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Today's Topics:
1. Re: mkanalysis-sess refeventdur (Greve, Douglas N.,Ph.D.)
2. Re: MP-RAGE protocol (Greve, Douglas N.,Ph.D.)
3. Re: Question about recon-all.v6.hires (Greve, Douglas N.,Ph.D.)
4. Re: mkanalysis-sess refeventdur (Nasiriavanaki, Zahra)
5. problem with mri_surfcluster (Barletta, Valeria)
6. Re: problem with mri_surfcluster (Greve, Douglas N.,Ph.D.)
7. Re: mris_label2annot empty Annot (Greve, Douglas N.,Ph.D.)
8. Re: problem with mri_surfcluster (Barletta, Valeria)
9. Re: Fixing of Morphometry Stats and Global Measure of Volume:
Longitudinal analysis (Greve, Douglas N.,Ph.D.)
10. Re: problem with mri_surfcluster (Greve, Douglas N.,Ph.D.)
11. Re: problem with mri_surfcluster (Barletta, Valeria)
----------------------------------------------------------------------
Message: 1
Date: Mon, 20 May 2019 16:52:39 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] mkanalysis-sess refeventdur
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <4f503934-d973-7563-2a14-235cb86012c6@mgh.harvard.edu>
Content-Type: text/plain; charset="Windows-1252"
No, you'll need to change your paradigm file to have two distinct 8 sec
events rather than one 16 sec event.
On 5/20/19 10:12 AM, Nasiriavanaki, Zahra wrote:
>
> Hi Freesurfer experts
>
>
> I am?making an analysis in Freesurfer version 6 and?I have a question
> about the "refeventdur" in mkanalysis-sess command.
>
> My stimulus duration is 16 seconds, but for a specific analysis, I
> only want to include half of the stimulus duration (ex:?the?first 8
> seconds only OR the?last 8 seconds only).
>
> I was wondering if I can do this, by setting the "refeventdur" to 8
> seconds.? Will that work? and if it does, is it including the first 8
> seconds or the last 8 seconds?
>
>
> Thanks
>
> Mona
>
>
>
> *Zahra?(Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 2
Date: Mon, 20 May 2019 16:55:39 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] MP-RAGE protocol
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <e482d81c-774b-00ea-a70e-809139c87bb5@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Your attachment says that none of the commands could be found. Make sure
you set up your environment correctly
On 5/20/19 4:53 AM, mustafa amin wrote:
>
> ????????External Email - Use Caution
>
> Hi Bruce,
>
> Thank you for your swift response as always, may I know how to convert
> the more than 100 DICOM files to mgz or nifti? I noticed that the
> command is for 1 file/image, please correct me if I am wrong. The
> MP-RAGE file that I sent you is more than 50 images.
>
> I tried to follow your instruction however it did not work smoothly.
> The diacom files couldn't be converted to mgz. I have attached the
> command that still did not work when I used them in this email. Please
> have a look and share some thoughts. Thank you for your kind attention
> and cooperation.
>
>
> Pada Jumat, 17 Mei 2019 21.14.44 WIB, Bruce Fischl
> <fischl@nmr.mgh.harvard.edu> menulis:
>
>
> Hi Mustafa
>
> 1. Your mprage ran through recon-all fine and the results look good. The
> saggital field of view is tight, so make sure that they don't crop
> brain in
> that direction.
>
> 2. Your recon-all command line is incorrect. You should point the
> SUBJECTS_DIR environment variable to whereever you want to store all of
> your FreeSurfer-processed data, then use the -i switch to path to the
> input
> volume. You can also specify SUBJECTS_DIR on the command line. So in your
> case something like:
>
>
> recon-all -i $FREESURFER_HOME/subjects/sample-001.mgz -s FS_subject001
> -sd \
> ??? ? /path/to/my/subjecs -all
>
> should do the trick. There is also no need to convert to nifti first
>
> cheers
> Bruce
>
>
> On Fri,
> 17 May 2019, mustafa amin wrote:
>
> >
> > ????????External Email - Use Caution
>
> >
> > Hi Bruce,
> >
> > Herewith I attach within the email the command that didn't work when
> I wanted to reconall. Please
> > have a look. What about the previous dicom that I have sent to you?
> Please share some thoughts.Thank
> > you very much.
> >
> > Yours faithfully,
> >
> > Mustafa
> >
> >
> > Pada Kamis, 16 Mei 2019 20.18.35 WIB, Bruce Fischl
> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> menulis:
> >
> >
> > Hi Mustafa
> >
> > can you give us some detials? What didn't work? Can you send us the full
> > command line, screen output and recon-all.log?
> >
> > cheers
> > Bruce
> >
> >
> > On Thu, 16 May 2019, mustafa amin wrote:
> >
> > >
> > > ????????External Email - Use Caution
> > >
> > > Hi Douglas,
> > >
> > > I tried to follow the instruction to recon-all the data however it
> didn't work. Please give
> > > some thoughts. Thank you in advance.
> > >
> > > Yours faithfully,
> > >
> > > Mustafa
> > >
> > > Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
> > > menulis:
> > >
> > >
> > > Hi Mustafa, why not just run recon-all on the data you have and see
> > > whether it looks ok?
> > >
> > > On 4/15/19 7:06 AM, mustafa amin wrote:
> > > >? ? ? ? ? External Email - Use Caution
> > > >
> > > > Hi Bruce,
> > > >
> > > > I?ve talked to the MRI operator and she told me that the best
> thing to do the MP-RAGE
> > > protocol is doing the T1 weighted 3D gradient echo with SENSE, she
> can?t set the TE, TR, TI
> > > just like the ADNI protocol asked, though. She can set the
> thickness to 1 mm. Is this set
> > > up okay?
> > > >
> > > > I have the DIACOM files of some subjects with the set up above.
> Can I send them to you to
> > > look at them?
> > > >
> > > >? I am terribly sorry for keep asking this basic question due to
> we never had experience
> > > doing it in Indonesia.
> > > >
> > > > Many thanks!
> > > >
> > > >
> > > > Mustafa M. Amin
> > > > Consultant Psychiatrist in Biological Psychiatry
> > > > Department of Psychiatry
> > > > Faculty of Medicine
> > > > Universitas Sumatera Utara
> > > >
> > > >> On 2 Apr 2019, at 20.49, Bruce Fischl
> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
> > > >>
> > > >> Hi Mustafa
> > > >>
> > > >> MRI is an amazingly versatile technology that can be messed up
> in an
> > > >> astonishing number of ways. By far the best thing to do would
> be to acquire
> > > >> a dataset and run it through recon-all and see if the results look
> > > >> accurate. If you have permission to do so, you are welcome to
> acquire one
> > > >> and send it to us to try out instead.
> > > >>
> > > >> cheers
> > > >> Bruce
> > > >>
> > > >> On Tue, 2 Apr 2019, mustafa amin
> > > >> wrote:
> > > >>
> > > >>>? ? ? ? External Email - Use Caution
> > > >>>
> > > >>> Dear Freesurfer experts,
> > > >>>
> > > >>> I need advice, the MRI operator need to confirm whether she
> had done the
> > > >>> right protocol of MP-RAGE. I have attached the picture that
> has been
> > > >>> taken by her. Please share some thoughts. Thank you in advance.
> > > >>>
> > > >>>
> > > >> _______________________________________________
> > > >> 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
> > >
> > >
> > > _______________________________________________
> > > 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
> >
> >
> _______________________________________________
> 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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 3
Date: Mon, 20 May 2019 16:59:08 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] Question about recon-all.v6.hires
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <c6c9e090-4ae9-1307-aad4-ac0822b1eed3@mgh.harvard.edu>
Content-Type: text/plain; charset="Windows-1252"
They should be there. Can you send recon-all.log and conf2hires.log files?
On 5/20/19 9:59 AM, Bruce Fischl wrote:
> Hi Victor
>
> the lh.white.{KH} are generated from the lh.white file, so I don't
> think it can have skipped creating it. Was it deleted? Can you double
> check?
>
> Bruce
> On Mon, 20 May 2019, Zeng,Victor (BIDMC - Psychiatry) wrote:
>
>>
>> Hi all,
>>
>>
>> I am running 7T scans through FS6, and I have been recommended to
>> install the tools
>> in?ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/
>> . So I ran the new
>> recon-all.v6.hires, specifically with the command "recon-all.hires.v6
>> -s subj -conf2hires -all"
>>
>>
>> For the most part, it ran, but I while QCing, it couldn't seem to
>> load the surfs files. Recon-all
>> seemed to have generated files called ?h.white.H and ?h.white.K, but
>> apparently skipped the steps
>> for ?h.white? I don't think I can load the surfs files without it,
>> and I don't?know if this is
>> intentional.
>>
>>
>> Victor Zeng
>> Beth Israel Deaconess Medical Center
>> Keshavan Lab
>> --
>>
>> ____________________________________________________________________________________________________
>>
>>
>> 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.
>>
>>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 4
Date: Mon, 20 May 2019 18:08:34 +0000
From: "Nasiriavanaki, Zahra" <ZNASIRIAVANAKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] mkanalysis-sess refeventdur
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<DM6PR04MB44432A081ED580B5F392F5F199060@DM6PR04MB4443.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
Got it.
Thank you very much for your reply
Mona
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Monday, May 20, 2019 12:52:39 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mkanalysis-sess refeventdur
No, you'll need to change your paradigm file to have two distinct 8 sec
events rather than one 16 sec event.
On 5/20/19 10:12 AM, Nasiriavanaki, Zahra wrote:
>
> Hi Freesurfer experts
>
>
> I am making an analysis in Freesurfer version 6 and I have a question
> about the "refeventdur" in mkanalysis-sess command.
>
> My stimulus duration is 16 seconds, but for a specific analysis, I
> only want to include half of the stimulus duration (ex: the first 8
> seconds only OR the last 8 seconds only).
>
> I was wondering if I can do this, by setting the "refeventdur" to 8
> seconds. Will that work? and if it does, is it including the first 8
> seconds or the last 8 seconds?
>
>
> Thanks
>
> Mona
>
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------
Message: 5
Date: Mon, 20 May 2019 18:40:25 +0000
From: "Barletta, Valeria" <VBARLETTA@mgh.harvard.edu>
Subject: [Freesurfer] problem with mri_surfcluster
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BN7PR04MB5185FB256479B0E8AF6171F1F9060@BN7PR04MB5185.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear Freesurfers,
I am trying to obtain clusters of vertices whit a certain value over a threshold inside a lesion mask projected to the surface, with the command:
mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos --minarea 0.01 --sum summary.txt
But I obtain this result saying there are no vertices in my mask.
thsign = pos, id = 1
version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
hemi = lh
srcid = /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh
srcsubjid = MS075_R01_07_R1year
srcsurf = lh.pial
srcframe = 0
thsign = pos
thmin = 1
thmax = 49.9581
fdr = -1
minarea = 0.01
xfmfile = talairach.xfm
nth = -1
sumfile = /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt
subjectsdir = /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
FixMNI = 1
Found 0 vertices in mask
Can you help me figure out why?
Thanks,
Vale
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Message: 6
Date: Mon, 20 May 2019 18:46:54 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] problem with mri_surfcluster
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <6a91d804-b0e6-bed2-dd04-24cb42a020c1@mgh.harvard.edu>
Content-Type: text/plain; charset="Windows-1252"
How did you choose thresholds of 1 and 49.95? In general, you don't need
to set --thmax. If you input is a binary mask, then you should set
--thmin to somethiing below 1 (eg, 0.5)
On 5/20/19 2:40 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I am trying to obtain clusters of vertices whit a certain value?over a
> threshold inside a lesion mask projected to the surface,?with the command:
>
>
> mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in
> lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask
> lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos
> --minarea 0.01 --sum summary.txt
>
> But I obtain this result saying there are no vertices in my mask.
>
> thsign = pos, id = 1
> version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
> hemi? ? ? ? ? ?= lh
> srcid? ? ? ? ? =
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh
>
> srcsubjid? ? ? = MS075_R01_07_R1year
> srcsurf? ? ? ? = lh.pial
> srcframe? ? ? ?= 0
> thsign? ? ? ? ?= pos
> thmin? ? ? ? ? = 1
> thmax? ? ? ? ? = 49.9581
> fdr? ? ? ? ? ? = -1
> minarea? ? ? ? = 0.01
> xfmfile? ? ? ? = talairach.xfm
> nth? ? ? ? ?= -1
> sumfile? =
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt
> subjectsdir? ? =
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
> FixMNI = 1
> Found 0 vertices in mask
>
>
> Can you help me figure out why?
>
> Thanks,
> Vale
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 7
Date: Mon, 20 May 2019 18:50:25 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_label2annot empty Annot
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <e13d70d6-4856-a7fb-935d-31104f073301@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Can you send the terminal output?
On 5/20/19 8:51 AM, Michal Tanzer wrote:
>
> ????????External Email - Use Caution
>
> Dear Freesurfer experts,
> I am having some difficulties in creating annot file for specific ROIs
> using the 2009atlas. When I am using this command, it saves the annot
> but I am getting empty files. Using the same command with the
> aparc.annot file and different ROIs seems fine, so I am not sure what
> is the problem.
>
> mris_label2annot --s fsaverage --h lh --ctab
> label/aparc.annot.a2009s.ctab --a myaprac--l
> dir/lh.G_insular_short.label --l dir/lh.G_Ins_lg&S_cent_ins.label --debug
>
> Thank you for your help,
>
> Kind regards,
> Michal
> --
> Michal Tanzer, PhD
>
> Postdoctoral fellow; Clinical Psychologist.
> Research Department of Clinical, Educational and Health Psychology,
> University College London,
> United Kingdom
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 8
Date: Mon, 20 May 2019 18:51:09 +0000
From: "Barletta, Valeria" <VBARLETTA@mgh.harvard.edu>
Subject: Re: [Freesurfer] problem with mri_surfcluster
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BN7PR04MB518570C9B3AFA4C4AF223B9DF9060@BN7PR04MB5185.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
I want to extract clusters within the cortical lesion mask in which the vertex values are below 49.95
The values are in the file lh.MS075_R01_07_R1year.subjspace.mgh
Thanks,
Vale
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Monday, May 20, 2019 2:46:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] problem with mri_surfcluster
How did you choose thresholds of 1 and 49.95? In general, you don't need
to set --thmax. If you input is a binary mask, then you should set
--thmin to somethiing below 1 (eg, 0.5)
On 5/20/19 2:40 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I am trying to obtain clusters of vertices whit a certain value over a
> threshold inside a lesion mask projected to the surface, with the command:
>
>
> mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in
> lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask
> lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos
> --minarea 0.01 --sum summary.txt
>
> But I obtain this result saying there are no vertices in my mask.
>
> thsign = pos, id = 1
> version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
> hemi = lh
> srcid =
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh
>
> srcsubjid = MS075_R01_07_R1year
> srcsurf = lh.pial
> srcframe = 0
> thsign = pos
> thmin = 1
> thmax = 49.9581
> fdr = -1
> minarea = 0.01
> xfmfile = talairach.xfm
> nth = -1
> sumfile =
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt
> subjectsdir =
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
> FixMNI = 1
> Found 0 vertices in mask
>
>
> Can you help me figure out why?
>
> Thanks,
> Vale
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
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Message: 9
Date: Mon, 20 May 2019 18:54:36 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] Fixing of Morphometry Stats and Global
Measure of Volume: Longitudinal analysis
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <67db3b4a-4ea4-2640-f769-7600311da729@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
You will not need to run the entire stream again. Did you run it in
high-res mode? If the volumes are conformed (eg, orig.mgz is 1mm,
252^3), then you do not need to do anything. Otherwise, you will need to
re-run only part of it using the patch and running
recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3
-wmparc -balabels
I think this should work fine on longitudinal data, but run it on one to
make sure
See https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed for
more info
On 5/20/19 4:06 AM, Diana Tordesillas-Guti?rrez wrote:
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I have a question about the bug in FreeSurfer v.6? in the global metrics
> computation:
>
> I have run my data through the longitudinal pipeline. I would like to
> know if my analysis have been affected (3T, voxel size 0.94) and I have
> to rerun the whole analysis in case they have.
>
> Thank you!
>
> Diana
>
------------------------------
Message: 10
Date: Mon, 20 May 2019 18:56:38 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] problem with mri_surfcluster
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <8a6b12bc-9a30-ae81-aa68-3c69ebf24c1d@mgh.harvard.edu>
Content-Type: text/plain; charset="Windows-1252"
When you look at the overlay in freeview and set the min thresh to 1, do
you see blobs?
On 5/20/19 2:51 PM, Barletta, Valeria wrote:
>
> I want to extract clusters within the cortical lesion mask?in which
> the vertex values are below 49.95
>
> The values are in the file lh.MS075_R01_07_R1year.subjspace.mgh
>
>
> Thanks,
>
> Vale
>
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
> N.,Ph.D. <DGREVE@mgh.harvard.edu>
> *Sent:* Monday, May 20, 2019 2:46:54 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] problem with mri_surfcluster
> How did you choose thresholds of 1 and 49.95? In general, you don't need
> to set --thmax. If you input is a binary mask, then you should set
> --thmin to somethiing below 1 (eg, 0.5)
>
> On 5/20/19 2:40 PM, Barletta, Valeria wrote:
> >
> > Dear Freesurfers,
> >
> > I am trying to obtain clusters of vertices whit a certain value?over a
> > threshold inside a lesion mask projected to the surface,?with the
> command:
> >
> >
> > mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in
> > lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask
> > lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos
> > --minarea 0.01 --sum summary.txt
> >
> > But I obtain this result saying there are no vertices in my mask.
> >
> > thsign = pos, id = 1
> > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve
> Exp $
> > hemi? ? ? ? ? ?= lh
> > srcid? ? ? ? ? =
> >
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh
> >
> > srcsubjid? ? ? = MS075_R01_07_R1year
> > srcsurf? ? ? ? = lh.pial
> > srcframe? ? ? ?= 0
> > thsign? ? ? ? ?= pos
> > thmin? ? ? ? ? = 1
> > thmax? ? ? ? ? = 49.9581
> > fdr? ? ? ? ? ? = -1
> > minarea? ? ? ? = 0.01
> > xfmfile? ? ? ? = talairach.xfm
> > nth? ? ? ? ?= -1
> > sumfile? =
> >
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt
> > subjectsdir? ? =
> > /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
> > FixMNI = 1
> > Found 0 vertices in mask
> >
> >
> > Can you help me figure out why?
> >
> > Thanks,
> > Vale
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 11
Date: Mon, 20 May 2019 19:09:43 +0000
From: "Barletta, Valeria" <VBARLETTA@mgh.harvard.edu>
Subject: Re: [Freesurfer] problem with mri_surfcluster
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BN7PR04MB518533E1145813E9CD09B971F9060@BN7PR04MB5185.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
This is what I see if I set min 1 max 49 on the overlay (the subjectspace.mgh file in the command)
[cid:219fb126-a40e-4f06-9849-aac62b6aee0f]
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Monday, May 20, 2019 2:56:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] problem with mri_surfcluster
When you look at the overlay in freeview and set the min thresh to 1, do
you see blobs?
On 5/20/19 2:51 PM, Barletta, Valeria wrote:
>
> I want to extract clusters within the cortical lesion mask in which
> the vertex values are below 49.95
>
> The values are in the file lh.MS075_R01_07_R1year.subjspace.mgh
>
>
> Thanks,
>
> Vale
>
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
> N.,Ph.D. <DGREVE@mgh.harvard.edu>
> *Sent:* Monday, May 20, 2019 2:46:54 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] problem with mri_surfcluster
> How did you choose thresholds of 1 and 49.95? In general, you don't need
> to set --thmax. If you input is a binary mask, then you should set
> --thmin to somethiing below 1 (eg, 0.5)
>
> On 5/20/19 2:40 PM, Barletta, Valeria wrote:
> >
> > Dear Freesurfers,
> >
> > I am trying to obtain clusters of vertices whit a certain value over a
> > threshold inside a lesion mask projected to the surface, with the
> command:
> >
> >
> > mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in
> > lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask
> > lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos
> > --minarea 0.01 --sum summary.txt
> >
> > But I obtain this result saying there are no vertices in my mask.
> >
> > thsign = pos, id = 1
> > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve
> Exp $
> > hemi = lh
> > srcid =
> >
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh
> >
> > srcsubjid = MS075_R01_07_R1year
> > srcsurf = lh.pial
> > srcframe = 0
> > thsign = pos
> > thmin = 1
> > thmax = 49.9581
> > fdr = -1
> > minarea = 0.01
> > xfmfile = talairach.xfm
> > nth = -1
> > sumfile =
> >
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt
> > subjectsdir =
> > /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
> > FixMNI = 1
> > Found 0 vertices in mask
> >
> >
> > Can you help me figure out why?
> >
> > Thanks,
> > Vale
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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