Re: [Freesurfer] Hippocampal subfields

[Iglesias Gonzalez, Juan E.]

Dear Zheng,
Can you please send us the log files?
Kind regards,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of 郑凤莲 

Reply-To: Freesurfer support list 
Date: Wednesday, 7 August 2019 at 21:19
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields


External Email - Use Caution
Hi exports,

I am using FS6.0 to segment hippocampus. I run "recon-all -s bert 
-hippocampal-subfields-T1" and it said "recon all bert finished without error". 
However, in mri directory, there is no l(r)h.hippoSfLabels-T1.v10.mgz file. And 
in tmp directory, there are two directories, "hippoSF_T1_v10_left" and 
"hippoSF_T1_v10_right". But in these two directories, the 
l(r)h.hippoSfLabels-T1.v10.mgz file is still not exsit. What's the matter? I 
need your help. Thanks very muxh in advance.

Sincerely,
Zheng





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[Freesurfer] Hippocampal subfields

[郑凤莲]

External Email - Use Caution

Hi exports,


I am using FS6.0 to segment hippocampus. I run "recon-all -s bert 
-hippocampal-subfields-T1" and it said "recon all bert finished without error". 
However, in mri directory, there is no l(r)h.hippoSfLabels-T1.v10.mgz file. And 
in tmp directory, there are two directories, "hippoSF_T1_v10_left" and 
"hippoSF_T1_v10_right". But in these two directories, the 
l(r)h.hippoSfLabels-T1.v10.mgz file is still not exsit. What's the matter? I 
need your help. Thanks very muxh in advance.


Sincerely,
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Re: [Freesurfer] Help with MRI segstats

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

You should only pass one of --seg, --annot, or --slabel  to 
mri_segstats. I don't understand how you are trying to use this in the 
context of your permutation. Is this something that you are running on 
each iteration? If so, it is probably not what you want to do. Probably 
you want to run mri_surfcluster to get the cluster sizes out.

On 8/7/19 1:31 PM, Daliah Ross wrote:
>
> External Email - Use Caution
>
> This is the command line:
> mri_segstats --seg F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.mgh 
> --annot lh.aparc.annot lh parc --slabel fsaverage lh cortex --sum 
> F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.txt
>
> We are running the permutations within FS, but because our model is a 
> linear mixed model, and we didn't think that this would be compatible 
> with fspalm. So, we are running the permutations "manually" (i.e. we 
> are generating the random permutations, which in our case is just 
> switching the subject labels for the thickness data. We are then using 
> mri_surfcluster to extract the maximum cluster size per permutation 
> and will use the permutation distribution to determine our the 
> statistical significance of our results). In addition, our analyses 
> are a bit out of the ordinary in that the thickness data are an 
> independent variable in our model, for which we have a repeated 
> non-imaging measure as the outcome. Effectively, we are using the 
> thickness maps to generate vertex-wise regressors, with a fixed 
> outcome measure (fixed in the sense that it doesn't vary across the 
> brain).
>
> If you have any thoughts about how we could use fspalm in our case, 
> your advice would be most appreciated.
>
> Thanks again,
> Daliah
>
> *Daliah Ross* | dro...@mail.yu.edu 
>
> Ph.D. Student, Clinical Psychology with Health Emphasis
> Ferkauf Graduate School of Psychology
> Yeshiva University
> Albert Einstein College of Medicine
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> 
>  > On Behalf Of
> Greve, Douglas N.,Ph.D.
> Sent: Tuesday, August 6, 2019 12:56 PM
> To: freesurfer@nmr.mgh.harvard.edu
> 
> Subject: Re: [Freesurfer] Help with MRI segstats
>
> Can you send command lines? Also, are you using the built-in
> permutation tool or trying to do something outside of FS?
>
> On 8/6/19 8:40 AM, Daliah Ross wrote:
> >
> > External Email - Use Caution
> >
> > Hi FreeSurfer experts,
> >
> > I have a couple of questions regarding mri_segstats tool for an
> > analysis on vertex-wise cortical thickness data. We are
> attempting to
> > compare maximum cluster sizes among permutations. We are having
> > trouble figuring out how to get the anatomical label for each
> cluster
> > using the --slabel argument. We are also wondering if the
> difference
> > between cluster sizes between mri_surfcluster and mri_segstats
> is due
> > to partial volumes, and if so, how to correctly use the --pv
> argument.
> > It suggests in the wiki page that mri/norm.mgz volume is usually
> used
> > but I believe we need something surface-based since we are using
> > thickness data.
> >
> > Thank you in advance for any help you can provide.
> >
> > Best,
> > Daliah
> >
> > *Daliah Ross* | dro...@mail.yu.edu 
> >
> >
> > Ph.D. Student, Clinical Psychology with Health Emphasis Ferkauf
> > Graduate School of Psychology Yeshiva University Albert Einstein
> > College of Medicine
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
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> > https://mail
> > .nmr.mgh.harvard.edu
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> %2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C0
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> %7Cfde693609070412c457808d71a8f16f2%
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Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space

[Iglesias Gonzalez, Juan E.]

Dear Jessica,
You can register your image to the atlas, and then apply the same transform to 
the segmentations (“propagate”). That will bring the segmentations to atlas 
(Brainnetome) space.
I hope this helps,
/E

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Jessica Bourgin 

Reply-To: Freesurfer support list 
Date: Wednesday, 7 August 2019 at 13:44
To: freesurfer 
Subject: Re: [Freesurfer] Transform hippocampal/amygdala segmentation to 
another space


External Email - Use Caution
Dear Juan Eugenio,

Thanks a lot for your quick response.

I don't understand what you mean exactly by "propagate the hard segmentations".

And when you say to register the subjects to the Brainnetome, do you mean 
replace the atlas used by recon-all to do that ? (sorry, I am currently a PhD 
student with little experience in neuroimaging).

You also mention that the transformation is not trivial. But do you think this 
is "correct" to make it ?

Thanks for your help !

Cheers,

Jessica BOURGIN
Laboratoire de Psychologie et Neurocognition
CNRS UMR 5105
Université Savoie Mont Blanc (USMB)
BP 1104
73011 Chambery Cedex France

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Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space

[Jessica Bourgin]

External Email - Use Caution

Dear Juan Eugenio, 

Thanks a lot for your quick response. 

I don't understand what you mean exactly by "propagate the hard segmentations". 

And when you say to register the subjects to the Brainnetome, do you mean 
replace the atlas used by recon-all to do that ? (sorry, I am currently a PhD 
student with little experience in neuroimaging). 

You also mention that the transformation is not trivial. But do you think this 
is "correct" to make it ? 

Thanks for your help ! 

Cheers, 


Jessica BOURGIN 
Laboratoire de Psychologie et Neurocognition 
CNRS UMR 5105 
Université Savoie Mont Blanc (USMB) 
BP 1104 
73011 Chambery Cedex France 

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[Freesurfer] [FREESURFER] longitudinal processing base_tmps does not exist error

[Lee, Seonjoo]

External Email - Use Caution

Dear Freesurfer,
Could you help me to resolve this error? I looked up the previous postings, but 
the recommendation (copying files in the same folder etc.) did not help.
Thank you.



$ recon-all -base template -tp 002_S_0295_S32678 -tp 002_S_0295_S567612 -sd 
$SUBJECTS_DIR

Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /Users/seonjoolee/ADNI_long/tmp

Actual FREESURFER_HOME /Applications/freesurfer

Darwin Seonjoos-iMac.nyspi.local 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 
11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64



Started at Wed Aug 7 10:24:55 EDT 2019

Ended   at Wed Aug 7 10:24:56 EDT 2019

#@#%# recon-all-run-time-hours 0.000

recon-all -s template finished without error at Wed Aug  7 10:24:56 EDT 2019

done





$ recon-all -long 002_S_0295_S32678 template -all

ERROR: file /Users/ll/ADNI_long/tmp/template/base-tps does not exist!



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Re: [Freesurfer] Fwd: Recon-all output space and .annot file registration

[Bruce Fischl]

Hi Rachel

all processing is done in the subject's native space. If you want to 
downsample probably the easiest thing to do is map to one of the 
lower res fsaverage subjects (e.g. fsaverage3 or fsaverage4) using 
mri_surf2surf/mri_label2label and the like after running recon-all.


cheers
Bruce


On Wed, 7 Aug 2019, Rachel S wrote:



External Email - Use Caution

Hello freesurfer developers,
I am trying to get the user defined segmentation for a subject generated in
here (https://github.com/mattcieslak/easy_lausanne) . After recon-all, I
have the pial surface with ~250k vertices. My first question is about the
recon-all space. I thought the output of recon-all is already registered
with the fsaverage space since it uses bucker40 as the template for
segmentation. But some mentioned it is in the individual native space. Which
one is true? 

My second question is about the procedure to generate the segmentation for
downsampled surface. I have the .annot file and .label file for that subject
and also for fsaverage. Reading the .annot file can give me the region
mapping for ~250k matrix. I want to map the subject to fsaverage5 space and
also downsample the vertices for the cortical surface to ~20k. And I want to
get the region mapping for this ~20k vertices from the ~250k vertice .annot
file. I looked into the documentation and email archive, here is a few
things I tried.

I am using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

1. Try to map to fsaverage in the recon-all step by using
recon-all -i .dcm -s p6_fs5 -all -qcache -target fsaverage5
And here is the error:

---
#@# 1/1 p6_fs5 Wed 07 Aug 2019 04:49:09 AM EDT --
---
mri_surf2surf --srcsubject p6_fs5 --srchemi lh --srcsurfreg
fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg
sphere.reg --tval ./tmp.mris_preproc.7614/p6_fs5.1.mgh --sval
/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness --sfmt
curv --noreshape --cortex
MRISread(/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaver
age5.sphere.reg): could not open file
Source registration surface changed to fsaverage5.sphere.reg
Target registration surface changed to sphere.reg

$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $

setenv SUBJECTS_DIR /home/rachelsun/Software/freesurfer/subjects
cd /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf
mri_surf2surf --srcsubject p6_fs5 --srchemi lh --srcsurfreg
fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg
sphere.reg --tval ./tmp.mris_preproc.7614/p6_fs5.1.mgh --sval
/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness --sfmt
curv --noreshape --cortex

sysname  Linux
hostname rachel-pc
machine  x86_64
user     rachelsun
srcsubject = p6_fs5
srcval     =
/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness
srctype    = curv
trgsubject = fsaverage5
trgval     = ./tmp.mris_preproc.7614/p6_fs5.1.mgh
trgtype    =
srcsurfreg = fsaverage5.sphere.reg
trgsurfreg = sphere.reg
srchemi    = lh
trghemi    = lh
frame      = 0
fwhm-in    = 0
fwhm-out   = 0
label-src  = lh.cortex.label
label-trg  = lh.cortex.label
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface 
reg/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaverage5.sphe
re.reg
No such file or directory
mri_surf2surf: could not read 
surface/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaverage5.sphe
re.reg
No such file or directory
Linux rachel-pc 4.19.62-1-MANJARO #1 SMP PREEMPT Sun Jul 28 09:14:58 UTC
2019 x86_64 GNU/Linux
 

2. Use the basic recon-all step recon-all -i .dcm -s p6 -all, and run 
mri_surf2surf --srcsubject p6 --sval-xyz pial --trgsubject fsaverage5
--tval-xyz --tval lh.pial.p6 --hemi lh
And I can get the surface mapped to fsaverage space, but I am not sure how
to get the region segmentation for this new surface.
From what I learned, mri_surf2surf is to map .annot between subjects.

Sorry for the long email and thank you for your time. I would really
appreciate it your input.

Best regards,
Rachel

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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for help

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

Run mris_preproc with a single subject and send the terminal output

On 8/7/19 11:47 AM, Reza Rahmanzadeh wrote:
>  External Email - Use Caution
>
> Yes, i checked -projfrac 0.5 with old or new mris_preproc but didn’t work. I 
> checked all registration, they are perfect.
>
>> On 7 Aug 2019, at 17:29, Greve, Douglas N.,Ph.D.  
>> wrote:
>>
>> If you do not specify --projfrac-avg, does it come out as non-zero? If
>> so, I would think that it is a problem with the registration. Have you
>> checked the registrations?
>>
>>> On 8/7/19 11:25 AM, Reza Rahmanzadeh wrote:
>>>  External Email - Use Caution
>>>
>>> It means that for any given subjects i’ve had one -iv argument and then for 
>>> mri_glmfit i used .fsgd file with the same order.
>>>
 On 7 Aug 2019, at 17:23, Reza Rahmanzadeh  
 wrote:

 External Email - Use Caution

 Yes, for mris_preproc:

 mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out 
 lh.NDI_inflated.avg.mgh --iv  
 

> On 7 Aug 2019, at 17:14, Reza Rahmanzadeh  
> wrote:
>
> mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out 
> lh.NDI_inflated.avg.mgh
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 Freesurfer@nmr.mgh.harvard.edu
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>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.


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[Freesurfer] Fwd: Recon-all output space and .annot file registration

[Rachel S]

External Email - Use Caution

Hello freesurfer developers,

I am trying to get the user defined segmentation for a subject generated in
here (https://github.com/mattcieslak/easy_lausanne) . After recon-all, I
have the pial surface with ~250k vertices. My first question is about the
recon-all space. I thought the output of recon-all is already registered
with the fsaverage space since it uses bucker40 as the template for
segmentation. But some mentioned it is in the individual native space.
Which one is true?

My second question is about the procedure to generate the segmentation for
downsampled surface. I have the .annot file and .label file for that
subject and also for fsaverage. Reading the .annot file can give me the
region mapping for ~250k matrix. I want to map the subject to fsaverage5
space and also downsample the vertices for the cortical surface to ~20k.
And I want to get the region mapping for this ~20k vertices from the ~250k
vertice .annot file. I looked into the documentation and email archive,
here is a few things I tried.

I am using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

1. Try to map to fsaverage in the recon-all step by using
recon-all -i .dcm -s p6_fs5 -all -qcache -target fsaverage5
And here is the error:

---
#@# 1/1 p6_fs5 Wed 07 Aug 2019 04:49:09 AM EDT --
---
mri_surf2surf --srcsubject p6_fs5 --srchemi lh --srcsurfreg
fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg
sphere.reg --tval ./tmp.mris_preproc.7614/p6_fs5.1.mgh --sval
/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness
--sfmt curv --noreshape --cortex
MRISread(/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaverage5.sphere.reg):
could not open file
Source registration surface changed to fsaverage5.sphere.reg
Target registration surface changed to sphere.reg

$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $

setenv SUBJECTS_DIR /home/rachelsun/Software/freesurfer/subjects
cd /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf
mri_surf2surf --srcsubject p6_fs5 --srchemi lh --srcsurfreg
fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg
sphere.reg --tval ./tmp.mris_preproc.7614/p6_fs5.1.mgh --sval
/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness
--sfmt curv --noreshape --cortex

sysname  Linux
hostname rachel-pc
machine  x86_64
user rachelsun
srcsubject = p6_fs5
srcval =
/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness
srctype= curv
trgsubject = fsaverage5
trgval = ./tmp.mris_preproc.7614/p6_fs5.1.mgh
trgtype=
srcsurfreg = fsaverage5.sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = lh.cortex.label
label-trg  = lh.cortex.label
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg
/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaverage5.sphere.reg
No such file or directory
mri_surf2surf: could not read surface
/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaverage5.sphere.reg
No such file or directory
Linux rachel-pc 4.19.62-1-MANJARO #1 SMP PREEMPT Sun Jul 28 09:14:58 UTC
2019 x86_64 GNU/Linux


2. Use the basic recon-all step recon-all -i .dcm -s p6 -all, and run
mri_surf2surf --srcsubject p6 --sval-xyz pial --trgsubject fsaverage5
--tval-xyz --tval lh.pial.p6 --hemi lh
And I can get the surface mapped to fsaverage space, but I am not sure how
to get the region segmentation for this new surface.
From what I learned, mri_surf2surf is to map .annot between subjects.

Sorry for the long email and thank you for your time. I would really
appreciate it your input.

Best regards,
Rachel
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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for help

[Reza Rahmanzadeh]

External Email - Use Caution

Yes, i checked -projfrac 0.5 with old or new mris_preproc but didn’t work. I 
checked all registration, they are perfect.

> On 7 Aug 2019, at 17:29, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> If you do not specify --projfrac-avg, does it come out as non-zero? If 
> so, I would think that it is a problem with the registration. Have you 
> checked the registrations?
> 
>> On 8/7/19 11:25 AM, Reza Rahmanzadeh wrote:
>> External Email - Use Caution
>> 
>> It means that for any given subjects i’ve had one -iv argument and then for 
>> mri_glmfit i used .fsgd file with the same order.
>> 
>>> On 7 Aug 2019, at 17:23, Reza Rahmanzadeh  
>>> wrote:
>>> 
>>>External Email - Use Caution
>>> 
>>> Yes, for mris_preproc:
>>> 
>>> mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out 
>>> lh.NDI_inflated.avg.mgh --iv  
>>> 
>>> 
 On 7 Aug 2019, at 17:14, Reza Rahmanzadeh  
 wrote:
 
 mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out 
 lh.NDI_inflated.avg.mgh
>>> 
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> 
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.

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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for help

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

If you do not specify --projfrac-avg, does it come out as non-zero? If 
so, I would think that it is a problem with the registration. Have you 
checked the registrations?

On 8/7/19 11:25 AM, Reza Rahmanzadeh wrote:
>  External Email - Use Caution
>
> It means that for any given subjects i’ve had one -iv argument and then for 
> mri_glmfit i used .fsgd file with the same order.
>
>> On 7 Aug 2019, at 17:23, Reza Rahmanzadeh  wrote:
>>
>> External Email - Use Caution
>>
>> Yes, for mris_preproc:
>>
>> mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out 
>> lh.NDI_inflated.avg.mgh --iv  
>> 
>>
>>> On 7 Aug 2019, at 17:14, Reza Rahmanzadeh  
>>> wrote:
>>>
>>> mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out 
>>> lh.NDI_inflated.avg.mgh
>>
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>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for help

[Reza Rahmanzadeh]

External Email - Use Caution

It means that for any given subjects i’ve had one -iv argument and then for 
mri_glmfit i used .fsgd file with the same order.

> On 7 Aug 2019, at 17:23, Reza Rahmanzadeh  wrote:
> 
>External Email - Use Caution
> 
> Yes, for mris_preproc:
> 
> mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out 
> lh.NDI_inflated.avg.mgh --iv  
> 
> 
>> On 7 Aug 2019, at 17:14, Reza Rahmanzadeh  wrote:
>> 
>> mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out 
>> lh.NDI_inflated.avg.mgh
> 
> 
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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for help

[Reza Rahmanzadeh]

External Email - Use Caution

Yes, for mris_preproc:

mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out 
lh.NDI_inflated.avg.mgh --iv  


> On 7 Aug 2019, at 17:14, Reza Rahmanzadeh  wrote:
> 
> mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out 
> lh.NDI_inflated.avg.mgh


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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for help

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

That mris_preroc commad is incomplete.

On 8/7/19 11:13 AM, Reza Rahmanzadeh wrote:
>
> External Email - Use Caution
>
> My command lines:
>
> My command lines sequentially for the analysis are: ( I have done just 
> the same command lines for MWF maps and it worked very good, but for 
> NDI and ODI maps of NODDI does not work).
>
> 1-mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 
> --out lh.NDI_inflated.avg.mgh (i used the new mris_preproc you sent me).
>
> 2-mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval 
> lh.NDI_inflated.avg.mgh --tval lh.NDI_inflated.avg.05.mgh
>
> 3-mri_glmfit --y lh.NDI_inflated.avg.05.mgh --surf fsaverage lh --C 
> contrast --fsgd fsgd.fsgd --cortex --glmdir lh.NDI_inflated.avg.05.glmdir
>
>
> And the output for the mri_glmfit was:
>> ERROR: no voxels found in the mask
>>   make sure at least one voxel has a non-zero value for each input
>
> Reza
>
> On 7 Aug 2019, at 17:11, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
>> no idea until you tell me what you did, including command lines and
>> terminal output
>>
>> On 8/7/19 11:08 AM, Reza Rahmanzadeh wrote:
>>> External Email - Use Caution
>>>
>>> Thanks, I saw that before, what could be the reason for that and how 
>>> could i do mris_preproc correctly for NDI maps?
>>>
>>> Thanks,
>>> Reza
>>>
 On 7 Aug 2019, at 17:05, Greve, Douglas N.,Ph.D. 
 mailto:dgr...@mgh.harvard.edu>> wrote:

 Every vertex of every subject is 0 in lh.NDI_inflated.avg.05.mgh

> On 8/6/19 6:30 AM, Reza Rahmanzadeh wrote:
>
> External Email - Use Caution
>
> Hi Doug,
>
>
> When i click on the link you sent me for uploading the files, there is
> no bottom/way to upload something there. That is why i attached the
> outputs.
>
>
> My command lines sequentially for the analysis are: ( I have done just
> the same command lines for MWF maps and it worked very good, but for
> NDI and ODI maps of NODDI does not work).
>
> 1-mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25
> --out lh.NDI_inflated.avg.mgh (i used the new mris_preproc you 
> sent me).
>
> 2-mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval
> lh.NDI_inflated.avg.mgh --tval lh.NDI_inflated.avg.05.mgh
>
> 3-mri_glmfit --y lh.NDI_inflated.avg.05.mgh --surf fsaverage lh --C
> contrast --fsgd fsgd.fsgd --cortex --glmdir 
> lh.NDI_inflated.avg.05.glmdir
>
>
>
> The outputs of all three steps are attached.
>
>
>
> Looking forward for your helps
>
> Reza
>
>
>
>
>
>
>
> 
> *From:* Greve, Douglas N.,Ph.D.  >
> *Sent:* Monday, August 5, 2019 5:55:18 PM
> *To:* Reza Rahmanzadeh; Freesurfer support list
> *Cc:* gr...@nmr.mgh.harvard.edu 
> *Subject:* Re: [Freesurfer] need for help
> Can you upload the input (ie, argument to --y) here:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming
> Also, send your mri_glmfit command line.
>
>> On 8/2/2019 9:41 AM, Reza Rahmanzadeh wrote:
>>
>> External Email - Use Caution
>>
>> yes, I have the page below for all patients.
>>
>>
>> I think it means all values are zero. My registration for bbregister
>> is fine and i wrote my mris_preproc the same as MWF maps.
>>
>>
>> Thanks,
>>
>> Reza
>>
>> 
>> *From:* Greve, Douglas N.,Ph.D. > >
>> *Sent:* Friday, August 2, 2019 3:35:45 PM
>> *To:* Reza Rahmanzadeh; Freesurfer support list
>> *Cc:* gr...@nmr.mgh.harvard.edu 
>> *Subject:* Re: [Freesurfer] need for help
>> did you check each subject to make sure they had a non-zero map?
>>
>>> On 8/2/2019 6:25 AM, Reza Rahmanzadeh wrote:
>>>
>>> External Email - Use Caution
>>>
>>> Dear Doug,
>>>
>>>
>>> NODDI is diffusion imaging and we have vakue regarding neurite
>>> density (NDI in NDI map) and orientation dispersion (ODI value in
>>> ODI map). I do not know why mris_preproc works well on MWI maps but
>>> not on NODDI maps (both NDI and ODI maps). Beside using projfrac-avg
>>> 0 1 0.25 , i have run mris_preproc with projfrac 0.5 but again i got
>>> this error:
>>>
>>> ERROR: no voxels found in the mask
>>>   make sure at least one voxel has a non-zero value for each input
>>>
>>> I have run mris_preproc on three patients that i am sure about
>>> registration quality, again when i scroll through them , there is no
>>> value in none of them. How that is possible?
>>>
>>> NOD

[Freesurfer] Help us help you learn methods in Advanced Statistics in Neuroimaging and Genetics

[ROBERT CARY WELSH]

External Email - Use Caution

Hi,

We are in the midst of designing a short course on Advanced Statistics in 
Neuroimaging and Genetics. We would like to get a sense of the interest.

If you don’t mind, please take a moment to fill out this short survey.

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Associate Professor
Department of Psychiatry
University of Utah
robert.c.we...@utah.edu


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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for help

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

no idea until you tell me what you did, including command lines and 
terminal output

On 8/7/19 11:08 AM, Reza Rahmanzadeh wrote:
>  External Email - Use Caution
>
> Thanks, I saw that before, what could be the reason for that and how could i 
> do mris_preproc correctly for NDI maps?
>
> Thanks,
> Reza
>
>> On 7 Aug 2019, at 17:05, Greve, Douglas N.,Ph.D.  
>> wrote:
>>
>> Every vertex of every subject is 0 in lh.NDI_inflated.avg.05.mgh
>>
>>> On 8/6/19 6:30 AM, Reza Rahmanzadeh wrote:
>>>
>>>  External Email - Use Caution
>>>
>>> Hi Doug,
>>>
>>>
>>> When i click on the link you sent me for uploading the files, there is
>>> no bottom/way to upload something there. That is why i attached the
>>> outputs.
>>>
>>>
>>> My command lines sequentially for the analysis are: ( I have done just
>>> the same command lines for MWF maps and it worked very good, but for
>>> NDI and ODI maps of NODDI does not work).
>>>
>>> 1-mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25
>>> --out lh.NDI_inflated.avg.mgh (i used the new mris_preproc you sent me).
>>>
>>> 2-mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval
>>> lh.NDI_inflated.avg.mgh --tval lh.NDI_inflated.avg.05.mgh
>>>
>>> 3-mri_glmfit --y lh.NDI_inflated.avg.05.mgh --surf fsaverage lh --C
>>> contrast --fsgd fsgd.fsgd --cortex --glmdir lh.NDI_inflated.avg.05.glmdir
>>>
>>>
>>>
>>> The outputs of all three steps are attached.
>>>
>>>
>>>
>>> Looking forward for your helps
>>>
>>> Reza
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> 
>>> *From:* Greve, Douglas N.,Ph.D. 
>>> *Sent:* Monday, August 5, 2019 5:55:18 PM
>>> *To:* Reza Rahmanzadeh; Freesurfer support list
>>> *Cc:* gr...@nmr.mgh.harvard.edu
>>> *Subject:* Re: [Freesurfer] need for help
>>> Can you upload the input (ie, argument to --y) here:
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming
>>> Also, send your mri_glmfit command line.
>>>
 On 8/2/2019 9:41 AM, Reza Rahmanzadeh wrote:

  External Email - Use Caution

 yes, I have the page below for all patients.


 I think it means all values are zero. My registration for bbregister
 is fine and i wrote my mris_preproc the same as MWF maps.


 Thanks,

 Reza

 
 *From:* Greve, Douglas N.,Ph.D. 
 *Sent:* Friday, August 2, 2019 3:35:45 PM
 *To:* Reza Rahmanzadeh; Freesurfer support list
 *Cc:* gr...@nmr.mgh.harvard.edu
 *Subject:* Re: [Freesurfer] need for help
 did you check each subject to make sure they had a non-zero map?

> On 8/2/2019 6:25 AM, Reza Rahmanzadeh wrote:
>
>  External Email - Use Caution
>
> Dear Doug,
>
>
> NODDI is diffusion imaging and we have vakue regarding neurite
> density (NDI in NDI map) and orientation dispersion (ODI value in
> ODI map). I do not know why mris_preproc works well on MWI maps but
> not on NODDI maps (both NDI and ODI maps). Beside using projfrac-avg
> 0 1 0.25 , i have run mris_preproc with projfrac 0.5 but again i got
> this error:
>
> ERROR: no voxels found in the mask
>make sure at least one voxel has a non-zero value for each input
>
> I have run mris_preproc on three patients that i am sure about
> registration quality, again when i scroll through them , there is no
> value in none of them. How that is possible?
>
> NODDI does not have a lot of zero value but all values in cortex are
> between 0.2-0.4.
>
>
> Thanks,
> Reza
>
>
> 
> *From:* Greve, Douglas N.,Ph.D. 
> *Sent:* Wednesday, July 31, 2019 12:50:45 AM
> *To:* Reza Rahmanzadeh; Freesurfer support list
> *Cc:* gr...@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] need for help
> I don't know what is in the NODDI maps. The way mri_glmfit works is
> that
> if any subject has a 0-value at a vertex, then it will mask out that
> vertex for all subjects. Is NODDI something that might have a lot of
> 0-values? It also may be that one subject has all 0s (eg, if the
> regitration was really bad), so you can check the map created by
> mris_preproc (load it in as an overlay, then hit the configure button,
> then change the frame number to scroll through your subjects)
>
>> On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote:
>>
>>  External Email - Use Caution
>>
>> (sorry for bombaeding you with e-mails)
>>
>>
>> It seems that the error happens only when i use NODDI diffusion image
>> e.g. NDI map i get that error, but for MWIs the new mris_preproc
> works
>> well.
>>
>>
>> Should i do anything special for NODDI images? BTW, the bbregister
>> works well for NODDI and i ent

Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr

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

The 3 spaces is for left hemi, right hemi, and subcortical, so, if you 
are using all three then correct for all 3

On 8/7/19 9:26 AM, miracle ozzoude wrote:
>
> External Email - Use Caution
>
> Got it. Thanks a lot doug. If i have to correct for multiple 
> comparison in surface based pet analysis and mutlimodal analysis (pet 
> and thickness), should i use --3spaces?
> Thank you.
>
> best,
> Paul
>
> On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> I think there is still something not right. You should just have
> one mri_glmfit command for each hemisphere in which the input is
> ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then
> specify the pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz
> --pvr ?h.pvr_grp2_pet.niigz) and then use that first contrast. The
> second is the same as the first but with a reversed sign, but it
> is not necessary since we always use unsigned tests and show both
> signs (but you can still do it).
>
> On 8/5/2019 8:14 PM, miracle ozzoude wrote:
>>
>> External Email - Use Caution
>>
>> I think i got it now. Something like this:
>>
>> ## group1 comes first in my fsgd file. removing the effects of
>> age and education
>> ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2.
>> mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c
>> pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \
>> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz  -surf
>> fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir
>> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c
>> pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \
>> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage
>> lh --cortex --glmdir rh.pet.thickness.glmdir
>>
>> contrast =  0 0 0 0 0 0 1 -1
>>
>> ##group 2 is second in my fsgd file. removing the effects of age
>> and education
>> ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2
>>  mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c
>> pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \
>> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
>> rh.pet.thickness.glmdir
>> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c
>> pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \
>> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
>> rh.pet.thickness.glmdir
>>
>> contrast = 0 0 0 0 0 0 -1 1
>>
>> On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D.
>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>
>> It still looks like you are using a group specific input
>> (--y). The input should be a simple file with both groups
>> (same input as you would use without pvr)
>>
>> On 8/5/2019 4:39 PM, miracooloz wrote:
>>>
>>> External Email - Use Caution
>>>
>>> Thanks Doug. How about the mri_glmfit commands? Since the
>>> contrasts are correct, I think the commands should be right.
>>>
>>> Best,
>>> Paul.
>>>
>>>
>>>
>>> Sent from my Samsung Galaxy smartphone.
>>>
>>>  Original message 
>>> From: "Greve, Douglas N.,Ph.D." 
>>> 
>>> Date: 2019-08-05 15:52 (GMT-05:00)
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> 
>>> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and
>>> cortical thickness relationship) using --pvr
>>>
>>> Yes, that contrast is correct.
>>>
>>> On 8/5/2019 3:11 PM, miracle ozzoude wrote:

 External Email - Use Caution

 Hello Doug,

 Thanks very much for your help. Your assumption was right
 in that i want to run a group comparison (i.e. test for a
 difference in amyloid-thickness slopes between the two
 groups). However, I am having a hard time creating the
 correct mri_glmfit and contrasts in this case. Based on
 your advice and searching through the forum
 
 (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html),
  i
 need 2 PVRs for each hemisphere in the mri_glmfit command.
 I gave it another shot below. Please let me know if i am
 correct.

 Thank you.
 Paul.

 ## group1 comes first in my fsgd file. removing the effects
 of age and education
 ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for
 group 2.
 mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd
 project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \
 --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz  -

Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr

[miracle ozzoude]

External Email - Use Caution

Got it. Thanks a lot doug. If i have to correct for multiple comparison in
surface based pet analysis and mutlimodal analysis (pet and thickness),
should i use --3spaces?
Thank you.

best,
Paul

On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> I think there is still something not right. You should just have one
> mri_glmfit command for each hemisphere in which the input is
> ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then specify the
> pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz --pvr
> ?h.pvr_grp2_pet.niigz) and then use that first contrast. The second is the
> same as the first but with a reversed sign, but it is not necessary since
> we always use unsigned tests and show both signs (but you can still do it).
>
> On 8/5/2019 8:14 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> I think i got it now. Something like this:
>
> ## group1 comes first in my fsgd file. removing the effects of age and
> education
> ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2.
> mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx
> --pvr  lh.pvr_grp1_pet.nii.gz \
> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz  -surf fsaverage lh
> --cortex --glmdir lh.pet.thickness.glmdir
> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx
> --pvr rh.pvr_grp1_pet.nii.gz \
> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh
> --cortex --glmdir rh.pet.thickness.glmdir
>
> contrast =  0 0 0 0 0 0 1 -1
>
> ##group 2 is second in my fsgd file. removing the effects of age and
> education
> ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2
>  mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx
> --pvr  allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \
> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
> rh.pet.thickness.glmdir
> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx
> --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \
> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
> rh.pet.thickness.glmdir
>
> contrast = 0 0 0 0 0 0 -1 1
>
> On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> It still looks like you are using a group specific input (--y). The input
>> should be a simple file with both groups (same input as you would use
>> without pvr)
>>
>> On 8/5/2019 4:39 PM, miracooloz wrote:
>>
>> External Email - Use Caution
>> Thanks Doug. How about the mri_glmfit commands? Since the contrasts are
>> correct, I think the commands should be right.
>>
>> Best,
>> Paul.
>>
>>
>>
>> Sent from my Samsung Galaxy smartphone.
>>
>>  Original message 
>> From: "Greve, Douglas N.,Ph.D." 
>> 
>> Date: 2019-08-05 15:52 (GMT-05:00)
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical
>> thickness relationship) using --pvr
>>
>> Yes, that contrast is correct.
>>
>> On 8/5/2019 3:11 PM, miracle ozzoude wrote:
>>
>> External Email - Use Caution
>> Hello Doug,
>>
>> Thanks very much for your help. Your assumption was right in that i want
>> to run a group comparison (i.e. test for a difference in amyloid-thickness
>> slopes between the two groups). However, I am having a hard time creating
>> the correct mri_glmfit and contrasts in this case. Based on your advice and
>> searching through the forum (
>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html),
>>  i
>> need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it
>> another shot below. Please let me know if i am correct.
>>
>> Thank you.
>> Paul.
>>
>> ## group1 comes first in my fsgd file. removing the effects of age and
>> education
>> ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2.
>> mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c
>> pvr1.mtx --pvr  lh.pvr_grp1_pet.nii.gz \
>> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz  -surf fsaverage lh
>> --cortex --glmdir lh.pet.thickness.glmdir
>> mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c
>> pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \
>> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh
>> --cortex --glmdir rh.pet.thickness.glmdir
>>
>> contrast =  0 0 0 0 0 0 1 -1
>>
>> ##group 2 is second in my fsgd file. removing the effects of age and
>> education
>> ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2
>>  mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c
>> pvr2.mtx --pvr  allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \
>> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
>> rh.pet.thickness.glmdir
>> mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c
>> pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \
>> --pvr rh.pv

Re: [Freesurfer] error in longitudinal stream command

[Alexandru Hanganu]

External Email - Use Caution

Hello Martin,

I was wondering - how solved the "Unmatched" error ?

In our case, this error appears for both 5.3, 6.0 and dev, on 2 different
clusters.

All folders exist, are filled with data and reecon-all finished without
error, plus hippocampus and brainstem
all folders and readable: drwxrwsrwx (chmod 777 -R)
In the base-tps - all time points are listed correctly.
Re-running -base - did not solve the issue.
Name has no underscores '_'

I didn't have this error on the local installation, so, I suspect it might
be linked to sourcing some libraries/folders, since we had to source the
mni folder to make it work.

Best,
Alexandru.
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Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space

[Iglesias Gonzalez, Juan E.]

Dear Jessica,
There is no intensity image associated with the atlases, so this is not trivial.
I guess you could register your subjects to the atlas, and propagate the hard 
segmentations?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Jessica Bourgin 

Reply-To: Freesurfer support list 
Date: Wednesday, 7 August 2019 at 04:49
To: freesurfer 
Subject: [Freesurfer] Transform hippocampal/amygdala segmentation to another 
space


External Email - Use Caution
Dear all,

I would like to use the Hippocampal Subfields and Nuclei Of Amygdala tool 
concomitantly with the Brainnetome Atlas for a resting-state analysis.

For this purpose, I need the hippocampal/amygdala nuclei to be in the same 
space as the Brainnetome.

Can you advise me on the method to use to transform the segmentation to another 
space ?

Thank you in advance for your help.

Best regards,


Jessica BOURGIN
Laboratoire de Psychologie et Neurocognition
CNRS UMR 5105
Université Savoie Mont Blanc (USMB)
BP 1104
73011 Chambery Cedex France
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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for help

[Reza Rahmanzadeh]

External Email - Use Caution

I tried to log in with the username and password you mentioned, but logging in 
failed. Could you please have a look into the file already i attached to my 
previous email, or let me know why i could not log in to transfer the file,


Thanks,

Reza


From: Greve, Douglas N.,Ph.D. 
Sent: Tuesday, August 6, 2019 6:40:28 PM
To: Reza Rahmanzadeh; Freesurfer support list
Cc: gr...@nmr.mgh.harvard.edu
Subject: Re: [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: [Freesurfer] need for 
help

Sorry, that should be
ftp surfer.nmr.mgh.harvard.edu

On 8/6/19 12:39 PM, Douglas N. Greve wrote:
> You can try it from the command line,
> ftp surfer.nmr.mgh.harvard.edut
> It will ask you for a user name; use your email address
> It will ask you for a password; use "anonymous" (no quotes)
> cd transfer/incoming
> put file.tar
>
>
> On 8/6/19 6:30 AM, Reza Rahmanzadeh wrote:
>>
>> External Email - Use Caution
>>
>> Hi Doug,
>>
>>
>> When i click on the link you sent me for uploading the files, there
>> is no bottom/way to upload something there. That is why i attached
>> the outputs.
>>
>>
>> My command lines sequentially for the analysis are: ( I have done
>> just the same command lines for MWF maps and it worked very good, but
>> for NDI and ODI maps of NODDI does not work).
>>
>> 1-mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25
>> --out lh.NDI_inflated.avg.mgh (i used the new mris_preproc you sent me).
>>
>> 2-mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval
>> lh.NDI_inflated.avg.mgh --tval lh.NDI_inflated.avg.05.mgh
>>
>> 3-mri_glmfit --y lh.NDI_inflated.avg.05.mgh --surf fsaverage lh --C
>> contrast --fsgd fsgd.fsgd --cortex --glmdir
>> lh.NDI_inflated.avg.05.glmdir
>>
>>
>>
>> The outputs of all three steps are attached.
>>
>>
>>
>> Looking forward for your helps
>>
>> Reza
>>
>>
>>
>>
>>
>>
>>
>> 
>> *From:* Greve, Douglas N.,Ph.D. 
>> *Sent:* Monday, August 5, 2019 5:55:18 PM
>> *To:* Reza Rahmanzadeh; Freesurfer support list
>> *Cc:* gr...@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] need for help
>> Can you upload the input (ie, argument to --y) here:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming
>> Also, send your mri_glmfit command line.
>>
>> On 8/2/2019 9:41 AM, Reza Rahmanzadeh wrote:
>>>
>>> External Email - Use Caution
>>>
>>> yes, I have the page below for all patients.
>>>
>>>
>>> I think it means all values are zero. My registration for bbregister
>>> is fine and i wrote my mris_preproc the same as MWF maps.
>>>
>>>
>>> Thanks,
>>>
>>> Reza
>>>
>>> 
>>>
>>> *From:* Greve, Douglas N.,Ph.D. 
>>> *Sent:* Friday, August 2, 2019 3:35:45 PM
>>> *To:* Reza Rahmanzadeh; Freesurfer support list
>>> *Cc:* gr...@nmr.mgh.harvard.edu
>>> *Subject:* Re: [Freesurfer] need for help
>>> did you check each subject to make sure they had a non-zero map?
>>>
>>> On 8/2/2019 6:25 AM, Reza Rahmanzadeh wrote:

 External Email - Use Caution

 Dear Doug,


 NODDI is diffusion imaging and we have vakue regarding neurite
 density (NDI in NDI map) and orientation dispersion (ODI value in
 ODI map). I do not know why mris_preproc works well on MWI maps but
 not on NODDI maps (both NDI and ODI maps). Beside using
 projfrac-avg 0 1 0.25 , i have run mris_preproc with projfrac 0.5
 but again i got this error:

 ERROR: no voxels found in the mask
   make sure at least one voxel has a non-zero value for each input

 I have run mris_preproc on three patients that i am sure about
 registration quality, again when i scroll through them , there is
 no value in none of them. How that is possible?

 NODDI does not have a lot of zero value but all values in cortex
 are between 0.2-0.4.


 Thanks,
 Reza


 

 *From:* Greve, Douglas N.,Ph.D. 
 *Sent:* Wednesday, July 31, 2019 12:50:45 AM
 *To:* Reza Rahmanzadeh; Freesurfer support list
 *Cc:* gr...@nmr.mgh.harvard.edu
 *Subject:* Re: [Freesurfer] need for help
 I don't know what is in the NODDI maps. The way mri_glmfit works is
 that
 if any subject has a 0-value at a vertex, then it will mask out that
 vertex for all subjects. Is NODDI something that might have a lot of
 0-values? It also may be that one subject has all 0s (eg, if the
 regitration was really bad), so you can check the map created by
 mris_preproc (load it in as an overlay, then hit the configure button,
 then change the frame number to scroll through your subjects)

 On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote:
 >
 > External Email - Use Caution
 >
 > (sorry for bombaeding you

[Freesurfer] Transform hippocampal/amygdala segmentation to another space

[Jessica Bourgin]

External Email - Use Caution

Dear all, 

I would like to use the Hippocampal Subfields and Nuclei Of Amygdala tool 
concomitantly with the Brainnetome Atlas for a resting-state analysis. 

For this purpose, I need the hippocampal/amygdala nuclei to be in the same 
space as the Brainnetome. 

Can you advise me on the method to use to transform the segmentation to another 
space ? 

Thank you in advance for your help. 

Best regards, 


Jessica BOURGIN 
Laboratoire de Psychologie et Neurocognition 
CNRS UMR 5105 
Université Savoie Mont Blanc (USMB) 
BP 1104 
73011 Chambery Cedex France 
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