SAME question: 
Do people in Group 1 differ from Group 2 on cortical thickness? 
Version 1 is the one provided by FS and Version 2 is an analog of 
another setup I have been provided by colleagues. Are these models 
answering the same or different questions? The freesurfer link below 
also shows an example of how to do an interaction (Group x Age) using 
Version 1 setup; for Version 2 setup of an interaction, I know I would 
multiply the IV and Moderator before this step so that I would have an 
additional "interaction variable" column to add as one of the 
'Variables' listed in the fsgd code.  So, I'm also curious if the two 
different methods of testing an interaction (in addition to the first 
question about the main effect) will get you the identical answer OR 
if there is something conceptually different? Do the nuances of this 
setup have to do with the difference between using DODS or DOSS?


_
_
_Main effect of Group on cortical thickness Version 1 (copied from FS 
example. link here 
)_

GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
Variables Age Weight
Input subject1 Group1 30 100
Input subject2 Group2 40 120

Contrasts: 1 -1 0 0 0 0 (to test main effect of group; this feels like 
an anova approach?)


_Main effect of Group on cortical thickness Version 2_
GroupDescriptorFile 1
Title OSGM
Class Subjects
Variables Group Age Weight
Input subject1 Subjects 0.5 30 100
Input subject2 Subjects -.5 40 120

contrasts: 0 1 0 0 (to test main effect of group; this feels like a 
linear regression approach?)


Thank you in advance for your help!

Lydia
--


Lydia Wu-Chung, M.A.
Doctoral candidate
BMED Lab
Department of Psychological Sciences
Rice University
6500 Main St - MS201
Houston, TX 77030
Lab Phone: 713-348-8126
Email: lydia...@rice.edu 

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Re: [Freesurfer] outcome directions of longitudinal two stage model

[Douglas N. Greve]

not sure what you mean and/or referring to. can  you elaborate?

On 5/7/2024 4:03 PM, L wrote:


External Email - Use Caution


Dear exports,

I am wondering whether the outcomes of the longitudinal two stage 
model is tp1 - tp2 or tp2 - tp1.


Thank you,

Lihong Wang

--
- Lihong


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Re: [Freesurfer] recon-all process still not finishing properly

[Douglas N. Greve]

It should just run the fill step. However, I've been slowly 
reprogramming recon-all to just see what needs to be run and rerun it, 
so you might get more than just the fill.


On 5/3/2024 4:38 PM, Dong, Yilei wrote:


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Hi Freesurfer Developers,

Just to reply to this thread again, if I want to see if recon-all will 
just run the -fill step, do I submit it on the files that have already 
been run? In addition, does this error count as Freesurfer running out 
of RAM or it's more of a cluster issue I have to talk with the staff 
that manage it?


Sincerely,
Yilei

*From:* Dong, Yilei 
*Sent:* Tuesday, April 23, 2024 3:34 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] recon-all process still not finishing 
properly

Hi Freesurfer support,

I have several questions regarding recon-all -fill and -debug.

If we run recon-all -fill, what is the command set-up for that? From 
the ReconAllDevTable here, *MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable 
<https://secure-web.cisco.com/1lmfyKn6Pvakq-RQxgJbE5k4RDGG6d0Vpvb5lGcjzph3h7UE3rIOK94h4_vGK8oa4q_FYtrbTmYfXg9SF-sFCkj4DY_oUkqnlqG_VRr6zv-uPviunfO901Vr4Llra2RZoL7k2SaVz5b8sHZwz9tr28nK4K01ItC1QwtyMTw-gA6LKU-lK3jTTjAHXqq0NK-7yqLmD6TCtsqdbNsdoxGLEfnWyV4rlB4ypTtbp8RQCkTKa8EWWLysYONW6-m24iLcIBbOt0l9i4UxjEV-DHag-8gIkxA9SeCthGdnNmHPEyy8ngikQbSR5ckvogYu-nsAi/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllDevTable>, 
do we structure the recon-all command to be: recon-all -autorecon2 
-fill -subjid ? I attempted to run recon-all -fill with -debug 
with the structure as follows: recon-all -s $subject -i $1 -fill 
-debug and I was wondering if this was the wrong format. I have also 
attached our recon-all-slurm-apr19.sb cluster submission file for 
reference.


Does recon-all -fill only run the fill step, while ignoring the 
previous steps before that or does recon-all run through all the 
initial steps including the -fill step ideally?


Regarding recon-all -debug, does the stdout file have the huge amounts 
of text specifying what each line is doing? I have included .out and 
.err files from the same recon-all -fill with -debug command for 
reference.


Sincerely,
Yilei

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


*Sent:* Thursday, April 18, 2024 2:57 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] recon-all process still not finishing 
properly
not sure what is happening. You can run recon-all with -debug and 
capture the output (both stdout and stderr) into a file. This will 
cause it to print out huge amounts of text specifying what it is doing 
on each line. You should also see if there is some stderr output that 
is not being caught. You can try running recon-all -fill on the 
subject that you created to see if the fill will run at all (this may 
be easier than waiting 4 hours).


On 4/8/2024 3:18 PM, Dong, Yilei wrote:


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Hi Freesurfer Support,

The past few weeks, I've emailed about my recon-all processing stream 
never completely finishing.
We are still encountering the same problem. For context, our 
recon-all job submission script runs recon-all for 1 image. Given a 
folder of 100 MRI images, we have another script that calls upon the 
recon-all script for each image within the folder via a for loop. The 
result is 100 jobs running in parallel on the cluster.


I have attached a screenshot of the parameters we set whenever we 
submit each recon-all job for each image by SLURM to UCSD's cluster. 
The maximum time we are allowed for each job is 48 hours. Our jobs 
are shared-node jobs, which means we run more than 1 job on a single 
node. This time, we increased RAM from 8GB to 16GB in hopes the 
entire recon-all processing stream can fully run through for each 
image, but it still stops at "mri_pretess done" and does not go on to 
the -fill step. Each job submitted to the cluster took around 4 hours 
and 20 minutes each to run in our most recent attempt.


If increasing the RAM did not change anything for us, how else can we 
get more verbose error messages? What other reasons could be why our 
recon-all aborts before finishing? I have attached a recon-all.log 
from one of our subjects for reference and a screenshot of the 
parameters we set for submitting jobs in our cluster for reference.



Freesurfer version: 7.2.0, but already available as module on UCSD's 
cluster system


Platform: Rocky Linux release 8.8 (Green Obsidian)

uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 
28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux


Recon-all log: see attached


Than

Re: [Freesurfer] brain volumes normalization

[Douglas N. Greve]

On 5/2/2024 4:03 AM, yunus soleymani wrote:


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Hello freesurfers,

I have some questions about the output variables of Freesurfer:

1. In the case of brain volume normalization, do I need to normalize 
all the volumetric results to the eTIV or just the subcortical volumes?

All volumes. And area too as you note in #4


2. Are there any formulas other than simple division in order to 
normalize the volumes?
People will sometimes use eTIV as a regressor in the GLM instead of 
dividing (make sure to normalize so that the scale does not mess up the GLM)


3. How are the .ThckStd values (like FS_R_Insula_ThckStd) calculated? 
What does the "std" mean here?

standard deviation across vertices


4. I believe that the surface area outputs are also affected by brain 
size differences in the population. Are there any reference values in 
the Freesurfer outputs to which surface areas can be normalized?

I just use eTIV


Thank you in advance for your help.

Best regards,
Yunus



*Yunus Soleymani*
**
*Ph.D. Candidate of Neuroimaging *
/*Tehran University of Medical Sciences*/
/**/
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+98 914 526 9298


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Re: [Freesurfer] Figures for publication

[Douglas N. Greve]

I would use either the ocn (cluster annotation) or the cluster-wise 
corrected map: overlay as you generally don't want to show uncorrected 
data. As for the max, it is a personal choice, just what you think looks 
good or makes your point.


On 4/22/2024 7:52 AM, Asuka Toyofuku wrote:


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Dear Freesurfer experts,

Thanks to all the help from this community, we're finally done with 
GLM analysis(mri_glimfit) and the cluster-wise correction 
(mri_glmfit_sim), and now I'm making figures for publication.


My question is

1.
Which output mgh files are commonly used for making figures for
publication? Do people use, for example,
cache.th40.abs.sig.cluster.mgh (cluster-wise corrected map:
overlay) or cache.th40.abs.sig.masked.mgh (uncorrected sig values
masked by the clusters that survive correction) or even
uncorrected ones, such as sig.mgh file in the contrast directory
before running the correction? From my impression, not many people
use e.g., cache.th40.abs.sig.cluster.mgh (which shows no colour
gradation inside the clusters)...
2.
How do you select the colour-bar cut-off and max values? Most
publications I saw use min cut-off value: -log10(p) = 2.00 and
max: -log10(p) = 5.00, but some uses min: p=0.05 and max: p=0.01.
Obviously, if you set the max value (with the configure section)
very low (e.g., 2.0), the size of the cluster gets bigger and
looks more significant. Are there any suggestions for setting the
configure/threshold for the figures?


Many thanks,
Asuka



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Re: [Freesurfer] Registration in PETSurfer

[Douglas N. Greve]

bbregister is more sensitive to the smoothing in the PET images. This 
can create a confound between atrophy and registration. bbregister 
should only be used on non-smoothed data.


On 5/1/2024 5:06 AM, Ruben Dörfel wrote:


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Hi FreeSurfer Team,

I am currently using PETSurfer to analyze FDG data. Following the 
guide *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer 
, 
it is suggested that you use /mri_coreg/ to register PET and MRI 
images. However, I was wondering whether /bbregister/ might not be the 
more appropriate tool to use, especially in a case like FDG, where we 
have a lot of uptake in the brain.


Best regards,

--
Ruben Dörfel, MSc
PhD Student

Center for Psychiatry Research
Karolinska Institutet

Neurobiology Research Unit
Copenhagen University Hospital, Rigshospitalet



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Re: [Freesurfer] recon-all process still not finishing properly

[Douglas N. Greve]

not sure what is happening. You can run recon-all with -debug and 
capture the output (both stdout and stderr) into a file. This will cause 
it to print out huge amounts of text specifying what it is doing on each 
line. You should also see if there is some stderr output that is not 
being caught. You can try running recon-all -fill on the subject that 
you created to see if the fill will run at all (this may be easier than 
waiting 4 hours).


On 4/8/2024 3:18 PM, Dong, Yilei wrote:


External Email - Use Caution

Hi Freesurfer Support,

The past few weeks, I've emailed about my recon-all processing stream 
never completely finishing.
We are still encountering the same problem. For context, our recon-all 
job submission script runs recon-all for 1 image. Given a folder of 
100 MRI images, we have another script that calls upon the recon-all 
script for each image within the folder via a for loop. The result is 
100 jobs running in parallel on the cluster.


I have attached a screenshot of the parameters we set whenever we 
submit each recon-all job for each image by SLURM to UCSD's cluster. 
The maximum time we are allowed for each job is 48 hours. Our jobs are 
shared-node jobs, which means we run more than 1 job on a single node. 
This time, we increased RAM from 8GB to 16GB in hopes the entire 
recon-all processing stream can fully run through for each image, but 
it still stops at "mri_pretess done" and does not go on to the -fill 
step. Each job submitted to the cluster took around 4 hours and 20 
minutes each to run in our most recent attempt.


If increasing the RAM did not change anything for us, how else can we 
get more verbose error messages? What other reasons could be why our 
recon-all aborts before finishing? I have attached a recon-all.log 
from one of our subjects for reference and a screenshot of the 
parameters we set for submitting jobs in our cluster for reference.



Freesurfer version: 7.2.0, but already available as module on UCSD's 
cluster system


Platform: Rocky Linux release 8.8 (Green Obsidian)

uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 
15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux


Recon-all log: see attached


Thank you!


Sincerely,

Yilei


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Re: [Freesurfer] Enorm threshold for dynamic PET images

[Douglas N. Greve]

Sorry, I don't know what you mean by enorm threshold. Can you elaborate?

On 4/4/2024 4:39 PM, Sneha Pandya wrote:


External Email - Use Caution

Dear team,

I am using mc-afni2 to perform motion correction on dynamic PET images 
(ref: petsurfer wiki page). I am planning to use an average of 
un-censored frames as a template to do so. What should the threshold 
be to estimate these set of un-censored frames? For fMRI we usually 
use 0.2 or 0.3 for motion. However, for PET data we have values in the 
enorm file ranges from 0-40.


Thank you,

Sneha


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Re: [Freesurfer] GLM Using 2 Surfaces - Thickness and Area

[Douglas N. Greve]

On 4/18/2024 1:59 PM, Tejaswi D. Sudhakar wrote:


External Email - Use Caution

Hello Freesurfer team,

I am interested in doing one glm analysis using both the thickness and 
cortical surface area.


My question is two-fold:

First, is it possible to provide both the thickness and area files to 
mris_preproc and mri_surf2surf commands or is it only possible to run 
two separate glms (one for thickness and one for area)?



You must run two separate glms


Second, can we consider thickness and area as separate values or are 
they both correlated? In other words, how correlated are the thickness 
and area values?


They should be uncorrelated by construction (ie, the noise in the 
thickness should be uncorrelated from that in the area), but they may 
biologically correlated (don't know). When doing an area analysis, make 
sure to turn on jacobian correction (on by default when you spec area to 
mris_preproc) and correct for total head size. You will also need to do 
the permutation corrections for multiple comparisons (for both thickness 
and area but esp for area).


Thanks in advances,

Tejaswi


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Re: [Freesurfer] gunzip error in load_mgh.m when file path contains spaces

[Douglas N. Greve]

thanks, just checked in your change.

On 4/17/2024 9:37 PM, Tyler Slouf wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I found what I believe to be a bug. Typically I can load mgz files 
into my Matlab program without any trouble.

But if the path containing the mgz file has a space then I get an error.

When I run this very short script in Matlab calling the MRIread 
function (/Applications/freesurfer/7.4.1/matlab/MRIread.m):


filepath = char("/Users/user/Documents/folder space test/data/mri.mgz");
mri = MRIread(filepath);

I get the following error:

gunzip: can't stat: /Users/user/Documents/folder 
(/Users/user/Documents/folder.gz): No such file or directory

gunzip: can't stat: space (space.gz): No such file or directory
gunzip: can't stat: test/data/mri.mgz (test/data/mri.mgz.gz): No such 
file or directory


ERROR: problem reading fname
SWITCH expression must be a scalar or a character vector.

Error in load_mgh (line 163)
switch type

Error in MRIread (line 90)
[mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);

Error in test_load_mgz (line 2)
mri = MRIread(filepath);

I traced this down to the function *load_mgh.m 
(*/Applications/freesurfer/7.4.1/matlab/load_mgh.m) where a file path 
string
(char array) is dynamically populated with randomly generated folder 
names to unzip into.

It's about line 69 and looks like this:
[status,msg] = unix(sprintf('gunzip -c %s > %s', fname, new_fname));

You may notice that potential spaces in the path names fname and 
new_fname are not escaped with single quotes.

I edited the file to escape the parameterized strings like so:
[status,msg] = unix(sprintf("gunzip -c '%s' > '%s'", fname, new_fname));

This solved the problem for me.

Computer details:
OS: MacOS Sonoma (latest)
Chipset: Apple M1 (aarch64)
Calling Program: Matlab R2023b
Freesurfer: 7.4.1

Thank you for your time.

Sincerely,
Tyler Slouf

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Re: [Freesurfer] Skin-Skull-Brain segmentation

[Douglas N. Greve]

You can try running samseg. This will generate most of the layers you 
want, but in segmentations. You will have to convert them to surfaces 
(eg, mri_tesssellate or mri_binarize with --surf output)


On 4/15/2024 5:31 AM, XIE Jing wrote:


External Email - Use Caution

Hello all,

We would like to use FreeSurfer to remodel the head, not only 
including the detailed brain structural information, but also 
considering skin and skull. I am wondering if the FreeSurfer is 
possible to split the skin, skull and brain surfaces at the same time?


We tried the syntax "mri_make_bem_surfaces -all" , and the error notes 
were received as follows:

/nvertices=2562, nfaces=5120 /
/mri_strip_skull: triangle file 
/home/customer/Desktop/headmodel/FREESURFER/freesurfer/lib/bem/ic4.tri 
read trishrink: File 
/home/customer/Desktop/headmodel/MRI/-all/mri/brain/COR-.info not found /

/Best guess at inner_skull.tri is in inner_skull_tmp.tri/

What's your suggestions and comments on this question? We appreciate 
it very much!


Thanks in advance!
Jing
*---*
*Jing XIE*
Associate Professor
Mechatronical Engineering
Beijing Institute of Technology
Beijing 180001, PR China


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Re: [Freesurfer] surface-based filtering

[Douglas N. Greve]

Yes, you can also run
mris_fwhm --smooth-only --i input.surf-values.mgz --fwhm FWHM --s 
subject --hemi hemi --o output.surf-values-smoothed.mgz --cortex

This will give the same result as mri_surf2surf

On 4/12/2024 10:07 PM, Jiaen Liu wrote:


External Email - Use Caution

I found in the source code about the use of fwhm. It decides the 
number of iterations to achieve a gaussian filter with the specified 
fwhm in mm


Best,
Jiaen
Sent with my mobile device

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Jiaen Liu 


*Sent:* Thursday, April 11, 2024 3:58:18 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

External Email - Use Caution

I thought N controls the number of smoothing iterations and the 
smoothing in each iteration is defined by fwhm which is some 
measurement of the smoothing kernel width.


Can I ask how to achieve smoothing effect similar to gaussian 
smoothing with certain sigma, where sigma is defined by voxel unit?


Thanks!

Best

Jiaen

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Fischl, Bruce 
R.,PHD

*Sent:* Thursday, April 11, 2024 15:50
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

Hi Jiaen

I’m not sure what you mean by “stacked smoothing”. I think the N in 
nsmooth is the number of iterations of nearest neighbor smoothing to 
apply, which  converges to Gaussian as N gets bigger. Not sure about 
the units for fwhm – I defer to Doug on that


Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Jiaen Liu

*Sent:* Thursday, April 11, 2024 4:41 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

*External Email - Use Caution *

Hi Bruce

Thanks for your response. In the help, I found the following options. 
Is the fwhm based on voxel unit? Does nsmooth-in or-out control the 
number of stacked smoothing?


--fwhm-src fwhmsrc: smooth the source to fwhmsrc

--fwhm-trg fwhmtrg: smooth the target to fwhmtrg

--nsmooth-in N  : smooth the input

--nsmooth-out N : smooth the output

Best

Jiaen

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Fischl, Bruce 
R.,PHD

*Sent:* Thursday, April 11, 2024 14:24
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

*EXTERNAL MAIL*

Yes, we support surface-based smoothing. Check out the help for 
mri_surf2surf


Cheers

Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Jiaen Liu

*Sent:* Thursday, April 11, 2024 2:14 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] surface-based filtering

*External Email - Use Caution *

I’m wondering if freesurfer provides functions to filter the surface 
data within certain neighborhood exclusively on the surface. It’s 
essentially similar to regular smoothing in 3D space. But the 
filtering kernel only runs on the surface.


I can think of a solution to filter adjacent vertex in the surface 
file. But I’m not sure if the adjacent vertex is also close in space.


Thanks!

Best regards,

*Jiaen Liu Ph.D.*

Assistant Professor

*/Advanced Imaging Research Center & Radiology/*

UT Southwestern Medical Center

2201 Inwood Ln

Dallas, TX, USA, 75390

Office: 214.645.2750

Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, Texas 

Re: [Freesurfer] BBRegistration with FSL topup

[Douglas N. Greve]

The vsm (voxel shift map) needs to be in the same voxel space as the 
fMRI (ie, it has to have the same voxel size, number of voxels, and the 
voxels must line up with the fMRI)


On 4/11/2024 8:11 PM, Gianluca Guglietti wrote:


External Email - Use Caution

Hi,

I had a question as to how to integrate fsl's topup command for 
correcting B0 distortion with freesurfer's boundary-based 
registration. I am working with high-resolution epi data (0.8mm 
isotropic) with a reduced FOV and am trying to register it to an 
MP2RAGE structural scan that I've already run through free surfer's 
recon-all. When I use the BBR command it works perfectly fine but when 
I try to add the topup field map it fails, returning this error 
"MRIvol2surfVSM: vsm dimension mismatch 1".


the field map was generated using two reverse phase encoded SE-EPI 
volumes with the same resolution and field of view as the GE-EPI BOLD 
data I am trying to register.


Any advice would be greatly appreciated!

Best,

Gianluca

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Re: [Freesurfer] vertices are -1 when using vol2label

[Douglas N. Greve]

vertices require a surface. There is no surface for cerebellum, so the 
vertices are all marked -1 to indicate that the vertex indices are not 
valid. The XYZ values are valid though


On 4/9/2024 6:36 AM, Sam W wrote:


External Email - Use Caution

Hello!
I'm trying to convert the cerebellum cortex in the aparc+aseg.mgz into 
a label so I tried:


mri_vol2label --c bert/mri/aparc+aseg.mgz --id 8 --l lh.cerebellum.label

but the resulting output file only has -1 as vertices. Is there 
anything wrong with the command above?


Best regards,
Sam

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Re: [Freesurfer] Support for GPU on Freesurfer

[Douglas N. Greve]

No, not any more. We used to have it, but it was too hard to maintain. 
You can always run in parallel on the CPU (-threads N)


On 4/3/2024 2:58 PM, Camargo, Aldo wrote:


External Email - Use Caution

Hi there,

I was wondering if there is support for GPU on FreeSurfer. I really 
would like to use it on GPU because is taking 9 hours per subject to 
recon-all.


Thanks a lot and have a nice day,

Aldo Camargo
Senior Postdoctoral Fellow at the University of Maryland, Baltimore



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Re: [Freesurfer] recon-all mri_convert error: extra argument ("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")

[Douglas N. Greve]

You have a space in your current path (between severe and similar). That 
is causing the problem


On 4/1/2024 8:26 AM, Huang, Yujing wrote:


There is a space in your path 
‘/home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe 
similar/first_sT1W_3D_TFE_tra_MR350895.nii’.


Rename the directory name and try again.

Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *???

*Sent:* Sunday, March 31, 2024 11:18 PM
*To:* FreeSurfer 
*Subject:* [Freesurfer] recon-all mri_convert error: extra argument 
("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")


*External Email - Use Caution *

Hello FreeSurfer Developers,

  I'm writing to ask for help while using "recon-all" command.

  I have converted some dcm format files to to nii format. Then I ran 
the command "recon-all -s maoyipeng -i 
first_sT1W_3D_TFE_tra_MR350895.nii -all", an error appeared:


/ mri_convert /home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe 
similar/first_sT1W_3D_TFE_tra_MR350895.nii 
/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz //
/mri_convert: extra argument 
("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")/

/type mri_convert -u for usage/
/Command exited with non-zero status 1/
/@#@FSTIME  2024:04:01:09:09:04 mri_convert N 3 e 0.00 S 0.00 U 0.00 P 
100% M 5972 F 0 R 236 W 0 c 0 w 1 I 0 O 0 L 0.43 0.24 0.19/

/@#@FSLOADPOST 2024:04:01:09:09:04 mri_convert N 3 0.43 0.24 0.19/
/Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 
00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux/
/recon-all -s maoyipeng exited with ERRORS at Mon Apr 1 09:09:04 HKT 
2024 //


I've searched the list and didn't find a similar question. I'm a bit 
new to FreeSurfer, so I am unsure how to resolve this issue. I've 
attached the recon-all.log if that might help.


1) FreeSurfer 
version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
2) uname -a: Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP 
Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

3) recon-all.log: see attached


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Re: [Freesurfer] mri_volsynth fails but exits with 0 exit status

[Douglas N. Greve]

Done

On 3/29/2024 3:31 PM, Aaron Tanenbaum wrote:


External Email - Use Caution

I am currently running FreeSurfer 7.4.  I wrote a script using the 
program mri_volsynth.  I noticed for the first time the program was 
trying to write files where it did not have write permissions. It 
outputted a few error messages but gave a 0 exit status. It would be 
nice to have it exit with a nonzero exit status.


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Re: [Freesurfer] Extracting significant regions - Longitudinal two stage model

[Douglas N. Greve]

what do you mean "extract" the cluster? Do you want mean thickness for 
each cluster? Or the mean contrast? Of all the voxels in a cluster? For 
the first two, you can use something like

mri_segstats --seg clusterseg.mgz --i contrast.mgz --sum summary.txt


On 3/26/2024 9:47 AM, Liliana Wu wrote:


External Email - Use Caution

Hi,

I ran a longitudinal two stage model analysis in 83 participants 
comparing two groups. After applying cluster correction, I am seeing 
several significant regions, and I was wondering if there is a way to 
extract each significant cluster from each participant.


I appreciate any help!

Thank you,

Liliana


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Re: [Freesurfer] autorecon1 issue

[Douglas N. Greve]

What are the errors that you are facing? Can you provide more detail?

On 3/26/2024 9:12 AM, Saifullah Tumrani wrote:


External Email - Use Caution

I am using freesurfer to preprocess my t1w 3d Mris using autorecon1 
which includes first 5 preprocessing techniques till skullstripping it 
worked well for 4 different datasets including ixi one from open neuro 
SRBPS but when i am using it for another dataset which has alsmost 
same configuration it’s talairach transformation fails for some 
samples and brain matter is removed in the final brainmask.mgz file 
moreover i applied autorecon-all for this dataset and even the process 
stopped for some showing error talaraich failed and for some samples 
the whole pipeline was executed without any error but in manual 
inspection i found brain matter removed by freesurfer kindly help me 
solving this problem. I later found bad skull stripping fix at this 
link FsTutorial/SkullStripFix_freeview - Free Surfer Wiki 
 using 
some commands but i am facing errors using these command recon-all 
-skullstrip -wsthresh -clean-bm -no-wsgcaatlas -subjid skullstrip1_before


kindly look into this if you have also experience same issues or have 
any insight on this. A response will be appriciated.


Thanks


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Re: [Freesurfer] Part brain is missing

[Douglas N. Greve]

Is that an MP2RAGE? The background may be messing things up. You can try 
masking it, eg,
mri_synthstrip --i yourimage.mgz --o stripped.mgz
Then pass stripped.mgz to recon-all

On 3/25/2024 6:33 AM, Chen Yang wrote:
>  External Email - Use Caution
>
> Dear FreeSurfer Developers,
>
> I am trying to do the processing for structural MRI data. I found that part 
> of brain is missing in one data (see Fig.1). Then I tried to change the 
> watershed parameter, but it didnt work at all (no matter which number I use), 
> the brainmask looks the same as before. So I did the manual editing, cloned 
> voxel from T1.mgz to brainmask.mgz. Then I run the -autorecon-pial, but it 
> froze in this step - fix topology. I checked 'wm.mgz', it contained a lot 
> skull and a lot of WM are missing (see Fig.2).
>
> I also tried to manually edit the brainmask.mgz and wm.mgz, then run 
> '-autorecon-wm' but it also froze in -fix topology. I put other might 
> relevant information in the end.
>
> I've searched in the mail archive but didn't find similar errors. I am not 
> sure if I did anything wrong. Does anyone have any thoughts on how to 
> trouble-shoot this problem? Also, Ive attached the recon-all.log in case it's 
> of any use.
>
> Thanks in advance!
>
> Best regards,
> Chen
>
>
> Other might relevant Information:
> 1) Coil element is wrong. 'HE2,4;NE2'.
> 2) I got an error message when I wad doing the recon-all first time: 
> watershed error: indices out of bounds. Then I added the command line 
> 'mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz 
> $mir/nu.mgz' based on this page 
> .
> Then I got another error message in recon-all: mri_em_register: could not 
> open brainmask.mgz so I added some cp to nu.mgz. It worked but the part of 
> brain is missing, as I mentioned in the beginning (Fig.1).
>
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
> 2) Platform: Linux 5.10.0-28-amd64
> 3) uname -a: Linux ramones 5.10.0-28 -amd64 #1 SMP Debian 5.10.209-2 
> (2024-01-31) x86_64 GNU/Linux
> 4) recon-all.log: see attached
>
>
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Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

[Douglas N. Greve]

That 2mm for the gaussian is just the post-processing filter and does 
not represent the full amount of partial volume effect. What kind of 
scanner is it?


On 3/22/2024 12:42 AM, WONG Wan Wa wrote:


External Email - Use Caution

Hi Douglas,

Thanks for your clarification. This is my first time to run PetSurfer. 
We did want to normalize by cerebellar grey matter, and I will add the 
"--rescale 8 47". I just copied "6" from the example command. I know 
"6" should be the FWHM of the point-spread function (PSF) of the 
scanner as measured in image space. I did ask the technician at the 
PET centre, and he replied that the reconstruction method was "OP-OSEM 
8i21s" and the filter was "XYZ gaussian 2.00". Can I use "2" for psf 
in the command?


Thanks,
Angel


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


*Sent:* Thursday, March 21, 2024 9:44 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied 
to PET data with single frame?
Yes, though that will normalize by the pons. If you want to normalize 
by something else, you will need to specify it with --rescale. Eg, if  
you want to normalize by ceberbellar gray matter, add

--rescale 8 47
Where did you get "6" from for the psf?

On 3/20/2024 10:57 PM, WONG Wan Wa wrote:


External Email - Use Caution

Hi Douglas,

Thanks for your reply. We used different tracers for diagnosis of AD 
or other neurodegenerative diseases, including PIB, FDG, Flutemetamol 
and TAU. If an SUV analysis is used, is it done by mri_gtmpvc? Is 
there any subsequent analysis needed?


This is my mri_gtmpvc command:

mri_gtmpvc \
  --i

$SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.nii.gz
\
  --reg

$SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.reg.lta
\
  --psf 6 \
  --seg $SUBJECTS_DIR/sub-QM001/mri/gtmseg.mgz \
  --default-seg-merge  \
  --auto-mask 1 .01 \
  --mgx .01 \
  --o $SUBJECTS_DIR/sub-QM001/pet/gtmpvc.output


Is this command okay?

Thanks,
Angel


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

*Sent:* Wednesday, March 20, 2024 11:27 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] PetSurfer: Can kinetic modeling be 
applied to PET data with single frame?
you cannot apply kinetic modeling to one frame. What is you ligand? 
For a one frame acquisition, you usually use an SUV analysis.


On 3/20/2024 12:03 AM, WONG Wan Wa wrote:


External Email - Use Caution

Hi experts,

As stated in the subject, can kinetic modeling be applied to PET 
data with only one frame? Or we just stop at ROI analysis without 
kinetic modeling?


Best,
Angel


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Re: [Freesurfer] Fw: Discrepancy between mris_preproc and mri_surf2surf results when mapping individual's measures to fsaverage space

[Douglas N. Greve]

oops, should have read your 2nd email. Yes, jacobian is the reason

On 3/20/2024 5:34 AM, tyzh...@ibp.ac.cn wrote:


External Email - Use Caution

Dear FreeSurfer Experts,


Sorry, I think I've found the answer. It's because Jacobian correction 
was performed for mris_preproc, right?



Tongyu Zhang



-原始邮件-
*发件人:*tyzh...@ibp.ac.cn
*发送时间:*2024-03-20 16:31:23 (星期三)
*收件人:* freesurfer@nmr.mgh.harvard.edu
*抄送:*
*主题:* Discrepancy between mris_preproc and mri_surf2surf results
when mapping individual's measures to fsaverage space

Dear FreeSurfer Experts,

I'm currently working on mapping cortical morphometric
measurements from each individual in the HCP dataset to the
fsaverage space.

I have noticed that both the mris_preproc and mri_surf2surf
commands can achieve this function. However, I found that the
vertex-level measurements for cortical thickness, sulcal depth,
and curvatures are consistent between these two commands, but the
results for surface area and gray matter volume are totally different.

I am puzzled by this inconsistency and speculate that perhaps
these two commands are calculated on different surfaces? I don't
understand why the two commands get different results since the
inputs are the same.

My command are as follows: (Different surface area values will be
obtained in lh.area.fsaverage.mgh and lh.area.fsaverage.gii files)

mris_preproc --s  id  --meas  area --target fsaverage --hemi lh
–out /Results/CorticalFeatures/id/lh.area.fsaverage.mgh

mri_surf2surf --srcsubject id --trgsubject fsaverage --hemi lh
--sval /HCP/id/surf/lh.area --tval
/Results/CorticalFeatures/id/lh.area.fsaverage.gii

Thank you so much!

Tongyu Zhang


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Re: [Freesurfer] Discrepancy between mris_preproc and mri_surf2surf results when mapping individual's measures to fsaverage space

[Douglas N. Greve]

When working with area, you need to turn on jacobian correction. 
mris_preproc will do this automatically, but you have to add --jac to 
mri_surf2surf explicitly


On 3/20/2024 4:31 AM, tyzh...@ibp.ac.cn wrote:


External Email - Use Caution

Dear FreeSurfer Experts,

I'm currently working on mapping cortical morphometric measurements 
from each individual in the HCP dataset to the fsaverage space.


I have noticed that both the mris_preproc and mri_surf2surf commands 
can achieve this function. However, I found that the vertex-level 
measurements for cortical thickness, sulcal depth, and curvatures are 
consistent between these two commands, but the results for surface 
area and gray matter volume are totally different.


I am puzzled by this inconsistency and speculate that perhaps these 
two commands are calculated on different surfaces? I don't understand 
why the two commands get different results since the inputs are the same.


My command are as follows: (Different surface area values will be 
obtained in lh.area.fsaverage.mgh and lh.area.fsaverage.gii files)


mris_preproc --s  id  --meas  area --target fsaverage --hemi lh –out 
/Results/CorticalFeatures/id/lh.area.fsaverage.mgh


mri_surf2surf --srcsubject id --trgsubject fsaverage --hemi lh --sval 
/HCP/id/surf/lh.area --tval 
/Results/CorticalFeatures/id/lh.area.fsaverage.gii


Thank you so much!

Tongyu Zhang


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Re: [Freesurfer] aparc & wm underestimation

[Douglas N. Greve]

Oh, I see you are using 7.1.1. You can upgrade to 7.4.1. This will not 
change the basic recon-all output and you'll have access to those new 
features.


On 3/16/2024 4:21 PM, Stanica, Maria wrote:


External Email - Use Caution

We checked and the ?h.orig surface looks right. We tried the -expert 
options file that you suggested anyway, but it exited with errors 
unfortunately and didn’t work. Is there anything else we can try?


Thanks again for your help!

Best,

Maria

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


*Date: *Wednesday, March 6, 2024 at 9:20 AM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] aparc & wm underestimation

This is difficult to debug remotely. The first thing to look at is the 
?h.orig surface. Does that look more-or-less right? If not, then it 
means that the wm.mgz is wrong. If it does not look right, it means 
that the surface placement algorithm is pushing the surface into 
subcortical gray. One way to overcome this is to create a 
brain.finalsurfs.manedit.mgz by copying the brain.finalsurfs.mgz, then 
edit the brain.finalsurfs.manedit.mgz to set those areas where the 
surface is off to 255. Then create an expert options file with

WhitePreAparc --rip-bg-no-annot --restore-255  --outvol mrisps.wpa.mgz
PlaceWhiteSurf --restore-255 --outvol mrisps.white.mgz
T1PialSurf --restore-255 --outvol mrisps.pial.mgz
And pass that to recon-all with the -expert option

On 3/5/2024 7:10 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Yes, the problem is that the white surface on the left side of the
image is extending too far into subcortical gray matter. We did
delete the control points and ran some white matter edits, but the
image I sent you is after we applied those edits (it was even
worse before). I don’t see any other wm edits we can make to the
image. It didn’t resolve our issue enough to make the image usable
for our analyses, so I wanted to see if there was anything else we
could do to resolve the problem.

Thank you!

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

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
    Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
*Date: *Tuesday, March 5, 2024 at 9:11 AM
*To: *freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] aparc & wm underestimation

Just to make sure I understand, the problem is that the white
surface on the left side of the image is extending too far into
subcortical gray matter, right? This can be difficult to fix, but
the right fix is to edit the wm.mgz. Make sure to delete your
control points as that is not the right fix. Also, remember that
the surfaces in this area may always be inaccurate if you can see
where the boundary is.

On 3/3/2024 6:09 PM, Stanica, Maria wrote:

*External Email - Use Caution *

This is after the most recent round of edits for one of the
subjects.

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu <mailto:mstan...@uab.edu>

Pronouns: she/her/hers

Image

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

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
*Date: *Sunday, March 3, 2024 at 3:38 PM
*To: *freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] aparc & wm underestimation

Can you send pictures of the slices showing the problem?

On 3/3/2024 3:18 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Hello FS developers,

I ran my subjects through skullstripping and recon-all.
Everything processed correctly (and exited without
errors), except 4 images which have an underestimation in
coronal subcortical region. The underestimation is
significant and goes on for about 10-12 slices (for one
image it was 153-162, for another it was 150-164).

After searching the list, we attempted control points,
which ended up not working (I don’t believe this was the
right method to correct the error). Then we tried white
matter edits, and one of the images was resolved, but the
other 3 did not get better. Is there anything else we
could do to try to resolve the issue? I can provide any
other information needed. Any help would be appreciated!

 1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
  

Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

[Douglas N. Greve]

Yes, though that will normalize by the pons. If you want to normalize by 
something else, you will need to specify it with --rescale. Eg, if  you 
want to normalize by ceberbellar gray matter, add

--rescale 8 47
Where did you get "6" from for the psf?

On 3/20/2024 10:57 PM, WONG Wan Wa wrote:


External Email - Use Caution

Hi Douglas,

Thanks for your reply. We used different tracers for diagnosis of AD 
or other neurodegenerative diseases, including PIB, FDG, Flutemetamol 
and TAU. If an SUV analysis is used, is it done by mri_gtmpvc? Is 
there any subsequent analysis needed?


This is my mri_gtmpvc command:

mri_gtmpvc \
  --i

$SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.nii.gz
\
  --reg

$SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.reg.lta
\
  --psf 6 \
  --seg $SUBJECTS_DIR/sub-QM001/mri/gtmseg.mgz \
  --default-seg-merge  \
  --auto-mask 1 .01 \
  --mgx .01 \
  --o $SUBJECTS_DIR/sub-QM001/pet/gtmpvc.output


Is this command okay?

Thanks,
Angel


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


*Sent:* Wednesday, March 20, 2024 11:27 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied 
to PET data with single frame?
you cannot apply kinetic modeling to one frame. What is you ligand? 
For a one frame acquisition, you usually use an SUV analysis.


On 3/20/2024 12:03 AM, WONG Wan Wa wrote:


External Email - Use Caution

Hi experts,

As stated in the subject, can kinetic modeling be applied to PET data 
with only one frame? Or we just stop at ROI analysis without kinetic 
modeling?


Best,
Angel


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Re: [Freesurfer] What do the stats files tell us?

[Douglas N. Greve]

See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

On 3/18/2024 4:38 PM, Vivek Kandasamy wrote:


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Hello,

So I ran FreeSurfer to get numeric data from MRI images and got these 
files under the stats page.


Screenshot 2024-03-18 144107.png

Do you know what each file tells us about our MRI images such as 
the lh.aparc.DKTatlas.mapped, lh.BA_exvivo.stats, lh.BA_exvivo.thresh, 
lh.curv, lh.w-g.pct, and wmparc.DKTatlas.mapped files?


Thanks,

Vivek Kandasamy

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Re: [Freesurfer] if: Expression Syntax - preproc-sess

[Douglas N. Greve]

What is your fcseed-config command line? If the input is not fmcpr, then 
you have to set the input when you config, eg, -funcstem f.even


On 3/19/2024 11:37 AM, Stefano Delli Pizzi wrote:


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Thank you Doug.
The preproc-sess command line runs fine.
An error occurs on:
fcseed-sess -s ID -cfg wm.config -overwrite
ERROR: could not determine file for rs-fMRI_AROMA/ID/rest/001/fmcpr

Best regards
Stefano

Il giorno 19 mar 2024, alle ore 15:54, Douglas N. Greve 
 ha scritto:


Hi Stefano, I think I found and fixed the problem. Can you try these?

On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:


External Email - Use Caution

Hi Doug,

The raw functional file is firstly passed with motion correction 
(i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering.

Next, I have renamed the ICA filtered file as f.nii.gz.
Then, I run:

preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 
-fsd rest -per-run -sliceorder even -force


There are issues with labels since excluding motion correction 
doesn't produce key files necessary for concatenating the files.
The preprocessing script is searching for the fmcpr.nii.gz file, 
which cannot be found because it is not created using the -nomc option.


When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and 
rerun preproc, the operation is done and the 
fmcpr.odd.sm0.fsaverage.lh is created.


However, when I run the next steps (fcseed-sess -s ID -cfg wm.config 
-overwrite), a second error occurs (reported below) because the 
script searches for fmcpr, which cannot be produced since I used -mc.


ERROR: could not determine file for 
/Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr 
This error seems to be related to the script searching for the fmcpr 
file, which isn't available due to the use of -mc.


Thank you.

Best regards,


Stefano




Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi 
 ha scritto:


Hi Doug have you any news
Thank you very much!
Stefano

Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi 
 ha scritto:


Thank you.
I’m attaching the file.
Stefano


Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve 
 ha scritto:


can you send me this file 
/Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess



On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote:


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It seems to me that I've done what you suggest. Attached is a 
new outputs.

Thanks
Stefano

Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve 
 ha scritto:


Are you sure that you are using the new version that I gave 
you? It looks like the previous version. Also, it does not look 
like the entire terminal output.


On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:


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The entire terminal output is attached.
Thanks!

Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve 
 ha scritto:


entire terminal output




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Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

[Douglas N. Greve]

you cannot apply kinetic modeling to one frame. What is you ligand? For 
a one frame acquisition, you usually use an SUV analysis.


On 3/20/2024 12:03 AM, WONG Wan Wa wrote:


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Hi experts,

As stated in the subject, can kinetic modeling be applied to PET data 
with only one frame? Or we just stop at ROI analysis without kinetic 
modeling?


Best,
Angel


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Re: [Freesurfer] if: Expression Syntax - preproc-sess

[Douglas N. Greve]

Hi Stefano, I think I found and fixed the problem. Can you try these?

On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:


External Email - Use Caution

Hi Doug,

The raw functional file is firstly passed with motion correction 
(i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering.

Next, I have renamed the ICA filtered file as f.nii.gz.
Then, I run:

preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 
-fsd rest -per-run -sliceorder even -force


There are issues with labels since excluding motion correction doesn't 
produce key files necessary for concatenating the files.
The preprocessing script is searching for the fmcpr.nii.gz file, which 
cannot be found because it is not created using the -nomc option.


When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and 
rerun preproc, the operation is done and the 
fmcpr.odd.sm0.fsaverage.lh is created.


However, when I run the next steps (fcseed-sess -s ID -cfg wm.config 
-overwrite), a second error occurs (reported below) because the script 
searches for fmcpr, which cannot be produced since I used -mc.


ERROR: could not determine file for 
/Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr 
This error seems to be related to the script searching for the fmcpr 
file, which isn't available due to the use of -mc.


Thank you.

Best regards,


Stefano




Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi 
 ha scritto:


Hi Doug have you any news
Thank you very much!
Stefano

Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi 
 ha scritto:


Thank you.
I’m attaching the file.
Stefano


Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve 
 ha scritto:


can you send me this file 
/Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess



On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote:


External Email - Use Caution

It seems to me that I've done what you suggest. Attached is a new 
outputs.

Thanks
Stefano

Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve 
 ha scritto:


Are you sure that you are using the new version that I gave you? 
It looks like the previous version. Also, it does not look like 
the entire terminal output.


On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:


External Email - Use Caution

The entire terminal output is attached.
Thanks!

Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve 
 ha scritto:


entire terminal output




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.






#! /bin/tcsh -f

#
# preproc-sess - runs preprocessing (mc, spatsmooth, mkbrainmask, inorm)
#
# Original Author: Doug Greve
#
# Copyright © 2021
# The General Hospital Corporation (Boston, MA). 
# All rights reserved.
#
# Distribution, usage and copying of this software is covered under the
# terms found in the License Agreement file named 'COPYING' found in the
# FreeSurfer source code root directory, and duplicated here:
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense
#
# General inquiries: freesurfer@nmr.mgh.harvard.edu
# Bug reports: analysis-b...@nmr.mgh.harvard.edu
#

# To get per-run reg with smoothing, make sure -fwhm is after -per-run:
# preproc-sess -s risk001 -per-run -fwhm 5 -fsd bold 
# This creates fmcpr.sm5, then
# mkanalysis-sess -native -funcstem fmcpr.sm5 ...

set VERSION = 'preproc-sess @FS_VERSION@';

set inputargs = ($argv);
set DateStr = "`date '+%y%m%d%H%M'`"

set instem   = ();
set mcinstem   = ();
set mcoutstem  = ();
set stcinstem   = ();
set stcoutstem  = ();
set sminstem   = ();
set smoutstem  = ();
set inormstem  = ();
set maskdir= masks
set maskstem   = brain;
set UseSmoothMask = 0;
set fwhm = ();
set surffwhm = ();
set volsurffwhm  = (); # for testing
set SliceOrder = ();
set SliceDelayFile = ()
set

Re: [Freesurfer] Large discrepancy in left and right volumes of perirhinal/entorhinal cortices on FreeSurfer 7.1

[Douglas N. Greve]

I've looked into this a little bit.
I looked at the area of the original manual labels for entorhinal as 
found in the aparc. They do show a lh>rh asym of 3%, but it is not 
significant (p=.45).
I looked at the automatic labels in two other large data sets. I found 
significant lh>rh asym of ento area in both of about 8-10%.
I don't consider 10% asym in area to be a symptom of something 
problematic. This would represent an expansion or contraction of the 
entorhinal border of about 0.5mm. I'm guessing that this is beyond the 
accuracy that we can expect.
I was looking at surface area, but now I see that you are looking at 
volume. The manual labels were defined on an areal basis, and I assume 
that that was the basis of the volume asym, but it could be due to 
differences in thickness.
How big a difference are you seeing in volume? Can you look at area and 
thickness to see if you see differences there?
Also, the surfaces are really hard to place in this area. Oftentimes, 
the ento will have a big bite in it that has to be fixed manually. I 
don't think there is asym in the bites, but it could make a particular 
case look extreme.
In general, we don't recommend doing laterality studies with the aparc 
as none of the steps involved have been developed to make sure that 
laterality artifacts are removed. In this case, it sounds like you are 
checking laterality for QA purposes?



On 3/13/2024 9:30 PM, Katie Vandeloo wrote:
>  External Email - Use Caution
>
> Hi Dr. Greve,
>
> I hope you are doing well. I am hoping to get in touch with someone from MGH 
> about some issues with Freesurfer 7. Our group hasn’t yet been successful in 
> finding the right person to talk to about this!
>
> We noticed that there are large discrepancies between left and right 
> hemisphere volumes of the perirhinal cortex (exceptionally small volumes in 
> the right hemisphere) in the outputs of recon-all for Freesurfer 7 but NOT 
> Freesurfer 6. I have reached out to other labs who observed the same pattern. 
> I think there is something systemic about Freesurfer 7 that should be looked 
> into. Just wanted to make someone aware - please let me know if there is 
> someone else I should contact about this.
>
> Thank you for your time!
>
> Kind Regards,
> Katie Vandeloo

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Re: [Freesurfer] GCS file format specification and conversion to GIFTI

[Douglas N. Greve]

It is not really something that can be converted to an overlay (gifti or 
otherwise). It is a probabalistic atlas with prior probabilities for 
each label as well as curvature mean and stddev for each label at each 
point in space. If you know some C++, you can look at GCSAread() in 
gcsa.cpp to see what gets read in.


On 3/13/2024 7:00 AM, Oscar Esteban wrote:


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Dear all,

I'm trying to understand the GCS file format as I failed to try an 
easy conversion with mris_convert.


If mris_convert cannot convert GCS to GIFTI, is there any open 
description of how the format is implemented?


Thanks very much

Best,
Oscar

*___*
*Oscar Esteban, Ph.D.*
Research and Teaching Ambizione FNS Fellow
Dept. of Radiology, CHUV, University of Lausanne

+41 77 957 00 77
+1 (650) 733 33 82

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Re: [Freesurfer] if: Expression Syntax - preproc-sess

[Douglas N. Greve]

Are you sure that you are using the new version that I gave you? It 
looks like the previous version. Also, it does not look like the entire 
terminal output.


On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:


External Email - Use Caution

The entire terminal output is attached.
Thanks!

Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve 
 ha scritto:


entire terminal output


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Re: [Freesurfer] Trouble Project Surface Annotation to Volume

[Douglas N. Greve]

Hi Bram, try using mris_surfseg2vol. Look in the recon-all log file for 
an example usage

doug


On 3/10/2024 12:43 PM, Bram Diamond wrote:


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Hello FreeSurfer Experts!

I’m having trouble projecting the Yeo 17n annotation to volume space. 
I’ve tried on FS v7.4.1 on Mac OS (14.3.1) and FS v7.3.2 on Linux (7.9).


I’ve tried the following two methods:

 1. aparc2aseg 

cd $FREESURFER_HOME/subjects/fsaverage/label

mri_aparc2aseg \

--s fsaverage \

--o Yeo2011_17Networks_N1000.mgz \

--annot Yeo2011_17Networks_N1000

 Output 

SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects

subject fsaverage

outvol Yeo2011_17Networks_N1000.mgz

useribbon 0

baseoffset 0

RipUnknown 0

Reading lh white surface

 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.white

Reading lh pial surface

 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.pial

Loading lh annotations from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot


Have color table for lh white annotation

Building hash of lh white

Building hash of lh pial

Reading rh white surface

 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/rh.white

Reading rh pial surface

 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/rh.pial

Loading rh annotations from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot


Have color table for rh white annotation

Building hash of rh white

Building hash of rh pial

Loading ribbon segmentation from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/mri/ribbon.mgz


Loading aseg from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/mri/aseg.mgz


ASeg Vox2RAS: ---

-1.0   0.0   0.0   128.0;

 0.0   0.0   1.0  -128.0;

 0.0 -1.0   0.0   128.0;

 0.0   0.0   0.0   1.0;

-

Labeling Slice (256)

  0 1   2   3   4   5   6   7   8   9  10  11  12  13  14  15 16  17  
18  19


 20 21  22  23  24  25  26  27  28  29  30  31  32  33  34  35 36  37  
38  39


 40 41  42  43  44  45  46  47  48  49  50  51  52  53  54  55 56  57  
58  59


 60 61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 76  77  
78  79


 80 81  82  83  84  85  86  87  88  89  90  91  92  93  94  95 96  97  
98  99


100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 
117 118 119


120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 
137 138 139


140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 
157 158 159


160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 
177 178 179


180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 
197 198 199


200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 
217 218 219


220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 
237 238 239


240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 
332584


Used brute-force search on 0 voxels

Writing output aseg to Yeo2011_17Networks_N1000.mgz

error: mghWrite(Yeo2011_17Networks_N1000.mgz, -1): could not open file

#VMPC# mri_aparc2aseg VmPeak  0

mri_aparc2aseg done

 2. label2vol 

cd $FREESURFER_HOME/subjects/fsaverage/label

mri_label2vol \

--annot lh.Yeo2011_17Networks_N1000.annot \

--o lh.Yeo2011_17Networks_N1000.mgz \

--hemi lh \

--fill-ribbon \

--identity \

--subject fsaverage

 Output 

Number of labels: 0

Annot File:      lh.Yeo2011_17Networks_N1000.annot

Template Volume: (null)

Outut Volume: lh.Yeo2011_17Networks_N1000.mgz

Registration File: (null)

Fill Threshold: 0

Label Vox Vol:  1

ProjType:       (null)

ProjTypeId:     0

ProjStart:     0

ProjStop:       0

ProjDelta:     0.1

Subject: fsaverage

Hemi:     lh

UseNewASeg2Vol: 0

DoLabelStatVol 0

LabelCodeOffset 0

setenv SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects

7.4.1

INFO: loading surface 
/Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.white


nvertices = 163842

Reading thickness 
/Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.thickness


Loading annotations from lh.Yeo2011_17Networks_N1000.annot

annotidmax = 18

nlabels = 18

Loading /Applications/freesurfer/7.4.1/subjects/fsaverage/mri/ribbon.mgz

Mapping

error: mghWrite(lh.Yeo2011_17Networks_N1000.mgz, -1): could not open file



I’ve done this before, so I feel like I must be doing something wrong. 
Any ideas?


Cheers,

Bram

*Bram R. Diamond, MS*

Clinical Psychology Doctoral Candidate

Northwestern University Feinberg School of Medicine

Mesulam Center for Cognitive Neurology & Alzheimer’s Disease

300 E. Superior Street | Tarry 8 | Chicago, IL 60611

www.brain.northwestern.edu


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Re: [Freesurfer] Cortical parcellation showing dots

[Douglas N. Greve]

And how does the parcellation look on the surface?

On 3/7/2024 9:53 AM, Hyunchul Lee wrote:


External Email - Use Caution

Yes, it looks fine to me
Those dots seem to lie on the pial surface

On Thu, Mar 7, 2024, 10:07 PM Douglas N. Greve 
 wrote:


Have you looked at the actual surface?

On 3/7/2024 2:29 AM, Hyunchul Lee wrote:


External Email - Use Caution

Hello,
I'm using Freesurfer recon-all to create reconstructions to use
with MNE-python for source estimation of SEEG data. My work
relies on having correct labeling of segmentation data. For most
cases, there has been no trouble but I am having trouble where
the cortical parcellation shows up as dots in one hemisphere.
Please see image attached. I also noticed that the lh.ribbon.mgz
is also 'dotty' (also attached). There is no issue with the right
hemisphere. This reconstruction was not manually edited, but only
recon-all was used.

I have tried using mris_volmask --label_left_ribbon, setting the
argument to various values. That didn't work that great -
reducing to 0 basically whites everything out except for the
white matter on the ipsilateral hemisphere and anything 1 or more
produces the same 'dots'. Interestingly the pial and wm surfaces
all look ok. Also, I am not sure if creating the correct
ribbon.mgz is going to fix the aparc.a2009+aseg file.

I would really appreciate your advice.

Best regards,
*
*
*Hyunchul Lee*  MBBS PhD

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Re: [Freesurfer] Cortical parcellation showing dots

[Douglas N. Greve]

Have you looked at the actual surface?

On 3/7/2024 2:29 AM, Hyunchul Lee wrote:


External Email - Use Caution

Hello,
I'm using Freesurfer recon-all to create reconstructions to use with 
MNE-python for source estimation of SEEG data. My work relies on 
having correct labeling of segmentation data. For most cases, there 
has been no trouble but I am having trouble where the cortical 
parcellation shows up as dots in one hemisphere. Please see image 
attached. I also noticed that the lh.ribbon.mgz is also 'dotty' (also 
attached). There is no issue with the right hemisphere. This 
reconstruction was not manually edited, but only recon-all was used.


I have tried using mris_volmask --label_left_ribbon, setting the 
argument to various values. That didn't work that great - reducing to 
0 basically whites everything out except for the white matter on the 
ipsilateral hemisphere and anything 1 or more produces the same 
'dots'. Interestingly the pial and wm surfaces all look ok. Also, I am 
not sure if creating the correct ribbon.mgz is going to fix the 
aparc.a2009+aseg file.


I would really appreciate your advice.

Best regards,
*
*
*Hyunchul Lee*  MBBS PhD

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Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area

[Douglas N. Greve]

Yujing, you can just send Taylor a binary that can be put in the local 
version of $FREESURFER/bin


On 3/6/2024 11:45 AM, Huang, Yujing wrote:


Hi Taylor,

Thanks for sharing the data.

I see the problem now.  The first 14336 bytes of your rh.area fit 
SIGNA_FILE criteria. So, it is read as SIGNA_FILE instead of 
MRI_CURV_FILE.


We will have a fix in dev version. But I’m not sure how to get around 
this in FS 7.2.


Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Ariko, Taylor

*Sent:* Wednesday, March 6, 2024 9:47 AM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: 
mris_calc could not establish read access to rh.area


*External Email - Use Caution *

Hello Yujing,

If I rerun this command:

mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

It says it is writing curvature file in the command line output:

writing curvature file ../surf/rh.area

Though the problem persists (mri_info says same thing as before). I 
have attached rh.white and rh.area for your review.


Many thanks,

Taylor

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 


*Date: *Wednesday, March 6, 2024 at 8:37 AM
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: 
mris_calc could not establish read access to rh.area


It doesn’t look like rh.area is recognized correctly. ‘mri_info 
rh.area’ should show it is a ‘curv’ file with nvertices x 1 x 1 
dimensions.


I’m not sure where exactly the area values are calculated. What happen 
if you re-run this step?


mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

Can you share the ?h.white and ?h.area?

Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Ariko, Taylor

*Sent:* Tuesday, March 5, 2024 7:24 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: 
mris_calc could not establish read access to rh.area


*External Email - Use Caution *

Hello Yujing,

Thank you for your quick response!

When I run:

mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add 
/path/to/subject/surf/rh.area.pial


I get the following error:

error: No such file or directory

error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): 
could not open file


error: No such file or directory

error:

mris_calc: could not establish read access to 
'/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.


But when I run:

mri_info rh.area

I get the following output:

Volume information for rh.area

        type: unknown

  dimensions: 831 x 10015 x 25953

voxel sizes: -0.00, -0.00,    nan

        type: SHORT (4)

        fov: 1016.473

        dof: 1

      xstart: 0.0, xend: 990983162970892849632569550308376576.0

      ystart: -0.0, yend: 3079152361728581627851833344.0

      zstart: -0.0, zend: -3815443229699337177012458129513775104.0

          TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 
0.00 degrees


    nframes: 1

    PhEncDir: UNKNOWN

    FieldStrength: 0.00

ras xform present

  xform info: x_r =  -1., y_r =   0., z_r = 0., c_r = 
-18770011487391973376.


            : x_a =   0., y_a =   0., z_a = 1., c_a =      
  nan


            : x_s =   0., y_s =  -1., z_s = 0., c_s =    
-0.


Orientation   : LIA

Primary Slice Direction: coronal

voxel to ras transform:

              0.  -0.      nan        nan

            -0.  -0.      nan        nan

            -0.   0.      nan        nan

              0.   0.   0.     1.

voxel-to-ras determinant nan

ras to voxel transform:

error: mat = NULL!

It appears that this is where the issue is coming from. Any ideas on 
why this is occurring? The brain is normal and has good rh.white and 
rh.pial surfaces.


Many thanks,

Taylor

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 


*Date: *Tuesday, March 5, 2024 at 4:25 PM
*To: *Freesurfer support list 
*Subject: *[EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc 
could not establish read access to rh.area


*CAUTION:*This email originated from outside the organization. *DO NOT 
CLICK ON LINKS* _or_ *OPEN ATTACHMENTS* unless you know and trust the 
sender.


Hi Taylor,

I don’t understand how you could get that error.  It seems to me that 
read_signa() is for reading .signa files.


Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ 
directly? Pass full path to your rh.area and rh.area.pial.


What does ‘mri_info rh.area’ report?

Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Ariko, Taylor

*Sent:* Tuesday, March 5, 2024 2:35 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] recon-all hard error: mris_calc could not 
establish read access to rh.area


*External Email - Use Caution *

Hello FreeSurfer Developers,

I am attempting 

Re: [Freesurfer] xhemi

[Douglas N. Greve]

When creating a laterality-free atlas one needs to make sure to do the 
same thing to the left and right hemi. Eg, the mni152 is not laterally 
symmetric, so you will get a different registration when you register 
your volume directly to the mni152 vs left-right reversing your volume 
and then registering (and why people will register to a symmetric mni152 
when doing such studies). These biases can creep in in other ways. Eg, 
when manually labeling the brain, the labeler might do the left slightly 
different than the right, and this might creep into the atlas (though 
this can be reduced by including left-right reversed labels in the 
atlas). Our standard labels (eg, aparc) are susceptible to these 
problems. Any clearer?


On 3/6/2024 10:52 AM, Joost Janssen wrote:


External Email - Use Caution

Dear Doug,

Thanks. A regional Laterality Index can be calculated using XHEMI (as 
described on the wiki) but also in a different way, e.g. using the 
default FS output from ?h*.stats files and e.g. doing 
(LH-RH)/((LH+RH)/2) or some other formula. You once mentioned about 
this latter approach "But the atlas was not created in a symmetrical 
way, so there might be biases". Could you elaborate on what these 
biases might be?
I read *MailScanner has detected a possible fraud attempt from 
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767398/ 
<https://secure-web.cisco.com/1TELdMKGVJpKa4ZNA0JT1c2M5j92hscTUXojMSwfCRgHWMi4h330-7qb3M2OGXIYrgOSZICxTxnpti-05ncWdhR6JaJbIx73FVjtEzOdBqK1bpmrufIS7sOC5rf9sTVNVfUF_2k02iDbUNyl8qoOsQMWS5KZS1t7h7JfI_o3K8yrj9LhxQ2EB54r2L_4CsVC3HXfzZQIQW58QvmALvYxzjqKSlL7ZlrmqwXDwD2yTC98P_wzNSIBNXBRqjKkZWOhCZR0piY0tJiFCGuAw6DMfILX-TiwrTwsyjwWmBqI1d_rxSHX5j2-2gRTFnUWbv9ua4qItxp5KwGEhL5PxfcxxZg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3767398%2F> 
and it mentions biases when doing registration of a hemisphere to 
either LH or RH but I am not sure if these are the same biases.

Thanks!
-joost

On Wed, Nov 29, 2023 at 12:02 AM Douglas N. Greve 
 wrote:


Yes, they are. BTW, you should not need to mri_convert the
thickness to mgh format

On 11/27/2023 10:01 AM, Joost Janssen wrote:


External Email - Use Caution

Dear Doug,

The objective is to have _regional_ laterality index for
thickness for aparc mapped to the left hemisphere. The following
commands work without error but are they correct for meeting my
objective? Thanks.

surfreg --s $subject --t fsaverage_sym --lh --no-annot

surfreg --s $subject --t fsaverage_sym --lh --no-annot --xhemi

mri_convert $subject/surf/lh.thickness $subject/surf/lh.thickness.mgh

mri_convert $subject/surf/rh.thickness $subject/surf/rh.thickness.mgh

mris_apply_reg --src $subject/surf/lh.thickness.mgh --trg
$subject/surf/lh.thickness.lh.fsaverage_sym.mgh --streg
$subject/surf/lh.fsaverage_sym.sphere.reg
fsaverage_sym/surf/lh.sphere.reg

mris_apply_reg --src $subject/surf/rh.thickness.mgh --trg
$subject/surf/rh.thickness.lh.fsaverage_sym.mgh --streg
$subject/xhemi/surf/lh.fsaverage_sym.sphere.reg
fsaverage_sym/surf/lh.sphere.reg

fscalc $subject/surf/lh.thickness.lh.fsaverage_sym.mgh pctdiff0
$subject/surf/rh.thickness.lh.fsaverage_sym.mgh div 200 -o
$subject/surf/li.thickness.lh.fsaverage_sym.mgh

mri_segstats --annot fsaverage lh aparc --i
$subject/surf/li.thickness.lh.fsaverage_sym.mgh --sum
$subject/stats/li.thickness.aparc.stats

-joost




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Re: [Freesurfer] remote access to freesurfer installation...

[Douglas N. Greve]

No, sorry. We do have FS containers that you could use on AWS

On 3/6/2024 9:28 AM, Gonzalo Rojas Costa wrote:


External Email - Use Caution

Hi:

Is there a freesurfer facility where an MRI study can be processed 
remotely?


  Sincerely,


Gonzalo Rojas Costa


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Re: [Freesurfer] Unexpected skull shape after wraped to MNI

[Douglas N. Greve]

Can you be more specific about what abnormality you are seeing? The 
Screenshot2 does not look so bad to me. I'm assuming that this is the 
talairach.xfm transform you are talking about? If so, that is hardly 
used in the stream (and certainly not for placing surfaces), so it is no 
surprise that the results look ok even if the xfm is off a little


On 3/6/2024 5:08 AM, GOFFINET Sara wrote:


External Email - Use Caution

Hello,

I ran freesurfer recon_all on a T1 MRI sequence (you can find the orig 
T1 in Screenshtot1) and my participant's brain warped to MNI 
(worig.nii) looks deformed (Screenshot2). Do you know why is there a 
bump (the worig file does not overlay well on MNI) while the 
reconstruction of the pial surface (lh.pial, rh.pial) shows no 
abnormality?



Thanks in advance,


Sara Goffinet


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Re: [Freesurfer] aparc & wm underestimation

[Douglas N. Greve]

This is difficult to debug remotely. The first thing to look at is the 
?h.orig surface. Does that look more-or-less right? If not, then it 
means that the wm.mgz is wrong. If it does not look right, it means that 
the surface placement algorithm is pushing the surface into subcortical 
gray. One way to overcome this is to create a 
brain.finalsurfs.manedit.mgz by copying the brain.finalsurfs.mgz, then 
edit the brain.finalsurfs.manedit.mgz to set those areas where the 
surface is off to 255. Then create an expert options file with

WhitePreAparc --rip-bg-no-annot --restore-255  --outvol mrisps.wpa.mgz
PlaceWhiteSurf --restore-255 --outvol mrisps.white.mgz
T1PialSurf --restore-255 --outvol mrisps.pial.mgz
And pass that to recon-all with the -expert option

On 3/5/2024 7:10 PM, Stanica, Maria wrote:


External Email - Use Caution

Yes, the problem is that the white surface on the left side of the 
image is extending too far into subcortical gray matter. We did delete 
the control points and ran some white matter edits, but the image I 
sent you is after we applied those edits (it was even worse before). I 
don’t see any other wm edits we can make to the image. It didn’t 
resolve our issue enough to make the image usable for our analyses, so 
I wanted to see if there was anything else we could do to resolve the 
problem.


Thank you!

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


*Date: *Tuesday, March 5, 2024 at 9:11 AM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] aparc & wm underestimation

Just to make sure I understand, the problem is that the white surface 
on the left side of the image is extending too far into subcortical 
gray matter, right? This can be difficult to fix, but the right fix is 
to edit the wm.mgz. Make sure to delete your control points as that is 
not the right fix. Also, remember that the surfaces in this area may 
always be inaccurate if you can see where the boundary is.


On 3/3/2024 6:09 PM, Stanica, Maria wrote:

*External Email - Use Caution *

This is after the most recent round of edits for one of the subjects.

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu <mailto:mstan...@uab.edu>

Pronouns: she/her/hers

Image

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

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
*Date: *Sunday, March 3, 2024 at 3:38 PM
*To: *freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] aparc & wm underestimation

Can you send pictures of the slices showing the problem?

On 3/3/2024 3:18 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Hello FS developers,

I ran my subjects through skullstripping and recon-all.
Everything processed correctly (and exited without errors),
except 4 images which have an underestimation in coronal
subcortical region. The underestimation is significant and
goes on for about 10-12 slices (for one image it was 153-162,
for another it was 150-164).

After searching the list, we attempted control points, which
ended up not working (I don’t believe this was the right
method to correct the error). Then we tried white matter
edits, and one of the images was resolved, but the other 3 did
not get better. Is there anything else we could do to try to
resolve the issue? I can provide any other information needed.
Any help would be appreciated!

 1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
 2. Operating System: Red Hat Enterprise Linux 7
 3. OS Version: 7.9 (Maipo)

Best,

Maria

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu <mailto:mstan...@uab.edu>

Pronouns: she/her/hers

Image

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Re: [Freesurfer] TRACULA GLM output question

[Douglas N. Greve]

The easiest thing is to set up contrasts to pull out the parameters you 
want. The next easiest (or maybe the easiest) is to look in the beta 
file. It will have a frame for each column in the design matrix. The 
value is the regression coefficient.


On 3/5/2024 11:33 AM, Hoskinson, Kristen wrote:


External Email - Use Caution

We’re working on a project where we ran 3 groups, 1 covariate, and ran 
a glm looking at white matter at cross-sections from TRACULA output, 
covarying for functional activation. We’re now wanting to plot out the 
interaction/slopes per group, but are having trouble locating the data 
that would allow that step.  Could anyone direct us?


Thank you!

--

*Kristen R. Hoskinson, Ph.D. *(she/her)

Associate Professor of Pediatrics

The Ohio State University College of Medicine

Principal Investigator, /Social Cognition, Adjustment, and 
Neurodevelopment (SCAN) Lab/


Center for Biobehavioral Health

The Abigail Wexner Research Institute at Nationwide Children's Hospital

700 Children's Drive
Columbus, Ohio  43205

(614) 722-3021

kristen.hoskin...@nationwidechildrens.org 




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Re: [Freesurfer] Citing the bert dataset

[Douglas N. Greve]

Most of the info has been lost for that scan. It was a GE 1.5T scanner; 
subject is a male, approx 37yo


On 3/4/2024 2:49 PM, Shounak Nandi wrote:


External Email - Use Caution

Hi,

I have used the *bert 
*dataset 
in one of the scientific works and was curious how I cite it?


I am eager to know your thoughts.

Thanks,
Shounak Nandi

Radiology Trainee,
Department of Radiology and Radiological Science,
Division of Cancer Imaging Research,
Johns Hopkins School of Medicine,
Baltimore, MD

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Re: [Freesurfer] aparc & wm underestimation

[Douglas N. Greve]

Just to make sure I understand, the problem is that the white surface on 
the left side of the image is extending too far into subcortical gray 
matter, right? This can be difficult to fix, but the right fix is to 
edit the wm.mgz. Make sure to delete your control points as that is not 
the right fix. Also, remember that the surfaces in this area may always 
be inaccurate if you can see where the boundary is.


On 3/3/2024 6:09 PM, Stanica, Maria wrote:


External Email - Use Caution

This is after the most recent round of edits for one of the subjects.

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu <mailto:mstan...@uab.edu>

Pronouns: she/her/hers

Image

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


*Date: *Sunday, March 3, 2024 at 3:38 PM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] aparc & wm underestimation

Can you send pictures of the slices showing the problem?

On 3/3/2024 3:18 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Hello FS developers,

I ran my subjects through skullstripping and recon-all. Everything
processed correctly (and exited without errors), except 4 images
which have an underestimation in coronal subcortical region. The
underestimation is significant and goes on for about 10-12 slices
(for one image it was 153-162, for another it was 150-164).

After searching the list, we attempted control points, which ended
up not working (I don’t believe this was the right method to
correct the error). Then we tried white matter edits, and one of
the images was resolved, but the other 3 did not get better. Is
there anything else we could do to try to resolve the issue? I can
provide any other information needed. Any help would be appreciated!

 1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
 2. Operating System: Red Hat Enterprise Linux 7
 3. OS Version: 7.9 (Maipo)

Best,

Maria

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu <mailto:mstan...@uab.edu>

Pronouns: she/her/hers

Image



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Re: [Freesurfer] aparc & wm underestimation

[Douglas N. Greve]

Can you send pictures of the slices showing the problem?

On 3/3/2024 3:18 PM, Stanica, Maria wrote:


External Email - Use Caution

Hello FS developers,

I ran my subjects through skullstripping and recon-all. Everything 
processed correctly (and exited without errors), except 4 images which 
have an underestimation in coronal subcortical region. The 
underestimation is significant and goes on for about 10-12 slices (for 
one image it was 153-162, for another it was 150-164).


After searching the list, we attempted control points, which ended up 
not working (I don’t believe this was the right method to correct the 
error). Then we tried white matter edits, and one of the images was 
resolved, but the other 3 did not get better. Is there anything else 
we could do to try to resolve the issue? I can provide any other 
information needed. Any help would be appreciated!


 1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
 2. Operating System: Red Hat Enterprise Linux 7
 3. OS Version: 7.9 (Maipo)

Best,

Maria

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu 

Pronouns: she/her/hers

Image


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Re: [Freesurfer] Freesurfer white matter overestimated

[Douglas N. Greve]

Can you include an image with and without the surfaces? Make sure to 
include slices where you think the white surface extends too far.


On 2/28/2024 9:13 AM, Luisa Klahn wrote:


External Email - Use Caution

Dear Douglas,
Please find the nu.mgz screenshot attached.
Best,
Luisa



*Von:* Luisa Klahn 
*Gesendet:* Montag, 26. Februar 2024 08:53
*An:* dgr...@mgh.harvard.edu 
*Betreff:* Re: [Freesurfer] Freesurfer white matter overestimated
Dear Douglas,
Please find attached the pictures for the following issue:
I am processing structural data from a 3T scanner using Freesurfer
version 7.3.2. For some subjects, the grey matter looks very thin, and
the white matter looks overestimated. I'll attach screenshots of the
brainmask, wm mask, and T1 including wm and pial surface lines.
I have tried to set control points into the wm but this did not change
the results.
Does anyone have an idea? Would it be possible to change the intensity
settings in the recon-all command?

Thanks for helping!
Best,
Luisa
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Re: [Freesurfer] Is the slice delay of each slice needed for slice time correction with preprocess-sess?

[Douglas N. Greve]

Yes, you can use the siemens STC option (ie, -stc siemens)

On 2/26/2024 9:02 PM, Maria Hakonen wrote:


External Email - Use Caution

Dear all,

Have I understood correctly that the slice delay of each slice is not 
needed when performing slice time correction with preprocess-sess?


I am processing an open OASIS fMRI dataset. The dataset has fMRI data 
in nifti format and JSON files that contain information about the data.
In the instructions they say: "Slice timing is included in the JSON 
when available. Some original DICOM files did not have slice timing 
info. When slice timing information is unavailable use the ratio 
TR/#slices."


The data is collected with a Siemens scanner.
If the slice timing is available it seems to be interleaved:

"SliceTiming": [
    1.1025,
    0,
    1.165,
    0.059998,
    1.2251,
    0.1225,
    1.28750001,
    0.1825,
    1.3474,
    0.245,
    1.4099,
    0.30499,
    1.47,
    0.36749,
    1.5325,
    0.42749,
    1.595,
    0.48999,
    1.655,
    0.55004,
    1.7175,

Could I just run slice time correction with the siemens option?

Best regards,
Maria



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Re: [Freesurfer] Segmentation White matter bad

[Douglas N. Greve]

I can't tell from those pics what is happening. Does it look like an 
imaging artifact? You can try putting control points


On 2/26/2024 12:58 PM, lejia2011411409 wrote:


External Email - Use Caution

Hi，
  I used command:  recon-all  -s subject1 -i subject1.nii   -all -sd  
/home/t1. I think it is FrreSurfer default method to segementation.


Lejia



At 2024-02-27 01:24:00, "Douglas N. Greve"  wrote:

what did you use the do the segmentation? Include command line and
terminal output

On 2/26/2024 10:46 AM, lejia2011411409 wrote:


External Email - Use Caution

Dear freesurfer experts,

A large amount of subjects got segmentation white matter bad
(some dark white matter cannot be recognition below 57 slices). 
Attachment show this problem.  I used 'kvlEMSegment brainmask.mgz
3 4 4 '  to segment white matter again.  while there reported   
 kvlEMSegment: command not found. Do you have any solutions for
this? Thanks in advance.

Best wishes,
Lejia

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Re: [Freesurfer] Permission denied error from -localGI

[Douglas N. Greve]

That is weird -- ft_read_mri is not one of our files. Can you send the 
command line and the *full* terminal output? The lGI stuff is pretty old 
and does not have a maintainer.


On 2/26/2024 1:40 PM, Michael Ruvalcaba wrote:


External Email - Use Caution

Hi Douglas,

Yes I can definitely do that!

After I run the recon -all part for a specific subject using 
freesurfer 7.2.0 in MATALB, I then run the below code:


%% 4c. Load Freesurfer Pre-Op MRI (do not edit)
addpath('/usr/local/freesurfer_x86_64-7.2.0/matlab');
fsmri_pre_acpc = ft_read_mri([subdir 
'3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);


Which gives me the following error:

/bin/bash: 
/scratch/tp0a8d7d21_790a_4945_a04d_b0cc7d38be4f.load_mgh.m.mgh: 
Permission denied


ERROR: could not open 
/scratch/tp0a8d7d21_790a_4945_a04d_b0cc7d38be4f.load_mgh.m.mgh for reading
ERROR: loading 
/home/knight/ecog/DATA_FOLDER/UCSD/SD11/3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz 
as MGH

Dot indexing is not supported for variables of this type.

Error in ft_read_mri (line 401)
    ndims = numel(size(tmp.vol));

Error in SD11_Recon_Pipeline (line 197)
fsmri_pre_acpc = ft_read_mri([subdir 
'3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);



I don't get this error when using freesurfer 6.0.0 and using those 
above commands. So I'm guessing it's because freesurfer 7.2.0 is 
trying to write something to a scratch file that doesn't even exist?


Thank you for your help!

Best,
Michael Ruvalcaba
Knight Lab
Helen Wills Neuroscience Institute
University of California, Berkeley


On Fri, Feb 23, 2024 at 10:26 AM Douglas N. Greve 
 wrote:


Can you send more info? Eg, command line, all terminal output,
version of FS you are using?

On 2/6/2024 6:18 PM, Michael Ruvalcaba wrote:


External Email - Use Caution

Hello,

I had a similar question you had in the past thread
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg72609.html

<https://secure-web.cisco.com/1zJkMv9aRmMM6PokM8jDCRUGLybtdGCgeH3ZTgzjLrgSV_Psg_PyipqWV0v3sXbvB4_kb2A09lkKzETq6p-Q72y_fLJpYAnivZ4sE6U8wa3OLcRcFsJk0pDqWI3jzvqCxrbp0pnCYTzlhRCne1CYNAdMoxB0ORfhE16LGiGIx3c7zpeRHDvzb_WkvNj-0ed0Xhwjs6Moiijl9lhtwkJHIFunH6CWkBHCO9YRg23zb5D0wWbxRcR5VBiMAEUQbw6m5cecc6wHXPMoaR8R0dYuln5D7FyLEF2jkY7VCKhKPrZBwR4aZ2PiSMztXbtH6So-p/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg72609.html>)
but I cannot seem to access the link where you solved this issue.
It looks like Tashrif helped you and he informed me to ask you

Can you help me with this by chance? I tried opening an account
and logging in but it says my account hasn't been approved yet :(
and I'm not sure who to contact to get it approved. It's been
months.

Thank you!

Best,
Michael Ruvalcaba


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Re: [Freesurfer] Segmentation White matter bad

[Douglas N. Greve]

what did you use the do the segmentation? Include command line and 
terminal output


On 2/26/2024 10:46 AM, lejia2011411409 wrote:


External Email - Use Caution

Dear freesurfer experts,

A large amount of subjects got segmentation white matter bad (some 
dark white matter cannot be recognition below 57 slices). Attachment 
show this problem.  I used 'kvlEMSegment brainmask.mgz 3 4 4 '  to 
segment white matter again.  while there reported     kvlEMSegment: 
command not found. Do you have any solutions for this? Thanks in advance.


Best wishes,
Lejia

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Re: [Freesurfer] Creating a custom registration template with FreeSurfer template

[Douglas N. Greve]

You need to specify a format for the output (eg, ...thickness.mgz)

On 2/26/2024 10:31 AM, Asuka Toyofuku wrote:


External Email - Use Caution

Hi, many thanks for your reply.
Here's the terminal output;

asuka@rigi:/media/.../FS7_Teen$ for d in Teen* EPK* epk*
> do mris_preproc --surfreg sphere.reg.teenheart_average_template --s 
$d --hemi lh --out lh.surfreg.teenheart_average_template.thickness 
--meas thickness

> done
ERROR: format for lh.surfreg.teenheart_average_template.thickness not 
recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not 
recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not 
recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not 
recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not 
recognized


Error continued so I stopped running at a certain point.
What do you think?

Best regards,
Asuka

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


*Sent:* 23 February 2024 19:30
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] Creating a custom registration template 
with FreeSurfer template
Can you include the full terminal output for one of the mris_preproc 
commands that is failing?


On 2/22/2024 7:12 AM, Asuka Toyofuku wrote:

*External Email - Use Caution *

Dear Freesurfer experts,


I have issues with creating a custom registration template. (I'm
following this instruction: *MailScanner has detected a possible
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 )


According to the instructions, we need to

1) Create an average subject (Creates $SUBJECTS_DIR/newtemplate)

2) Register each subject to the new template (do for both lh and
rh), resulting in lh.sphere.reg.newtemplate and
rh.sphere.reg.newtemplate
3) Get thickness values in the newtemplate space for GLM analysis
4) Create another average template based on the previous one:
(Creates $SUBJECTS_DIR/newnewtemplate)

I'm stuck with the 3) command.
Instruction suggests:
mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2
--s subj3 ...

and this is my code:
for d in Teen*
do mris_preproc --surfreg sphere.reg.teenheart_average_template
--s $d --hemi lh --out
lh.surfreg.teenheart_average_template.thickness --meas thickness
done

( I specified hemi and output because, without it, I got ERROR: no
source hemi specified)

My command led to an error saying:

ERROR: format for lh.surfreg.teenheart_average_template.thickness
not recognized

So my questions are:

a) what does it mean that "format for
lh.surfreg.average_template.thickness not recognised"? Any ideas
on how to fix this?

b) Does this mris_preproc --surfreg command produce different
smoothing mgh files? (e.g., fwhm10, fwhm15, fwhm20...?)

Because standard mris_preproc before GLM analysis(*MailScanner has
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<https://

Re: [Freesurfer] Freesurfer white matter overestimated

[Douglas N. Greve]

It looks like the volume has very poor contrast. What volume are you 
displaying it on? Can you take a pic on the nu.mgz?


On 2/26/2024 2:53 AM, Luisa Klahn wrote:


External Email - Use Caution

Dear Douglas,
Please find attached the pictures for the following issue:
I am processing structural data from a 3T scanner using Freesurfer
version 7.3.2. For some subjects, the grey matter looks very thin, and
the white matter looks overestimated. I'll attach screenshots of the
brainmask, wm mask, and T1 including wm and pial surface lines.
I have tried to set control points into the wm but this did not change
the results.
Does anyone have an idea? Would it be possible to change the intensity
settings in the recon-all command?

Thanks for helping!
Best,
Luisa
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Re: [Freesurfer] Fwd: Vertex / voxel lesion symptom mapping

[Douglas N. Greve]

Can you be even more specific? Operationally, what does it entail? Are 
you just trying to correlate, say, cognitive deficits to, say, thickenss?


On 2/25/2024 9:12 PM, Martin Juneja wrote:


External Email - Use Caution

Hi Doug,

Sorry for not elaborating in my previous email.

Voxel lesion symptom mapping (VLSM) is a method to calculate symptom 
localization by estimating statistical relationships between damage to 
specific brain regions (it could be stroke lesion, tumor lesion or TBI 
lesion etc.) and resulting deficits (e.g., *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724038/ 
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and *MailScanner has detected a possible fraud attempt from 
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https://academic.oup.com/brain/article/137/9/2532/2848278 
<https://secure-web.cisco.com/1Sv3DQt7ECt7yYskA3qSYiurVnqwYgQMrW8bVWoluBQmsM_yLtTYU5rsNedrt7kfxvXWRFNBdsUI4A1g3RXw72SMBIG6ZQrrv9cyiZQGDsnk8bidCzCK_lFen7x0alY7ZhJs5O1HBwG06GFvTNxoPfkbR1hD87w8QzlmPBxoAV_migSoy78DKyb73PilyF7D9vRCcWNAx4UOdo0SSrO_Shf1_py0ygzhtUB2FOJo-0Z-5e1wnn3cKO0-MJMcDUhRdVzUXTYWyey2rVOBEqbKBye_yDzoaxLIKzESNFAVFJGY8t8AlAjZS0kE9aqzZKXXtHqmihL1X2aNJDuA_eQsRZA/https%3A%2F%2Facademic.oup.com%2Fbrain%2Farticle%2F137%2F9%2F2532%2F2848278>). 
This method can guide the development of targeted interventions and 
rehabilitation strategies aimed at improving symptoms by targeting 
specific brain regions (or networks, if we use network lesion symptom 
mapping: *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
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<https://secure-web.cisco.com/10LgUitf4Y4lehNjHOInoyAOPPrjXpKyw8QudhBNFrI-HEs531siCcOCZApchqgDvWDYKy7cM6QODz-i1dQPhiBuCX-00bXDcm2EF8XZrhB_Rknetjx1FVS8u1BBOZ16mMYnGswaNPzNgbt15-7OR0ZajBrz3jJMaAXx2tGeFbJuIT_cwpTPX2u7uVcKu40byzK3CksUD9sBXUODMzo1dWFYJ7dqv9jzjPyhXiM51d49k7iGamx_SlWvcrdjka0R328JXdXbqwiXqt2FEwAVsz1ioBdFbSPNdth73sqgmm1hDt5vQsBMMp8Txr8bGJeZxE6q-ZHf8yqwxiFsXOOVtBw/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC9724189%2F>).


On Fri, Feb 23, 2024 at 10:27 AM Douglas N. Greve 
 wrote:


Sorry, don't know what VLSM is. Can you elaborate?

On 2/6/2024 3:19 PM, Martin Juneja wrote:


External Email - Use Caution

Dear FreeSurfer community and experts,

I would greatly appreciate any help/response with the following.

Thanks.

-- Forwarded message -
From: *Martin Juneja* 
Date: Wed, Jan 31, 2024 at 7:51 PM
Subject: Vertex / voxel lesion symptom mapping
To: Freesurfer support list 


Greetings FreeSurfer community,

I was just wondering if it's possible to perform vertex/voxel
lesion symptom mapping (VLSM) using FreeSurfer? In other words, I
would like to assess the impact of lesion topography (of course,
heterogenous locations across patients) on
neurocognitive function in brain tumor patients.

I would greatly appreciate any help/response.

Thanks!

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Re: [Freesurfer] consistency in recon-all parallel pipeline

[Douglas N. Greve]

Can you try it with -threads instead? We don't typically use -parallel

On 2/23/2024 2:44 PM, Horn, Mitchell Jacob wrote:


This is all with ‘recon-all -parallel’

Thanks,

Mitch

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Huang, Yujing

*Sent:* Friday, February 23, 2024 2:30 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] consistency in recon-all parallel pipeline

Do you run ‘recon-all -parallel’ or ‘recon-all –threads ’?

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Horn, Mitchell 
Jacob

*Sent:* Friday, February 23, 2024 12:28 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] consistency in recon-all parallel pipeline

Bottom line is that when I run any FreeSurfer version 7+ in parallel 
on COS8 I get different results each time.


Thanks,

Mitch

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* Friday, February 23, 2024 11:03 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] consistency in recon-all parallel pipeline

So, is the bottom line that when you run 7.4.1 on COS8 in parallel 
that you get (slightly) different results each time?


On 2/2/2024 11:20 AM, Horn, Mitchell Jacob wrote:

Hi FS Devs,

I’m experiencing unreproducible thickness results when running any
7+ version with parallelization enabled. Running recon-all without
parallelization produces consistent thickness results. I’m running
this in AlmaLinux8 (a library-equivalent downstream OS to CentOS8).

I’m attaching a table (table1) of 12 recons with bert:

 1. 3 parallelized with CentOS8-compiled 7.4.1
 2. 3 non-parallelized with CentOS8-compiled 7.4.1
 3. 3 parallelized with CentOS7-compiled 7.4.1
 4. 3 non-parallelized with CentOS7-compiled 7.4.1

I suspected the downstream CentOS8 libm was the culprit (because
of testing I did this last 2023 summer). I ran 3 more recons
parallelized with the CentOS7-compiled 7.4.1, but before running
the recon-all command, set LD_PRELOAD to a copy of the CentOS7
libm libraries. The thickness results were then consistent, see
the second table below (table2). I could not run this experiment
on the CentOS8-compiled version, as that one is obviously not
backward compatible with CentOS7 libm.

As a quick test of the OS-dependency, I submitted 3 parallel
recons on MLSC with 7.3.3. Each reported different thickness. See
table 3 (table3).

I’m asking if you can please confirm whether running any 7.+
version with parallelization is generating reproducible results
for you in CentOS8 (or equivalent)?

P.S. - I tested 6.0 (CentOS6-compilation) with parallelization,
and the results were consistent.

Best,

Mitch

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Re: [Freesurfer] Temporal lobe mask

[Douglas N. Greve]

you can run recon-all on the mni152 to get the aparc+aseg.mgz, then take 
the temporal lobe from that


On 2/23/2024 11:29 AM, Camargo, Aldo wrote:


External Email - Use Caution

Hi there,

I would like to know where I can find a mask in MNI space for the 
temporal lobe.


Thanks a lot in advance for your help,

Aldo Camargo


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Re: [Freesurfer] overlay activation map on flattened surface

[Douglas N. Greve]

Just sample the activation onto the full surface (eg, --surf white 
--projfrac 0.5), then just load it as an overlay when you view the patch 
in freeview


On 2/22/2024 12:18 PM, Atena Akbari wrote:


External Email - Use Caution

Hello Freesurfer team,

I have flattened the occipital patch using "mris_flatten -w 10 
subj04/surf/lh.occip.patch.3d subj04/surf/lh.occip.flattened" and it 
worked without any error and I can load the flattened patch in 
freeview. However, I have difficulty overlaying the activation map 
onto the flattened surface. Is the following command correct for this 
purpose?
(mri_vol2surf --mov   spmT_0001.nii --out  
subj04/surf/lh.bold.flat.mgz  --reg  fsl_reg.dat.lta   --surf 
occip.flattened  --hemi  lh)


Many thanks,

Atena


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Re: [Freesurfer] creating a cortical label using a 3D image ROI and calculating its volume and average thickness

[Douglas N. Greve]

You can run mri_vol2surf to sample the ROI onto the surface, eg,
mri_vol2surf --regheader subject --mov yourROI.mgz --projfrac-max 0 1 .1 
--hemi lh --o lh.yourROI.mgz

yourROI.mgz should be voxel-for-voxel aligned with the orig.mgz
View your sample with
tksurferfv subject lh inflated -aparc -ov lh.yourROI.mgz -fminmax 0.5 1
You can then get the thickness, area, vol with something like
mri_segstats --i lh.thickness --seg lh.yourROI.mgz --id 1 --sum 
summary.thickness.dat
When applying it to the area or volume files, make sure to add 
--accumulate to the command line



On 2/22/2024 8:24 AM, Yakupov, Renat /DZNE wrote:


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Dear Freesurfer users,


I would like to do the following:

- there is an ROI mask image file in the same space as the T1-weighted 
image


- I would like to use that mask to define the borders of a cortical area

- and then calculate volume and average thickness of the above defined 
cortical area



I know that I can get a rough estimate of the volume by applying the 
ROI mask to the the aparc* file and calculating the number of voxels, 
but what I would really like to do is use the ROI mask to constrain 
the WM and pial surfaces to the volume inside the ROI and then 
calculate statistics using the surfaces approach.



I also know that I can combine existing labels, but unfortunately this 
custom ROI contains parts of various cortical regions, not whole regions.



Any advice would be appreciated!


Best wishes,

Renat.


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Re: [Freesurfer] Creating a custom registration template with FreeSurfer template

[Douglas N. Greve]

Can you include the full terminal output for one of the mris_preproc 
commands that is failing?


On 2/22/2024 7:12 AM, Asuka Toyofuku wrote:


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Dear Freesurfer experts,


I have issues with creating a custom registration template. (I'm 
following this instruction: *MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates 
 )



According to the instructions, we need to

1) Create an average subject (Creates $SUBJECTS_DIR/newtemplate)

2) Register each subject to the new template (do for both lh and rh), 
resulting in lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate

3) Get thickness values in the newtemplate space for GLM analysis
4) Create another average template based on the previous one: (Creates 
$SUBJECTS_DIR/newnewtemplate)


I'm stuck with the 3) command.
Instruction suggests:
mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s 
subj3 ...


and this is my code:
for d in Teen*
do mris_preproc --surfreg sphere.reg.teenheart_average_template --s $d 
--hemi lh --out lh.surfreg.teenheart_average_template.thickness --meas 
thickness

done

( I specified hemi and output because, without it, I got ERROR: no 
source hemi specified)


My command led to an error saying:

ERROR: format for lh.surfreg.teenheart_average_template.thickness not 
recognized


So my questions are:

a) what does it mean that "format for 
lh.surfreg.average_template.thickness not recognised"? Any ideas on 
how to fix this?


b) Does this mris_preproc --surfreg command produce different 
smoothing mgh files? (e.g., fwhm10, fwhm15, fwhm20...?)


Because standard mris_preproc before GLM analysis(*MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming 
to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis 
) 
are done with previously qcashed data (e.g., need 
thickness.fwhm10.fsaverage to run mris_preproc), but at this point, I 
don't have any of these thickness files with different smoothing levels.


c ) If this mris_preproc --surfreg command does not generate a set of 
thickness maps in **newtemplate space** at different smoothing levels, 
what kind of command should I run?



Any input is appreciated!


Best regards,

Asuka


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Re: [Freesurfer] How to write rh.w-g.pct from recon-all stats output into a table

[Douglas N. Greve]

Do you see a subject/stats/lh.w-g.pct.stats file?
You can use asegstats2table to compile this across subjects. Run it with 
-help to get more info


On 2/22/2024 3:26 AM, ERNEST KISSI wrote:


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I processed several items of data. And I have rh.w-g.pct file in my stats
folders.
How can I get process this file to get table reading file? I tried to use
asegstats2table and aparcstats2table but it didn’t work.
Could you provide me with necessary information about getting of stats 
from

rh.w-g.pct to table file like asegstats2table?
Thank you.

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Re: [Freesurfer] Using MRI_segstats to calculate grey matter intensity

[Douglas N. Greve]

Yes, you just have to make sure the input and seg volumes are in voxel 
for voxel alignment


On 2/21/2024 4:30 AM, ERNEST KISSI wrote:


External Email - Use Caution

Hello freesurfer Team,

I have the grey matter segmentation from FSL and I have freesurfer 
recon-all output but the recon-all outputs do not have regional grey 
matter intensities. Can I use MRI_segstats to calculate the regional 
grey matter output using the FSL grey matter segmentation and the 
recon-all subject hemi parc and subject hemi labels to get the various 
brain parts and labels for the grey matter?


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Re: [Freesurfer] formula calculating percent signal change

[Douglas N. Greve]

In what context? For fMRI, it is the signal change divided by the signal 
mean (x100%)



On 2/20/2024 6:43 PM, Tina Zahrie wrote:


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Hi all,

How is the percent signal change calculated within a ROI? What is the 
formula for it?


Thanks,
Tina


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Re: [Freesurfer] psf formula PET SURFER

[Douglas N. Greve]

I'm not sure what you are looking for as it is just the equation of a 
gaussian. The PSF is given as the full-width-half-max. This is converted 
to a std dev with

gstd = fwhm/sqrt(log(256.0))


On 2/18/2024 7:03 AM, Federica Di Antonio wrote:


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Dear experts,

I'm employing PETsurfer for partial volume correction.
Could you share the definition or formula you use to define the psf 
(flag --psf of mri_gtmpvc) that is used to correct the PET image?
I understand that it is an isotropic gaussian filter, but could you 
maybe provide the precise formula you employ or the reference you 
refer to?


Thank you so much for your kindness and availability,

Federica Di Antonio


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Re: [Freesurfer] if: Expression Syntax - preproc-sess

[Douglas N. Greve]

I cannot reproduce this locally. If you still want help, attach logs. 
You can also try running it with -debug as the first option and capture 
the copious terminal output.


On 2/6/2024 8:39 AM, Huang, Yujing wrote:


Not sure where this happened. Does it produce any log files that you 
can share? Maybe both logs with and without the -nomc option.


Best,

Yujing

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Stefano Delli 
Pizzi

*Sent:* Saturday, February 3, 2024 2:33 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] if: Expression Syntax - preproc-sess

*External Email - Use Caution *

Hello FreeSurfer Developers,
I'm attempting to run preproc-sess with -nomc option
preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 
-fsd rest

-per-run -sliceorder up -force
if: Expression Syntax.
This error occurred before to create the file with slice timing correction
The error did not occur when I run the preproc-sess command line 
without the

-nomc option.
I've searched the list and no similar errors have been reported. Does 
anyone

have any thoughts on how to trouble-shoot this one?
FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
Platform: Darwin Kernel Version 21.6.0

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Re: [Freesurfer] Fwd: Vertex / voxel lesion symptom mapping

[Douglas N. Greve]

Sorry, don't know what VLSM is. Can you elaborate?

On 2/6/2024 3:19 PM, Martin Juneja wrote:


External Email - Use Caution

Dear FreeSurfer community and experts,

I would greatly appreciate any help/response with the following.

Thanks.

-- Forwarded message -
From: *Martin Juneja* 
Date: Wed, Jan 31, 2024 at 7:51 PM
Subject: Vertex / voxel lesion symptom mapping
To: Freesurfer support list 


Greetings FreeSurfer community,

I was just wondering if it's possible to perform vertex/voxel lesion 
symptom mapping (VLSM) using FreeSurfer? In other words, I would like 
to assess the impact of lesion topography (of course, heterogenous 
locations across patients) on neurocognitive function in brain tumor 
patients.


I would greatly appreciate any help/response.

Thanks!

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Re: [Freesurfer] aseg QA questions

[Douglas N. Greve]

On 2/6/2024 2:01 PM, Sarah Skinner wrote:


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Question 1 - We found a few voxels that are labeled as the right 
choroid-plexus, but it is nowhere near the rest of the structure. See 
attached image. Is this a problem? If yes, what is the best way to fix 
this?

Probably not a problem as it is just a few voxels.


Question 2 - The right-lateral-ventricle appears to be separated into 
2 unconnected areas. We are assuming this is okay, but we wanted a 
second opinion. See attached image.
Yes, this is ok and often happens in younger subjects where the channel 
between the two areas is very narrow.


Thanks!

Sarah Skinner
Research Specialist
Institute on Aging
University of Wisconsin-Madison

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Re: [Freesurfer] Cortical WM parcellation for DKT atlas?

[Douglas N. Greve]

If  you look in the recon-all.log file (or recon-all.cmd file), you will 
find the command that creates the wmparc.mgz. You can adapt it to use 
the DKT


On 2/6/2024 6:53 AM, Hamied Haroon wrote:


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Hello Freesurfer Gurus,

Is it possible to obtain “wmparc” but for the DKT cortical atlas, please?

Many thanks.

Best wishes,

Hamied

*Dr Hamied A Haroon*[he/him/his], MSc, PhD, MInstP

Research Fellow in Quantitative Biomedical MR Imaging

The University of Manchester


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Re: [Freesurfer] Manual/reproduce conform

[Douglas N. Greve]

The TkR vox2ras will never have direction cosine info. The -conform-dc 
will keep the original DC in the "conformed" volume (eg, orig.mgz vs 
rawavg.mgz)


On 1/11/2024 3:22 PM, Dipterix Wang wrote:


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I tried `--conform-dc` and the flag was not recognized. `-conform-dc` 
didn't give me error. However, vox2ras-tkr still didn't include the 
cosine information.


This is the Torig:

mri_info --vox2ras-tkr T1.mgz

-1.0    0.0    0.0  128.0

0.0    0.0    1.0 -128.0

0.0   -1.0    0.0  128.0

0.0    0.0    0.0    1.0


While Norig is

mri_info --vox2ras T1.mgz

-0.99989    0.00604    0.01331  124.66034

0.01408    0.15990    0.98703 -164.17455

-0.00383   -0.98711    0.15997  108.14072

0.0    0.0    0.0    1.0


I wonder what steps I could take to make sure the Torig = Norig. Here 
Norig is acpc realigned.


Best,
- D

On Mon, Jan 1, 2024 at 4:27 PM Douglas N. Greve 
 wrote:


If you want to keep the original orientation, you can specify
--conform-dc. Would that fix your problem?

On 12/21/2023 9:30 AM, Dipterix Wang wrote:


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Dear FreeSurer Wizards,

I'm trying to run the recon-all command on one of my template
brains such that the resulting Norig and Torig are identical. I
understand that fs always conforms the MRI to 256^3 before
segmentation. I wonder if there is any way that I can resample
the original MRI to achieve the same Norig and Torig?

More specifically, currently the Torig (vox to tkrRAS) is
     [,1] [,2] [,3] [,4]
[1,]   -1    0    0  128
[2,]    0    0    1 -128
[3,]    0   -1    0  128
[4,]    0    0    0    1

If I resample the input image such that Norig (vox to scanRAS)
equals this matrix, can I expect that "conform" does not change
the orientation?

Alternatively, is there any method I can use to "predict" or
reproduce the Torig from the original MRI outside of FreeSurfer?

Thanks,
- Dipterix


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Re: [Freesurfer] Getting from MNI152 to fsaverage

[Douglas N. Greve]

Hi Lauri, that command does look right (and no need to worry about that 
warning). The projfrac is the projection fraction. This is the distance 
away from the white surface that fMRI will be sampled relative to the 
thickness at that location. So a value of 0.5 means to sample in the 
middle of the ribbon, which is probably where you want to sample. There 
are other options (eg, you can sampled a fixed mm distance).

doug


On 2/2/2024 1:15 PM, Lauri Tuominen wrote:


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Dear experts,

I am comparing freesurfer mri_vol2surf to nilearn surface.vol_to_surf. 
I am finding large differences so I just wanted to get this command 
absolutely right before making any sort of conclusions.



I would love if someone could confirm this is ok:


```

mri_vol2surf --mov task-rest_space-MNI152NLin6Asym.bold.nii.gz \

--mni152reg \

--hemi lh \

--surf white \

--o lh.task-rest_space-fsaverage.bold.nii.gz

```


Also I get complains about source volume voxel size (2,2,2) being 
different from target voxel size (1,1,1). I did read somewhere that 
this warning can be ignored. Is that correct?



fsfast pipeline seems to use default projection fraction 0.5, while 
the default in the above command is 0. Could someone explain me the 
reasoning behind this? I am wondering if I should be using 0.5 or 0 
with my data.



Thank you so much!!

Lauri






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Re: [Freesurfer] consistency in recon-all parallel pipeline

[Douglas N. Greve]

So, is the bottom line that when you run 7.4.1 on COS8 in parallel that 
you get (slightly) different results each time?


On 2/2/2024 11:20 AM, Horn, Mitchell Jacob wrote:


Hi FS Devs,

I’m experiencing unreproducible thickness results when running any 7+ 
version with parallelization enabled. Running recon-all without 
parallelization produces consistent thickness results. I’m running 
this in AlmaLinux8 (a library-equivalent downstream OS to CentOS8).


I’m attaching a table (table1) of 12 recons with bert:

  * 3 parallelized with CentOS8-compiled 7.4.1
  * 3 non-parallelized with CentOS8-compiled 7.4.1
  * 3 parallelized with CentOS7-compiled 7.4.1
  * 3 non-parallelized with CentOS7-compiled 7.4.1

I suspected the downstream CentOS8 libm was the culprit (because of 
testing I did this last 2023 summer). I ran 3 more recons parallelized 
with the CentOS7-compiled 7.4.1, but before running the recon-all 
command, set LD_PRELOAD to a copy of the CentOS7 libm libraries. The 
thickness results were then consistent, see the second table below 
(table2). I could not run this experiment on the CentOS8-compiled 
version, as that one is obviously not backward compatible with CentOS7 
libm.


As a quick test of the OS-dependency, I submitted 3 parallel recons on 
MLSC with 7.3.3. Each reported different thickness. See table 3 (table3).


I’m asking if you can please confirm whether running any 7.+ version 
with parallelization is generating reproducible results for you in 
CentOS8 (or equivalent)?


P.S. - I tested 6.0 (CentOS6-compilation) with parallelization, and 
the results were consistent.


Best,

Mitch


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Re: [Freesurfer] Freesurfer white matter overestimated

[Douglas N. Greve]

Hi, no snapshots were attached.

On 2/1/2024 6:02 AM, Luisa Klahn wrote:


External Email - Use Caution

Hello!
I am processing structural data from a 3T scanner using Freesurfer 
version 7.3.2. For some subjects, the grey matter looks very thin, and 
the white matter looks overestimated. I'll attach screenshots of the 
brainmask, wm mask, and T1 including wm and pial surface lines.
I have tried to set control points into the wm but this did not change 
the results.


Does anyone have an idea? Would it be possible to change the intensity 
settings in the recon-all command?


Thanks for helping!
Luisa

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Re: [Freesurfer] Fixing intensity normalization issue which leads to gray matter classified as WM

[Douglas N. Greve]

Are you saying that synthseg itself is generating the wrong seg or that 
something is going wrong further downstream? The recon-all stream with 
synthseg is not a supported pipeline at the moment. For the standard 
stream, can you send the full recon-all.log file?


On 1/29/2024 2:04 PM, Maya Yablonski wrote:


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Hello,

I am running freesurfer v7.3.2 reconall with -synthseg on a pediatric 
sample, and for one specific subject I keep getting a lot of gray 
matter classified as white matter, which leads to the ?h.white 
surfaces being too close to the pial surface. I have tried running 
with and without the --robust option but the issue recurs. Are there 
any expert options that I can play with before manually editing the 
WM.mgz? The issue is pervasive throughout the brain so will require 
heavily editing every single slice. The values for the misclassified 
gray matter are 85-97 in the brainmask.mgz and 100-110 in the WM.mgz 
and the T1 image looks ok by eye. When trying to run the same subject 
with the default pipeline (no synthseg), it crashes with the following 
error:


reading 1 input volumes...
logging results to talairach.log
reading 
'/share/software/user/open/freesurfer/7.3.2/average/RB_all_2020-01-02.gca'...

GCAread took 0 minutes and 1 seconds.
average std = 7.2   using min determinant for regularization = 5.2
0 singular and 884 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
error: mghRead(/MYPATH/freesurfer/sub-2341/mri/brainmask.mgz, -1): 
could not open file

error: mri_em_register: could not open mask volume brainmask.mgz.

I wonder if there's any parameter I can tweak in the expert.opts?
Thanks for any leads,
Maya

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Re: [Freesurfer] Calculation of MRI intensity

[Douglas N. Greve]

you will have to binarize it first, eg, mri_binarize --i inputimage.mgz 
--min threshold --o binary.mgz, then run mri_segstats --seg binary.mgz 
--id 1 --i inputimage.mgz --sum sum.dat


On 2/7/2024 8:55 AM, Huang, Yujing wrote:


I think mri_segstats –i option will do that - 
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats


Best,

Yujing

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *ERNEST KISSI

*Sent:* Wednesday, February 7, 2024 8:12 AM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] Calculation of MRI intensity

*External Email - Use Caution *

Hi Freesurfer Team,

Please I want to calculate the mean intensity of a skullstripped MRI 
image. I do not want to use recon-all because I do not want to 
parcellate or segment it. Is there such utility or function in freesurfer?


Thank you.

Sincerely,

Ernest Kissi Kontor.


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Re: [Freesurfer] No ROI name in summary of MNI305 group analysis

[Douglas N. Greve]

Try adding -seg fsaverage aparc+aseg.mgz


On 1/26/2024 4:59 AM, wangzhiwei3233 wrote:


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Dear Gouglas,
Thank you for your replay. There is still no ROI name in the summary 
after adding --reg $SUBJECTS_DIR/fsaverage/mri.2mm/reg.2mm.dat.

My updated command is as followed:
/mri_volcluster *--in* ./sig.${sigFormat} *--thmin* ${thvoxel} 
*--sign* ${sigsignTemp} *--cwpvalthresh 0.05 --minsize* 273 *--fwhm* 6 
*--no-adjust* *--sum* ${nameout}.cluster.summary *--out* 
${nameout}.cluster.nii.gz *--ocn* ${nameout}.ocn.nii.gz *--labelbase* 
$Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_${nameout}/label 
*--reg ${SUBJECTS_DIR}/fsaverage/mri.2mm/reg.2mm.dat* *--mask 
*${SUBJECTS_DIR}/fsaverage/mri.2mm/subcort.mask.mgz/

//
Best,
zhiwei
---
Date: Sat, 25 Nov 2023 14:04:08 -0500
From: "Douglas N. Greve"
Subject: Re: [Freesurfer] No ROI name in summary of MNI305 group
analysis
To:freesurfer@nmr.mgh.harvard.edu
Message-ID:
Content-Type: text/plain; charset="utf-8"

Try adding --reg $SUBJECTS_DIR/fsaverage/mri.2mm/reg.2mm.dat


On 11/23/2023 2:32 AM, wangzhiwei3233 wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Experts,
> I did group-level analysis in MNI305 space.? Then I output the summay 
> via command 'mri_volcluster' as follows:
> /*mri_volcluster --in* ./sig.nii.gz *--thmin* ${thvoxel} *--sign* 
> ${sigsignTemp} *--cwpvalthresh* 0.05 *--minsize* 273 *--fwhm 6* 
> *--no-adjust --sum* ${nameout}.cluster.summary*--out* 
> ${nameout}.cluster.nii.gz *--ocn* ${nameout}.ocn.nii.gz *--labelbase* 
> $Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_${nameout}/label 
> *--mask* 
> /mnt/hgfs/G/work/MetaCog/Human/subjects/fsaverage/mri.2mm/subcort.mask.mgz/

> /
> /
> the output is as follows. there are no ROI names in the table. Is it 
> because I missed the option '--reg' in the command line? Which 
> register file shoul I use if I should add it? I can't find the 
> 'register.dat' file in fsaverage folder.

>
> Very appricated if you can help me.
>
> Best,
> zhiwei

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Re: [Freesurfer] T1 maps longitudinal data

[Douglas N. Greve]

Currently, you'd have to convert them  to  t1-weighted images and then 
run recon-all on that. I think there is software out there to do this if 
you go the t1 maps from an mp2rage scan


On 1/25/2024 11:57 AM, AJ wrote:


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Hi,
I have T1 relaxation maps over 4 time points. In terms of longitudinal 
analysis, could these maps be fed into Freesurfer longitudinal 
pipeline to control for intersubject variability of signal intensity?  
Any other method you would recommend?


Many thanks

AJ

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Re: [Freesurfer] Freesurfer Intensity representation

[Douglas N. Greve]

See this tutorial 
https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0 on 
multimodal integration. Basically, you will need to run mri_vol2vol to 
map your MPF volume to the anatomical/conformed space, then run 
mri_segstats passing it the segmentation you want to use and the 
converted MPF image.


On 1/24/2024 11:04 AM, ERNEST KISSI wrote:


External Email - Use Caution

When MPF images are registered on T1 images, I think the intensity 
represents the MPF values, not the T1 values. This is because the 
registration process only transforms the spatial coordinates of the 
MPF images to match the T1 images, but does not alter the signal 
intensity or contrast of the MPF images. Therefore, the registered MPF 
images still reflect the macromolecular proton fraction of the brain 
tissue, which is independent of the T1 values.


Just wanna confirm. This is from a colleague.

On Wed, Jan 24, 2024 at 6:50 PM ERNEST KISSI 
 wrote:


I want to use the intensity of the macromolecular proton fraction
(MPF). I want to compare the intensity of the MPF of the various
brain regions or structures between two groups. I am not using the
volumes. The MPF was registered  on the T1 so does it mean that
the intensity is from the MPF.

On Wed, Jan 24, 2024 at 6:44 PM ERNEST KISSI
 wrote:

I want to use the intensity of the macromolecular proton
fraction (MPF). I want to compare the intensity of the MPF
between two groups.

On Wed, Jan 24, 2024 at 6:11 PM Fischl, Bruce R.,PHD
 wrote:

It is whatever volume you gave as input to recon-all. If
you tell us which statistics you want to regenerate for
another volume we can tell you know what commands to run.


cheers

Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu
 *On Behalf Of
*ERNEST KISSI
*Sent:* Wednesday, January 24, 2024 9:05 AM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] Freesurfer Intensity representation

*External Email - Use Caution *

Hi,

Please I made an initial enquiry about using freesurfer
for MPF maps. The feedback was that I register the MPF
maps on their corresponding T1 images using multimodal
registration. I used FSL to do the multimodal registration
and then use recon-all in freesurfer.

Now I want to know what the intensity and the volume of
the output in the aseg file represent. Is it the intensity
of the MPF or the TI and MPF?

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Re: [Freesurfer] Recon-all Longitudinal Talairach issue

[Douglas N. Greve]

Can you send the recon-all.log file that contains the error?

On 1/24/2024 4:01 AM, Kapteijns, Kirsten wrote:


External Email - Use Caution

Dear all,

I have run recon-all successfully on multiple subjects on multiple 
timepoints. If I open the mri folder, it shows the correct talairach 
files and no issues arose during processing.


However, when I then run the longitudinal pipeline (first base, which 
also shows correct files) on the subjects (recon-all -long SUBJXXtp1 
SUBJXXbase -all) the talairach shows an failure detection and the 
subsequent file is talairach.invalid.mgz.


The actual segmentation etc. seems fine when inspecting, but when I 
then want to run segmentBS.sh on these processed folders, it gives an 
error.


I have run this a few month back without issue, and had just a few 
subjects left, but now all of them show this same error. Any idea how 
this could be caused?


Kind regards,

Kirsten

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Re: [Freesurfer] MRIread and RAS orientation

[Douglas N. Greve]

The vol structure will reflect how the volume is stored on disk. If you 
have two files that have the same structure (ie, order of rows, cols, 
slices) then they will have the same vol in matlab regardless of the 
header orientation.


On 1/23/2024 11:00 AM, Fotiadis, Panagiotis wrote:


External Email - Use Caution

Thank you both! I am asking because I took a nifti file that was in 
RAS orientation (file1), flipped it into LAS (using /fslorient 
-swaporient file2/), and then opened both files in MATLAB with 
MRIread. The resulting .vol matrices for both files were, however, 
identical (i.e., voxel at location  in file1.vol had the exact 
same value as voxel in location  in file2.vol). Would you 
happen to know if the indexing of the vol structure is expected to 
come out the same with MRIread, regardless of the orientation?


Thanks,

Panos

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

*Date: *Tuesday, January 23, 2024 at 9:14 AM
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] MRIread and RAS orientation

*External Email - Use Caution *

I’m pretty sure that the Matlab code does not reorient.

Cheers,

Eugenio

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 


*Date: *Tuesday, January 23, 2024 at 08:49
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] MRIread and RAS orientation

I’m not sure about the MATLAB codes. When the C codes read in images, 
no automatically transformation is done.


I think you can verify it by checking several [c, r, s] locations of 
both images loaded with MRIread().  I think c and r are reversed in 
MATLAB. And the index starts from 1.


Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Fotiadis, 
Panagiotis

*Sent:* Tuesday, January 23, 2024 1:54 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] MRIread and RAS orientation

*External Email - Use Caution *

Hello,

I have two nifti files that are both in the same MNI space, the former 
of which is saved in LAS orientation while the other in RAS 
orientation (as showcased by the “Orientation” field of mri_info). I 
just wanted to verify: When loading both on MATLAB using MRIread, both 
of their volumes are automatically loaded (or transformed in the case 
of the first file) in the same RAS orientation, right (using the 
vox2ras transformation)?


Thanks in advance!

Best,

Panos

**
Electronic Mail is not secure, may not be read every day, and should 
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Re: [Freesurfer] if: Expression Syntax - preproc-sess with -nomc option

[Douglas N. Greve]

Can you run it with -debug as the first option, capture the output, and 
send it to me? It will be a lot of output, so just capture it in a file 
and send the file, eg

preproc-sess -debug -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd 
rest -per-run -sliceorder up -force | tee pps.log



On 1/22/2024 11:20 AM, Stefano Delli Pizzi wrote:
>  External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I'm attempting to run preproc-sess with -nomc option
>
> preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest 
> -per-run -sliceorder up -force
> if: Expression Syntax.
>
> This error occurred before to create the file with slice timing correction
>
> The error did not occur when I run the preproc-sess command line without the 
> -nomc option.
>
> I've searched the list and no similar errors have been reported. Does anyone 
> have any thoughts on how to trouble-shoot this one?
>
> FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
> Platform: Darwin Kernel Version 21.6.0
>
> ___
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Re: [Freesurfer] FW: Create a Binarized ROI for Surface

[Douglas N. Greve]

Sorry, I don't understand what you are asking. Can you elaborate?

On 1/19/2024 4:37 PM, Na, Xiaoxu wrote:


External Email - Use Caution

Hi Dr. Doug,

Thanks for your prompt reply!

I’m sorry it was not clear. Basically, I would like to extract the 
cortical volume for each subject using a pre-defined ROI. As I have 
already created the surface ROI, thanks to your answer on the official 
website, I have no further question now on ROI.


This group analysiscan’s further survive the multiple correction using 
the mri_glmfit-sim that you gave me years ago, so there is no file 
like cache.th40.neg.sig.ocn.annot as before.


Instead, I tried to create a ROI and run command line as $mri_segstats 
--seg mask1.sm1.bin.mgh --exlude 0 --i 
groupAnalysis/lh.volume.g2v2.10.mgh --avgwf lh.volume.mask1.dat, where 
mask1.sm1.bin.mgh is the ROI and groupAnalysis/lh.volume.g2v2.10.mgh 
is the mris_proc processed file from a group of subjects. It did 
extract something, 1 number for each subject, but I believe there is a 
ratio or scalar between the actual volume of that vertex and those 
show in lh.volume.g2v2.10.mgh. Is there anywhere I can figure out 
where this ratio/scalar is? Thank you so much!


Regards,

Xiaoxu

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* Friday, January 19, 2024 3:16 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] FW: Create a Binarized ROI for Surface

On 1/19/2024 3: 45 PM, Na, Xiaoxu wrote: External Email - Use Caution 
Dear Freesurfer Expert, While the sphere can only be drawn using that 
Dr. Doug suggested, the sphere option would mess up. Do you need help 
with this? If so, can you give


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On 1/19/2024 3:45 PM, Na, Xiaoxu wrote:

*External Email - Use Caution *

Dear Freesurfer Expert,

While the sphere can only be drawn using that Dr. Doug  suggested,
the sphere option would mess up.

Do you need help with this? If so, can you give more info?

I have a further question as using this ROI to extract surface
information from ?h.area and ?h.volume. I’m using the command line
as below:

$mri_segstats --seg mask1.sm1.bin.mgh --exlude 0 --i
groupAnalysis/lh.volume.g2v2.10.mgh --sumwf lh.volume.mask1.dat

However, due to the calculation of surface and volume, we need
another input of sum file (ASCII file), how can I do that before I
can run the above?

Sorry, I don't know what you mean

Another simple question is, what is lh.volume.mgh in the group
analysis folder processed by mris_proc? Is that a simple merge of
all subjects lh.volume file? Why the number is between 0-10, is
there any way I can put ?h.volume or ?h.area back to gain each
subject’s real volume or area value on that surface vertex? Thank
you so much!

This is a vertex-wise measure of volume of the cortex at that point. 
Eg, a given vertex has an area defined by the mean area of the 
triangles that abut it. When this  is multiplied by the thickness, you 
get a volume measure (we actually compute it differently using a 
truncated pyramid, but that's the basic idea). You can use this in a 
VBM-like analysis.


Regards,

Xiaoxu

*From:* Na, Xiaoxu
*Sent:* Wednesday, December 13, 2023 4:25 PM
*To:* Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Create a Binarized ROI for Surface

Dear Freesurfer Expert,

We would like to extract mean Cth values for each subject within a
own-creaded ROI (surface defined), using freeview (for instance).
Is it possible to create a ROI (i.e. spherical surface)
surrounding a particular vertex of an sig.mgh file? (and then
extract its mean Cth values for each subject)?

I think this is not a new question, and it was posted somehow on
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers

<https://secure-web.cisco.com/14KqP_qoE2NgpsQ3WWt56RlBZkuC6REnTh_WGRL08hzCcuaKk7nfMdkDINT06xy8szEnMZ7sj5130u58ShCsklEJe1XpT7uF9TT7Z-1wwaefAUc-l1woSMFAT6vgy1UjauR35mq8tMT39ZT9VUOqgomqQoKY8W-e0Bikmgym_GIEwt762EGrMGAo8VgrdLdF0cj-07rkA2OhQJFC9bp1zlnD3p_VxHQCQeliudCQe8ovUnbSyuWQnbujrNqEjvce7qMcU1awT65u-f1_JcWQCgJ0oyicWs6s3zRf2T5QzgJSeaHK5H0JZfAOk4y6J6mUbKgdJ5QyGIm4UvXo7fdpy2w/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1p4y33YGPMt3Xr5IlZXBnYyxigfeQuk70cz1lkfaic6sGmC8qA5lauVhI1rT6YyYkzZwV4Nc5The50lU99NUP0P08OuZXZlGcV2awRfjyD8dnCwV-ej_DoLtv2aEl5L6H_XsKSYPlV5UQTHQOPgZ0OlzfqPWrMDLf7vEJTFgE0oIXHWTkjRWe-r_xTSUd-TnsGIxbMkTt75znip6awWwYkSDWqYBayh-gKCuDQewg8jam5eacT7xjQeIMCJ6PfiYZ6aRVvxfG53AvXI1SpeazLlp_w0DaKDZ2Z6lqz6bpU1tQe5fI97ACIq3V9v7itFjzK-EsQ3hCBgBEt6pwsZjn4A%2Fhttps%2A3A%2A2F%2A2Fsurfer.

Re: [Freesurfer] FW: Create a Binarized ROI for Surface

[Douglas N. Greve]

On 1/19/2024 3:45 PM, Na, Xiaoxu wrote:


External Email - Use Caution

Dear Freesurfer Expert,

While the sphere can only be drawn using that Dr. Doug  suggested, the 
sphere option would mess up.



Do you need help with this? If so, can you give more info?


I have a further question as using this ROI to extract surface 
information from ?h.area and ?h.volume. I’m using the command line as 
below:


$mri_segstats --seg mask1.sm1.bin.mgh --exlude 0 --i 
groupAnalysis/lh.volume.g2v2.10.mgh --sumwf lh.volume.mask1.dat


However, due to the calculation of surface and volume, we need another 
input of sum file (ASCII file), how can I do that before I can run the 
above?



Sorry, I don't know what you mean


Another simple question is, what is lh.volume.mgh in the group 
analysis folder processed by mris_proc? Is that a simple merge of all 
subjects lh.volume file? Why the number is between 0-10, is there any 
way I can put ?h.volume or ?h.area back to gain each subject’s real 
volume or area value on that surface vertex? Thank you so much!


This is a vertex-wise measure of volume of the cortex at that point. Eg, 
a given vertex has an area defined by the mean area of the triangles 
that abut it. When this  is multiplied by the thickness, you get a 
volume measure (we actually compute it differently using a truncated 
pyramid, but that's the basic idea). You can use this in a VBM-like 
analysis.


Regards,

Xiaoxu

*From:* Na, Xiaoxu
*Sent:* Wednesday, December 13, 2023 4:25 PM
*To:* Freesurfer support list 
*Subject:* Create a Binarized ROI for Surface

Dear Freesurfer Expert,

We would like to extract mean Cth values for each subject within a 
own-creaded ROI (surface defined), using freeview (for instance). Is 
it possible to create a ROI (i.e. spherical surface) surrounding a 
particular vertex of an sig.mgh file? (and then extract its mean Cth 
values for each subject)?


I think this is not a new question, and it was posted somehow on 
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers 
, 
and *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67677.html 
, 
but I’m still encountering questions.


These commands did run, but together they didn’t create a binarized 
mask with 1 for the sphere around the coordinates, and 0 for the other 
voxels. Would you recommend what I should change? Thank you so much!


$mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness 
--pdf sphere --sphere-center -7.4 67.22 60.27 --radius 5 --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

Regards,

Xiaoxu


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Re: [Freesurfer] Issue with mri_glmfit-sim

[Douglas N. Greve]

mmm, still not sure. I'm assuming that you don't really have those 
backslashes ("\") in there. Can you try it with mcz instead of perm just 
to see if you can get it running. I would also try version 7.4.1; 
version 6.0 is from a long time ago and so hard to debug.


On 1/19/2024 3:03 PM, O'Neill, Alexandra Grace wrote:

Hi Doug,

Thanks so much for getting back to me. Below is our previous 
correspondence:


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


*Date: *Friday, January 12, 2024 at 4:19 PM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] Issue with mri_glmfit-sim

I think v6 might be broken when using -bg. Try removing that.

On 1/8/2024 11:19 AM, O'Neill, Alexandra Grace wrote:



Hello FS community,

To correct for multiple comparisons for the results of a
parametric modulation GLM analysis, I have run mri_glmfit-sim
using Freesurfer version 6.0 with the following command:

mri_glmfit-sim \ --debug --glmdir

/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepSec/OSGM/osgm
\ --perm 1000 2.0 abs \ --cwp 0.05 \ --2spaces \ --bg 1

The code completes without errors, however none of the output
files mentioned in this tutorial

<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm>
 are
created. Below are the contents of the mriglm-fit.log file in case
that is helpful.*

*



$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $

cwd /autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago

cmdline mri_glmfit.bin --y

/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz
--wls

/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz
--fsgd /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd --osgm
--glmdir

/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM
--surf fsaverage rh --fwhm 6

sysname  Linux

hostname tempest.nmr.mgh.harvard.edu

machine  x86_64

user     ago5

FixVertexAreaFlag = 1

UseMaskWithSmoothing     1

fwhm     6.00

niters    26.00

OneSampleGroupMean 1

y
 
/autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz

logyflag 0

usedti  0

FSGD /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd

labelmask
 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/fsaverage/label/rh.cortex.label

maskinv 0

glmdir

/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM

IllCondOK 0

ReScaleX 1

DoFFx 0

wFile

/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz

weightinv  1

weightsqrt 1

ResidualFWHM 12.847434

SearchSpace 74490.844410

anattype surface

Do you have any idea how to fix this problem? Thanks so much in
advance!

Alexandra



*Alexandra G. O'Neill**(she/her)*

/Clinical Research Coordinator/
Massachusetts General Hospital
Department of Psychiatry
Division of Neuropsychiatry and Neuromodulation
149 13th Street, Charlestown, MA 02129

T: (617) 726-8753 | E: agone...@mgh.harvard.edu
<mailto:agone...@mgh.harvard.edu>


Thank you,
Alexandra

*From:* Greve, Douglas N.,Ph.D. 
*Sent:* Friday, January 19, 2024 2:44 PM
*To:* O'Neill, Alexandra Grace ; Freesurfer 
support list 

*Subject:* Re: [Freesurfer] Issue with mri_glmfit-sim
Sorry, I already forgot  what the problem was. Can you include our 
previous correspondence? Also, make sure to reply to the list. Thanks!


On 1/19/2024 10:07 AM, O'Neill, Alexandra Grace wrote:

Hi Doug,

Thank you for getting back to me. Unfortunately, the issue is
persisting, and the command is still running but with no output
files. Is there anything else that could potentially be the
problem? I’m attaching the most recent log file (as a txt file)
from the command I ran. Please let me know if any other
information would be helpful!

Thank you so much,

Alexandra


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Re: [Freesurfer] Issue with mri_glmfit-sim

[Douglas N. Greve]

Sorry, I already forgot  what the problem was. Can you include our 
previous correspondence? Also, make sure to reply to the list. Thanks!


On 1/19/2024 10:07 AM, O'Neill, Alexandra Grace wrote:


Hi Doug,

Thank you for getting back to me. Unfortunately, the issue is 
persisting, and the command is still running but with no output files. 
Is there anything else that could potentially be the problem? I’m 
attaching the most recent log file (as a txt file) from the command I 
ran. Please let me know if any other information would be helpful!


Thank you so much,

Alexandra

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Re: [Freesurfer] Applying Wang Atlas to Group Analysis Results in FreeSurfer

[Douglas N. Greve]

what is the wang atlas? volume or surface?

On 1/19/2024 12:20 AM, Sujeevini Sujanthan wrote:


External Email - Use Caution

Hi,

I would like to apply the wang atlas over the group activation maps 
produced from Freesurfer analysis. I would appreciate any 
guidance/instructions you can offer for how I can do that.


Thank you for your time!

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Re: [Freesurfer] Ex-vivo adult brain MRI segmentation and surface analysis

[Douglas N. Greve]

That does not look like it is a problem with the input image. Do you 
have a normal, invivo MRI that you can run samseg on to see if it is 
just a problem with your platform?


On 1/18/2024 3:57 AM, K Eswar wrote:


External Email - Use Caution

Dear FS community

I have an ex-vivo human adult brain MRI, both in T1 MPRAGE and Fiesta. 
I have recently come across a paper on MRI segmentation using a 
function called- samseg. From the webpage( *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon 
) 
I realized that there is a different approach altogether to processing 
these fixative brains. However, as a first step, when I tried the 
samseg function, I noticed that the function exited with errors.


The steps where it fails are:
Read mesh collection: 
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz

Transforming points
Transforming points
Read mesh collection: 
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
Read mesh collection: 
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz

Killed

I am using the Ubuntu 22.04 version with RAM 32GB
Freesurver version: 
freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275


I would greatly appreciate it if you could help me with MRI 
segmentation and cortical surface analysis on these brains.


Thanks for your time and consideration.

Regards
K Eswar
Project Scientist
Sudha Gopalakrishnan Brain Centre
IIT Madras, India

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Re: [Freesurfer] T1map processing error

[Douglas N. Greve]

The way I have done this was do compute T1w images (MPRAGE) through 
simulations, then run recon-all on that.


On 1/17/2024 11:55 AM, Maksim Slivka wrote:


External Email - Use Caution

Dear FS community,


Recently our lab started collecting 3D-QALAS (Cho et al., 2023). Using 
this method, a quantitative T1map was constructed.



Trying to process this map, FS (v7.1.0) recon-all would output the 
following error:


mri_cc: no WM voxels found with norm > 40 -- check skull stripping


I would like to ask if anyone here has experience in processing 
quantitative T1maps with FS? Did you also run into that error? Were 
you able to solve it?



I am looking forward to hearing from you.


Best regards,

Maksim Slivka

Head engineer

Center for Lifespan Changes in Brain and Cognition (LCBC)

Department of Psychology

University of Oslo

POB 1094 Blindern

0317 Oslo

Norway


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Re: [Freesurfer] Sample registration question

[Douglas N. Greve]

Yes, that would be an ROI analysis

On 1/13/2024 1:00 PM, Mirsol Choi wrote:


External Email - Use Caution

Hello,

My goal is to compare the FA and MD values of hippocampal subfields 
(only inside the hippocampus) between cognitively normal, MCI, and AD 
subjects. I am unsure if this would require a voxel wise analysis or 
an ROI analysis… to my understanding this is more of a ROI analysis 
between subjects - is this assumption incorrect?


Thank you,
Peter

On Sat, Jan 13, 2024 at 10:44 AM Douglas N. Greve 
 wrote:


So this is where I get confused on your intentions because you say
that you want to do a voxel-wise analysis of an ROI. Do you mean
you want to do a voxelwise analysis but only inside, eg, whole
hippocampus?

On 1/12/2024 6:07 PM, Mirsol Choi wrote:


External Email - Use Caution

Hello,

Sorry I should have clarified. Yes, I would like to perform
voxelwise analysis of FA and MD values of hippocampal subfield
between subjects. Is this possible with free surfer?

Thank you again for your time.

M

On Fri, Jan 12, 2024 at 4:05 PM Douglas N. Greve
 wrote:

oh, I thought you wanted to do an ROI analysis. You mean for
a voxelwise analysis?

On 1/12/2024 5:46 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there,


Following the first registration step, should I also run
another registration command to put all fa-in-subfields.mgz
for each subject onto the same space for inter subject
analysis of FA values?

Thanks again,
M

On Fri, Jan 12, 2024 at 3:00 PM Douglas N. Greve
 wrote:

Map the diffusion data to the subfield space, eg,
mri_vol2vol --mov fa.nii.gz --reg register.lta --targ
subfields.mgz --o fa-in-subfields.mgz
Then run mri_segstats
mri_segstats  --ctab-default --i fa-in-subfields.mgz
--seg subfields.mgz --sum fa-in-subfields.dat



On 1/12/2024 4:53 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there,

Is there a way to successfully obtain FA/MD values from
the hippocampus subfields?

Thank you,
M

On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve
 wrote:

I'm not sure what you mean. The subfields are an
ROI-based analysis. Are you saying you want to do a
voxel-based analysis (without reference to ROIs)?

On 1/9/2024 12:05 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there Freesurfer,

I am currently using freesurfer to take DTI
metrics (FA, MD) from hippocampal subfields.
At this point of my exploration with freesurfer, I
am able to correctly register the hippocampal
subfields and diffusion data, and obtain my FA
values from the subfields. However, this is at the
individual subject level.

I will eventually need to register all of my
samples in the same space for me to do a group
analysis. However I am unsure what the order of
registration should be for this process to be
feasible.

Does this order seem feasible for accurate analysis?

1) recon-all all of my subjects
2) dt_recon all of my subjects (one of the outputs
is a registration file, which has registered the
DTI data to outputs of recon-all)
3) run the hippocampus segmentation command on all
subjects (segmentHA_T1.sh) to obtain hippocampal
subfield segmentation
4) register the segmentation file to the FA maps
(output of dt_recon) using vol2subfield command
5) After creating a subfield-FA map for each
subject, spatial normalize the samples onto the
same space using *mri_vol2vol*
*
*
Thank you so much for taking the time reading my
question. If there is a different method to
spatially normalizing my datasets, or if there is
a more optimal order of registration, I'd be happy
to hear from you.

Thank you,
M

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Re: [Freesurfer] Midline white/pial surface

[Douglas N. Greve]

I would also be helpful to have some pics of what you are seeing. The 
surface is not valid in the "medial well" -- ie all the non-cortical 
structures on the central sagittial plane such as thalamus an VDC.


On 1/16/2024 7:50 AM, Huang, Yujing wrote:


Can you try the troubleshooting methods from this page:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData

Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Sunniva Fenn-Moltu

*Sent:* Monday, January 15, 2024 6:35 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] Midline white/pial surface

*External Email - Use Caution *

Hi,

i'm running recon-all and have encountered an issue with the surface 
boundaries on several subjects. What I'm experiencing is that the 
midline surface is included in the white surface in one hemisphere, 
and in the pial surface on the other hemisphere. This results in the 
midline boundary of the thalamus and ventral DC being white surface in 
one hemisphere, and pial surface in the other. Do you have any idea 
why this is happening?


I am running freesurfer on NoMachine (freesurfer/7.4.1).

Best,

Sunniva


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Re: [Freesurfer] [External] Re: extracting measurements for mean gray matter thickness/LGI

[Douglas N. Greve]

why not just average them together? Or are you hoping that FS provides 
this last small step? I don't think that we do ...


On 1/16/2024 10:04 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

Sorry, to be clear, there is a measurement for bilateral mean 
thickness offered by default? I'm able to gather the left mean 
thickness and the right mean thickness easily.


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

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


*Sent:* Friday, January 12, 2024 4:26 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* [External] Re: [Freesurfer] extracting measurements for 
mean gray matter thickness/LGI
I don't understand. Why not use the mean thickness from FS? We have an 
lGI module; we have not supported it in years, but maybe it still 
works. *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
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On 1/10/2024 9:52 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

Hi,

We were wondering what the preferred command is for extracting mean 
gray matter thickness/LGI


I am aware that FS outputs left/right mean thickness but wanted to be 
conscious of the fact that left/right hemisphere might have different 
sizes.


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

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Re: [Freesurfer] Sample registration question

[Douglas N. Greve]

So this is where I get confused on your intentions because you say that 
you want to do a voxel-wise analysis of an ROI. Do you mean you want to 
do a voxelwise analysis but only inside, eg, whole hippocampus?


On 1/12/2024 6:07 PM, Mirsol Choi wrote:


External Email - Use Caution

Hello,

Sorry I should have clarified. Yes, I would like to perform voxelwise 
analysis of FA and MD values of hippocampal subfield between subjects. 
Is this possible with free surfer?


Thank you again for your time.

M

On Fri, Jan 12, 2024 at 4:05 PM Douglas N. Greve 
 wrote:


oh, I thought you wanted to do an ROI analysis. You mean for a
voxelwise analysis?

On 1/12/2024 5:46 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there,


Following the first registration step, should I also run another
registration command to put all fa-in-subfields.mgz for each
subject onto the same space for inter subject analysis of FA values?

Thanks again,
M

On Fri, Jan 12, 2024 at 3:00 PM Douglas N. Greve
 wrote:

Map the diffusion data to the subfield space, eg,
mri_vol2vol --mov fa.nii.gz --reg register.lta --targ
subfields.mgz --o fa-in-subfields.mgz
Then run mri_segstats
mri_segstats  --ctab-default --i fa-in-subfields.mgz --seg
subfields.mgz --sum fa-in-subfields.dat



On 1/12/2024 4:53 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there,

Is there a way to successfully obtain FA/MD values from the
hippocampus subfields?

Thank you,
M

On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve
 wrote:

I'm not sure what you mean. The subfields are an
ROI-based analysis. Are you saying you want to do a
voxel-based analysis (without reference to ROIs)?

On 1/9/2024 12:05 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there Freesurfer,

I am currently using freesurfer to take DTI metrics
(FA, MD) from hippocampal subfields.
At this point of my exploration with freesurfer, I am
able to correctly register the hippocampal subfields
and diffusion data, and obtain my FA values from the
subfields. However, this is at the individual subject
level.

I will eventually need to register all of my samples in
the same space for me to do a group analysis. However I
am unsure what the order of registration should be for
this process to be feasible.

Does this order seem feasible for accurate analysis?

1) recon-all all of my subjects
2) dt_recon all of my subjects (one of the outputs is a
registration file, which has registered the DTI data to
outputs of recon-all)
3) run the hippocampus segmentation command on all
subjects (segmentHA_T1.sh) to obtain hippocampal
subfield segmentation
4) register the segmentation file to the FA maps
(output of dt_recon) using vol2subfield command
5) After creating a subfield-FA map for each subject,
spatial normalize the samples onto the same space using
*mri_vol2vol*
*
*
Thank you so much for taking the time reading my
question. If there is a different method to spatially
normalizing my datasets, or if there is a more optimal
order of registration, I'd be happy to hear from you.

Thank you,
M

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Re: [Freesurfer] Registration of MPF to FLASH 3D image

[Douglas N. Greve]

If you can program, then write a script with a loop

On 1/12/2024 5:41 PM, ERNEST KISSI wrote:


External Email - Use Caution

Thanks,I have been able to fix the problem.  But is there a way to run 
multiple samples at a time on windows? Because I have over 50 images 
to process.


On Sat, Jan 13, 2024, 12:31 AM Douglas N. Greve 
 wrote:


That is the bbregister command. You should look at the output of
recon-all

On 1/11/2024 5:37 PM, ERNEST KISSI wrote:


External Email - Use Caution

This what the output shows doing the bbregister.

image.png


On Thu, Jan 11, 2024 at 6:09 PM Fischl, Bruce R.,PHD
 wrote:

A T1-weighted FLASH should work. When you say “it did not
work” what do you mean? Can you give us some details?

Cheers

Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu
 *On Behalf Of
*ERNEST KISSI
*Sent:* Thursday, January 11, 2024 3:54 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] Registration of MPF to FLASH 3D image

*External Email - Use Caution *

Dear Freesurfer team,

I messaged the team on my MPF map analysis and a suggestion
was made that I register the MPF maps on the T1 MPRAGE
images. However, I did not acquire MPRAGE  but FLASH images.

Can I used those instead ?  Again, I tried even using only
the T1 FLASH images and it did not work so I am not sure
whether the registration of the MPF maps on it will work or
not. Is there anyway around this?

Thank you.

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Re: [Freesurfer] Sample registration question

[Douglas N. Greve]

oh, I thought you wanted to do an ROI analysis. You mean for a voxelwise 
analysis?


On 1/12/2024 5:46 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there,


Following the first registration step, should I also run another 
registration command to put all fa-in-subfields.mgz for each subject 
onto the same space for inter subject analysis of FA values?


Thanks again,
M

On Fri, Jan 12, 2024 at 3:00 PM Douglas N. Greve 
 wrote:


Map the diffusion data to the subfield space, eg,
mri_vol2vol --mov fa.nii.gz --reg register.lta --targ
subfields.mgz --o fa-in-subfields.mgz
Then run mri_segstats
mri_segstats  --ctab-default --i fa-in-subfields.mgz --seg
subfields.mgz --sum fa-in-subfields.dat



On 1/12/2024 4:53 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there,

Is there a way to successfully obtain FA/MD values from the
hippocampus subfields?

Thank you,
M

On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve
 wrote:

I'm not sure what you mean. The subfields are an ROI-based
analysis. Are you saying you want to do a voxel-based
analysis (without reference to ROIs)?

On 1/9/2024 12:05 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there Freesurfer,

I am currently using freesurfer to take DTI metrics (FA, MD)
from hippocampal subfields.
At this point of my exploration with freesurfer, I am able
to correctly register the hippocampal subfields and
diffusion data, and obtain my FA values from the subfields.
However, this is at the individual subject level.

I will eventually need to register all of my samples in the
same space for me to do a group analysis. However I am
unsure what the order of registration should be for this
process to be feasible.

Does this order seem feasible for accurate analysis?

1) recon-all all of my subjects
2) dt_recon all of my subjects (one of the outputs is a
registration file, which has registered the DTI data to
outputs of recon-all)
3) run the hippocampus segmentation command on all subjects
(segmentHA_T1.sh) to obtain hippocampal subfield segmentation
4) register the segmentation file to the FA maps (output of
dt_recon) using vol2subfield command
5) After creating a subfield-FA map for each subject,
spatial normalize the samples onto the same space using
*mri_vol2vol*
*
*
Thank you so much for taking the time reading my question.
If there is a different method to spatially normalizing my
datasets, or if there is a more optimal order of
registration, I'd be happy to hear from you.

Thank you,
M

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Re: [Freesurfer] Sample registration question

[Douglas N. Greve]

Map the diffusion data to the subfield space, eg,
mri_vol2vol --mov fa.nii.gz --reg register.lta --targ subfields.mgz --o 
fa-in-subfields.mgz

Then run mri_segstats
mri_segstats  --ctab-default --i fa-in-subfields.mgz --seg subfields.mgz 
--sum fa-in-subfields.dat



On 1/12/2024 4:53 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there,

Is there a way to successfully obtain FA/MD values from the 
hippocampus subfields?


Thank you,
M

On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve 
 wrote:


I'm not sure what you mean. The subfields are an ROI-based
analysis. Are you saying you want to do a voxel-based analysis
(without reference to ROIs)?

On 1/9/2024 12:05 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there Freesurfer,

I am currently using freesurfer to take DTI metrics (FA, MD) from
hippocampal subfields.
At this point of my exploration with freesurfer, I am able to
correctly register the hippocampal subfields and diffusion data,
and obtain my FA values from the subfields. However, this is at
the individual subject level.

I will eventually need to register all of my samples in the same
space for me to do a group analysis. However I am unsure what the
order of registration should be for this process to be feasible.

Does this order seem feasible for accurate analysis?

1) recon-all all of my subjects
2) dt_recon all of my subjects (one of the outputs is a
registration file, which has registered the DTI data to outputs
of recon-all)
3) run the hippocampus segmentation command on all subjects
(segmentHA_T1.sh) to obtain hippocampal subfield segmentation
4) register the segmentation file to the FA maps (output of
dt_recon) using vol2subfield command
5) After creating a subfield-FA map for each subject, spatial
normalize the samples onto the same space using *mri_vol2vol*
*
*
Thank you so much for taking the time reading my question. If
there is a different method to spatially normalizing my datasets,
or if there is a more optimal order of registration, I'd be happy
to hear from you.

Thank you,
M

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Re: [Freesurfer] Including superficial white matter in cortical parcellation

[Douglas N. Greve]

I suspect the problem is with the aseg.mgz input. You can regenerate 
that with the new surfs with a different call to mri_surf2volseg. 
However, that will take a --fix-presurf-with-ribbon argument, so you 
will also have to regenerate the ribbon.mgz file for the new surfaces 
with mris_volmask


On 1/9/2024 7:23 AM, Thomas, George wrote:


External Email - Use Caution

Dear Freesurfer Experts,

I am interested in generating a volumetric segmentation and 
parcellation of the HCP-MMP1 atlas using mri_surf2volseg - and I have 
previously done this like so:


mri_surf2volseg --o $sub/HCP-MMP1_fsSpace.mgz \
                      --label-cortex --i $sub/mri/aseg.mgz --threads 4 \
                      --lh-annot $sub/label/lh.HCP-MMP1.annot 1000 
--lh-cortex-mask $sub/label/lh.cortex.label \
                      --lh-white $sub/surf/lh.white --lh-pial 
$sub/surf/lh.pial \
                      --rh-annot $sub/label/rh.HCP-MMP1.annot 2000 
--rh-cortex-mask $sub/label/rh.cortex.label \
                      --rh-white $sub/surf/rh.white --rh-pial 
$sub/surf/rh.pial



However rather than use the regular white matter surface generated by 
recon-all (as above), I want to parcellate between the pial surface 
and a superficial white matter surface 1mm below the GM/WM boundary.


I have generated this superficial white matter (SWM) surface for both 
hemispheres like so:

mris_expand lh.white -1 lh.SWM.1mm

My first though was just to replace the --rh-white / --lh-white inputs 
with the SWM surface, but after running this, the output remains the 
same.


I think I may also need use a different input than aseg.mgz, but not 
sure what this would be or how to generate it.


Any assistance you could offer with the would be greatly appreciated.

Many thanks,
George


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Re: [Freesurfer] poor inferior cerebellum segmentation

[Douglas N. Greve]

You can try using mri_synthseg --i orig.mgz --o synthseg.mgz
it generally does a better job on cerebellum than the native FS command

On 1/5/2024 4:11 PM, Carlos Alcocer wrote:


External Email - Use Caution

Hello,

Inferior portion of cerebellum are not segmented well. It is included 
in skullstrip and I tried adding control points in cerebellar WM but 
this did not help. I am not interested in cerebellum but I do need 
eTIV. Will this poor cerebellar segmentation affect eTIV calculation?


Thank you,

Carlos



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Re: [Freesurfer] extracting measurements for mean gray matter thickness/LGI

[Douglas N. Greve]

I don't understand. Why not use the mean thickness from FS? We have an 
lGI module; we have not supported it in years, but maybe it still works. 
https://surfer.nmr.mgh.harvard.edu/fswiki/LGI


On 1/10/2024 9:52 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

Hi,

We were wondering what the preferred command is for extracting mean 
gray matter thickness/LGI


I am aware that FS outputs left/right mean thickness but wanted to be 
conscious of the fact that left/right hemisphere might have different 
sizes.


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

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Re: [Freesurfer] Sample registration question

[Douglas N. Greve]

I'm not sure what you mean. The subfields are an ROI-based analysis. Are 
you saying you want to do a voxel-based analysis (without reference to 
ROIs)?


On 1/9/2024 12:05 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there Freesurfer,

I am currently using freesurfer to take DTI metrics (FA, MD) from 
hippocampal subfields.
At this point of my exploration with freesurfer, I am able to 
correctly register the hippocampal subfields and diffusion data, and 
obtain my FA values from the subfields. However, this is at the 
individual subject level.


I will eventually need to register all of my samples in the same space 
for me to do a group analysis. However I am unsure what the order of 
registration should be for this process to be feasible.


Does this order seem feasible for accurate analysis?

1) recon-all all of my subjects
2) dt_recon all of my subjects (one of the outputs is a registration 
file, which has registered the DTI data to outputs of recon-all)
3) run the hippocampus segmentation command on all subjects 
(segmentHA_T1.sh) to obtain hippocampal subfield segmentation
4) register the segmentation file to the FA maps (output of dt_recon) 
using vol2subfield command
5) After creating a subfield-FA map for each subject, spatial 
normalize the samples onto the same space using *mri_vol2vol*

*
*
Thank you so much for taking the time reading my question. If there is 
a different method to spatially normalizing my datasets, or if there 
is a more optimal order of registration, I'd be happy to hear from you.


Thank you,
M

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Re: [Freesurfer] Issue with mri_glmfit-sim

[Douglas N. Greve]

I think v6 might be broken when using -bg. Try removing that.

On 1/8/2024 11:19 AM, O'Neill, Alexandra Grace wrote:

*Hello FS community,*
*

To correct for multiple comparisons for the results of a parametric 
modulation GLM analysis, I have run mri_glmfit-sim using Freesurfer 
version 6.0 with the following command:


mri_glmfit-sim \ --debug --glmdir 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepSec/OSGM/osgm 
\ --perm 1000 2.0 abs \ --cwp 0.05 \ --2spaces \ --bg 1


*
*The code completes without errors, however none of the output files 
mentioned inthis tutorial 
are 
created. Below are the contents of the mriglm-fit.log file in case 
that is helpful.

*
*
*
*
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago
cmdline mri_glmfit.bin --y 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz 
--wls 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz 
--fsgd /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd --osgm 
--glmdir 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM 
--surf fsaverage rh --fwhm 6

sysname  Linux
hostname tempest.nmr.mgh.harvard.edu
machine  x86_64
user     ago5
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
fwhm     6.00
niters    26.00
OneSampleGroupMean 1
y 
 /autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz

logyflag 0
usedti  0
FSGD /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd
labelmask 
 /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/fsaverage/label/rh.cortex.label

maskinv 0
glmdir 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM

IllCondOK 0
ReScaleX 1
DoFFx 0
wFile 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz

weightinv  1
weightsqrt 1
ResidualFWHM 12.847434
SearchSpace 74490.844410
anattype surface



Do you have any idea how to fix this problem? Thanks so much in advance!
*
*Alexandra*
*
*
*Alexandra G. O'Neill* *(she/her)*
/Clinical Research Coordinator/
Massachusetts General Hospital
Department of Psychiatry
Division of Neuropsychiatry and Neuromodulation
149 13th Street, Charlestown, MA 02129
T: (617) 726-8753 | E: agone...@mgh.harvard.edu 





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Re: [Freesurfer] Tksurfer and freeview

[Douglas N. Greve]

please send the command line and the terminal output. Also, try using 
tksurferfv (this is a wrapper around freeview that takes tksurfer-like 
commands)


On 1/6/2024 8:59 PM, JAEHYUN KIM wrote:


External Email - Use Caution

Hello,

I attempted to switch tksurfer to freeview in the script, but it seems 
like I need to change arguments "tcl" to something that can be applied 
to freeview.


Option 'tcl' not recognized.



What argument could possibly be used to replace /tcl/ in the 
script such as /*tmp.tcl*/**and /*lh pial -tcl*/??



Best,
Ed

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