Re: [Freesurfer] Recon-all Soft Errors

Douglas N. Greve Tue, 04 Aug 2020 07:02:46 -0700

Can you send a picture of the type of errors you are seeing?


On 7/31/2020 9:03 AM, Elana Sarabin wrote:

         External Email - Use Caution

Here is the recon-all.log file.

Thanks,
Elana

-----Original Message-----
From: Elana Sarabin
Sent: July 30, 2020 10:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: Recon-all Soft Errors

Here is the recon-all.log file.

Thanks,
Elana

-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of 
freesurfer-requ...@nmr.mgh.harvard.edu
Sent: July 30, 2020 10:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 197, Issue 59

[△EXTERNAL]



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Today's Topics:

    1. FS 7.1.0 - Editing intensity values for WM (Nils B?er)
    2. Re: FS 7.1.0 - Editing intensity values for WM (Fischl, Bruce)
    3. Creating .annot file for a mri_decimate downsampeld       version
       of pial surface (Donelson Berger)
    4. GONE: -make to recon-all (Johnson, Hans J)
    5. Re: fsgd file - glmfit error
       (Lab of Autism and Developmental Neuroscience,    Lab of Autism and 
Developmental Neuroscience)
    6. Re: Recon-all Soft Errors (Zollei, Lilla,Ph.D.)
    7. bad interpreter: No such file or directory error
       (Hengameh Marzbani)
    8. Re: overlapping/ superimposing regions of one analysis over
       another (Douglas N. Greve)
    9. Re: Creating .annot file for a mri_decimate downsampeld
       version of pial surface (Douglas N. Greve)
   10. Re: Recon-all Soft Errors (Douglas N. Greve)
   11. Re: Coregistration to MNI (Douglas N. Greve)
   12. mri_aparc2aseg: how to remove redundant output labels? (Ellen Ji)
   13. Re: bad interpreter: No such file or directory error (fsbuild)


----------------------------------------------------------------------

Message: 1
Date: Wed, 29 Jul 2020 21:27:03 +0200
From: Nils B?er <nils.tobia...@gmail.com>
Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
         <CALZW1G2=-ovwkl81szxtbimckbwion6ewsfd2xp0nzewqyb...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

         External Email - Use Caution

Hello everyone,

I just have a short question, because I can't find anything helpful in the 
tutorials.

In my MRI scans freesurfer includes areas to the white matter, even though 
visual inspection concludes that the area should be grey matter. Is there a 
possibility to change the value at which freesurfer includes areas to the WM, 
which i can just change? For example freesurfer includes areas to the WM with 
intensity values below 85 and i want to change that.

I'd be thankful for any feedback/links to guides.

Best regards,

Nils
--

Nils B?er
Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* 
University of Paderborn Department of Sports and Health Warburger Str. 100
33098 Paderborn
Room: Sp 1.401

Email: nils.tobia...@gmail.com / nbo...@mail.uni-paderborn.de 
<nils.tobia...@gmail.com>
Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/
          https://sug.uni-paderborn.de/department/it/
<https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/>

<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
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Message: 2
Date: Wed, 29 Jul 2020 20:32:34 +0000
From: "Fischl, Bruce" <bfis...@mgh.harvard.edu>
Subject: Re: [Freesurfer] FS 7.1.0 - Editing intensity values for WM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
         
<bl0pr04mb660985ec505deecb596362adef...@bl0pr04mb6609.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="utf-8"

Hi Nils

There are expert options for this. You can specify things like -min_white 90 to 
some of the programs like mri_segment and the surface placement stuff

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Nils B?er
Sent: Wednesday, July 29, 2020 3:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM


         External Email - Use Caution
Hello everyone,

I just have a short question, because I can't find anything helpful in the 
tutorials.

In my MRI scans freesurfer includes areas to the white matter, even though 
visual inspection concludes that the area should be grey matter. Is there a 
possibility to change the value at which freesurfer includes areas to the WM, 
which i can just change? For example freesurfer includes areas to the WM with 
intensity values below 85 and i want to change that.

I'd be thankful for any feedback/links to guides.

Best regards,

Nils
--

Nils B?er
Research Assistant with Bachelor Degree (WHB) Psychology and Movement 
University of Paderborn Department of Sports and Health Warburger Str. 100
33098 Paderborn
Room: Sp 1.401
Email: nils.tobia...@gmail.com / 
nbo...@mail.uni-paderborn.de<mailto:nils.tobia...@gmail.com>
Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/
          
https://sug.uni-paderborn.de/department/it/<https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/>

[https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
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Message: 3
Date: Wed, 29 Jul 2020 15:51:03 -0500
From: Donelson Berger <donelsongrahamber...@gmail.com>
Subject: [Freesurfer] Creating .annot file for a mri_decimate
         downsampeld     version of pial surface
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
         <CAAKWbtXL5vQOPXEoO6TUeRM_dHowghOYVX=ptxwpe8+gkam...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

         External Email - Use Caution

Hello FreeSurfer Expert,

I've run into a problem that I just can't seem to solve. After downsampling teh 
?.pial surfaces using mri_decimate to 20,000 surfaces and 10,002 points, I 
don't know how to create .annot files for the new surfaces I created. I want to 
be able to tell which ROI each vertex is in for my new surface based off a 
parcellation.

I've been trying to use mri_ca_label, mri_ca_train, and mris_sample_parc, but I 
can't seem to get anything to work.

Do you have any suggestions?

Thanks for your help,
Donelson Graham Berger
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Message: 4
Date: Wed, 29 Jul 2020 22:22:47 +0000
From: "Johnson, Hans J" <hans-john...@uiowa.edu>
Subject: [Freesurfer] GONE: -make to recon-all
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <9db20083-d647-47e0-9396-c24308b50...@uiowa.edu>
Content-Type: text/plain; charset="utf-8"

         External Email - Use Caution

The release notes for 7.0.0 claim that the -make option is "Gone" from 
recon-all.  This option, however, is still available and does not seem to fail.

I am running several thousand data sets on a cluster through Freesurfer 7.1.0, and 
periodically the process fails for some subjects. In the past the "recon-all -make 
all" feature was a very convenient way to complete freesurfer runs that were 
terminated early for some unknown reason

Q1)  should "recon-all -make all" be avoided for FreeSurfer 7.1.0?
Q2) is there an alternate way to "continue form the point where results are 
missing" in the pipeline?

Thanks,
Hans



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Message: 5
Date: Wed, 29 Jul 2020 15:49:44 -0700
From: "Lab of Autism and Developmental Neuroscience,    Lab of Autism and
         Developmental Neuroscience" <l...@email.gwu.edu>
Subject: Re: [Freesurfer] fsgd file - glmfit error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
         <cace7mb+vav5uypsnrsfnyda8xt0_ddhe1sxd2-rumcf3z0_...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

         External Email - Use Caution

Thank you Douglas!


On Tue, Jul 28, 2020 at 9:34 AM Douglas N. Greve <dgr...@mgh.harvard.edu>
wrote:

Try putting 1 after GroupDescriptorFile, ie,

GroupDescriptorFile 1

On 7/28/2020 12:21 PM, Lab of Autism and Developmental Neuroscience,
Lab of Autism and Developmental Neuroscience wrote:

         External Email - Use Caution
Here is my fsgd file.
Thank you!


On Mon, Jul 27, 2020 at 8:44 PM Douglas N. Greve
<dgr...@mgh.harvard.edu>
wrote:

Please send the fsgd file

On 7/27/2020 11:34 PM, Lab of Autism and Developmental Neuroscience,
Lab of Autism and Developmental Neuroscience wrote:

         External Email - Use Caution
Dear Freesurfer experts,

Hope this email finds you well. I am having some trouble with the
fsgd file for glmfit and I'm confused why. This is the error I'm
getting when running glmfit:

iMac-Pro:BAP_complete ajobsaid$ mri_glmfit --y
mrip.rh_volume_F7_BNB.00.mgh --fsgd fsgd_8.fsgd --C Cor_2.mtx --surf
fsaverage rh --cortex --glmdir contrast2.rh_volume_BNB.glmdir
gdfRead(): reading fsgd_8.fsgd
ERROR: FSGDF version 0 unsupported (fsgd_8.fsgd)
iMac-Pro:BAP_complete ajobsaid$

If needed, I can send you my fsgd file, but I have triple checked the
design and format of the file (it is saved as .fsgd), and I'm still
getting this error message.

Thank you,
Alex

_______________________________________________
Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/ma
ilman/listinfo/freesurfer


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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


_______________________________________________
Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mai
lman/listinfo/freesurfer


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Message: 6
Date: Thu, 30 Jul 2020 09:34:12 +0000
From: "Zollei, Lilla,Ph.D." <lzol...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all Soft Errors
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:

<dm6pr04mb44127c2db157bb07ab669f41e3...@dm6pr04mb4412.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="windows-1252"

Hi Elena,
What is the age range of your subjects?
Best, Lilla
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> 
on behalf of Elana Sarabin <elana.sarab...@ucalgary.ca>
Sent: Wednesday, July 29, 2020 11:02 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Recon-all Soft Errors

         External Email - Use Caution

Hi Freesurfer experts,

I am a first time user of FreeSurfer and I haven?t been able to find any 
threads for how to fix some of my problems. I have a very large dataset and as 
I am editing on freeview I am noticing that ? or more of my participants have a 
large area missing in the brainmask.mgz file but the region is visible from the 
T1.file. In some participant scans the areas missing arent too big however 
other scans (the photo I attached) have a very large portion of the brain 
missing. I have tried quite a few things to fix this including re running 
recon-all, adding control points, and adjusting the wsthresh value, however, 
none have worked. Wondering if there is a way to fix this kind of error and if 
there is a way to prevent this from happening as I run recon-all on future 
participants. In addition, I have been duplicating my files before editing in 
order to always have the original files as a backup. With some participants 
when I duplicate the files their T1.mgz file ends up completely white (image 
attached). I have yet to see this in a none duplicated file however with some 
participants I can duplicate the files and have no issue. I have attached 
photos of both of my problems. Any suggestions for fixes would be greatly 
appreciated.

Thanks,

Elana

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Message: 7
Date: Thu, 30 Jul 2020 17:49:49 +0430
From: Hengameh Marzbani <marzban...@gmail.com>
Subject: [Freesurfer] bad interpreter: No such file or directory error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
         <CAFn2Bowe=LPArymmLwu=k_3wgezc0gng9okv5qaebpdzugv...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

         External Email - Use Caution

Hello Freesurfer developers,

I have installed FreeSurfer v7 on 2 machines running Ubuntu and made sure that 
the setting are fine.

Also, freeview works by simply typing the freeview command.

However,I have tried to run recon-all. but, I have got the following error 
message on all PCs:

*bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such 
file or directory*

also The build-stamps.txt file contents:
*freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b*

Thank you in advance,
Best regards,
Hengameh
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Message: 8
Date: Thu, 30 Jul 2020 10:20:07 -0400
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] overlapping/ superimposing regions of one
         analysis over another
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <c4e336e0-b3b8-89eb-e59b-1894fdf85...@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

To obtain the common regions, first binarize the clusterwise significance maps 
with something like mri_binarize --min 2.0 --i clustersigmap1.mgh --o 
bin.clustersigmap1.mgh Same for the other groups Then take the intersection 
fscalc clustersigmap1.mgh and clustersigmap2.mgh -o intersection.mgh

On 7/27/2020 2:17 PM, Sunil Khokhar wrote:

????????External Email - Use Caution

To operate the visualization and obtain the common regions of my
between-group difference results and the correlation results in one
image. In other?words, overlapping/ superimposing?my correlation
results on the between-group results (to obtain the common regions
from the two separate analysis).

Thanks
_______________
Sunil K Khokhar
PhD Scholar,
Department of Neuroimaging & Interventional Radiology, NIMHANS,
Bengaluru, INDIA.
khokharsun...@gmail.com <mailto:khokharsun...@gmail.com>
+91-9413101839


On Mon, Jul 27, 2020 at 8:21 PM Douglas N. Greve
<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote:

     are you asking how to create positive and negative regions or are
     you asking how to operate the visualization?

     On 7/25/2020 9:40 AM, Sunil Khokhar wrote:

     ????????External Email - Use Caution

     Dear Experts,

     I have done a between group (2 groups) difference in whole brain
     voxel based cortical thickness using QDEC, which showed
     significant regional differences in certain clusters
     bilaterally?in the brain. I also did a correlation between
     cortical thickness and behavioral scores separately?in these two
     groups. Now, I want to superimpose regions (clusters) which
     showed positive and negative correlation on the?results/
     regions?I obtained in my between group analysis. How can I do this?

     Thanks in advance!
     Sunil.
     _______________
     Sunil K Khokhar
     PhD Scholar,
     Department of Neuroimaging & Interventional Radiology,
     NIMHANS, Bengaluru, INDIA.
     khokharsun...@gmail.com <mailto:khokharsun...@gmail.com>
     +91-9413101839

     _______________________________________________
     Freesurfer mailing list
     Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

     _______________________________________________
     Freesurfer mailing list
     Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Message: 9
Date: Thu, 30 Jul 2020 10:21:14 -0400
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Creating .annot file for a mri_decimate
         downsampeld version of pial surface
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <ec2eef74-6cd8-0c36-dbeb-983240090...@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Use
mris_apply_reg --sval-annot lh.your.annot --streg lh.pial lh.pial.decimated --o 
lh.your.decimated.annot


On 7/29/2020 4:51 PM, Donelson Berger wrote:

????????External Email - Use Caution

Hello FreeSurfer Expert,

I've run into a problem that I just can't seem to solve. After
downsampling teh ?.pial surfaces using mri_decimate to 20,000 surfaces
and 10,002 points, I don't know how to create .annot files for the new
surfaces I created. I want to be able to tell which ROI each vertex is
in for my new surface based off a parcellation.

I've been trying to use mri_ca_label, mri_ca_train, and
mris_sample_parc, but I can't seem to get anything to work.

Do you have any suggestions?

Thanks for your help,
Donelson Graham Berger

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 10
Date: Thu, 30 Jul 2020 10:26:22 -0400
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all Soft Errors
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <78c6cfdd-63ba-9ed1-1c26-fcbc76472...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

for the first error, can you send the recon-all.log file?
For the second error, you need to adjust the intensity ranges. For some reason 
they are coming up as 0s.

On 7/29/2020 11:02 AM, Elana Sarabin wrote:

????????External Email - Use Caution

Hi Freesurfer experts,

I am a first time user of FreeSurfer and I haven?t been able to find
any threads for how to fix some of my problems. I have a very large
dataset and as I am editing on freeview I am noticing that ? or more
of my participants have a large area missing in the brainmask.mgz file
but the region is visible from the T1.file. In some participant scans
the areas missing arent too big however other scans (the photo I
attached) have a very large portion of the brain missing. I have tried
quite a few things to fix this including re running recon-all, adding
control points, and adjusting the wsthresh value, however, none have
worked. Wondering if there is a way to fix this kind of error and if
there is a way to prevent this from happening as I run recon-all on
future participants. In addition, I have been duplicating my files
before editing in order to always have the original files as a backup.
With some participants when I duplicate the files their T1.mgz file
ends up completely white (image attached). I have yet to see this in a
none duplicated file however with some participants I can duplicate
the files and have no issue. I have attached photos of both of my
problems. Any suggestions for fixes would be greatly appreciated.


Thanks,

Elana


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 11
Date: Thu, 30 Jul 2020 11:31:47 -0400
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Coregistration to MNI
To: "Camargo, Aldo" <acama...@som.umaryland.edu>, Freesurfer support
         list    <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <9af8c73e-46a8-e9b6-4b84-ce507589e...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

It looks like cvs failed. Can you send the log? Also, please remember to post 
to the list and not us personally.


On 7/30/2020 11:13 AM, Camargo, Aldo wrote:

????????External Email - Use Caution

Hi Douglas,


I was able to run the script to create the cvs folder and its files
but still I can not run the script that does the coregistration of the
Pet image to the MNI space.

I am getting the following error:

(base)
acamargo@acamargo-System-Product-Name:~/PET/MPRAGE/2006-09-27_14_15_46
.0/S19445/subj1/mri$
mri_vol2vol --gcam
/home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/me
anPET.nii.gz
register.dof6.lta
$SUBJECS_DIR/subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
$FREESURFER_HOME/subject/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1
pet.cvs.2mm.sm00.ni.gz Loading mov
/home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/me
anPET.nii.gz
Loading source LTA register.dof6.lta
Loading GCAM /subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
ERROR: cannot find or read
/subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z



----------------------------------------------------------------------
--
*From:* Douglas N. Greve <dgr...@mgh.harvard.edu>
*Sent:* Wednesday, July 29, 2020 10:39 AM
*To:* Camargo, Aldo <acama...@som.umaryland.edu>; Freesurfer support
list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Coregistration to MNI Here is the command
mri_cvs_register --mov $subject --mni --openmp N

This command can take a very long time to run. The --openmp N
indicates the number of processors to use if you have a multiprocessor
system. Even with N=3, it can take 18 hours.




On 7/29/2020 12:35 AM, Camargo, Aldo wrote:

????????External Email - Use Caution

Hi Douglas,

I don't have the folder cvs and I don't have the files bellow:

cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta

How can I get these files,

Aldo

---------------------------------------------------------------------
---
*From:* Camargo, Aldo <acama...@som.umaryland.edu>
<mailto:acama...@som.umaryland.edu>
*Sent:* Monday, July 27, 2020 11:46 PM
*To:* Douglas N. Greve <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Coregistration to MNI Thanks a lot
Douglas for your great input,

Aldo
---------------------------------------------------------------------
---
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Sent:* Monday, July 27, 2020 10:46 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Coregistration to MNI This command will
allow you to have a registration file and sample into MNI152 2mm
space

mri_vol2vol --gcam pet.nii.gz register.dof6.lta
$SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1
pet.cvs.2mm.sm00.nii.gz

you can get the registration file with mri_coreg --mov pet.nii.gz --s
$subject --reg register.dof6.lta



On 7/26/2020 9:19 AM, Zollei, Lilla,Ph.D. wrote:

Hi Aldo,
If you have a recon-ned structural MRI corresponding to your PET
scan then the answer is yes.
Lilla
--------------------------------------------------------------------
----
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Camargo, Aldo <acama...@som.umaryland.edu>
<mailto:acama...@som.umaryland.edu>
*Sent:* Saturday, July 25, 2020 12:19 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] Coregistration to MNI

????????External Email - Use Caution

Hi Freesurfer experts,

I want to coregister a PET image to the MNI space, can I use
mri_cvs_register ?

Thanks a lot,

Aldo Camargo

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Message: 12
Date: Thu, 30 Jul 2020 17:39:06 +0200
From: Ellen Ji <ellen...@bli.uzh.ch>
Subject: [Freesurfer] mri_aparc2aseg: how to remove redundant output
         labels?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <24cc8874-81ee-1e68-85ad-b8fe662c4...@bli.uzh.ch>
Content-Type: text/plain; charset="utf-8"; format="flowed"

         External Email - Use Caution

Dear experts,

I am running mri_aparc2aseg using two annotations as input (one for each 
hemisphere), each with 159 labels, and wish to end up with a single output 
segmentation of 318 labels. However, when I run the below, this is not the case:

mri_aparc2aseg \
  ??????????????? --s subject1 \
  ??????????????? --annot 500_sym.aparc \  ??????????????? --wmparc-dmax 2 \  
??????????????? --labelwm \  ??????????????? --hypo-as-wm? \  ??????????????? 
--o subject1/mri/parcellation.nii.gz

In fact, the output has 680 labels rather than 318 labels. A few questions.

- How can I see what exactly the 680 label names are (how to extract from the 
.nii.gz output file)? Currently, I have just quantified it to be 680 by doing 
this in matlab: gunzip('parcellation.nii.gz')  ???? a = 
MRIread('parcellation.nii');  ???? u = unique(a.vol(:));  ???? length(u) % 
total number of labels

- I believe the extra labels are from the Freesurfer LUT. How can I make sure 
they are not added when running mri_aparc2aseg? (such that only my annotation 
labels are included in the output)

Thank you very much,

Ellen

*****
Ellen Ji, PhD
Postdoctoral Research Fellow
Psychiatric University Hospital
University of Z?rich
ellen...@bli.uzh.ch
homanlab.github.io/ellen/

------------------------------

Message: 13
Date: Thu, 30 Jul 2020 17:48:25 +0200
From: fsbuild <fsbu...@contbay.com>
Subject: Re: [Freesurfer] bad interpreter: No such file or directory
         error
To: freesurfer@nmr.mgh.harvard.edu
Cc: marzban...@gmail.com
Message-ID: <1596124105.5f22ebc98f...@trashmail.com>
Content-Type: text/plain; charset="utf-8"

         External Email - Use Caution

Hello Hengameh,
You probably need to install tcsh (and or csh).
I would try,
$&nbsp;sudo&nbsp;apt-get install csh tcsh
- R..

On Jul 30, 2020, at 09:19, Hengameh Marzbani &lt;marzban...@gmail.com&gt; 
wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use 
Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello Freesurfer developers,I have installed FreeSurfer v7 on 2 
machines running Ubuntu and made sure that the setting are fine. Also, freeview works by simply typing the freeview command.However,I have tried to run 
recon-all. but, I have got the following error message on all PCs:bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or 
directoryalso&nbsp;The build-stamps.txt file contents:freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297bThank you in advance, Best regards, 
Hengameh_______________________________________________Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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End of Freesurfer Digest, Vol 197, Issue 59
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Re: [Freesurfer] Recon-all Soft Errors

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