[Freesurfer] issue with lesions

[Sam W]

External Email - Use Caution

Hello,
I have run recon-all on T1 scans of patients with WM lesions. I noticed
however that for some patients the lesion is excluded from
aparc.a2009s+aseg.mgz but for other patients it is included (and labelled
as non-lesion).
Ultimately I'd like to extract a) volume information in WM and b) volume
information of the WM lesion. I think I can get the the WM volume from the
wmparc.stats file. For the lesion volume I think I can take the
WM-hypointensities from the aseg file right? However I noticed that if a
lesion is on the right hemisphere, the Right-WM-hypointensities shows 0s in
all columns, which cannot be right.
I have a mask of the lesion (1s where lesion occurs, 0s elsewhere) in
anatomical space, can I use this mask somehow in FS to inform recon-all
where the lesion occurs?
Thanks in advance!
Sam
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[Freesurfer] qdec contrast and data extraction

[Maximo, Jose Omar]

External Email - Use Caution

Hi,

Which specific file should I load? I see cluster.mgh, cluster.summary, 
sign.ocn.annot, sig.ocn.mgh, sig.vertex.mgh, and pdf.dat. 

How can I extract the values from fsaverage space?

Basically, what is the correct way to extract values from these significant 
clusters?

Many thanks,
Omar

Date: Tue, 3 Sep 2019 15:15:02 +
From: "Greve, Douglas N.,Ph.D." 
Subject: Re: [Freesurfer] qdec contrast and data extraction
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID: <2286f9bf-37a4-1be9-2252-0bccc833a...@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

You might have done something wrong along the way. When you run the 
montecarlo correction, it will create a file with the thickness values in it 
for each cluster. the first thing to do is to load that and see if you see the 
expected differences. The other thing is to not go back into native space to 
extract the numbers. There are several operations that happen as it moves into 
fsaverage space and in preparation for group analysis (interpolation, and 
smoothing); sometimes these make a big difference. if the ROI is small, it may 
not map accurately back into the native space (and you should not need to draw 
it in the first place)

On 8/30/2019 11:36 AM, Maximo, Jose Omar wrote:

External Email - Use Caution
Hi,

I have a question:

My design is 2 groups (HC and Patients in that respective order) and 2 
nuisance factors (age and eTIV). When I look at the average volume difference 
between the 2 groups, I get blue and red clusters. I presume the color coding 
is where each group is greater than the other (Blue = Patients > HC and Red = 
HC > Patients).

Then, I processed to extract individual values from each cluster in order 
to plot them. When I extract data from the blue clusters and plot them, the two 
groups show no difference in thickness at all, whereas when I look at volume, 
HC show more than patients in blue clusters (see attached figure). I would 
assume that both figures would show patients > HC based on the negative 
statistic.

Am I interpreting the colors wrong? Or am I doing something wrong?

These are my steps 1) After applying montecarlo correction, I drew my ROIs 
to extract the data from; 2) map it onto every single subject; and then 3) used 
mris_anatomical_stats to extract the data from each subject.

Any suggestions are welcome.

Best,
Omar

Jose O. Maximo, Ph.D. | Postdoctoral Fellow
Department of Psychiatry & Behavioral Neurobiology
UAB School of Medicine
University of Alabama at Birmingham
Cell Phone: (619) 252-3492
Email: jomax...@uabmc.edu




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[Freesurfer] (Revised) Clusterwise correction for multiple comparisons

[Gwang-Won Kim]

External Email - Use CautionHi there, To perform a cluster-wise correction for multiple comparisons, I ran monte carlo simulation as follows: mri_glmfit-sim --glmdir g1v2.wls --3spaces --grf  2 abs I know that "- -3spaces" means adjusting p-values for both hemispheres and subcortical structures.I have a question. How can I do if I use p-values corrected only for subcortical structure? Good luck,Gwang-Won Kim 













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Re: [Freesurfer] Compare vertexwise correlation maps

[Matthieu Vanhoutte]

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So if I obtained two correlation maps from the same population but based on 
different input parameters, how could I demonstrate that vertex correlation 
values are statistically « strongest »/« lowest »  in one of the map compared 
to the other ?

Best,
Matthieu

> Le 3 sept. 2019 à 17:00, Greve, Douglas N.,Ph.D.  a 
> écrit :
> 
> You want to see if the correlation values themselves? You can't do that 
> (unless you have a bunch of correlation maps). You have to incorporate 
> your question/hypothesis into the design and contrast.
> 
> On 9/2/2019 11:14 AM, Matthieu VANHOUTTE wrote:
>> External Email - Use Caution
>> 
>> Dear experts,
>> 
>> I would like now to determine if there is statistically difference
>> between vertexwise correlation maps (whether one is statistically
>> "stronger" than the other). Would there be a way to do this with
>> Freesurfer? (r-to-z Fisher transformation and statistical method?)
>> 
>> Best regards,
>> 
>> Matthieu
>> 
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[Freesurfer] Clusterwise correction for multiple comparisons

[Gwang-Won Kim]

External Email - Use CautionHi there, To perform a cluster-wise correction for multiple comparisons, I ran monte carlo simulation as follows: mri_glmfit-sim --glmdir g1v2.wls --3spaces --cache 2 abs I know that "- -3spaces" means adjusting p-values for both hemispheres and subcortical structures.I have a question. How can I do if I use p-values corrected only for subcortical structure? Good luck,Gwang-Won Kim 













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[Freesurfer] make_average_subject error

[Maxime Perron]

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​Dear Freesurfer Experts,



I have the following issue when running the make_average_subject command (

make_average_subject --subjects (Subjid) --out BrainaverageN72) : 







Building hash of lh white


Building hash of lh pial


Building hash of rh white


Building hash of rh pial


Loading aseg from /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72/mri/aseg.presurf.hypos.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;
mghRead(mri/norm.mgz, -1): could not open file
-


Labeling Slice
relabeling unlikely voxels in interior of white matter
Segmentation fault
Darwin tulipe.crulrg.local 17.7.0 Darwin Kernel Version 17.7.0: Sun Jun  2 20:31:42 PDT 2019; root:xnu-4570.71.46~1/RELEASE_X86_64 x86_64


recon-all -s BrainaverageN72 exited with ERRORS at Tue Sep  3 11:33:02 EDT 2019



I appreciate any help.


​Regards, 


Maxime 


















​






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[Freesurfer] Problem with lGI

[Avi Gharehgazlou]

External Email - Use Caution

Hi,

I have ran the lGI flag many times in the past. However, now that I am
trying to run the flag on a new group of participants I get the below
error. Will you please tell me how I can fix this?

Thanks so much,

Avi



New invocation of recon-all



Fri Aug 30 16:47:49 EDT 2019
/d/mjt/9/users/avideh/data/recon/MR160-114-0370_01
/usr/local/freesurfer/bin/recon-all
-s MR160-114-0370_01 -localGI -openmp 2
subjid MR160-114-0370_01
setenv SUBJECTS_DIR /d/mjt/9/users/avideh/data/recon
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux apollo.sickkids.ca 4.15.0-50-generic #54-Ubuntu SMP Mon May 6
18:46:08 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 16384 kbytes
maxproc  321903
maxlocks unlimited
maxsignal321903
maxmessage   819200
maxnice  0
maxrtprio0
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   824734641899414026581924  3746363689740062364472
Swap:   8388604 1922560 6466044


program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info
ProgramName: mri_convert.bin  ProgramArguments: -all-info
ProgramVersion: $Name: stable6 $  TimeStamp: 2019/08/30-20:47:49-GMT
BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226
2016/02/26 16:15:24 mreuter Exp $  User: avideh  Machine:
apollo.sickkids.ca  Platform: Linux  PlatformVersion:
4.15.0-50-generic  CompilerName: GCC  CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info
ProgramVersion: $Name: stable6 $  TimeStamp: 2019/08/30-20:47:49-GMT
BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v
1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: avideh  Machine:
apollo.sickkids.ca  Platform: Linux  PlatformVersion:
4.15.0-50-generic  CompilerName: GCC  CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier
(x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info
ProgramVersion: $Name: stable6 $  TimeStamp: 2019/08/30-20:47:49-GMT
BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4
2011/03/02 00:04:14 nicks Exp $  User: avideh  Machine:
apollo.sickkids.ca  Platform: Linux  PlatformVersion:
4.15.0-50-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_normalize  ProgramArguments: -all-info
ProgramVersion: $Name:  $  TimeStamp: 2019/08/30-20:47:49-GMT
BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v
1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: avideh  Machine:
apollo.sickkids.ca  Platform: Linux  PlatformVersion:
4.15.0-50-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_watershed  ProgramArguments: -all-info
ProgramVersion: $Name: stable6 $  TimeStamp: 2019/08/30-20:47:49-GMT
BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v
1.103 2016/06/17 18:00:49 zkaufman Exp $  User: avideh  Machine:
apollo.sickkids.ca  Platform: Linux  PlatformVersion:
4.15.0-50-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion:
$Name: stable6 $  TimeStamp: 2019/08/30-20:47:49-GMT  BuildTimeStamp:
Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02
00:04:16 nicks Exp $  User: avideh  Machine: apollo.sickkids.ca
Platform: Linux  PlatformVersion: 4.15.0-50-generic  CompilerName: GCC
 CompilerVersion: 40400
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion:
$Name:  $  TimeStamp: 2019/08/30-20:47:49-GMT  BuildTimeStamp: Jan 18
2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52
zkaufman Exp $  User: avideh  Machine: apollo.sickkids.ca  Platform:
Linux  PlatformVersion: 4.15.0-50-generic  CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_label2label.bin  ProgramArguments: -all-info
ProgramVersion: $Name:  $  TimeStamp: 2019/08/30-20:47:50-GMT
BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_label2label.c,v
1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: avideh  Machine:
apollo.sickkids.ca  Platform: Linux  PlatformVersion:
4.15.0-50-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_em_register  ProgramArguments: -all-info
ProgramVersion: $Name:  $  TimeStamp: 2019/08/30-20:47:50-GMT
BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_em_register.c,v
1.105.2.1 2016/10/27 

[Freesurfer] Extracting contrast data from mri_glmfit to graph

[cody samth]

External Email - Use Caution

Hello,

I have a question regarding how to graph results that came from a vertex
wise analysis using the command mri_glmfit and mri_glmfit-sim.

I was interested in investigating an interaction effect between groups and
my variable of interest (continuous) while co-varying for three nuisance
variables. After running mri_glmfit and mri_glmfit-sim to correct for
multiple comparisons. I visualized the results and found significant
clusters.

I'm interested in graphing these results. Based on archived questions to
this mailing list the individual values for each cluster can be found
within the ocn.dat file and the cluster information can be found in the
summary file. My analysis looked at volume, thickness and surface area.
Since mean volume and area is difficult to interpret I want to convert the
values to a total measure. It has been suggested in the past this can be
done by multiplying each individuals values within the ocn.dat file by the
number of vertices the cluster has. However, from my understanding this
could be done by altering the mri_segstats command (that mri_glmfit-sim
automatically runs) to include the --accumulate option.

When I do these methods to convert mean area and volume to total area and
volume the results are different.

My first question is 1) Shouldn't these values be identical? The values
from multiplying mean volume by number of vertices are roughly around 3500.
Whereas using the --accumulate in mri_segstats are around 2500. What could
be causing this discrepancy?

2) If my cluster has a size of 1500 mm^2 (in a model for area) does it make
sense that every individual's values after extraction and conversion to
total area are larger than the cluster size?

3) ocn.dat files are the input values meaning they're raw and would need to
be corrected in a statistically (in a similar way that I modeled it in
freesurfer) before graphing right?
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Re: [Freesurfer] mri_surf2surf without sphere.reg {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Thanks Doug, that worked! Caspar

Am Di., 3. Sept. 2019 um 17:03 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> Yes, just specify --surfreg white (or some other surface you do have).
>
> On 9/3/2019 9:51 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
> Hi!
> I am having some issues projecting retinotopic mapping data from a monkey
> analyzed in surface space onto its surface using rtview. The issue seems to
> be that the data need to be converted into paint format through
> mri_surf2surf, and that we do not have a ?h.sphere.reg file because the
> surface is not aligned to a template.
> Is it possible to run mri_surf2surf without reference to ?h.sphere.reg
> somehow? I tried with --s instead of source and target subject, but that
> didn't work.
> Alternatively, can we provide an identity matrix for ?h.sphere.reg,
> perhaps through mris_register?
>
> Any advice would be appreciated.
> Thanks, Caspar
>
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>  
> 
>
>
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Re: [Freesurfer] qdec contrast and data extraction

[Greve, Douglas N.,Ph.D.]

You might have done something wrong along the way. When you run the montecarlo 
correction, it will create a file with the thickness values in it for each 
cluster. the first thing to do is to load that and see if you see the expected 
differences. The other thing is to not go back into native space to extract the 
numbers. There are several operations that happen as it moves into fsaverage 
space and in preparation for group analysis (interpolation, and smoothing); 
sometimes these make a big difference. if the ROI is small, it may not map 
accurately back into the native space (and you should not need to draw it in 
the first place)

On 8/30/2019 11:36 AM, Maximo, Jose Omar wrote:

External Email - Use Caution
Hi,

I have a question:

My design is 2 groups (HC and Patients in that respective order) and 2 nuisance 
factors (age and eTIV). When I look at the average volume difference between 
the 2 groups, I get blue and red clusters. I presume the color coding is where 
each group is greater than the other (Blue = Patients > HC and Red = HC > 
Patients).

Then, I processed to extract individual values from each cluster in order to 
plot them. When I extract data from the blue clusters and plot them, the two 
groups show no difference in thickness at all, whereas when I look at volume, 
HC show more than patients in blue clusters (see attached figure). I would 
assume that both figures would show patients > HC based on the negative 
statistic.

Am I interpreting the colors wrong? Or am I doing something wrong?

These are my steps 1) After applying montecarlo correction, I drew my ROIs to 
extract the data from; 2) map it onto every single subject; and then 3) used 
mris_anatomical_stats to extract the data from each subject.

Any suggestions are welcome.

Best,
Omar

Jose O. Maximo, Ph.D. | Postdoctoral Fellow
Department of Psychiatry & Behavioral Neurobiology
UAB School of Medicine
University of Alabama at Birmingham
Cell Phone: (619) 252-3492
Email: jomax...@uabmc.edu



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Re: [Freesurfer] mri_surf2surf without sphere.reg

[Greve, Douglas N.,Ph.D.]

Yes, just specify --surfreg white (or some other surface you do have).

On 9/3/2019 9:51 AM, Caspar M. Schwiedrzik wrote:

External Email - Use Caution

Hi!
I am having some issues projecting retinotopic mapping data from a monkey 
analyzed in surface space onto its surface using rtview. The issue seems to be 
that the data need to be converted into paint format through mri_surf2surf, and 
that we do not have a ?h.sphere.reg file because the surface is not aligned to 
a template.
Is it possible to run mri_surf2surf without reference to ?h.sphere.reg somehow? 
I tried with --s instead of source and target subject, but that didn't work.
Alternatively, can we provide an identity matrix for ?h.sphere.reg, perhaps 
through mris_register?

Any advice would be appreciated.
Thanks, Caspar



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Re: [Freesurfer] Compare vertexwise correlation maps

[Greve, Douglas N.,Ph.D.]

You want to see if the correlation values themselves? You can't do that 
(unless you have a bunch of correlation maps). You have to incorporate 
your question/hypothesis into the design and contrast.

On 9/2/2019 11:14 AM, Matthieu VANHOUTTE wrote:
>  External Email - Use Caution
>
> Dear experts,
>
> I would like now to determine if there is statistically difference
> between vertexwise correlation maps (whether one is statistically
> "stronger" than the other). Would there be a way to do this with
> Freesurfer? (r-to-z Fisher transformation and statistical method?)
>
> Best regards,
>
> Matthieu
>
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Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

[Bruce Fischl]

hmmm. Can you tar and gzip the whole subject dir and upload it to our ftp 
site?

On Tue, 3 Sep 2019, Rovai Antonin wrote:


   External Email - Use Caution

Hey

So opening only the conformed image in freeview, mricro and fsleyes constantly 
gives me crazy results. Also, the wm segmentation is completely wrong so I 
really think there something wrong in the file….

Best

Antonin

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer


On 3 Sep 2019, at 15:55, Bruce Fischl  wrote:

Hi Antonin

hmmm. Can you try *only* loading the conformed image and seeing how it looks? 
freeview will use one of the images as the basis for it's display coordinates, 
which can cause apparent slicing artifacts that are only display issues for 
other volumes.

cheers
Bruce

On Tue, 3 Sep 2019, Rovai Antonin wrote:


External Email - Use Caution
Hello again
I have the following issue when running mri_convert. When using the option
-conform option (as in the reconall pipeline), the sag slices seems to be
shifted at some point (see attached pictures). What is happening?
By the way the option description is not super clear, could you please give
some extra details?
Best
Antonin
[IMAGE][IMAGE]
Hôpital Erasme
Lien vers Disclaimer

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Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

[Rovai Antonin]

External Email - Use Caution

Hey

So opening only the conformed image in freeview, mricro and fsleyes constantly 
gives me crazy results. Also, the wm segmentation is completely wrong so I 
really think there something wrong in the file….

Best

Antonin

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

> On 3 Sep 2019, at 15:55, Bruce Fischl  wrote:
>
> Hi Antonin
>
> hmmm. Can you try *only* loading the conformed image and seeing how it looks? 
> freeview will use one of the images as the basis for it's display 
> coordinates, which can cause apparent slicing artifacts that are only display 
> issues for other volumes.
>
> cheers
> Bruce
>
> On Tue, 3 Sep 2019, Rovai Antonin wrote:
>
>> External Email - Use Caution
>> Hello again
>> I have the following issue when running mri_convert. When using the option
>> -conform option (as in the reconall pipeline), the sag slices seems to be
>> shifted at some point (see attached pictures). What is happening?
>> By the way the option description is not super clear, could you please give
>> some extra details?
>> Best
>> Antonin
>> [IMAGE][IMAGE]
>> Hôpital Erasme
>> Lien vers Disclaimer
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Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

[Bruce Fischl]

Hi Antonin

hmmm. Can you try *only* loading the conformed image and seeing how it 
looks? freeview will use one of the images as the basis for it's display 
coordinates, which can cause apparent slicing artifacts that are only 
display issues for other volumes.


cheers
Bruce

On Tue, 3 Sep 2019, Rovai Antonin wrote:



External Email - Use Caution

Hello again


I have the following issue when running mri_convert. When using the option
-conform option (as in the reconall pipeline), the sag slices seems to be
shifted at some point (see attached pictures). What is happening? 

By the way the option description is not super clear, could you please give
some extra details?

Best

Antonin

[IMAGE][IMAGE]

Hôpital Erasme

Lien vers Disclaimer


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Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

[Bruce Fischl]

oh, I see. Yes it is defaulted to being on in recon-all. You can specify 
-no-mprage to recon-all to turn it off, although it might be worth trying 
both out on a set of subjects and seeing which does a better job


cheers
Bruce

On Tue, 3 Sep 2019, Rovai Antonin 
wrote:




External Email - Use Caution

Hi Bruce,


Thanks for your response. From what I read on the wiki
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) the
switch in on by default since freesurfer6.0 (but that doesn’t seem to be the
case in 5.3).
At any rate we use the BRAVO sequence (on a GE MRI) and it also has an
inversion pulse (also CNR isn’t as good as in a MPRAGE).

Best

Antonin

  On 3 Sep 2019, at 15:44, Bruce Fischl
   wrote:

Hi AR

1. mprage in general has higher CNR and lower SNR than non
inversion-prepared T1w sequences like FLASH. THe -mprage switch takes
advantage of this to loosen the intensity gradient threshold in the
region filling of the wm.

2. If you just leave out the -mprage switch it will revert to the
default behavior

cheers
Bruce



On Tue, 3 Sep 2019, Rovai Antonin wrote:

  External Email - Use Caution
  Hello,
  From the ReconAllTable
  (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0)
  I see
  that the mri_normalize step (producing the T1.mgz file) has
  the -mprage
  option.
  I have two questions:
  1. What is this option doing exactly? There is no
  description in the
  mri_normalize man page
  (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize);
  similarly, the CLI
  help doesn’t mention this option.
  2. How do I change this when launching a ReconAll without
  re-writing a custom
  pipeline? (For context our T1 is not MPRAGE and we had some
  segmentation
  issues so this is an attempt to debug this).
  Thanks for you help
  AR
  Hôpital Erasme
  Lien vers Disclaimer

Hôpital Erasme

Lien vers Disclaimer

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[Freesurfer] mri_surf2surf without sphere.reg

[Caspar M. Schwiedrzik]

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Hi!
I am having some issues projecting retinotopic mapping data from a monkey
analyzed in surface space onto its surface using rtview. The issue seems to
be that the data need to be converted into paint format through
mri_surf2surf, and that we do not have a ?h.sphere.reg file because the
surface is not aligned to a template.
Is it possible to run mri_surf2surf without reference to ?h.sphere.reg
somehow? I tried with --s instead of source and target subject, but that
didn't work.
Alternatively, can we provide an identity matrix for ?h.sphere.reg, perhaps
through mris_register?

Any advice would be appreciated.
Thanks, Caspar
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Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

[Rovai Antonin]

External Email - Use Caution

(Continued)

Of course I meant using the recon-all command!

On 3 Sep 2019, at 15:48, Rovai Antonin 
mailto:antonin.ro...@erasme.ulb.ac.be>> wrote:


External Email - Use Caution

Hi Bruce,

Thanks for your response. From what I read on the wiki 
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) the switch 
in on by default since freesurfer6.0 (but that doesn’t seem to be the case in 
5.3).
At any rate we use the BRAVO sequence (on a GE MRI) and it also has an 
inversion pulse (also CNR isn’t as good as in a MPRAGE).

Best

Antonin

On 3 Sep 2019, at 15:44, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:

Hi AR

1. mprage in general has higher CNR and lower SNR than non inversion-prepared 
T1w sequences like FLASH. THe -mprage switch takes advantage of this to loosen 
the intensity gradient threshold in the region filling of the wm.

2. If you just leave out the -mprage switch it will revert to the default 
behavior

cheers
Bruce



On Tue, 3 Sep 2019, Rovai Antonin wrote:

External Email - Use Caution
Hello,
From the ReconAllTable
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see
that the mri_normalize step (producing the T1.mgz file) has the -mprage
option.
I have two questions:
1. What is this option doing exactly? There is no description in the
mri_normalize man page
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize); similarly, the CLI
help doesn’t mention this option.
2. How do I change this when launching a ReconAll without re-writing a custom
pipeline? (For context our T1 is not MPRAGE and we had some segmentation
issues so this is an attempt to debug this).
Thanks for you help
AR
Hôpital Erasme
Lien vers Disclaimer


Lien vers Disclaimer

[Hôpital Erasme]

Lien vers Disclaimer

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Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

[Rovai Antonin]

External Email - Use Caution

Hi Bruce,

Thanks for your response. From what I read on the wiki 
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) the switch 
in on by default since freesurfer6.0 (but that doesn’t seem to be the case in 
5.3).
At any rate we use the BRAVO sequence (on a GE MRI) and it also has an 
inversion pulse (also CNR isn’t as good as in a MPRAGE).

Best

Antonin

On 3 Sep 2019, at 15:44, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:

Hi AR

1. mprage in general has higher CNR and lower SNR than non inversion-prepared 
T1w sequences like FLASH. THe -mprage switch takes advantage of this to loosen 
the intensity gradient threshold in the region filling of the wm.

2. If you just leave out the -mprage switch it will revert to the default 
behavior

cheers
Bruce



On Tue, 3 Sep 2019, Rovai Antonin wrote:

External Email - Use Caution
Hello,
From the ReconAllTable
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see
that the mri_normalize step (producing the T1.mgz file) has the -mprage
option.
I have two questions:
1. What is this option doing exactly? There is no description in the
mri_normalize man page
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize); similarly, the CLI
help doesn’t mention this option.
2. How do I change this when launching a ReconAll without re-writing a custom
pipeline? (For context our T1 is not MPRAGE and we had some segmentation
issues so this is an attempt to debug this).
Thanks for you help
AR
Hôpital Erasme
Lien vers Disclaimer

[Hôpital Erasme]

Lien vers Disclaimer

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Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

[Bruce Fischl]

Hi AR

1. mprage in general has higher CNR and lower SNR than non 
inversion-prepared T1w sequences like FLASH. THe -mprage switch takes 
advantage of this to loosen the intensity gradient threshold in the region 
filling of the wm.


2. If you just leave out the -mprage switch it will revert to the default 
behavior


cheers
Bruce



On Tue, 3 Sep 2019, Rovai 
Antonin wrote:




External Email - Use Caution

Hello,


From the ReconAllTable
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see
that the mri_normalize step (producing the T1.mgz file) has the -mprage
option.

I have two questions:
1. What is this option doing exactly? There is no description in the
mri_normalize man page
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize); similarly, the CLI
help doesn’t mention this option.
2. How do I change this when launching a ReconAll without re-writing a custom
pipeline? (For context our T1 is not MPRAGE and we had some segmentation
issues so this is an attempt to debug this).

Thanks for you help

AR

Hôpital Erasme

Lien vers Disclaimer


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[Freesurfer] Question about how to build .gca files from non-human atlas and images

[arsene ella]

External Email - Use Caution

*Dear **Freesurfer experts,*
*I’ve built an atlas of structures of a non-human average brain and
now **I would like to build **its** .gca files from scratch. **From
the Freesurfer mailing list, I saw that this is possible using
**rebuild_gca_atlas.csh* *which trains labelled brai**ns
(**seg_edited.mgz**) and their intensity volumes (it is said to use
the **norm.mgz** for this purpose) from several subjects through
**mri_ca_train**. **My questions are :**1) How to normalize my native
intensity volume to a **norm.mgz**  volume without .gca and .lta files
asking by  **mri_ca_normalize **?**Y**ou’ve suggested to give
**mri_ca_normalize** a flag to tell it to use a manual segmentation
instead of the gca by trying **-seg **. Then the
gca name won't matter - it should ignore it… I tried this as followed
:**let : **- **Brain_Template_T1_MPR.mgz **  be my
intensity native volume**- **Brain_Cortex_Atlas.mgz*  *
  be my manual segmented volume**-
**Brain_Template_T1_MPR_norm.mgz*  *  be **my **norm** output**
volume*
*Command lines :**mri_ca_normalize**  Brain_Template_T1_MPR.mgz
**-seg** Brain_Cortex_Atlas.mgz
Brain_Template_T1_MPR_norm.mgz**gave the following error message
:**reading 1 input volume**reading atlas from
'-seg'...**GCAread(-seg): could not open file**No such file or
directory**mri_ca_normalize: could not open GCA -seg.**No such file or
directory*
*mri_ca_normalize* *-seg **  Brain_Cortex_Atlas.mgz
Brain_Template_T1_MPR.mgz Brain_Template_T1_MPR_norm.mgz**gave the
following message  and stopped:**using segmentation volume
/home/arsene/Bureau/FS_GCA/FS_SHEEP_CGA/Brain_Cortex_Atlas.mgz to
generate control points...**usage: mri_ca_normalize []
  ...
...*
*What is wrong with theses **mri_ca_normalize* *commands ?*
*2) My second question is to know how to transfert labels from my*
*manual seg**mented** volume **(ex : **atlas.mgz**) to each single
image volume (ex : vol1**.mgz**) ?**You’ve suggested to use
**mri_label2label**, but **I didn’t see anything allowing me to do a
**volume_to_volume** transfert **from **its **–help**…** If I got it
wrong, could you suggest a command ?*


*cheers*


*Arsene*
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[Freesurfer] Reconall with no-MPRAGE T1w image?

[Rovai Antonin]

External Email - Use Caution

Hello,

From the ReconAllTable 
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see that 
the mri_normalize step (producing the T1.mgz file) has the -mprage option.

I have two questions:
1. What is this option doing exactly? There is no description in the 
mri_normalize man page 
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize); similarly, the CLI 
help doesn’t mention this option.
2. How do I change this when launching a ReconAll without re-writing a custom 
pipeline? (For context our T1 is not MPRAGE and we had some segmentation issues 
so this is an attempt to debug this).

Thanks for you help

AR

[Hôpital Erasme]

Lien vers Disclaimer
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