Hi Doug,
Our freeview command is: freeview -v ${fs_id}/mri/T1.mgz
${fs_id}/mri/brainmask.mgz:colormap=heat:opacity=0.4
Thank you,
Kaley
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
freesurfer-requ...@nmr.mgh.harvard.edu <freesurfer-requ...@nmr.mgh.harvard.edu>
Sent: Wednesday, June 14, 2017 11:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 160, Issue 25
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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. Re: difference in T1 and T2 resolution (Douglas Greve)
2. Re: viewing surfaces in 3D using freeview (Ruopeng Wang)
3. Re: mri_vol2surf: visualising the edges at projfrac 0.1 - 0.5
(Elijah Mak)
4. Re: difference in T1 and T2 resolution (John Anderson)
5. Re: recon-all exits with error at surf/lh.thickness, mghRead
looks for .mgh/.mgz filename extension (Bruce Fischl)
6. Re: difference in T1 and T2 resolution (Douglas Greve)
7. Re: Brainmask Shifted (Douglas Greve)
8. Re: separate medial from lateral part in superiorfrontal
parcel of Desikan-Killiany atlas (Bruce Fischl)
9. Re: Applying an affine transformation to a surface (Douglas Greve)
10. Re: Surface area of a define volume projection on cortical
surface (Douglas Greve)
11. Re: viewing surfaces in 3D using freeview (Michael Davies)
12. Re: Merging outputs of mri_label2vol across hemi (Douglas Greve)
13. Re: Merging outputs of mri_label2vol across hemi (Elijah Mak)
14. Re: Merging outputs of mri_label2vol across hemi (Douglas Greve)
15. Re: Longitudinal Pipeline (Martin Reuter)
16. Re: viewing surfaces in 3D using freeview (Ruopeng Wang)
----------------------------------------------------------------------
Message: 1
Date: Wed, 14 Jun 2017 16:02:10 +0200
From: Douglas Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] difference in T1 and T2 resolution
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <9ddd5b02-e0df-ffbb-1515-e5bf02a62...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
This is not due to a difference between T1 and T2 resolution. The
problem is that the two T1 volumes (001.mgz and 002.mgz) are difference
sizes. It is probably not a good idea to try to combine them, but if you
really want to, I can supply you with a solution.
On 6/14/17 1:12 PM, John Anderson wrote:
> Thank you for your response. The log file is attached
> *Sent:* Tuesday, June 13, 2017 at 2:02 AM
> *From:* "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution
>
> can you send the log file?
>
> On 6/11/17 10:08 PM, John Anderson wrote:
>
> In the log file the error was:
> ERROR: MultiRegistration::loadMovables: images have different
> voxel sizes.
> Currently not supported, maybe first make conform?
> Debug info: size(1) = 1, 1, 1 size(0) = 0.7, 0.7, 0.8
> MultiRegistration::loadMovables: voxel size is different
> /recons/subj1/mri/orig/002.mgz.
> Jon
> *Sent:* Sunday, June 11, 2017 at 2:12 PM
> *From:* "Matt Glasser" <m...@ma-tea.com>
> *To:* "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution
> What was the error message?
> Peace,
> Matt.
> From: <freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of John
> Anderson <j.ander...@publicist.com <mailto:j.ander...@publicist.com>>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Date: Sunday, June 11, 2017 at 9:06 AM
> To: <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: [Freesurfer] difference in T1 and T2 resolution
> Dear Freesurfer experts,
> I have T1 and T2 images were unfortunately acquired with different
> resolution (i.e the voxel sizes is not the same)
> T1 is 280X280X208
> T2 is 270X270X200
>
> I tried to run "recon-all" but it failed to process the data. The
> command that I used is :
> pbsubmit -c " recon-all -subjid subj1 -T2 PATH_TO_/T2.nii.gz
> -qcache -T2pial -all"
> How can I analyze these images? Is it a correct procedure to
> conform the voxels using "mri_convert". Is this procedure correct?
> does it hurt the anatomy of the images?
> I highly appreciate your help
> John
> _______________________________________________ Freesurfer mailing
> list Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The
> information in this e-mail is intended only for the person to whom
> it is addressed. If you believe this e-mail was sent to you in
> error and the e-mail contains patient information, please contact
> the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error but does not contain patient information, please
> contact the sender and properly dispose of the e-mail.
> _______________________________________________ Freesurfer mailing
> list Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The
> information in this e-mail is intended only for the person to whom
> it is addressed. If you believe this e-mail was sent to you in
> error and the e-mail contains patient information, please contact
> the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error but does not contain patient information, please
> contact the sender and properly dispose of the e-mail.
>
> _______________________________________________
> 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 The
> information in this e-mail is intended only for the person to whom it
> is addressed. If you believe this e-mail was sent to you in error and
> the e-mail contains patient information, please contact the Partners
> Compliance HelpLine at http://www.partners.org/complianceline . If the
> e-mail was sent to you in error but does not contain patient
> information, please contact the sender and properly dispose of the e-mail.
>
>
> _______________________________________________
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Message: 2
Date: Wed, 14 Jun 2017 10:05:40 -0400
From: Ruopeng Wang <rpw...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <412df637-000d-481f-93c1-ccd861f15...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Please copy and paste the full command line you ran and the error message you
got.
Thanks,
Ruopeng
> On Jun 14, 2017, at 9:26 AM, Michael Davies <michael.davie...@hotmail.com>
> wrote:
>
> Hello i am trying to access the data files in 3D but i am having problems
> opening the files using the command syntax given on the website.
>
> I have set my own pathway using my own data;
>
> ?/projects/pbic1030/Micahel/subjects/Subj1/fsaverage/surf/?
>
> However, one i progress with the code past this point i am unable to load the
> data and get the error message No file or directory in the terminal even
> though this is the correct pathway to the data.
>
> When i enter the rest as follows this is when the problems begin to occur
> lh.pial:annot=aparc.annot:name=pial_aparc:visible=0
> \
>
> Could you please advise me how to proceed?
>
> Kind regards, Michael
> University of Birmingham
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 3
Date: Wed, 14 Jun 2017 15:14:20 +0100
From: Elijah Mak <fk...@medschl.cam.ac.uk>
Subject: Re: [Freesurfer] mri_vol2surf: visualising the edges at
projfrac 0.1 - 0.5
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<caauuvmybt1phl1xokawwb0smyzekgxuaw7otmzludfww4ry...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Freesurfer Team,
No worries, I have found a helpful solution from an old thread using
mris_expand.
<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40894.html>
http://i.imgur.com/CrF125X.png
Thanks.
Best Wishes,
Elijah
On Tue, Jun 13, 2017 at 8:47 PM, Elijah Mak <fk...@medschl.cam.ac.uk> wrote:
> Hi Freesurfer Team,
>
> Is there a way to visualise the sampling edges across a range of projfrac
> values (0.1 (closer to WM) - 0.5) and overlay them onto PET data?
>
> Any suggestions are greatly appreciated. Thanks.
>
> Best Wishes,
> Elijah
>
>
>
--
Elijah Mak, Gates Scholar
PhD Candidate *|* Psychiatry
University of Cambridge
Trinity College, Cambridge, CB2 1TQ
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Message: 4
Date: Wed, 14 Jun 2017 16:20:09 +0200
From: "John Anderson" <j.ander...@publicist.com>
Subject: Re: [Freesurfer] difference in T1 and T2 resolution
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<trinity-bd3c6d9e-38b2-4095-91f5-8a7ccbc85484-1497450009614@3capp-mailcom-lxa03>
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Message: 5
Date: Wed, 14 Jun 2017 10:25:20 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all exits with error at
surf/lh.thickness, mghRead looks for .mgh/.mgz filename extension
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1706141024260.28...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Anup
I suspect the problem is choosing a subject with ".mgz" in the ID. I
wouldn't include any of ".nii" ".mgz" or ".mgh" in a subject ID. Try
rerunning and just using fsMM
cheers
Bruce
On Wed, 14 Jun 2017, Anup Bidesi wrote:
>
> Hello FreeSurfer Users,
>
> New to Freesurfer, I'm attempting to recon-all using :
>
> recon-all -all -i T1.nii -s op.nii.mgz (Attached recon-all log)
>
> The automated process begins normally and seems to run Autorecon Prrocessing
> Stages 1-25, but at step 26
> (I think) and then exits with Error, per log as seen below:
>
> -------------------------------------------------------------
>
> mghRead(/home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.th
> ickness,
> -1): could not open file.
> Filename extension must be .mgh, .mgh.gz
> or .mgz
>
> -------------------------------------------------------------
>
> Within the subject .mgz folder in Surf there was a tmp.pctsurfcon.14807 fold
> er with
> a file named lh.wm.mgh (size 569 kb).
>
> I ran this process a couple of times and the autorecon process would exit at
> same step.I
> tried looking up the Archive for any similar previous error messages but did
> not find any.
> Please advise.
>
> 1) FreeSurfer version:
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>
> 2) Platform: Ubuntu 14.04
>
> 3) uname -a: Linux brainmindengineer-Precision-Tower-7910 3.13.0-117-generic
> #164-Ubuntu
> SMP Fri Apr 7 11:05:26 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>
> 4) recon-all.log: see attached
>
> Thanks for your help,
>
> Anup
>
>
------------------------------
Message: 6
Date: Wed, 14 Jun 2017 16:28:48 +0200
From: Douglas Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] difference in T1 and T2 resolution
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <01d6defd-4ccb-5fcb-8b02-37955bd49...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
It looks like at least the number of voxels is different between the two
(not sure about the voxel size). You may or may not want to average the
two images together. If they are different sizes, it is probably the
case that they have different acquisition parameters and so different
contrasts. If you want to analyze both, then you'll need to resample one
into the other, eg,
mv 002.mgz orig.002.mgz
mri_vol2vol --mov orig.002.mgz --targ 001.mgz --regheader --o 002.mgz
but this is probably not a good idea
On 6/14/17 4:20 PM, John Anderson wrote:
>
> Thank Doug for the response.
> This is very interesting!! I never thought about that! I was thinking
> that the two images (i.e. T1 and T2) must have the same resolution.
> I understand that when we talk about differnce in the size of the
> files that means either the thickness of the slices is different or
> the number of images is differnt correct?
> Kindly could you please shed more light on this issue and how we can
> handle it.
> Also is it matter if the resolution of the two images is different?
> How can I analyse such images correctly?
> Many thanks!
> John
> *Sent:* Wednesday, June 14, 2017 at 10:02 AM
> *From:* "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution
>
> This is not due to a difference between T1 and T2 resolution. The
> problem is that the two T1 volumes (001.mgz and 002.mgz) are
> difference sizes. It is probably not a good idea to try to combine
> them, but if you really want to, I can supply you with a solution.
>
> On 6/14/17 1:12 PM, John Anderson wrote:
>
> Thank you for your response. The log file is attached
> *Sent:* Tuesday, June 13, 2017 at 2:02 AM
> *From:* "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution
>
> can you send the log file?
>
> On 6/11/17 10:08 PM, John Anderson wrote:
>
> In the log file the error was:
> ERROR: MultiRegistration::loadMovables: images have different
> voxel sizes.
> Currently not supported, maybe first make conform?
> Debug info: size(1) = 1, 1, 1 size(0) = 0.7, 0.7, 0.8
> MultiRegistration::loadMovables: voxel size is different
> /recons/subj1/mri/orig/002.mgz.
> Jon
> *Sent:* Sunday, June 11, 2017 at 2:12 PM
> *From:* "Matt Glasser" <m...@ma-tea.com>
> *To:* "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution
> What was the error message?
> Peace,
> Matt.
> From: <freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of
> John Anderson <j.ander...@publicist.com
> <mailto:j.ander...@publicist.com>>
> Reply-To: Freesurfer support list
> <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Date: Sunday, June 11, 2017 at 9:06 AM
> To: <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: [Freesurfer] difference in T1 and T2 resolution
> Dear Freesurfer experts,
> I have T1 and T2 images were unfortunately acquired with
> different resolution (i.e the voxel sizes is not the same)
> T1 is 280X280X208
> T2 is 270X270X200
>
> I tried to run "recon-all" but it failed to process the data.
> The command that I used is :
> pbsubmit -c " recon-all -subjid subj1 -T2 PATH_TO_/T2.nii.gz
> -qcache -T2pial -all"
> How can I analyze these images? Is it a correct procedure to
> conform the voxels using "mri_convert". Is this procedure
> correct? does it hurt the anatomy of the images?
> I highly appreciate your help
> John
> _______________________________________________ Freesurfer
> mailing list Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> The information in this e-mail is intended only for the person
> to whom it is addressed. If you believe this e-mail was sent
> to you in error and the e-mail contains patient information,
> please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was
> sent to you in error but does not contain patient information,
> please contact the sender and properly dispose of the e-mail.
> _______________________________________________ Freesurfer
> mailing list Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> The information in this e-mail is intended only for the person
> to whom it is addressed. If you believe this e-mail was sent
> to you in error and the e-mail contains patient information,
> please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was
> sent to you in error but does not contain patient information,
> please contact the sender and properly dispose of the e-mail.
>
> _______________________________________________
> 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 The
> information in this e-mail is intended only for the person to whom
> it is addressed. If you believe this e-mail was sent to you in
> error and the e-mail contains patient information, please contact
> the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error but does not contain patient information, please
> contact the sender and properly dispose of the e-mail.
>
> _______________________________________________
> 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 The
> information in this e-mail is intended only for the person to whom it
> is addressed. If you believe this e-mail was sent to you in error and
> the e-mail contains patient information, please contact the Partners
> Compliance HelpLine at http://www.partners.org/complianceline . If the
> e-mail was sent to you in error but does not contain patient
> information, please contact the sender and properly dispose of the e-mail.
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 7
Date: Wed, 14 Jun 2017 16:32:38 +0200
From: Douglas Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Brainmask Shifted
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <02f67013-f90c-699f-0307-9f1bf9b13...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
what is your freeview command?
On 6/14/17 3:51 PM, KALEY E ELLIS wrote:
>
> Dear FreeSurfer Developers,
>
>
> We are using FreeSurfer v6.0 and our operating system is OS X El
> Capitan version 10.11.6.
>
>
> We are going through the manual editing process and are checking the
> brainmask by following these instructions:
>
> http://freesurfer.net/fswiki/FsTutorial/SkullStripFixV6.0
>
> We have two subjects who appear to have brainmasks that are shifted up
> considerably (see attached image). The recon-all.log file indicates
> that it finished without errors:
>
>
> reading volume
> /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/mri/wm.mgz...
> reading input surface
> /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white...
> reading input pial surface
> /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.pial...
> reading input white surface
> /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white...
> INFO: assuming MGZ format for volumes.
>
> table columns are:
> number of vertices
> total surface area (mm^2)
> total gray matter volume (mm^3)
> average cortical thickness +- standard deviation (mm)
> integrated rectified mean curvature
> integrated rectified Gaussian curvature
> folding index
> intrinsic curvature index
> structure name
>
> 277 173 970 3.493 0.659 0.107 0.039 3 0.4
> ./rh.entorhinal_exvivo.label
>
> #------------------------------------------
>
> Started at Thu Jun 8 10:50:24 CDT 2017
> Ended at Fri Jun 9 00:06:58 CDT 2017
> #@#%# recon-all-run-time-hours 13.276
> recon-all -s 2083_base finished without error at Fri Jun 9 00:06:58
> CDT 2017
>
> Could you please advise me on how to correct this issue? We have run
> all of these subjects the same way, but only two have had this problem.
>
>
> Thank you!
>
> Kaley
>
>
> Associate Research Specialist
> Center for Healthy Minds
> Waisman Center for Brain Imaging and Behavior
> University of Wisconsin-Madison
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 8
Date: Wed, 14 Jun 2017 10:33:55 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] separate medial from lateral part in
superiorfrontal parcel of Desikan-Killiany atlas
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Rahul Desikan <rahuldesi...@gmail.com>
Message-ID:
<alpine.lrh.2.20.1706141033400.28...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Rahul: any suggestions?
Bruce
On Wed, 14 Jun 2017, Caspar M. Schwiedrzik wrote:
> Hi!
> Is there by any chance a known demarcation line in in the XYZ coordinates of
> the Desikan-Killiany atlas that could be used to separate the
> superiorfrontal parcel into a medial and a lateral part?
>
> Thanks!
> Caspar
>
>
>
------------------------------
Message: 9
Date: Wed, 14 Jun 2017 16:56:17 +0200
From: Douglas Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Applying an affine transformation to a
surface
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <ba337251-ab46-8ef2-a1f3-25dbbd353...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
Can you try it with --reg instead of --reg-inv ?
On 6/13/17 8:55 PM, Daniel Gallichan wrote:
> Hello
>
> In a very similar situation to a post I found in the Freesurfer
> archive, I have low-resolution (3T) and high-resolution scans (7T) of
> the same subject - and would like to put the surfaces from the
> low-resolution scan into the space of the hi-res data. The
> instructions from the previous thread say to check example 4 when
> running ?mri_surf2surf --help? - which I tried, but I cannot get the
> result to overlap in freeview.
>
> I have a registration file which looks very good from running
> bbregister on the high-res data into the low-res space - but I cannot
> perform the registration the other way around as I?m still having
> trouble getting the hi-res data to process properly through recon-all
> (it?s acquired at 350um, and I?m currently running it downsampled to
> 500um, but that?s still a work-in-progress?).
>
> So this is the command-line that I tried to apply the transformation
> from the registration to a surface:
>
> mri_surf2surf --reg-inv hires_to_lowres.dat
> ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz --hemi lh --sval-xyz white
> --tval-xyz ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz --tval lh.white.hires
> --s subj_lowres
>
> If I then try to view the result:
>
> freeview -v ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz -f
> ${SUBJECTS_DIR}/subj_lowres/surf/lh.white.hires
>
> it is clear that the two are far from being aligned?
>
> I?m afraid I may be misunderstanding how to control the coordinate
> systems in the mri_surf2surf command - especially as the source and
> targets are different ?subjects? (the same actual subject, though?). I
> can?t used the ?--trgsubject? option because recon-all has not
> completed properly on the hires data, and there is no sphere.reg file
> (although I have to confess, I haven?t understood why it would need it
> if I am specifying my own registration file?) . Any suggestions very
> gratefully received.
>
> Thanks
>
> Daniel
>
>
>
>
>
>
>
>
>
>
>
>
> *Dr Daniel Gallichan*
> *Lecturer*
>
> CUBRIC
> School of Engineering
> Cardiff University
> Maindy Road
> Cardiff
> CF24 4HQ
> Wales, United Kingdom
>
> Tel: +44 (0) 29 208 70045
> Email: gallich...@cardiff.ac.uk <mailto:gallich...@cardiff.ac.uk>
>
>
>
> *Dr Daniel Gallichan*
> *Ddarlithydd*
>
> CUBRIC
> Ysgol Beirianneg
> Prifysgol Caerdydd
> Heol Maindy
> Caerdydd
> CF24 4HQ
> Cymru, y Deyrnas Unedig
>
> Ff?n: +44 (0) 29 208 70045
> E-bost: gallich...@caerdydd.ac.uk <mailto:gallich...@caerdydd.ac.uk>
>
> Personal website:
> http://www.cardiff.ac.uk/people/view/507850-gallichan-daniel
> CUBRIC - *C*ardiff *U*niversity *B*rain *R*esearch *I*maging
> *C*entre - http://sites.cardiff.ac.uk/cubric/
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 10
Date: Wed, 14 Jun 2017 16:59:12 +0200
From: Douglas Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Surface area of a define volume projection
on cortical surface
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <d4df9dba-3dc0-bb6c-d6cf-b16f371aa...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
It will not be one surface area for all voxels, each voxel will have
it's own surface area. If you have a particular voxel in mind, then you
can create a volume where that voxel is 1.0 and the rest 0, then map it
to the surface and to fsaverage and see how big it gets.
On 6/13/17 9:26 PM, Matthieu Vanhoutte wrote:
> Dear Freesurfer's experts,
>
> Given the well known size of a voxel I would like to know the
> equivalent surface area once projected on the white fsaverage cortical
> surface.
>
> Could anyone give me a proper way of computing this ?
>
> Best regards,
> Matthieu
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 11
Date: Wed, 14 Jun 2017 15:02:45 +0000
From: Michael Davies <michael.davie...@hotmail.com>
Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <3f0cfe28-9695-4220-9fe8-55bc68c07...@hotmail.com>
Content-Type: text/plain; charset="windows-1252"
Hi Ruopeng, this is the command i ran and resulting error message;
bash-4.1$
/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0
\
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> \
> projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visible=0
> \
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0 \
> projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> --viewport 3d
bash:
/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0:
No such file or directory
Kind regards, Michael
On 14 Jun 2017, at 15:05, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> wrote:
Please copy and paste the full command line you ran and the error message you
got.
Thanks,
Ruopeng
On Jun 14, 2017, at 9:26 AM, Michael Davies
<michael.davie...@hotmail.com<mailto:michael.davie...@hotmail.com>> wrote:
Hello i am trying to access the data files in 3D but i am having problems
opening the files using the command syntax given on the website.
I have set my own pathway using my own data;
?/projects/pbic1030/Micahel/subjects/Subj1/fsaverage/surf/?
However, one i progress with the code past this point i am unable to load the
data and get the error message No file or directory in the terminal even though
this is the correct pathway to the data.
When i enter the rest as follows this is when the problems begin to occur
lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
Could you please advise me how to proceed?
Kind regards, Michael
University of Birmingham
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The information in this e-mail is intended only for the person to whom it is
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Message: 12
Date: Wed, 14 Jun 2017 17:17:32 +0200
From: Douglas Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Merging outputs of mri_label2vol across hemi
To: Elijah Mak <fk...@medschl.cam.ac.uk>, Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Cc: Kwangyeol Baek <kwangyeol.b...@gmail.com>
Message-ID: <d5148453-4927-fd9c-8736-7707543b6...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hmmm, not sure. can you send the full terminal output?
On 6/13/17 7:03 PM, Elijah Mak wrote:
> Hi Doug,
>
> After resampling the aparc annotation into the functional native
> space, the LUT values no longer correspond to the correct regions. A
> screenshot is attached here: http://i.imgur.com/HNIgrKI.png
>
> The values for the labels range from 1 - 35 only.
>
> The command is mri_label2vol --annot $i/label/rh.aparc.annot --temp
> ${i}_medn.nii --reg $i/fmri/fmri_t1_mricoreg.dat --fillthresh 0.5
> --hemi rh --subject $i --proj frac 0 .1 1 --o ${i}.rh.aparc.in.func.nii
>
> The goal is to apply the annotation and extract the regional fMRI data
> (4D) using this 3D volume parcellation. Could we achieve that by using
> these steps?
>
> Thanks.
>
> Best Wishes,
> Elijah
>
>
>
> On 13 June 2017 at 07:05:13, Douglas Greve (gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>) wrote:
>
> You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz
>
> This will work if there are no overlapping voxels. If there are,
> you'll have to do something like
>
> mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz
>
> then use the masked in the mri_concat command
>
>
> On 6/11/17 11:18 AM, Elijah Mak wrote:
>> Hi Freesurfer Team,
>>
>> I am trying to resample the aparc annotation into functional space
>> using mri_label2vol. It works fine and the script produced the
>> segmentation for each hemisphere. Is there a way to merge both the
>> left and right volumes together? Thanks for your help.
>>
>> Best Wishes,
>> Elijah
>>
>>
>> _______________________________________________
>> 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
>
>
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
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Message: 13
Date: Wed, 14 Jun 2017 16:23:12 +0100
From: Elijah Mak <fk...@medschl.cam.ac.uk>
Subject: Re: [Freesurfer] Merging outputs of mri_label2vol across hemi
To: Douglas Greve <gr...@nmr.mgh.harvard.edu>, Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Cc: Kwangyeol Baek <kwangyeol.b...@gmail.com>
Message-ID: <etpan.594154e0.41743cb1....@medschl.cam.ac.uk>
Content-Type: text/plain; charset="utf-8"
Hi Doug,
The full log for 1 subject is here:
dhcp-10-240-201-16:T1_Bd elijahmak_imac$ for i in `cat bd_list`; do
mri_label2vol --annot $i/label/lh.aparc.annot --temp ${i}_medn.nii --reg
$i/fmri/fmri_t1_mricoreg.lta --fillthresh 0.5 --hemi lh --subject $i --proj
frac 0 .1 1 --o ${i}.lh.aparc.in.func.nii; done
Number of labels: 0
Annot File:? ? ? 23950/label/lh.aparc.annot
Template Volume: 23950_medn.nii
Outut Volume: 23950.lh.aparc.in.func.nii
Registration File: 23950/fmri/fmri_t1_mricoreg.lta
Fill Threshold: 0.5
Label Vox Vol:? 1
ProjType: ? ? ? frac
ProjTypeId: ? ? 2
ProjStart:? ? ? 0
ProjStop: ? ? ? 0.1
ProjDelta:? ? ? 1
Subject:? 23950
Hemi: ? ? lh
UseNewASeg2Vol:? 0
DoLabelStatVol? 0
LabelCodeOffset? 0
setenv SUBJECTS_DIR
/Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
Template RAS-to-Vox: --------
-0.42918? -0.00000? -0.00000 ? 31.00000;
-0.00000? -0.00000? -0.42918 ? 39.00000;
-0.00000 ? 0.42918? -0.00000 ? 33.50000;
-0.00000? -0.00000? -0.00000 ? 1.00000;
Template Voxel Volume: 12.6493
nHits Thresh: 6.32467
Loading registration from 23950/fmri/fmri_t1_mricoreg.lta
regio_read_register: loading lta
RegMat: --------
-0.99901? -0.04205? -0.01419? -0.53889;
-0.00761? -0.15273 ? 0.98824? -0.11671;
?0.04372? -0.98737? -0.15226? -9.41649;
?0.00000 ? 0.00000 ? 0.00000 ? 1.00000;
Label RAS-to-Vox: --------
?0.42876 ? 0.01805 ? 0.00609 ? 31.23128;
-0.01877 ? 0.42377 ? 0.06535 ? 43.04141;
-0.00327? -0.06555 ? 0.42414 ? 33.44991;
?0.00000 ? 0.00000 ? 0.00000 ? 1.00000;
? INFO: loading surface?
/Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd/23950/surf/lh.white
nvertices = 152772
Reading thickness
/Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd/23950/surf/lh.thickness
Loading annotations from 23950/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
annotidmax = 36
nlabels = 36
Allocating Hit Volume (11664432) voxels
PVF (null)
Thesholding hit volume.
mri_label2vol done?
Thanks. Appreciate your help.
Best Wishes,
Elijah?
On 14 June 2017 at 16:18:24, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote:
Hmmm, not sure. can you send the full terminal output?
On 6/13/17 7:03 PM, Elijah Mak wrote:
Hi Doug,
After resampling the aparc annotation into the functional native space, the LUT
values no longer correspond to the correct regions. A screenshot is attached
here:?http://i.imgur.com/HNIgrKI.png
The values for the labels range from 1 - 35 only.
The command is mri_label2vol --annot $i/label/rh.aparc.annot --temp
${i}_medn.nii --reg $i/fmri/fmri_t1_mricoreg.dat --fillthresh 0.5 --hemi rh
--subject $i --proj frac 0 .1 1 --o ${i}.rh.aparc.in.func.nii
The goal is to apply the annotation and extract the regional fMRI data (4D)
using this 3D volume parcellation. Could we achieve that by using these steps?
Thanks.
Best Wishes,
Elijah
On 13 June 2017 at 07:05:13, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote:
You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz
This will work if there are no overlapping voxels. If there are, you'll have to
do something like
mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz
then use the masked in the mri_concat command
On 6/11/17 11:18 AM, Elijah Mak wrote:
Hi Freesurfer Team,
I am trying to resample the aparc annotation into functional space using
mri_label2vol. It works fine and the script produced the segmentation for each
hemisphere. Is there a way to merge both the left and right volumes together?
Thanks for your help.
Best Wishes,
Elijah
_______________________________________________
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
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Message: 14
Date: Wed, 14 Jun 2017 17:30:39 +0200
From: Douglas Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Merging outputs of mri_label2vol across hemi
To: Elijah Mak <fk...@medschl.cam.ac.uk>, Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Cc: Kwangyeol Baek <kwangyeol.b...@gmail.com>
Message-ID: <b5e8ae32-3ea9-ae8f-b1d0-0643fe0cf...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Add --offset 2000 to the command line (use 1000 for lh)
On 6/14/17 5:23 PM, Elijah Mak wrote:
> Hi Doug,
>
> The full log for 1 subject is here:
>
> dhcp-10-240-201-16:T1_Bd elijahmak_imac$ for i in `cat bd_list`; do
> mri_label2vol --annot $i/label/lh.aparc.annot --temp ${i}_medn.nii
> --reg $i/fmri/fmri_t1_mricoreg.lta --fillthresh 0.5 --hemi lh
> --subject $i --proj frac 0 .1 1 --o ${i}.lh.aparc.in.func.nii; done
>
> Number of labels: 0
>
> Annot File: 23950/label/lh.aparc.annot
>
> Template Volume: 23950_medn.nii
>
> Outut Volume: 23950.lh.aparc.in.func.nii
>
> Registration File: 23950/fmri/fmri_t1_mricoreg.lta
>
> Fill Threshold: 0.5
>
> Label Vox Vol: 1
>
> ProjType: frac
>
> ProjTypeId: 2
>
> ProjStart: 0
>
> ProjStop: 0.1
>
> ProjDelta: 1
>
> Subject: 23950
>
> Hemi: lh
>
> UseNewASeg2Vol: 0
>
> DoLabelStatVol 0
>
> LabelCodeOffset 0
>
> setenv SUBJECTS_DIR
> /Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd
>
> $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
>
> Template RAS-to-Vox: --------
>
> -0.42918 -0.00000 -0.00000 31.00000;
>
> -0.00000 -0.00000 -0.42918 39.00000;
>
> -0.00000 0.42918 -0.00000 33.50000;
>
> -0.00000 -0.00000 -0.00000 1.00000;
>
> Template Voxel Volume: 12.6493
>
> nHits Thresh: 6.32467
>
> Loading registration from 23950/fmri/fmri_t1_mricoreg.lta
>
> regio_read_register: loading lta
>
> RegMat: --------
>
> -0.99901 -0.04205 -0.01419 -0.53889;
>
> -0.00761 -0.15273 0.98824 -0.11671;
>
> 0.04372 -0.98737 -0.15226 -9.41649;
>
> 0.00000 0.00000 0.00000 1.00000;
>
> Label RAS-to-Vox: --------
>
> 0.42876 0.01805 0.00609 31.23128;
>
> -0.01877 0.42377 0.06535 43.04141;
>
> -0.00327 -0.06555 0.42414 33.44991;
>
> 0.00000 0.00000 0.00000 1.00000;
>
> INFO: loading surface
> /Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd/23950/surf/lh.white
>
>
> nvertices = 152772
>
> Reading thickness
> /Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd/23950/surf/lh.thickness
>
> Loading annotations from 23950/label/lh.aparc.annot
>
> reading colortable from annotation file...
>
> colortable with 36 entries read (originally
> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>
> annotidmax = 36
>
> nlabels = 36
>
> Allocating Hit Volume (11664432) voxels
>
>
> PVF (null)
>
> Thesholding hit volume.
>
> mri_label2vol done
>
>
> Thanks. Appreciate your help.
>
> Best Wishes,
> Elijah
>
>
>
> On 14 June 2017 at 16:18:24, Douglas Greve (gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>) wrote:
>
> Hmmm, not sure. can you send the full terminal output?
>
> On 6/13/17 7:03 PM, Elijah Mak wrote:
>> Hi Doug,
>>
>> After resampling the aparc annotation into the functional native
>> space, the LUT values no longer correspond to the correct regions. A
>> screenshot is attached here: http://i.imgur.com/HNIgrKI.png
>>
>> The values for the labels range from 1 - 35 only.
>>
>> The command is mri_label2vol --annot $i/label/rh.aparc.annot --temp
>> ${i}_medn.nii --reg $i/fmri/fmri_t1_mricoreg.dat --fillthresh 0.5
>> --hemi rh --subject $i --proj frac 0 .1 1 --o ${i}.rh.aparc.in.func.nii
>>
>> The goal is to apply the annotation and extract the regional fMRI
>> data (4D) using this 3D volume parcellation. Could we achieve that by
>> using these steps?
>>
>> Thanks.
>>
>> Best Wishes,
>> Elijah
>>
>>
>>
>> On 13 June 2017 at 07:05:13, Douglas Greve (gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>) wrote:
>>
>> You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz
>>
>> This will work if there are no overlapping voxels. If there are,
>> you'll have to do something like
>>
>> mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz
>>
>> then use the masked in the mri_concat command
>>
>>
>> On 6/11/17 11:18 AM, Elijah Mak wrote:
>>> Hi Freesurfer Team,
>>>
>>> I am trying to resample the aparc annotation into functional space
>>> using mri_label2vol. It works fine and the script produced the
>>> segmentation for each hemisphere. Is there a way to merge both the
>>> left and right volumes together? Thanks for your help.
>>>
>>> Best Wishes,
>>> Elijah
>>>
>>>
>>> _______________________________________________ Freesurfer mailing
>>> list Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> _______________________________________________
>> Freesurfer mailing list
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>>
>>
>> The information in this e-mail is intended only for the person to
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
>> you in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>
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> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
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Message: 15
Date: Wed, 14 Jun 2017 17:52:08 +0200
From: Martin Reuter <mreu...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal Pipeline
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2873b8ac-fbc1-4606-b55f-cc453994f...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"
Hi Theo,
- not sure what test you mean. Have a second person correct the data and
compare ?
- you can run 1.5. and 3 T data in the longitudinal pipeline, however (similar
to cross sectional processing) you will not know if the differences of the
results are due to anatomical changes or due to scanner differences.
Best, Martin
> On 14. Jun 2017, at 03:27, AKUDJEDU, THEOPHILUS <t.akudje...@nuigalway.ie>
> wrote:
>
> Hi All,
>
> Is it standard practice to conduct test when corrections are made in
> freesurfer for subcortical structure volumes?
>
> Also, are you able to analyse data acquired (1.5T - time point one) with
> time-point two (3T) in the longitudinal pipeline?
>
>
> Thanks
>
>
> Theo
>
> From: AKUDJEDU, THEOPHILUS
> Sent: Tuesday, June 13, 2017 3:19:00 PM
> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: Longitudinal Pipeline
>
> Hi All,
>
> Is it standard practice to conduct reliability when corrections are made in
> freesurfer for subcortical structure volumes?
>
> Also, are you able to analyse data acquired (1.5T - time point one) with
> time-point two (3T) in the longitudinal pipeline?
>
>
> Thanks
>
>
> Theo
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Message: 16
Date: Wed, 14 Jun 2017 11:54:15 -0400
From: Ruopeng Wang <rpw...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <7a176159-c4c6-245e-acd8-afd13d042...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
You didn't call freeview there... Try adding "freeview -f " at the
beginning of the command.
On 06/14/2017 11:02 AM, Michael Davies wrote:
> Hi Ruopeng, this is the command i ran and resulting error message;
>
> bash-4.1$
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0
> \
> >
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> \
> >
> projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visible=0
> \
> >
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0
> \
> > projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > --viewport 3d
> bash:
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0:
> No such file or directory
>
>
> Kind regards, Michael
>
>> On 14 Jun 2017, at 15:05, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu>
>> wrote:
>>
>> Please copy and paste the full command line you ran and the error
>> message you got.
>>
>> Thanks,
>> Ruopeng
>>
>>> On Jun 14, 2017, at 9:26 AM, Michael Davies
>>> <michael.davie...@hotmail.com <mailto:michael.davie...@hotmail.com>>
>>> wrote:
>>>
>>> Hello i am trying to access the data files in 3D but i am having
>>> problems opening the files using the command syntax given on the
>>> website.
>>>
>>> I have set my own pathway using my own data;
>>>
>>> ?/projects/pbic1030/Micahel/subjects/Subj1/fsaverage/surf/?
>>>
>>> However, one i progress with the code past this point i am unable to
>>> load the data and get the error message No file or directory in the
>>> terminal even though this is the correct pathway to the data.
>>>
>>> When i enter the rest as follows this is when the problems begin to
>>> occur lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
>>>
>>> Could you please advise me how to proceed?
>>>
>>> Kind regards, Michael
>>> University of Birmingham
>>> _______________________________________________
>>> 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
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
>> you in error
>> but does not contain patient information, please contact the sender
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>> dispose of the e-mail.
>
>
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