Hi Elana
You say it happens on 50% of your participants. Can you pick one and upload the
entire gzipped and tarred directory for that subject?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Elana Sarabin
Sent: Saturday, August 8, 2020 10:07 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all Soft Errors
External Email - Use Caution
Sorry I’m not sure I know what you mean when you say an example dataset.
Regards,
Elana
Get Outlook for iOS<https://aka.ms/o0ukef>
________________________________
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 Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Sent: Friday, August 7, 2020 9:17:24 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Recon-all Soft Errors
[△EXTERNAL]
Can you upload an example dataset? It looked like an intensity normalization
failure that probably caused a topological defect
Cheers
Bruce
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 Elana Sarabin
Sent: Friday, August 7, 2020 11:08 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Recon-all Soft Errors
External Email - Use Caution
More so that the brainmask.mgz is missing a lot of both grey and white matter.
For some the area cut out in brainmask is much smaller and for others it is
large just like the photo I sent. I am wondering if there is a way to fix this
since 50% of my participants scans look like this.
Thanks,
Elana
Get Outlook for iOS<https://aka.ms/o0ukef>
________________________________
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: Friday, August 7, 2020 8:17:42 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] Recon-all Soft Errors
[△EXTERNAL]
This error shows a massive failure. Is this what you are describing as:
includes areas to the white matter, even though visual inspection concludes
that the area should be grey matter.
On 8/6/2020 9:00 PM, Elana Sarabin wrote:
External Email - Use Caution
Here is one photo. Seems this is the most I can send at once. Most errors look
just like this however sometimes larger and sometimes smaller.
Best,
Elana
From:
<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>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, August 4, 2020 at 8:01 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] Recon-all Soft Errors
[△EXTERNAL]
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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
On Behalf Of
freesurfer-requ...@nmr.mgh.harvard.edu<mailto:freesurfer-requ...@nmr.mgh.harvard.edu>
Sent: July 30, 2020 10:00 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Freesurfer Digest, Vol 197, Issue 59
[△EXTERNAL]
Send Freesurfer mailing list submissions to
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When replying, please edit your Subject line so it is more specific than "Re:
Contents of Freesurfer digest..."
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><mailto:nils.tobia...@gmail.com>
Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CALZW1G2=-ovwkl81szxtbimckbwion6ewsfd2xp0nzewqyb...@mail.gmail.com><mailto: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<mailto:nils.tobia...@gmail.com> /
nbo...@mail.uni-paderborn.de<mailto:nbo...@mail.uni-paderborn.de>
<nils.tobia...@gmail.com><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://sug.uni-paderborn.de/en/sport/sportpsychologie/team/>
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Message: 2
Date: Wed, 29 Jul 2020 20:32:34 +0000
From: "Fischl, Bruce" <bfis...@mgh.harvard.edu><mailto:bfis...@mgh.harvard.edu>
Subject: Re: [Freesurfer] FS 7.1.0 - Editing intensity values for WM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<bl0pr04mb660985ec505deecb596362adef...@bl0pr04mb6609.namprd04.prod.outlook.com><mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto: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<mailto: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<mailto:nils.tobia...@gmail.com> /
nbo...@mail.uni-paderborn.de<mailto:nbo...@mail.uni-paderborn.de><mailto:nils.tobia...@gmail.com><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://sug.uni-paderborn.de/en/sport/sportpsychologie/team/>
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------------------------------
Message: 3
Date: Wed, 29 Jul 2020 15:51:03 -0500
From: Donelson Berger
<donelsongrahamber...@gmail.com><mailto:donelsongrahamber...@gmail.com>
Subject: [Freesurfer] Creating .annot file for a mri_decimate
downsampeld version of pial surface
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAAKWbtXL5vQOPXEoO6TUeRM_dHowghOYVX=ptxwpe8+gkam...@mail.gmail.com><mailto: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><mailto:hans-john...@uiowa.edu>
Subject: [Freesurfer] GONE: -make to recon-all
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<9db20083-d647-47e0-9396-c24308b50...@uiowa.edu><mailto: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><mailto:l...@email.gwu.edu>
Subject: Re: [Freesurfer] fsgd file - glmfit error
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<cace7mb+vav5uypsnrsfnyda8xt0_ddhe1sxd2-rumcf3z0_...@mail.gmail.com><mailto: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><mailto: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><mailto: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<mailto:listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/ma>
ilman/listinfo/freesurfer
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_______________________________________________
Freesurfer mailing
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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><mailto:lzol...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all Soft Errors
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<dm6pr04mb44127c2db157bb07ab669f41e3...@dm6pr04mb4412.namprd04.prod.outlook.com><mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Elana Sarabin
<elana.sarab...@ucalgary.ca><mailto:elana.sarab...@ucalgary.ca>
Sent: Wednesday, July 29, 2020 11:02 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto: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><mailto:marzban...@gmail.com>
Subject: [Freesurfer] bad interpreter: No such file or directory error
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAFn2Bowe=LPArymmLwu=k_3wgezc0gng9okv5qaebpdzugv...@mail.gmail.com><mailto: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><mailto:dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] overlapping/ superimposing regions of one
analysis over another
To: <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<c4e336e0-b3b8-89eb-e59b-1894fdf85...@mgh.harvard.edu><mailto:c4e336e0-b3b8-89eb-e59b-1894fdf85...@mgh.harvard.edu>
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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>
<mailto: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>
<mailto: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>
<mailto:khokharsun...@gmail.com><mailto:khokharsun...@gmail.com>
+91-9413101839
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Message: 9
Date: Thu, 30 Jul 2020 10:21:14 -0400
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu><mailto: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><mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<ec2eef74-6cd8-0c36-dbeb-983240090...@mgh.harvard.edu><mailto:ec2eef74-6cd8-0c36-dbeb-983240090...@mgh.harvard.edu>
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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
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Message: 10
Date: Thu, 30 Jul 2020 10:26:22 -0400
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all Soft Errors
To: <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<78c6cfdd-63ba-9ed1-1c26-fcbc76472...@mgh.harvard.edu><mailto: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
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Message: 11
Date: Thu, 30 Jul 2020 11:31:47 -0400
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Coregistration to MNI
To: "Camargo, Aldo"
<acama...@som.umaryland.edu><mailto:acama...@som.umaryland.edu>, Freesurfer
support
list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<9af8c73e-46a8-e9b6-4b84-ce507589e...@mgh.harvard.edu><mailto: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><mailto:dgr...@mgh.harvard.edu>
*Sent:* Wednesday, July 29, 2020 10:39 AM
*To:* Camargo, Aldo
<acama...@som.umaryland.edu><mailto:acama...@som.umaryland.edu>; Freesurfer
support
list <freesurfer@nmr.mgh.harvard.edu><mailto: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>
<mailto: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>
<mailto: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>
<mailto: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>
<mailto: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>
<mailto: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>
<mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto: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>
<mailto: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>
<mailto: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>
<mailto: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>
<mailto: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><mailto:ellen...@bli.uzh.ch>
Subject: [Freesurfer] mri_aparc2aseg: how to remove redundant output
labels?
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<24cc8874-81ee-1e68-85ad-b8fe662c4...@bli.uzh.ch><mailto: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<mailto:ellen...@bli.uzh.ch>
homanlab.github.io/ellen/
------------------------------
Message: 13
Date: Thu, 30 Jul 2020 17:48:25 +0200
From: fsbuild <fsbu...@contbay.com><mailto:fsbu...@contbay.com>
Subject: Re: [Freesurfer] bad interpreter: No such file or directory
error
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: marzban...@gmail.com<mailto:marzban...@gmail.com>
Message-ID:
<1596124105.5f22ebc98f...@trashmail.com><mailto: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,
$ sudo apt-get install csh tcsh
- R..
On Jul 30, 2020, at 09:19, Hengameh Marzbani <marzban...@gmail.com>
wrote: 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 directoryalso 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<mailto:listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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