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Today's Topics:
1. Re: [External] Re: rostral anterior cingulate fix?
(Zeng,Victor (BIDMC - Psychiatry))
2. Re: [External] Re: rostral anterior cingulate fix? (Bruce Fischl)
3. Re: recon-all Error : inputs cannot have multiple frames.
( Yueming )
4. Re: recon-all Error : inputs cannot have multiple frames.
(Bruce Fischl)
5. error while running pial_lgi for gyrification index
(vittal korann)
6. Re: error while running pial_lgi for gyrification index
(Tim Sch?fer)
7. Viewing Uncorrected Significance Map in Freeview (Marie Hill)
----------------------------------------------------------------------
Message: 1
Date: Fri, 5 Jul 2019 17:42:28 +0000
From: "Zeng,Victor (BIDMC - Psychiatry)" <vzeng@bidmc.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: rostral anterior cingulate
fix?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <1562348548910.95994@bidmc.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
Sorry, I thought I attached something
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
ph: 617 754 1237
--
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Sent: Friday, July 5, 2019 10:24 AM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] rostral anterior cingulate fix?
Hi Victor
can you render the parcellation in that area on the surface (in freeview)
and show it to us?
cheers
Bruce
On Fri, 5 Jul 2019, Zeng,Victor (BIDMC - Psychiatry) wrote:
>
> Hi Freesurfer group -
>
>
> I'm using FS6.0 dev-20190118, and I'm processing a few brain scans. I'm seeing a misparcellation of
> the right rostral anterior cingulate using tkmedit (I know tkmedit is sorta deprecated), and it
> doesn't seem inappropriate to use control point fixes. How would you best fix this (I'm open to
> using freeview), without just editing the aparc+aseg.mgz?
>
>
> Victor Zeng
> Beth Israel Deaconess Medical Center
> Keshavan Lab
> ph: 617 754 1237
> --
>
> ____________________________________________________________________________________________________
>
> This message is intended for the use of the person(s) to whom it may be addressed. It may contain
> information that is privileged, confidential, or otherwise protected from disclosure under
> applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or
> use of this information is prohibited. If you have received this message in error, please
> permanently delete it and immediately notify the sender. Thank you.
>
>
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Message: 2
Date: Fri, 5 Jul 2019 13:45:40 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: rostral anterior cingulate
fix?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1907051345020.916@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed
you did, but not a surface rendering. Load it with freeview and show it as
a surface (maybe inflated and white)
On Fri, 5 Jul 2019, Zeng,Victor (BIDMC
- Psychiatry) wrote:
>
> Sorry, I thought I attached something
> Victor Zeng
> Beth Israel Deaconess Medical Center
> Keshavan Lab
> ph: 617 754 1237
> --
>
> ________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Sent: Friday, July 5, 2019 10:24 AM
> To: Freesurfer support list
> Subject: [External] Re: [Freesurfer] rostral anterior cingulate fix?
>
> Hi Victor
>
> can you render the parcellation in that area on the surface (in freeview)
> and show it to us?
>
> cheers
> Bruce
>
>
> On Fri, 5 Jul 2019, Zeng,Victor (BIDMC - Psychiatry) wrote:
>
>>
>> Hi Freesurfer group -
>>
>>
>> I'm using FS6.0 dev-20190118, and I'm processing a few brain scans. I'm seeing a misparcellation of
>> the right rostral anterior cingulate using tkmedit (I know tkmedit is sorta deprecated), and it
>> doesn't seem inappropriate to use control point fixes. How would you best fix this (I'm open to
>> using freeview), without just editing the aparc+aseg.mgz?
>>
>>
>> Victor Zeng
>> Beth Israel Deaconess Medical Center
>> Keshavan Lab
>> ph: 617 754 1237
>> --
>>
>> ____________________________________________________________________________________________________
>>
>> This message is intended for the use of the person(s) to whom it may be addressed. It may contain
>> information that is privileged, confidential, or otherwise protected from disclosure under
>> applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or
>> use of this information is prohibited. If you have received this message in error, please
>> permanently delete it and immediately notify the sender. Thank you.
>>
>>
------------------------------
Message: 3
Date: Sat, 6 Jul 2019 10:36:28 +0800
From: " Yueming " <1028551592@qq.com>
Subject: Re: [Freesurfer] recon-all Error : inputs cannot have
multiple frames.
To: " freesurfer " <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <tencent_1282426509F1FBABD7C044C444A589BB2209@qq.com>
Content-Type: text/plain; charset="iso-8859-1"
External Email - Use Caution
My command: recon-all -all -i /usr/local/110/UN18/1.DCM -s 18p
I DON'T KNOW,WHAT KIND OF frames will be considered unmultiple?
My inputs' format is dicom,when it is about 200kB,the software can run and has no such error.but when the dicom is more than 500kB,the next error will happen:
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/usr/local/freesurfer/subjects/18/mri/orig/001.mgz has 17 frames
My English is so bad that you know...... Forgive me,please!
WISH TO YOUR TEACHING AND REPLY.
>From a graduate student of China Liaoning University .
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Message: 4
Date: Fri, 5 Jul 2019 22:42:30 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all Error : inputs cannot have
multiple frames.
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1907052241330.916@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
I think the dicom series that 1.DCM is part of is not a 3D T1-weighted
structural. Can you run mri_info on it, or dcmdump (or both)?
On Sat, 6 Jul
2019, Yueming wrote:
>
> ????????External Email - Use Caution????????
>
> My command: recon-all -all -i /usr/local/110/UN18/1.DCM -s 18p?
> I DON'T KNOW,WHAT KIND OF frames will be considered unmultiple?
> My inputs' format is dicom,when it is about 200kB,the software can run and has no such error.but
> when the dicom is more than 500kB,the next error will happen:
>
> [IMAGE]
> Checking for (invalid) multi-frame inputs...
> ERROR: input(s) cannot have multiple frames!
> /usr/local/freesurfer/subjects/18/mri/orig/001.mgz has 17 frames
>
> My English is so bad that you know......? Forgive me,please!
>
> WISH TO YOUR TEACHING AND REPLY.
> From a graduate student?of China Liaoning University .?
>
>
------------------------------
Message: 5
Date: Sat, 6 Jul 2019 16:57:28 +0530
From: vittal korann <vittalkorann@gmail.com>
Subject: [Freesurfer] error while running pial_lgi for gyrification
index
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CACyMoT1CW-wS37dHyamo1WTf4NP-V1Ov0MMY6mjEaVtk3pV-uA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi FS experts,
I wanted to run the gyrification index for all patients with Schizophrenia
and volunteers. When I entered the command:
"recon-all -s SATM124 -qcache -measure pial_lgi" and the terminal output
" Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-r-- 1 root 1590 1054464 Jul 6 16:02
/usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log
Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
'/usr/local/freesurfer/bin/recon-all' ->
'/usr/local/freesurfer/subjects/SATM124/scripts/recon-all.local-copy'
#--------------------------------------------
#@# Qdec Cache preproc lh pial_lgi fsaverage Sat Jul 6 16:39:03 IST 2019
/usr/local/freesurfer/subjects/SATM124/surf
mris_preproc --s SATM124 --hemi lh --meas pial_lgi --target fsaverage
--out lh.pial_lgi.fsaverage.mgh
nsubjects = 1
ERROR: cannot find /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi
Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s SATM124 exited with ERRORS at Sat Jul 6 16:39:03 IST 2019
For more details, see the log file
/usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting"
I never faced this problem before while running gyrification index. To me,
it's looks bizarre.
Would appreciate any help.
Thanks & regards
-Korann
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------------------------------
Message: 6
Date: Sat, 6 Jul 2019 14:02:03 +0200 (CEST)
From: Tim Sch?fer <ts+ml@rcmd.org>
Subject: Re: [Freesurfer] error while running pial_lgi for
gyrification index
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <1748678951.441799.1562414523805@ox.hosteurope.de>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Just to be sure: *does* /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi exist?
Tim
> On July 6, 2019 at 1:27 PM vittal korann <vittalkorann@gmail.com> wrote:
>
>
> External Email - Use Caution
>
> Hi FS experts,
>
> I wanted to run the gyrification index for all patients with Schizophrenia
> and volunteers. When I entered the command:
> "recon-all -s SATM124 -qcache -measure pial_lgi" and the terminal output
>
> " Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> Actual FREESURFER_HOME /usr/local/freesurfer
> -rw-rw-r-- 1 root 1590 1054464 Jul 6 16:02
> /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log
> Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31
> UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
> '/usr/local/freesurfer/bin/recon-all' ->
> '/usr/local/freesurfer/subjects/SATM124/scripts/recon-all.local-copy'
> #--------------------------------------------
> #@# Qdec Cache preproc lh pial_lgi fsaverage Sat Jul 6 16:39:03 IST 2019
> /usr/local/freesurfer/subjects/SATM124/surf
>
> mris_preproc --s SATM124 --hemi lh --meas pial_lgi --target fsaverage
> --out lh.pial_lgi.fsaverage.mgh
>
> nsubjects = 1
> ERROR: cannot find /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi
> Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31
> UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s SATM124 exited with ERRORS at Sat Jul 6 16:39:03 IST 2019
>
> For more details, see the log file
> /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting"
>
> I never faced this problem before while running gyrification index. To me,
> it's looks bizarre.
> Would appreciate any help.
>
> Thanks & regards
> -Korann
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Dr. Tim Sch?fer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
------------------------------
Message: 7
Date: Sat, 6 Jul 2019 13:38:54 +0000
From: Marie Hill <marie_hill@outlook.com>
Subject: [Freesurfer] Viewing Uncorrected Significance Map in Freeview
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<LNXP123MB1817D23EE50CB4F16728A2E0F0F40@LNXP123MB1817.GBRP123.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="iso-8859-1"
External Email - Use Caution
Hi everyone,
I have just finished running glmfit. When I try to load the significance maps in freeview, they appear to load for a moment and then disappear, just showing the brain volume without any highlighted areas of significance. Does anyone have any idea why this could be?
I ran the command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.g4v1.glmdir/bipolar-vs-schizophrenia/sig.mgh:overlay_threshold=4,5 -viewport 3d
Kindest Regards,
Marie
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