[Freesurfer] Viewing the output of mris_preproc in Freeview + export to Matlab

[Alon Baram]

External Email - Use Caution

Hello,

I want to overlay the .mgh file which is the output of mris_preproc in
freeview on the fsaverage surface. This file has (according to mri_info)
the dimensions Nverteces x 1 x 1 x Nsubjects: my data in fsaverage space
for each of my subjects. But when I load it in freeview I can only see one
value in each vertex.

Is there a way to view "4D" (it's actually 2D: Nverteces x Nsubjects) data
in Freeview? If not, what is the single value (per vertex) that freeview
chooses to show me? is it just the data from the first subject? I tried to
look in the documentation for any clues about viewing time-series data in
Freeview, but failed.

I would also be very happy to understand what is the best way to save this
4D .mgh file in a format that I can then import it into Matlab.

Thanks for the help!
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[Freesurfer] New segmentation of thalamic nuclei

[Iglesias Gonzalez, Eugenio]

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Dear FreeSurfer users,

It is my pleasure to announce that our new tool to segment the thalamic nuclei 
from structural MR scans is available in the development version of FreeSurfer. 
The tool relies on an atlas derived from manual annotations made on 
histological sections. The module can analyze the main FreeSurfer T1 scan, but 
also supports MR images with contrasts other than T1 – as long as the 
corresponding T1 has been processed with recon-all. If you’ve got images 
processed with an earlier version of FreeSurfer, you don’t need to process them 
again with the development version; you can directly run the new module on your 
existing processed subjects.

You can find the documentation, including a link to a preprint of the paper, in 
the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei

As with any other FreeSurfer tool (particularly those that have been recently 
released), we appreciate any feedback that you might have.

Kind regards,

/Eugenio


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

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[Freesurfer] recon-all with mri_ca_normalize (longitudinal)

[miracle ozzoude]

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Hello FreeSurfer team,

In order to create the longitudinal base after norm.mgz, Is the command
below the right way to end recon-all after creating norm.mgz?

recon-all -s subjectID -autorecon1 -autorecon2  -i T1image -canorm.

Thank you.

Best,
Paul
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[Freesurfer] Hippocampal subfield registration question.

[Jamie Hanson]

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Dear FS List,

I was just started to run hippocampal subfield segmentation and had a
question about registration (and a related output warning).
In the ~5 test subjects I've tried the SF routine, I get a warning early on
that says--

**
*
* WARNING: Registration did not converge in 5 steps!
*  Problem might be ill posed.
*  Please inspect output manually!
*
**

Two questions--
1) Is that anything to be concerned about?
2) If so, are there relevant documents regarding checking the outputs to
flag potential poor registration/segmentation?

Any information or thoughts are greatly appreciated!
Thanks much!

All the best,
Jamie.

--
Jamie Hanson
Assistant Professor, Psychology
Research Scientist, Learning Research and Development Center
University of Pittsburgh
Personal website: jamiehanson.org
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Re: [Freesurfer] Hippocampal subfield registration question.

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Jamie,
It’s a message from mri_robust_register in the initialization of the atlas 
position. If the finaloutput looks reasonable (which it mostly likely will), 
don’t worry too much.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Jamie Hanson 

Reply-To: Freesurfer support list 
Date: Friday, 10 August 2018 at 17:13
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfield registration question.


External Email - Use Caution

Dear FS List,

I was just started to run hippocampal subfield segmentation and had a question 
about registration (and a related output warning).
In the ~5 test subjects I've tried the SF routine, I get a warning early on 
that says--

**
*
* WARNING: Registration did not converge in 5 steps!
*  Problem might be ill posed.
*  Please inspect output manually!
*
**

Two questions--
1) Is that anything to be concerned about?
2) If so, are there relevant documents regarding checking the outputs to flag 
potential poor registration/segmentation?

Any information or thoughts are greatly appreciated!
Thanks much!

All the best,
Jamie.

--
Jamie Hanson
Assistant Professor, Psychology
Research Scientist, Learning Research and Development Center
University of Pittsburgh
Personal website: jamiehanson.org
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Re: [Freesurfer] Surface Area in Toddlers/Children

[Douglas Greve]

It should be preserving total surface area. Can you send your 
mris_preproc command line and the terminal output? It might be something 
with 5.1 as well.



On 8/9/18 3:49 PM, Derek Sayre Andrews wrote:


External Email - Use Caution

Dear Freesurfer Developers and Experts,

I have been exploring various vertex wise (mass univariate) effects 
using freesurfer measures of cortical thickness and surface area in a 
cohort of toddlers/children aged 25-70 months.


When looking at the effect of age on surface area using individuals’ 
measures mapped to fsaverage and smoothed at 15mm fwhm (area.pial. 
fwhm15.fsaverage.mgh) I observed a widespread negative effect of age 
(i.e. decreased surface area with age). Given the age group of the 
cohort this seems implausible. Plotting the sum of each individuals 
lh+rh.area.pialfsaverage.fwhm15.mgh against age shows the relationship:


cid:image001.png@01D42FCE.C197B360

However, plotting the lh+rh total surface area returned by 
mris_anatomical_stats reveals a much more plausible relationship 
between surface area and age:


cid:image002.png@01D42FCE.C197B360

My working hypothesis is that the significantly smaller brain sizes of 
our cohort compared to fsaverage, and the fact(?) that -qcache does 
not preserve global surface area, is causing an “over adjustment” in 
our cohorts smallest brains when mapped to fsaverage.


Thus, my questions are three fold

 1. Is the mapping of our significantly smaller brains to fsaverage a
potential explanation for the results we are seeing in our mass
univariate analyses of surface area?

 2. If this is the case, would this effect be limited to surface area
or also extend to other freesurfer measures including cortical
thickness, lGI, sulcal depth etc.

 3. How would you recommend approaching vertex wise analyses in a
cohort of this age? Create a study specific average subject using
make_average_subject to map onto?

Thank you for your insight and guidance!

Best, Derek

PS: All processing was performed using freesurfer v5.1

cid:image003.png@01D42FCE.C197B360

*Derek Sayre Andrews, PhD*

Postdoctoral Scholar

Department of Psychiatry and Behavioral Sciences

The M.I.N.D Institute

University of California Davis


Telephone: +1 916 703 0360
Email: dandr...@ucdavis.edu 



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Re: [Freesurfer] Viewing the output of mris_preproc in Freeview + export to Matlab

[Douglas Greve]

It is showing you the map of the first frame (subject in this case). You 
can adjust the frame with a slider on the left. Also, there is a time 
plot icon on the top. If you click on that it will show you a graph of 
the subjects at the chosen vertex.


On 8/10/18 8:16 AM, Alon Baram wrote:


External Email - Use Caution

Hello,

I want to overlay the .mgh file which is the output of mris_preproc in 
freeview on the fsaverage surface. This file has (according to 
mri_info) the dimensions Nverteces x 1 x 1 x Nsubjects: my data in 
fsaverage space for each of my subjects. But when I load it in 
freeview I can only see one value in each vertex.


Is there a way to view "4D" (it's actually 2D: Nverteces x Nsubjects) 
data in Freeview? If not, what is the single value (per vertex) that 
freeview chooses to show me? is it just the data from the first 
subject? I tried to look in the documentation for any clues about 
viewing time-series data in Freeview, but failed.


I would also be very happy to understand what is the best way to save 
this 4D .mgh file in a format that I can then import it into Matlab.


Thanks for the help!



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Re: [Freesurfer] coregistering with bbregister

[Douglas Greve]

Sometimes the FSL initialization will fail. If you are using FS version 
6, then run it without specifying --init-fsl and it will use mri_coreg, 
which is more robust. If your anatomical and functional were acquired at 
the same time, you might be able to get away with --init-header instead.


On 8/9/18 2:12 PM, Ben M wrote:


External Email - Use Caution

Hi,
I'm trying to coregister the strucural image to the mean functional 
image using bbregister, so after reconall I did:


bbregister --t2 --init-fsl --reg /data/bbregister/reg.dat --mov 
/data/mean_func.nii.gz --s 001


bet /data/structural.nii.gz /data/bet_structural.nii.gz

#brain.nii.gz is the brain.mgz from reconall output (in freesurfer space)
mri_vol2vol --mov /data/bet_structural.nii.gz --targ 
/data/brain.nii.gz --o /data/coregistered_structural.nii.gz --reg 
/data/bbregister/reg.dat --inv –-nearest


But when I load the coregistered_structural.nii.gz and the 
mean_func.nii.gz they are not aligned. I'm sure I'm doing something 
wrong, could someone help me figure it out please?


Thanks in advance,
Ben


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Re: [Freesurfer] Plotting QDEC results

[Douglas Greve]

Each row is a subject and each column is a cluster. BTW, a threshold of 
1.3 is way too low for lGI. If you want to use a threshold that low, you 
should use permutation instead of monte carlo (in general, permutation 
is better, but certainly for lGI).


On 8/9/18 1:39 PM, Avi Gharehgazlou wrote:


External Email - Use Caution

Hi experts,

I looked at association between LGI and a behavioural scale on QDEC. 
after the analysis, to plot the significant clusters/ blobs, I wanted 
to export LGI values for each subject from each significant blob and 
based on instructions in previous archives I ran the following command 
line:


mri_glmfit-sim –glmdir (qdec output directory) --cache 1.3 abs

which generated a "cache.th13.abs.y.ocn.dat" file. This file contains 
3 columns and 36 rows. I'm assuming the values in the three columns 
correspond to LGI values for each significant blob for each subject? 
(I had 3 significant blobs and 36 participants)


Will you please confirm I am doing (and interpreting) this correctly?

Thanks so much,

Avi


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Re: [Freesurfer] mri_volcluster not recognize --mindistance

[Douglas Greve]

Try --mindist not --mindistance

On 8/9/18 9:08 AM, Yagmur Ozdemir 19 wrote:


External Email - Use Caution

Hello FreeSurfer experts,

I am trying to run mri_volcluster with the following command to later 
create masks of clustered regions from functional data. I get an error 
saying that the option --mindistance is not recognized, even though 
this option is shown in mri_volcluster --help and the FS wiki page. 
Any idea what might be causing this?


mri_volcluster --in thresh_highres.nii.gz --sum volcluster.txt --ocn 
clustered_thresh_highres.nii.gz --thmin 1.5 --sign pos --regheader 
 --mindistance 10 --minsizevox 800 --fwhm 3

ERROR: Option --mindistance unknown

Best
Idil


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Re: [Freesurfer] T1 mapping

[Douglas Greve]

mri_fit_parms should do it. BTW, if you are using a siemens scanner, you 
should just collect an MP2RAGE. That automatically outputs a 
quantitative T1 map using the two inversion technique. The results are 
much more accurate than using multiple flip angles


On 8/8/18 5:00 PM, Fotiadis, Panagiotis wrote:


Hello,


I am interested in doing some T1-mapping analyses on some ex vivo 
brains. We have collected flash sequences under multiple flip angles 
(5, 10, 15, 20, 25 and 30). How would you suggest that I proceed? 
Should I use the mri_ms_fitparms to come up with the T1 maps for each 
subject and then maybe calculate the signal intensity 1mm into the 
cortex, or is there another way that you would recommend?



Thanks in advance for any advice!


Best,

Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869


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Re: [Freesurfer] Correlations on QDEC

[Douglas Greve]

did you see the text where it says "If you seek help with this problem, 
make sure to send:" and then it gives a list of things to send? There 
will be a file called y.fsgd in the output, make sure to send that


On 8/8/18 4:40 PM, Avi Gharehgazlou wrote:


External Email - Use Caution

Hi experts,

I have examined the relation between LGI and a behavioural continuous 
scale (SCQ) on QDEC while controlling for sex, age and surface area in 
my model. When I want to do another analysis, doing exactly this but 
also controlling for diagnosis as well, QDEC gives the following error:


ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08



Possible problem with experimental design:

Check for duplicate entries and/or lack of range of

continuous variables within a class.

If you seek help with this problem, make sure to send:

1. Your command line:

mri_glmfit.bin --y 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/y.mgh 
--fsgd 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/qdec.fsgddods 
--glmdir 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0 
--surf fsaverage lh --label 
/d/mjt/9/users/avideh/data/recon/fsaverage/label/lh.aparc.label --C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Avg-Intercept-pial_lgi.mat 
--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Avg-pial_lgi-RBS-Cor.mat 
--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-ADHD-ASD-Intercept-pial_lgi.mat 
--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-ADHD-ASD-Cor-pial_lgi-RBS.mat 
--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-M-F-Intercept-pial_lgi.mat 
--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-M-F-Cor-pial_lgi-RBS.mat--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-X-Dx-Sex-Intercept-pial_lgi.mat 
--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-X-Dx-Sex-Cor-pial_lgi-RBS.mat


2. The FSGD file (if using one)

3. And the design matrix above

Attempting to diagnose further

SumSq: Min=0.488835 (col 11), Max=3.834060 (col 6)

... could not determine the cause of the problem


My understanding is that QDEC allows for controlling for 2 discrete 
variables, thus I don't know what I am doing wrong if I also control 
for diagnosis (in addition to sex)?


I would really appreciate your help,

Thanks so much,

Avi



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Re: [Freesurfer] Surface Area in Toddlers/Children

[Derek Sayre Andrews]

External Email - Use Caution

Hi Douglas,

Thank you for the response.

I did not use mris_preproc to prepared the data.

The data was mapped to fsaverage using recon-all with -qcache. I then loaded 
the l/rh.area.pial.fwhm15.fsaverage.mgh files into MATLAB using 
SurfStatReadData and summed them 
across each vertex.

Would the terminal output of recon-all -qcache be helpful?

Best, Derek



Derek Sayre Andrews, PhD
Postdoctoral Scholar
Department of Psychiatry and Behavioral Sciences
The M.I.N.D Institute
University of California Davis

Telephone: +1 916 703 0360
Email: dandr...@ucdavis.edu



From:  on behalf of Douglas Greve 

Reply-To: Freesurfer support list 
Date: Friday, August 10, 2018 at 10:25 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Surface Area in Toddlers/Children

It should be preserving total surface area. Can you send your mris_preproc 
command line and the terminal output? It might be something with 5.1 as well.

On 8/9/18 3:49 PM, Derek Sayre Andrews wrote:

External Email - Use Caution
Dear Freesurfer Developers and Experts,

I have been exploring various vertex wise (mass univariate) effects using 
freesurfer measures of cortical thickness and surface area in a cohort of 
toddlers/children aged 25-70 months.

When looking at the effect of age on surface area using individuals’ measures 
mapped to fsaverage and smoothed at 15mm fwhm (area.pial. fwhm15.fsaverage.mgh) 
I observed a widespread negative effect of age (i.e. decreased surface area 
with age). Given the age group of the cohort this seems implausible. Plotting 
the sum of each individuals lh+rh.area.pialfsaverage.fwhm15.mgh against age 
shows the relationship:
[cid:image001.png@01D42FCE.C197B360]

However, plotting the lh+rh total surface area returned by 
mris_anatomical_stats reveals a much more plausible relationship between 
surface area and age:
[cid:image002.png@01D42FCE.C197B360]


My working hypothesis is that the significantly smaller brain sizes of our 
cohort compared to fsaverage, and the fact(?) that -qcache does not preserve 
global surface area, is causing an “over adjustment” in our cohorts smallest 
brains when mapped to fsaverage.

Thus, my questions are three fold


  1.  Is the mapping of our significantly smaller brains to fsaverage a 
potential explanation for the results we are seeing in our mass univariate 
analyses of surface area?


  1.  If this is the case, would this effect be limited to surface area or also 
extend to other freesurfer measures including cortical thickness, lGI, sulcal 
depth etc.


  1.  How would you recommend approaching vertex wise analyses in a cohort of 
this age? Create a study specific average subject using make_average_subject to 
map onto?

Thank you for your insight and guidance!

Best, Derek


PS: All processing was performed using freesurfer v5.1



Derek Sayre Andrews, PhD
Postdoctoral Scholar
Department of Psychiatry and Behavioral Sciences
The M.I.N.D Institute
University of California Davis

Telephone: +1 916 703 0360
Email: dandr...@ucdavis.edu






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Re: [Freesurfer] Confusion about MRI_GLMFIT

[Douglas Greve]

On 8/8/18 2:17 PM, Funk, Quentin wrote:


External Email - Use Caution

Freesurfer experts,


I'm trying to figure out what values I get from mri_glmfit as in the 
tutorial. 
In 
particular, I'm interested in how I can compare these values to what I 
get from QDEC.


QDEC runs mri_glmfit, so they will be the same assuming you give it the 
same input, design, and contrast.



In that tutorial, the software does a linear regression for each 
gender and then computes a F_ratio for the two two fits. (How does 
this relate to the average in the contrast listed?)


If the average were 0, then you would have no result whereas the F test 
will test for any combination of  the two



The F_ratio then gives a way to get P-values (under certain 
assumptions)--so then from the F_ratio, pvals are computed--this leads 
to sig.mgh.



But what are the other files? The descriptions are a bit too vague for 
me to understand, unfortunately. The ones I'm interested in primarily are:



pcc.mgh -- partial (pearson) correlation coefficient (surface overlay)

Do you know what a pearson correlation is? The pearson can only be 
computed between two sets of numbers. When you have multiple regression, 
you use a partial pearson.


z.mgh -- z-stat that corresponds to the significance (surface overlay)


This is the p-value converted into a z.



The z-stat should be some sort of standard score--so a standard score 
of significance (so p-value?) compared to what distribution?



Second, what if I were interested in a different categorical 
variable--say I had a group of Alzheimer's patients and a group of 
Healthy patients. In QDEC, I click "diagnosis" as the variable to do 
the analysis on. What contrast does this correspond to? What type of 
linear fit is being compared--the slope of the regression with respect 
to age? If I leave out nuisance variables (like age), I should 
conceivably get an F-test between the two constant models, which 
should be more or less similar to a voxelwise t-test?


The contrast will be [-1 +1]. The sig.mgh will be the sig of the t-test 
(ie, a signed test).




Any help here is appreciated!


Quentin Funk, PhD
Houston Methodist Research Institute
713-363-9003 

Houston Methodist. Leading Medicine.

Houston Methodist is ranked by /U.S. News & World Report/ as the No. 1 
hospital in Texas for patient care. Houston Methodist is nationally 
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Re: [Freesurfer] Surface Area in Toddlers/Children

[Douglas Greve]

Yes. -qcache actually calls mris_preproc. At one point, FS did not 
preserve total area when  mapping to fsaverage. I fixed it a while ago, 
but maybe something was still off in 5.1


On 8/10/18 2:06 PM, Derek Sayre Andrews wrote:


External Email - Use Caution

Hi Douglas,

Thank you for the response.

I did not use mris_preproc to prepared the data.

The data was mapped to fsaverage using recon-all with -qcache. I then 
loaded the l/rh.area.pial.fwhm15.fsaverage.mgh files into MATLAB using 
SurfStatReadData  and 
summed them across each vertex.


Would the terminal output of recon-all -qcache be helpful?

Best, Derek

*Derek Sayre Andrews, PhD*

Postdoctoral Scholar

Department of Psychiatry and Behavioral Sciences

The M.I.N.D Institute

University of California Davis


Telephone: +1 916 703 0360
Email: dandr...@ucdavis.edu 

*From: * on behalf of Douglas 
Greve 

*Reply-To: *Freesurfer support list 
*Date: *Friday, August 10, 2018 at 10:25 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children

It should be preserving total surface area. Can you send your 
mris_preproc command line and the terminal output? It might be 
something with 5.1 as well.


On 8/9/18 3:49 PM, Derek Sayre Andrews wrote:

*External Email - Use Caution *

Dear Freesurfer Developers and Experts,

I have been exploring various vertex wise (mass univariate)
effects using freesurfer measures of cortical thickness and
surface area in a cohort of toddlers/children aged 25-70 months.

When looking at the effect of age on surface area using
individuals’ measures mapped to fsaverage and smoothed at 15mm
fwhm (area.pial. fwhm15.fsaverage.mgh) I observed a widespread
negative effect of age (i.e. decreased surface area with age).
Given the age group of the cohort this seems implausible. Plotting
the sum of each individuals lh+rh.area.pialfsaverage.fwhm15.mgh
against age shows the relationship:

cid:image001.png@01D42FCE.C197B360

However, plotting the lh+rh total surface area returned by
mris_anatomical_stats reveals a much more plausible relationship
between surface area and age:

cid:image002.png@01D42FCE.C197B360

My working hypothesis is that the significantly smaller brain
sizes of our cohort compared to fsaverage, and the fact(?) that
-qcache does not preserve global surface area, is causing an “over
adjustment” in our cohorts smallest brains when mapped to fsaverage.

Thus, my questions are three fold

 1. Is the mapping of our significantly smaller brains to
fsaverage a potential explanation for the results we are
seeing in our mass univariate analyses of surface area?

 2. If this is the case, would this effect be limited to surface
area or also extend to other freesurfer measures including
cortical thickness, lGI, sulcal depth etc.

 3. How would you recommend approaching vertex wise analyses in a
cohort of this age? Create a study specific average subject
using make_average_subject to map onto?

Thank you for your insight and guidance!

Best, Derek

PS: All processing was performed using freesurfer v5.1

cid:image003.png@01D42FCE.C197B360

*Derek Sayre Andrews, PhD*

Postdoctoral Scholar

Department of Psychiatry and Behavioral Sciences

The M.I.N.D Institute

University of California Davis


Telephone: +1 916 703 0360
Email: dandr...@ucdavis.edu 




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Re: [Freesurfer] T1 mapping

[Fotiadis, Panagiotis]

Hi Doug,


Thanks for your response! I had a couple follow-up questions:


1) If I used mri_fit_parms to calculate the T1 maps, then created a surface 
mid-cortex (with mris_expand) with that T1 map as a reference, and uploaded 
that file into MATLAB through MRIread, would the resulting values represent 
absolute "pure" T1 values?


2) Even though we are scanning on a Siemens scanner we have been acquiring a 
tfl_mgh_multiecho_4E_P2_1MM_ISO sequence. Do you think I could do T1 mapping 
based on that sequence (with the same method as the one described in the 
previous question)?


Thanks again, and I apologize for the potential triviality of the questions!


Best,

Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869

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

Sent: Friday, August 10, 2018 1:59:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] T1 mapping

mri_fit_parms should do it. BTW, if you are using a siemens scanner, you should 
just collect an MP2RAGE. That automatically outputs a quantitative T1 map using 
the two inversion technique. The results are much more accurate than using 
multiple flip angles

On 8/8/18 5:00 PM, Fotiadis, Panagiotis wrote:

Hello,


I am interested in doing some T1-mapping analyses on some ex vivo brains. We 
have collected flash sequences under multiple flip angles (5, 10, 15, 20, 25 
and 30). How would you suggest that I proceed? Should I use the mri_ms_fitparms 
to come up with the T1 maps for each subject and then maybe calculate the 
signal intensity 1mm into the cortex, or is there another way that you would 
recommend?


Thanks in advance for any advice!


Best,

Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869



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Re: [Freesurfer] Midline errors

[Bruce Fischl]

HI Maxime

check the aseg labels and make sure they are correct (and fix them if 
not). Probably a couple of left/right ventricle voxels are mislabeled

Bruce
On 
Fri, 10 Aug 2018, Maxime Perron wrote:




External Email - Use Caution

Hello FreeSurfer Developers,
 
I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found 
midline cutting error, that
is the midline does not go through exactly the center of the brain in coronal 
cut. For example, the
midline is a little bit fuzzy and goes through an hemisphere than the other 
(see attachment). I've
searched in the mail list and ​I don't find the way to fix it. Does anyone have 
any idea to fix it? 
Thank you,

Maxime Perron

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Re: [Freesurfer] coregistering with bbregister

[Ben M]

External Email - Use Caution

Hi Doug,

Thank you for your suggestions, I'll try them.
Could you please let me know if my code is actually doing what I intend it
to do? Specifically, the idea is to perform functional-to-structural
registration.

so first I did
$ bbregister --t2 --reg /data/bbregister/reg.dat --mov
/data/mean_func.nii.gz --s 001

I'm not sure if the --mov image should be the motion-corrected mean
functional image or the skull-stripped anatomical image. I think if I want
to do functional-to-structural registration it should actually be the
anatomical image as --mov right? Or it doesn't matter which one I choose?

I then did
$ mri_vol2vol --mov /data/bet_structural.nii.gz --targ /data/brain.nii.gz
--o /data/coregistered_structural.nii.gz --reg  /data/bbregister/reg.dat
--inv –-nearest
 which I thinks applies the transformation matrix to the structural image,
am I correct? In this case it would be a structural-to-functional
registration I think.
So, if I intend to perform functional-to-structural registration I should
actually rather do

$ bbregister --t2 --reg /data/bbregister/reg.dat --mov
/data/bet_structural.nii.gz --s 001
$ mri_vol2vol --mov /data/mean_func.nii.gz --targ /data/brain.nii.gz --o
/data/coregistered_functional.nii.gz --reg  /data/bbregister/reg.dat --inv
–-nearest

Could you please confirm if this is correct?

Thank you very much,
Ben






Sometimes the FSL initialization will fail. If you are using FS version
6, then run it without specifying --init-fsl and it will use mri_coreg,
which is more robust. If your anatomical and functional were acquired at
the same time, you might be able to get away with --init-header instead.

On 8/9/18 2:12 PM, Ben M wrote:
>>* External Email - Use Caution
*>>* Hi,
*>* I'm trying to coregister the strucural image to the mean functional
*>* image using bbregister, so after reconall I did:
*>>* bbregister --t2 --init-fsl --reg /data/bbregister/reg.dat --mov
*>* /data/mean_func.nii.gz --s 001
*>>* bet /data/structural.nii.gz /data/bet_structural.nii.gz
*>>* #brain.nii.gz is the brain.mgz from reconall output (in freesurfer space)
*>* mri_vol2vol --mov /data/bet_structural.nii.gz --targ
*>* /data/brain.nii.gz --o /data/coregistered_structural.nii.gz --reg
*>* /data/bbregister/reg.dat --inv –-nearest
*>>* But when I load the coregistered_structural.nii.gz and the
*>* mean_func.nii.gz they are not aligned. I'm sure I'm doing something
*>* wrong, could someone help me figure it out please?
*>>* Thanks in advance,
*>* Ben*
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[Freesurfer] Untar and sh files in dev version

[Schumman Resonance]

External Email - Use Caution

Hi,

Couple of newbie questions. I downloaded the dev version of freesurfer  and
did:
tar xvzf

freesurfer-linux-centos6_x86_64-dev.tar.gz


to get



gzip: stdin: unexpected end of file

tar: Unexpected EOF in archive

tar: Unexpected EOF in archive

tar: Error is not recoverable: exiting now


Also, when I ls the folder I couldn't see the SetUpFreesurfer.sh and
SurferEnv.sh only the csh files.


Any pointers how to solve these would be appreciated.


Thanks,

S
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Re: [Freesurfer] Untar and sh files in dev version

[Dicamillo, Robert]

Hello Schumman,

Try the following command on the tar archive (cut and paste it if you like)

$ tar zxpf freesurfer-linux-centos6_x86_64-dev.tar.gz

and then take a look at the files.

- Rob

On Aug 10, 2018, at 10:25 PM, Schumman Resonance 
mailto:schumm...@gmail.com>> wrote:


External Email - Use Caution

Hi,

Couple of newbie questions. I downloaded the dev version of freesurfer  and did:
tar xvzf
freesurfer-linux-centos6_x86_64-dev.tar.gz

to get



gzip: stdin: unexpected end of file
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now



Also, when I ls the folder I couldn't see the SetUpFreesurfer.sh and 
SurferEnv.sh only the csh files.

Any pointers how to solve these would be appreciated.

Thanks,
S
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Re: [Freesurfer] Untar and sh files in dev version

[Schumman Resonance]

External Email - Use Caution

Thanks for your response.
I run the command you suggested and this is what I got:

freesurfer/average/mult-comp-cor/fsaverage_sym/rh/cortex/fwhm04/pos/th33/mc-z.csd:
(Empty error message)

tar: Error exit delayed from previous errors.

Also, still no .sh files...

Best,
K

On Fri, Aug 10, 2018 at 7:52 PM, Dicamillo, Robert <
rdicami...@mgh.harvard.edu> wrote:

> Hello Schumman,
>
> Try the following command on the tar archive (cut and paste it if you like)
>
> $ tar zxpf freesurfer-linux-centos6_x86_64-dev.tar.gz
>
> and then take a look at the files.
>
> - Rob
>
> On Aug 10, 2018, at 10:25 PM, Schumman Resonance 
> wrote:
>
> External Email - Use Caution
>
> Hi,
>
> Couple of newbie questions. I downloaded the dev version of freesurfer
> and did:
> tar xvzf
> freesurfer-linux-centos6_x86_64-dev.tar.gz
>
> to get
>
>
> gzip: stdin: unexpected end of file
> tar: Unexpected EOF in archive
> tar: Unexpected EOF in archive
> tar: Error is not recoverable: exiting now
>
>
>
> Also, when I ls the folder I couldn't see the SetUpFreesurfer.sh and
> SurferEnv.sh only the csh files.
>
> Any pointers how to solve these would be appreciated.
>
> Thanks,
> S
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> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
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> properly
> dispose of the e-mail.
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