Message: 7
Date: Wed, 14 Jun 2017 16:32:38 +0200
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Brainmask Shifted
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <02f67013-f90c-699f-0307-9f1bf9b131be@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
>
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Message: 8
Date: Wed, 14 Jun 2017 10:33:55 -0400 (EDT)
From: Bruce Fischl <fischl@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 <rahuldesikan@gmail.com>
Message-ID:
<alpine.LRH.2.20.1706141033400.28087@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 <greve@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-a1f3-25dbbd353776@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: gallichand@cardiff.ac.uk <
mailto:gallichand@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: gallichand@caerdydd.ac.uk <
mailto:gallichand@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
>
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Message: 10
Date: Wed, 14 Jun 2017 16:59:12 +0200
From: Douglas Greve <greve@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-b16f371aa7b0@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.davies30@hotmail.com>
Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <3F0CFE28-9695-4220-9FE8-55BC68C0755E@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 <rpwang@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.davies30@hotmail.com<mailto:Michael.davies30@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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Message: 12
Date: Wed, 14 Jun 2017 17:17:32 +0200
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Merging outputs of mri_label2vol across hemi
To: Elijah Mak <fkm24@medschl.cam.ac.uk>, Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Cc: Kwangyeol Baek <kwangyeol.baek@gmail.com>
Message-ID: <d5148453-4927-fd9c-8736-7707543b6b68@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 (greve@nmr.mgh.harvard.edu
> <
mailto:greve@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
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Message: 13
Date: Wed, 14 Jun 2017 16:23:12 +0100
From: Elijah Mak <fkm24@medschl.cam.ac.uk>
Subject: Re: [Freesurfer] Merging outputs of mri_label2vol across hemi
To: Douglas Greve <greve@nmr.mgh.harvard.edu>, Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Cc: Kwangyeol Baek <kwangyeol.baek@gmail.com>
Message-ID: <etPan.594154e0.41743cb1.61c@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 (greve@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 (greve@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
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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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
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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
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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: 14
Date: Wed, 14 Jun 2017 17:30:39 +0200
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Merging outputs of mri_label2vol across hemi
To: Elijah Mak <fkm24@medschl.cam.ac.uk>, Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Cc: Kwangyeol Baek <kwangyeol.baek@gmail.com>
Message-ID: <b5e8ae32-3ea9-ae8f-b1d0-0643fe0cf2cc@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 (greve@nmr.mgh.harvard.edu
> <
mailto:greve@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 (greve@nmr.mgh.harvard.edu
>> <
mailto:greve@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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> in error
> but does not contain patient information, please contact the sender
> and properly
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Message: 15
Date: Wed, 14 Jun 2017 17:52:08 +0200
From: Martin Reuter <mreuter@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal Pipeline
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2873B8AC-FBC1-4606-B55F-CC453994FDDA@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.AKUDJEDU1@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 <rpwang@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-afd13d04201d@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 <rpwang@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.davies30@hotmail.com <
mailto:Michael.davies30@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
>> 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
>
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_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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End of Freesurfer Digest, Vol 160, Issue 25
*******************************************
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Message: 8
Date: Wed, 14 Jun 2017 14:39:53 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Subcortical Segmentation
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1706141439460.28087@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed
yes, you can use freeview to do this.
cheers
Bruce
On Wed, 14 Jun 2017, AKUDJEDU,
THEOPHILUS wrote:
>
> Hi FreeSurfers,
>
>
> Are we able to correct the anatomical boundaries of subcortical structures
> delineated with FreeSurfer? On which output file do we do this if it's
> possible?
>
>
> Thank you
>
>
> Theo
>
>
>
>
------------------------------
Message: 9
Date: Wed, 14 Jun 2017 18:44:10 +0000
From: Michael Davies <Michael.Davies30@hotmail.com>
Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<MM1P123MB1372937B6CEB92A948FD8B1089C30@MM1P123MB1372.GBRP123.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="windows-1252"
Hi, the server has been down and i currently cannot access my account. I did however try putting freeview -f at the beginning before without any luck but i will try again when possible.
Kind regards, Michael
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Sent: 14 June 2017 15:54:15
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview
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 <rpwang@nmr.mgh.harvard.edu><mailto:rpwang@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.davies30@hotmail.com<mailto:Michael.davies30@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
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
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Message: 10
Date: Wed, 14 Jun 2017 14:46:00 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1706141445330.28087@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
Hi Michael
can you send us the full command line and screen output of any command
that you ran that fails and you want our help with?
thanks
Bruce
On Wed, 14
Jun 2017, Michael Davies wrote:
>
> Hi, the server has been down and i currently cannot access my account. I did
> however try putting freeview -f at the beginning before without any luck but
> i will try again when possible.
>
>
> Kind regards, Michael
>
> ____________________________________________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang
> <rpwang@nmr.mgh.harvard.edu>
> Sent: 14 June 2017 15:54:15
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview ?
> 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=apar
> c.annot:name=pial_aparc:visible=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overla
> y=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=apar
> c.annot:name=pial_aparc:visible=0: No such file or directory
>
>
> Kind regards, Michael
>
> On 14 Jun 2017, at 15:05, Ruopeng Wang
> <rpwang@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.davies30@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
>
>
> _______________________________________________
> 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
>
>
>
>
------------------------------
Message: 11
Date: Wed, 14 Jun 2017 19:42:33 +0000
From: "Almarshad F." <F.Almarshad@soton.ac.uk>
Subject: [Freesurfer] aparc.a2009s+aseg.mgz
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<F957B5E1040AEF46898AEE2797758850663457D2@SRV00357.soton.ac.uk>
Content-Type: text/plain; charset="iso-8859-1"
Dear FreeSurfer expert
is it possible to create "aparc.a2009s+aseg.mgz" from custom parcellation i have..
i used label2annot to create the 2.annot files from my none overlapping labels.. !
i think mri_aparc2aseg<
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg> --s <subjid> --ribbon --annot aparc.a2009s would create the file .. however i could not understand how the
command works, in terms of my two (label/lh.aparc.annot and label/rh.aparc.annot).. if you please can clarify what are the steps i need to make to get the aparc.a2009s+aseg.mgz based on my parcellation
many thinks
fatima
------------------------------
Message: 12
Date: Wed, 14 Jun 2017 19:54:29 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] aparc.a2009s+aseg.mgz
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <D5670C24.10A25%ayendiki@mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
Hi Fatima - mri_aparc2aseg is the right command, but you should specify
the name of your annotation instead of aparc.a2009s (which is one of the
standard freesurfer annotations). So if your annotation is lh.mine.annot
and rh.mine.annot, then you need "--annot mine?.
Anastasia.
On 6/14/17, 3:42 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
Almarshad F." <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
F.Almarshad@soton.ac.uk> wrote:
>
>Dear FreeSurfer expert
>
>is it possible to create "aparc.a2009s+aseg.mgz" from custom parcellation
>i have..
>
>i used label2annot to create the 2.annot files from my none overlapping
>labels.. !
>i think
>mri_aparc2aseg<
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg>
>--s <subjid> --ribbon --annot aparc.a2009s would create the file ..
>however i could not understand how the command works, in terms of my two
>(label/lh.aparc.annot and label/rh.aparc.annot).. if you please can
>clarify what are the steps i need to make to get the
>aparc.a2009s+aseg.mgz based on my parcellation
>
>
>many thinks
>
>fatima
>
>
>
>
>
>_______________________________________________
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 13
Date: Wed, 14 Jun 2017 20:22:56 +0000
From: Michael Davies <Michael.Davies30@hotmail.com>
Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<MM1P123MB1372D26CD8EA4A79840D9FC589C30@MM1P123MB1372.GBRP123.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="windows-1252"
Hi Bruce this is the command i am attempting to run but having no luck as yet. Any help would be greatly appreciated.
bash-4.1$ freeview -f \
> /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: freeview: command not found
bash-4.1$
Kind regards, Michael
University of Birmingham
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Sent: 14 June 2017 18:46:00
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview
Hi Michael
can you send us the full command line and screen output of any command
that you ran that fails and you want our help with?
thanks
Bruce
On Wed, 14
Jun 2017, Michael Davies wrote:
>
> Hi, the server has been down and i currently cannot access my account. I did
> however try putting freeview -f at the beginning before without any luck but
> i will try again when possible.
>
>
> Kind regards, Michael
>
> ____________________________________________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang
> <rpwang@nmr.mgh.harvard.edu>
> Sent: 14 June 2017 15:54:15
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview
> 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=apar
> c.annot:name=pial_aparc:visible=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overla
> y=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=apar
> c.annot:name=pial_aparc:visible=0: No such file or directory
>
>
> Kind regards, Michael
>
> On 14 Jun 2017, at 15:05, Ruopeng Wang
> <rpwang@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.davies30@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
>
>
> _______________________________________________
> 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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>
>
>
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Message: 14
Date: Thu, 15 Jun 2017 07:29:54 +0000
From: Michael Davies <Michael.davies30@hotmail.com>
Subject: [Freesurfer] viewing 3D surfaces
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<MM1P123MB1372E6BCA87911F82ADF5FDE89C00@MM1P123MB1372.GBRP123.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="us-ascii"
Hello, i am having problems accessing the 3D surfaces of my data. Is there any advice you could provide for me please?
bash-4.1$ freeview -f \
> /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: freeview: command not found
Kind regards, Michael
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Message: 15
Date: Thu, 15 Jun 2017 11:15:08 +0200
From: Gabor Perlaki <petzinger.gabor@gmail.com>
Subject: [Freesurfer] DKT vs. DK Freesurfer atlases
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CA+f2votkD8f86RCvZAWj0jxFhdBM0F=d7OuYptyAVLKbXm+YCQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear all,
I've found an article comparing DK and DKT atlas based automatic
segmentations to manual labels (Klein and Tourville, Front Neurosci. 2012;
6:171,
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514540/). It seems
that using DKT40 works better than DK in most of the cortical regions
(based on Dice).
Does anybody know that the DKTatlas related results created by Freesurfer
(e.g. aparc.DKTatlas+aseg.mgz, lh.aparc.DKTatlas.stats) are based on the
same DKT40 atlas used in the article and whether the DKT40 atlas related
results were also created by Freesurfer in the article by Klein and
Tourville? Are the Freesurfer created results in lh.aparc.DKTatlas.stats
generally more reliable than the results in lh.aparc.stats?
--
Gabor Perlaki
research associate
Diagnostic Center of P?cs
H-7623 P?cs, R?t str. 2.
Tel.: 0036-30-2084367
E-mail: petzinger.gabor@gmail.com
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Message: 16
Date: Thu, 15 Jun 2017 12:16:48 +0000
From: Michael Davies <Michael.Davies30@hotmail.com>
Subject: [Freesurfer] Viewing 3D surfaces
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<MM1P123MB1372E11D9AB13DDC9BCAFE3C89C00@MM1P123MB1372.GBRP123.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="iso-8859-1"
Hello, i am having problems loading the 3D surface for my data. I was wondering if you could provide any advice please? This is the command code i put into the terminal;
bash-4.1$ freeview -f/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: freeview: command not found
bash-4.1$
Kind regards, Michael
University of Birmingham
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Message: 17
Date: Thu, 15 Jun 2017 15:02:13 +0200
From: Ismail Koubiyr <ismail.koubiyr@gmail.com>
Subject: [Freesurfer] Cortical thickness differences displayed on
surface
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAL_WnEyRK+KTkjD1R+_-0mw3ELqn=kGknSttFTaQv-OpYwu=eA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear all,
I have performed cortical thickness analysis with FS 5.3 and have found
some differences in some areas ( I have used the --lobesStrict option).
Now, I would like to display the p-values I have found for each lobe on a
surface . Would anyone have any idea how to do it ?
Many thanks,
Ismail
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Message: 18
Date: Thu, 15 Jun 2017 13:46:45 +0000
From: "Lim, Lena" <lena.lim@kcl.ac.uk>
Subject: [Freesurfer] volume, thickness and surface area analyses
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<AM3PR03MB10441496FAFAF3FD46287250C2C00@AM3PR03MB1044.eurprd03.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
Dear Freesurfer Experts,
A review questioned the validity of examining volume in addition to cortical thickness and surface area within the same study. In particular, he commented that "The volume is the product of the thickness and area ...As the product of two Gaussian-distributed
variables is not Gaussian-distributed, the volume is likely to violate assumptions of the statistical methods." Could you please kindly advice on this?
Many thanks,
Lena
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Message: 19
Date: Thu, 15 Jun 2017 10:11:54 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] viewing 3D surfaces
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1706151010570.28087@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Michael
you need to have FreeSurfer in your path or nothing will work. Have you
sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
environment?
cheers
Bruce
On Thu, 15 Jun 2017, Michael Davies wrote:
> Hello, i am having problems accessing the 3D surfaces of my data. Is there
> any advice you could provide for me please?
> bash-4.1$ freeview -f \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apar
> c.annot:name=pial_aparc:visible=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overla
> y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visibl
> e=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0
> \
> > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > --viewport 3d
> bash: freeview: command not found
>
> Kind regards, Michael
>
>
------------------------------
Message: 20
Date: Thu, 15 Jun 2017 16:20:07 +0200
From: Lisa Kramarenko <lisa.kramarenko@gmail.com>
Subject: Re: [Freesurfer] Libnetcdf.so.6 error during
mris_make_surfaces
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAET4nGJ1Ldnh=J9U9tiZZrk=zJy4fTG8WxtaQGwFa2dmk+8bWA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi,
sure, it's
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
thanks!
On 13 June 2017 at 19:38, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:
> Hello Lisa,
>
> Can you provide me with the contents of your
> FREESURFER_HOME/build-stamp.txt file
>
> On 06/12/2017 05:44 PM, Lisa Kramarenko wrote:
> > Hi,
> >
> > I am getting the following error when my HCP pipelines come to the
> > mris_make surfaces step:
> >
> > mris_make_surfaces: error while loading shared libraries:
> > libnetcdf.so.6: cannot open shared object file: No such file or directory
> >
> > I saw this response:
> >
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02418.html
> > but the files are not available anymore and I cannot find where to
> > download it. I have Ubuntu 14.04 (64-bit). Do you have any idea about
> > what causes this problem and how to solve it?
> >
> > Thanks a lot!
> > Lisa
> >
> >
> > _______________________________________________
> > 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: 21
Date: Thu, 15 Jun 2017 15:12:57 +0000
From: Michael Davies <Michael.Davies30@hotmail.com>
Subject: Re: [Freesurfer] viewing 3D surfaces
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<MM1P123MB1372A26995B6F2D0C4538FED89C00@MM1P123MB1372.GBRP123.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="iso-8859-1"
Hi Bruce, i am still getting error messages. is there anything else i could try doing?
Kind regards, Michael
bash-4.1$ freesurfer_setup_freeview
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer_v6.0.0
FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects
MNI_DIR /usr/local/freesurfer_v6.0.0/mni
FSL_DIR /usr/local/fsl
bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \
> /surf/lh.inflated:visible=0 \
> /surf/lh.white:visible=0 \
> /surf/lh.pial \
> --viewport 3d
bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such file or directory
bash-4.1$
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Sent: 15 June 2017 14:11
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces
Hi Michael
you need to have FreeSurfer in your path or nothing will work. Have you
sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
environment?
cheers
Bruce
On Thu, 15 Jun 2017, Michael Davies wrote:
> Hello, i am having problems accessing the 3D surfaces of my data. Is there
> any advice you could provide for me please?
> bash-4.1$ freeview -f \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apar
> c.annot:name=pial_aparc:visible=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overla
> y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visibl
> e=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0
> \
> > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > --viewport 3d
> bash: freeview: command not found
>
> Kind regards, Michael
>
>
_______________________________________________
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
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: 22
Date: Thu, 15 Jun 2017 11:19:21 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] viewing 3D surfaces
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1706151119020.28087@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
you are not calling freeview in this command. Try putting freeview at the
start
On Thu, 15 Jun 2017, Michael Davies wrote:
>
> Hi Bruce, i am still getting error messages. is there anything else i could
> try doing?
>
> Kind regards, Michael
>
>
> bash-4.1$ freesurfer_setup_freeview
> -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME?? /usr/local/freesurfer_v6.0.0
> FSFAST_HOME?????? /usr/local/freesurfer_v6.0.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR????? /usr/local/freesurfer_v6.0.0/subjects
> MNI_DIR?????????? /usr/local/freesurfer_v6.0.0/mni
> FSL_DIR?????????? /usr/local/fsl
> bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat
> ed_thickness:visible=0 \
> > /surf/lh.inflated:visible=0 \
> > /surf/lh.white:visible=0 \
> > /surf/lh.pial \
> > --viewport 3d
> bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such
> file or directory
> bash-4.1$
>
>
>
> ____________________________________________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> <fischl@nmr.mgh.harvard.edu>
> Sent: 15 June 2017 14:11
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces ?
> Hi Michael
>
> you need to have FreeSurfer in your path or nothing will work. Have you
> sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
> environment?
>
> cheers
> Bruce
>
>
> On Thu, 15 Jun 2017, Michael Davies wrote:
>
> > Hello, i am having problems accessing the 3D surfaces of my data. Is there
> > any advice you could provide for me please?
> > bash-4.1$ freeview -f \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apa
> r
> > c.annot:name=pial_aparc:visible=0 \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overl
> a
> > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visib
> l
> > e=0 \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=
> 0
> > \
> > > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > > --viewport 3d
> > bash: freeview: command not found
> >
> > Kind regards, Michael
> >
> >
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> Freesurfer Info Page - Harvard University
> mail.nmr.mgh.harvard.edu
> To see the collection of prior postings to the list, visit the Freesurfer
> Archives. A searchable archive which of messages PRIOR to March 2004 is at
> ...
>
>
>
> 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: 23
Date: Thu, 15 Jun 2017 15:45:37 +0000
From: Michael Davies <Michael.Davies30@hotmail.com>
Subject: Re: [Freesurfer] viewing 3D surfaces
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<MM1P123MB137229FF280646D87E03069D89C00@MM1P123MB1372.GBRP123.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="iso-8859-1"
Hi Bruce, i'm getting closer to opening it now. But the final command /surf/lh.pial \ didnt work this time. Any further suggestions?
Kind regards, Michael
bash-4.1$ freesurfer_setup_freeview
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer_v6.0.0
FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects
MNI_DIR /usr/local/freesurfer_v6.0.0/mni
FSL_DIR /usr/local/fsl
bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
bash-4.1$ freeview -f \
> /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \
> /surf/lh.inflated:visible=0 \
> /surf/lh.white:visible=0 \
> /surf/lh.pial \
> --viewport 3d
MRISread(/surf/lh.pial): could not open file
No such file or directory
MRISread failed
No such file or directory
ould not open file
bash-4.1$
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Sent: 15 June 2017 15:19:21
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces
you are not calling freeview in this command. Try putting freeview at the
start
On Thu, 15 Jun 2017, Michael Davies wrote:
>
> Hi Bruce, i am still getting error messages. is there anything else i could
> try doing?
>
> Kind regards, Michael
>
>
> bash-4.1$ freesurfer_setup_freeview
> -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME /usr/local/freesurfer_v6.0.0
> FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects
> MNI_DIR /usr/local/freesurfer_v6.0.0/mni
> FSL_DIR /usr/local/fsl
> bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat
> ed_thickness:visible=0 \
> > /surf/lh.inflated:visible=0 \
> > /surf/lh.white:visible=0 \
> > /surf/lh.pial \
> > --viewport 3d
> bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such
> file or directory
> bash-4.1$
>
>
>
> ____________________________________________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> <fischl@nmr.mgh.harvard.edu>
> Sent: 15 June 2017 14:11
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces
> Hi Michael
>
> you need to have FreeSurfer in your path or nothing will work. Have you
> sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
> environment?
>
> cheers
> Bruce
>
>
> On Thu, 15 Jun 2017, Michael Davies wrote:
>
> > Hello, i am having problems accessing the 3D surfaces of my data. Is there
> > any advice you could provide for me please?
> > bash-4.1$ freeview -f \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apa
> r
> > c.annot:name=pial_aparc:visible=0 \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overl
> a
> > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visib
> l
> > e=0 \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=
> 0
> > \
> > > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > > --viewport 3d
> > bash: freeview: command not found
> >
> > Kind regards, Michael
> >
> >
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> Freesurfer Info Page - Harvard University
> mail.nmr.mgh.harvard.edu
> To see the collection of prior postings to the list, visit the Freesurfer
> Archives. A searchable archive which of messages PRIOR to March 2004 is at
> ...
>
>
>
> 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: 24
Date: Thu, 15 Jun 2017 11:48:31 -0400
From: Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] viewing 3D surfaces
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <194bf0e0-7652-b2ec-0a6d-20e626ec7d99@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
Remove the '/' in front of "surf".
On 06/15/2017 11:45 AM, Michael Davies wrote:
>
> Hi Bruce, i'm getting closer to opening it now. But the final command
> /surf/lh.pial \ didnt work this time. Any further suggestions?
>
>
> Kind regards, Michael
>
>
> bash-4.1$ freesurfer_setup_freeview
> -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> --------
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME /usr/local/freesurfer_v6.0.0
> FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects
> MNI_DIR /usr/local/freesurfer_v6.0.0/mni
> FSL_DIR /usr/local/fsl
> bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> bash-4.1$ freeview -f \
> > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> >
> /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> \
> > /surf/lh.inflated:visible=0 \
> > /surf/lh.white:visible=0 \
> > /surf/lh.pial \
> > --viewport 3d
> MRISread(/surf/lh.pial): could not open file
> No such file or directory
> MRISread failed
> No such file or directory
> ould not open file
> bash-4.1$
>
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> <fischl@nmr.mgh.harvard.edu>
> *Sent:* 15 June 2017 15:19:21
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] viewing 3D surfaces
> you are not calling freeview in this command. Try putting freeview at the
> start
> On Thu, 15 Jun 2017, Michael Davies wrote:
>
> >
> > Hi Bruce, i am still getting error messages. is there anything else
> i could
> > try doing?
> >
> > Kind regards, Michael
> >
> >
> > bash-4.1$ freesurfer_setup_freeview
> > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> --------
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME /usr/local/freesurfer_v6.0.0
> > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects
> > MNI_DIR /usr/local/freesurfer_v6.0.0/mni
> > FSL_DIR /usr/local/fsl
> > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> >
> >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat
> > ed_thickness:visible=0 \
> > > /surf/lh.inflated:visible=0 \
> > > /surf/lh.white:visible=0 \
> > > /surf/lh.pial \
> > > --viewport 3d
> > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such
> > file or directory
> > bash-4.1$
> >
> >
> >
> >
> ____________________________________________________________________________
> > From: freesurfer-bounces@nmr.mgh.harvard.edu
> > <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> > <fischl@nmr.mgh.harvard.edu>
> > Sent: 15 June 2017 14:11
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] viewing 3D surfaces
> > Hi Michael
> >
> > you need to have FreeSurfer in your path or nothing will work. Have you
> > sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
> > environment?
> >
> > cheers
> > Bruce
> >
> >
> > On Thu, 15 Jun 2017, Michael Davies wrote:
> >
> > > Hello, i am having problems accessing the 3D surfaces of my data.
> Is there
> > > any advice you could provide for me please?
> > > bash-4.1$ freeview -f \
> >
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apa
> > r
> > > c.annot:name=pial_aparc:visible=0 \
> >
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overl
> > a
> > >
> y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> > \
> >
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visib
> > l
> > > e=0 \
> >
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=
> > 0
> > > \
> > > > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > > > --viewport 3d
> > > bash: freeview: command not found
> > >
> > > Kind regards, Michael
> > >
> > >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > Freesurfer Info Page - Harvard University
> > mail.nmr.mgh.harvard.edu
> > To see the collection of prior postings to the list, visit the
> Freesurfer
> > Archives. A searchable archive which of messages PRIOR to March 2004
> is at
> > ...
> >
> >
> >
> > 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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